From c021c4816b8f0d8aa81c990439771f26684f93b0 Mon Sep 17 00:00:00 2001 From: Hendrik Ranocha Date: Thu, 25 Jan 2024 14:34:19 +0100 Subject: [PATCH 01/63] set version to v0.6.7 --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index f246bdfdab4..8532e47f761 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "Trixi" uuid = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb" authors = ["Michael Schlottke-Lakemper ", "Gregor Gassner ", "Hendrik Ranocha ", "Andrew R. Winters ", "Jesse Chan "] -version = "0.6.7-pre" +version = "0.6.7" [deps] CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2" From 246dc5be204c8937f077a1d12b5603bb70138357 Mon Sep 17 00:00:00 2001 From: Hendrik Ranocha Date: Thu, 25 Jan 2024 14:34:36 +0100 Subject: [PATCH 02/63] set development version to v0.6.8-pre --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 8532e47f761..1a0aa0103dc 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "Trixi" uuid = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb" authors = ["Michael Schlottke-Lakemper ", "Gregor Gassner ", "Hendrik Ranocha ", "Andrew R. Winters ", "Jesse Chan "] -version = "0.6.7" +version = "0.6.8-pre" [deps] CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2" From 70d365f405c2494e314277f22e63dcc32d04f095 Mon Sep 17 00:00:00 2001 From: Daniel Doehring Date: Thu, 25 Jan 2024 16:09:57 +0100 Subject: [PATCH 03/63] Fix Docs rendering: Avoid Markdown hyperlink (#1814) * Avoid hyperlink in doc * Update docs/src/meshes/p4est_mesh.md Co-authored-by: Michael Schlottke-Lakemper * Apply suggestions from code review Co-authored-by: Michael Schlottke-Lakemper --------- Co-authored-by: Michael Schlottke-Lakemper --- docs/src/meshes/p4est_mesh.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/src/meshes/p4est_mesh.md b/docs/src/meshes/p4est_mesh.md index db75346cab3..3b35ffcad6f 100644 --- a/docs/src/meshes/p4est_mesh.md +++ b/docs/src/meshes/p4est_mesh.md @@ -55,7 +55,7 @@ This heading is used to indicate to the mesh constructor which of the above mapp create a curvilinear mesh. If the Abaqus file header is **not** present then the `P4estMesh` is created with the first strategy above. -#### List of corner nodes +#### [List of corner nodes](@id corner-node-list) Next, prefaced with `*NODE`, comes a list of the physical `(x,y,z)` coordinates of all the corners. The first integer in the list of the corners provides its id number. @@ -71,7 +71,7 @@ Thus, for the two-dimensional example mesh this block of corner information is 7, 3.0, -1.0, 0.0 ``` -#### List of elements +#### [List of elements](@id element-list) The element connectivity is given after the list of corners. The header for this information block is ``` @@ -237,7 +237,7 @@ For completeness, we provide the entire Abaqus mesh file for the example mesh in As an alternative to an Abaqus mesh generated by `HOHQMesh`, `.inp` files with boundary information encoded as nodesets `*NSET,NSET=` can be used to construct a `p4est` mesh. This is especially useful for usage of existing meshes (consisting of bilinear elements) which could stem from the popular [`gmsh`](https://gmsh.info/) meshing software. -In addition to the list of [nodes](#nodes) and [elements](#elements) given above, there are nodesets of the form +In addition to the list of [nodes](@ref corner-node-list) and [elements](@ref element-list) given above, there are nodesets of the form ``` *NSET,NSET=PhysicalLine1 1, 4, 52, 53, 54, 55, 56, 57, 58, From 367881bb713f8671acc1a42ae28a3d68f3000935 Mon Sep 17 00:00:00 2001 From: Daniel Doehring Date: Mon, 29 Jan 2024 09:29:02 +0100 Subject: [PATCH 04/63] Correct NACA6412 BC assignment (#1815) --- docs/literate/src/files/p4est_from_gmsh.jl | 8 ++++---- .../p4est_2d_dgsem/elixir_euler_NACA6412airfoil_mach2.jl | 4 ++-- test/test_p4est_2d.jl | 8 ++++---- 3 files changed, 10 insertions(+), 10 deletions(-) diff --git a/docs/literate/src/files/p4est_from_gmsh.jl b/docs/literate/src/files/p4est_from_gmsh.jl index 356339cdd47..abfe70eebc4 100644 --- a/docs/literate/src/files/p4est_from_gmsh.jl +++ b/docs/literate/src/files/p4est_from_gmsh.jl @@ -347,8 +347,8 @@ end #hide #md # // labeling of the boundary parts # Physical Line(1) = {4}; // Inflow. Label in Abaqus .inp file: PhysicalLine1 # Physical Line(2) = {2}; // Outflow. Label in Abaqus .inp file: PhysicalLine2 -# Physical Line(3) = {1, 3}; // Airfoil. Label in Abaqus .inp file: PhysicalLine3 -# Physical Line(4) = {5, 6}; //Upper and lower wall/farfield/... Label in Abaqus .inp file: PhysicalLine4 +# Physical Line(3) = {1, 3}; // Upper and lower wall/farfield/... Label in Abaqus .inp file: PhysicalLine3 +# Physical Line(4) = {5, 6}; // Airfoil. Label in Abaqus .inp file: PhysicalLine4 # ``` # which are crucial for the correct assignment of boundary conditions in `Trixi.jl`. # In particular, it is the responsibility of a user to keep track on the physical boundary names between the mesh generation and assignment of boundary condition functions in an elixir. @@ -437,8 +437,8 @@ end #hide #md # # boundary_conditions = Dict(:PhysicalLine1 => boundary_condition_supersonic_inflow, # Left boundary # :PhysicalLine2 => boundary_condition_supersonic_outflow, # Right boundary -# :PhysicalLine3 => boundary_condition_slip_wall, # Airfoil -# :PhysicalLine4 => boundary_condition_supersonic_outflow) # Top and bottom boundary +# :PhysicalLine3 => boundary_condition_supersonic_outflow, # Top and bottom boundary +# :PhysicalLine4 => boundary_condition_slip_wall) # Airfoil # # semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver, # boundary_conditions = boundary_conditions) diff --git a/examples/p4est_2d_dgsem/elixir_euler_NACA6412airfoil_mach2.jl b/examples/p4est_2d_dgsem/elixir_euler_NACA6412airfoil_mach2.jl index 6673053d88f..fcd2ca00e10 100644 --- a/examples/p4est_2d_dgsem/elixir_euler_NACA6412airfoil_mach2.jl +++ b/examples/p4est_2d_dgsem/elixir_euler_NACA6412airfoil_mach2.jl @@ -79,8 +79,8 @@ mesh = P4estMesh{2}(mesh_file, polydeg = polydeg, boundary_symbols = boundary_sy boundary_conditions = Dict(:PhysicalLine1 => boundary_condition_supersonic_inflow, # Left boundary :PhysicalLine2 => boundary_condition_supersonic_outflow, # Right boundary - :PhysicalLine3 => boundary_condition_slip_wall, # Airfoil - :PhysicalLine4 => boundary_condition_supersonic_outflow) # Top and bottom boundary + :PhysicalLine3 => boundary_condition_supersonic_outflow, # Top and bottom boundary + :PhysicalLine4 => boundary_condition_slip_wall) # Airfoil semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver, boundary_conditions = boundary_conditions) diff --git a/test/test_p4est_2d.jl b/test/test_p4est_2d.jl index b034091a175..121001b35ff 100644 --- a/test/test_p4est_2d.jl +++ b/test/test_p4est_2d.jl @@ -394,12 +394,12 @@ end @trixi_testset "elixir_euler_NACA6412airfoil_mach2.jl" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_NACA6412airfoil_mach2.jl"), l2=[ - 1.9752162683735258e-9, 3.150450205812513e-9, - 1.8885499402935914e-9, 7.273629602920966e-9, + 0.19107654776276498, 0.3545913719444839, + 0.18492730895077583, 0.817927213517244, ], linf=[ - 6.007577890709825e-7, 1.005273289944597e-6, - 5.948514542597182e-7, 2.3111764217986774e-6, + 2.5397624311491946, 2.7075156425517917, 2.200980534211764, + 9.031153939238115, ], tspan=(0.0, 0.1)) # Ensure that we do not have excessive memory allocations From 38100d0a855b0a370c0fd65fbe9bfbe301f5d096 Mon Sep 17 00:00:00 2001 From: Hendrik Ranocha Date: Mon, 29 Jan 2024 09:44:45 +0100 Subject: [PATCH 05/63] set version to v0.6.8 --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 1a0aa0103dc..29e36a46dc5 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "Trixi" uuid = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb" authors = ["Michael Schlottke-Lakemper ", "Gregor Gassner ", "Hendrik Ranocha ", "Andrew R. Winters ", "Jesse Chan "] -version = "0.6.8-pre" +version = "0.6.8" [deps] CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2" From fcf2652f8ce3f16ba640a66990134632c9f8d3d5 Mon Sep 17 00:00:00 2001 From: Hendrik Ranocha Date: Mon, 29 Jan 2024 09:44:57 +0100 Subject: [PATCH 06/63] set development version to v0.6.9-pre --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 29e36a46dc5..0bbdec206d8 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "Trixi" uuid = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb" authors = ["Michael Schlottke-Lakemper ", "Gregor Gassner ", "Hendrik Ranocha ", "Andrew R. Winters ", "Jesse Chan "] -version = "0.6.8" +version = "0.6.9-pre" [deps] CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2" From f4e6e494846784e513987a91d2248c04fd616029 Mon Sep 17 00:00:00 2001 From: Benjamin Bolm <74359358+bennibolm@users.noreply.github.com> Date: Tue, 30 Jan 2024 11:07:31 +0100 Subject: [PATCH 07/63] (Thread-)Parallelize bounds check routine for subcell IDP limiting (#1736) * Implement parallel bounds check for IDP limiting * Add missing warning as "experimental" from last PR * Updating `idp_bounds_delta_threaded` for all bounds at once * Revise parallel memory structure * Using maximum instead of reduce * Expand vector length to fix False Sharing problem * Generalize stride size in vector * Add suggested comment --- src/callbacks_stage/subcell_bounds_check.jl | 10 ++- .../subcell_bounds_check_2d.jl | 81 ++++++++++++------- .../dgsem_tree/dg_2d_subcell_limiters.jl | 3 + src/solvers/dgsem_tree/subcell_limiters_2d.jl | 23 ++++-- 4 files changed, 80 insertions(+), 37 deletions(-) diff --git a/src/callbacks_stage/subcell_bounds_check.jl b/src/callbacks_stage/subcell_bounds_check.jl index d7e30ab1621..9f34a6b3b4b 100644 --- a/src/callbacks_stage/subcell_bounds_check.jl +++ b/src/callbacks_stage/subcell_bounds_check.jl @@ -118,7 +118,7 @@ end @inline function finalize_callback(callback::BoundsCheckCallback, semi, limiter::SubcellLimiterIDP) (; local_minmax, positivity) = limiter - (; idp_bounds_delta) = limiter.cache + (; idp_bounds_delta_global) = limiter.cache variables = varnames(cons2cons, semi.equations) println("─"^100) @@ -128,8 +128,10 @@ end for v in limiter.local_minmax_variables_cons v_string = string(v) println("$(variables[v]):") - println("-lower bound: ", idp_bounds_delta[Symbol(v_string, "_min")][2]) - println("-upper bound: ", idp_bounds_delta[Symbol(v_string, "_max")][2]) + println("- lower bound: ", + idp_bounds_delta_global[Symbol(v_string, "_min")]) + println("- upper bound: ", + idp_bounds_delta_global[Symbol(v_string, "_max")]) end end if positivity @@ -138,7 +140,7 @@ end continue end println(string(variables[v]) * ":\n- positivity: ", - idp_bounds_delta[Symbol(string(v), "_min")][2]) + idp_bounds_delta_global[Symbol(string(v), "_min")]) end end println("─"^100 * "\n") diff --git a/src/callbacks_stage/subcell_bounds_check_2d.jl b/src/callbacks_stage/subcell_bounds_check_2d.jl index d52eb6edb9e..545d19b5136 100644 --- a/src/callbacks_stage/subcell_bounds_check_2d.jl +++ b/src/callbacks_stage/subcell_bounds_check_2d.jl @@ -10,26 +10,37 @@ time, iter, output_directory, save_errors) (; local_minmax, positivity) = solver.volume_integral.limiter (; variable_bounds) = limiter.cache.subcell_limiter_coefficients - (; idp_bounds_delta) = limiter.cache + (; idp_bounds_delta_local, idp_bounds_delta_global) = limiter.cache + + # Note: Accessing the threaded memory vector `idp_bounds_delta_local` with + # `deviation = idp_bounds_delta_local[key][Threads.threadid()]` causes critical performance + # issues due to False Sharing. + # Initializing a vector with n times the length and using every n-th entry fixes this + # problem and allows proper scaling: + # `deviation = idp_bounds_delta_local[key][n * Threads.threadid()]` + # Since there are no processors with caches over 128B, we use `n = 128B / size(uEltype)` + stride_size = div(128, sizeof(eltype(u))) # = n if local_minmax for v in limiter.local_minmax_variables_cons v_string = string(v) key_min = Symbol(v_string, "_min") key_max = Symbol(v_string, "_max") - deviation_min = idp_bounds_delta[key_min] - deviation_max = idp_bounds_delta[key_max] - for element in eachelement(solver, cache), j in eachnode(solver), - i in eachnode(solver) - - var = u[v, i, j, element] - deviation_min[1] = max(deviation_min[1], - variable_bounds[key_min][i, j, element] - var) - deviation_max[1] = max(deviation_max[1], - var - variable_bounds[key_max][i, j, element]) + deviation_min_threaded = idp_bounds_delta_local[key_min] + deviation_max_threaded = idp_bounds_delta_local[key_max] + @threaded for element in eachelement(solver, cache) + deviation_min = deviation_min_threaded[stride_size * Threads.threadid()] + deviation_max = deviation_max_threaded[stride_size * Threads.threadid()] + for j in eachnode(solver), i in eachnode(solver) + var = u[v, i, j, element] + deviation_min = max(deviation_min, + variable_bounds[key_min][i, j, element] - var) + deviation_max = max(deviation_max, + var - variable_bounds[key_max][i, j, element]) + end + deviation_min_threaded[stride_size * Threads.threadid()] = deviation_min + deviation_max_threaded[stride_size * Threads.threadid()] = deviation_max end - deviation_min[2] = max(deviation_min[2], deviation_min[1]) - deviation_max[2] = max(deviation_max[2], deviation_max[1]) end end if positivity @@ -38,17 +49,28 @@ continue end key = Symbol(string(v), "_min") - deviation = idp_bounds_delta[key] - for element in eachelement(solver, cache), j in eachnode(solver), - i in eachnode(solver) - - var = u[v, i, j, element] - deviation[1] = max(deviation[1], - variable_bounds[key][i, j, element] - var) + deviation_threaded = idp_bounds_delta_local[key] + @threaded for element in eachelement(solver, cache) + deviation = deviation_threaded[stride_size * Threads.threadid()] + for j in eachnode(solver), i in eachnode(solver) + var = u[v, i, j, element] + deviation = max(deviation, + variable_bounds[key][i, j, element] - var) + end + deviation_threaded[stride_size * Threads.threadid()] = deviation end - deviation[2] = max(deviation[2], deviation[1]) end end + + for (key, _) in idp_bounds_delta_local + # Calculate maximum deviations of all threads + idp_bounds_delta_local[key][stride_size] = maximum(idp_bounds_delta_local[key][stride_size * i] + for i in 1:Threads.nthreads()) + # Update global maximum deviations + idp_bounds_delta_global[key] = max(idp_bounds_delta_global[key], + idp_bounds_delta_local[key][stride_size]) + end + if save_errors # Print to output file open("$output_directory/deviations.txt", "a") do f @@ -56,8 +78,10 @@ if local_minmax for v in limiter.local_minmax_variables_cons v_string = string(v) - print(f, ", ", idp_bounds_delta[Symbol(v_string, "_min")][1], ", ", - idp_bounds_delta[Symbol(v_string, "_max")][1]) + print(f, ", ", + idp_bounds_delta_local[Symbol(v_string, "_min")][stride_size], + ", ", + idp_bounds_delta_local[Symbol(v_string, "_max")][stride_size]) end end if positivity @@ -65,14 +89,17 @@ if v in limiter.local_minmax_variables_cons continue end - print(f, ", ", idp_bounds_delta[Symbol(string(v), "_min")][1]) + print(f, ", ", + idp_bounds_delta_local[Symbol(string(v), "_min")][stride_size]) end end println(f) end - # Reset first entries of idp_bounds_delta - for (key, _) in idp_bounds_delta - idp_bounds_delta[key][1] = zero(eltype(idp_bounds_delta[key][1])) + # Reset local maximum deviations + for (key, _) in idp_bounds_delta_local + for i in 1:Threads.nthreads() + idp_bounds_delta_local[key][stride_size * i] = zero(eltype(idp_bounds_delta_local[key][stride_size])) + end end end diff --git a/src/solvers/dgsem_tree/dg_2d_subcell_limiters.jl b/src/solvers/dgsem_tree/dg_2d_subcell_limiters.jl index 2fc62f548d2..9af8b65b4cd 100644 --- a/src/solvers/dgsem_tree/dg_2d_subcell_limiters.jl +++ b/src/solvers/dgsem_tree/dg_2d_subcell_limiters.jl @@ -470,6 +470,9 @@ end For subcell limiting, the calculation of local bounds for non-periodic domains require the boundary outer state. This function returns the boundary value at time `t` and for node with spatial indices `indices`. + +!!! warning "Experimental implementation" + This is an experimental feature and may change in future releases. """ @inline function get_boundary_outer_state(boundary_condition::BoundaryConditionDirichlet, cache, t, equations, dg, indices...) diff --git a/src/solvers/dgsem_tree/subcell_limiters_2d.jl b/src/solvers/dgsem_tree/subcell_limiters_2d.jl index 384f4178bc9..3d272359fe4 100644 --- a/src/solvers/dgsem_tree/subcell_limiters_2d.jl +++ b/src/solvers/dgsem_tree/subcell_limiters_2d.jl @@ -13,21 +13,32 @@ function create_cache(limiter::Type{SubcellLimiterIDP}, equations::AbstractEquat bound_keys) # Memory for bounds checking routine with `BoundsCheckCallback`. - # The first entry of each vector contains the maximum deviation since the last export. - # The second one contains the total maximum deviation. - idp_bounds_delta = Dict{Symbol, Vector{real(basis)}}() + # Local variable contains the maximum deviation since the last export. + # Using a threaded vector to parallelize bounds check. + idp_bounds_delta_local = Dict{Symbol, Vector{real(basis)}}() + # Global variable contains the total maximum deviation. + idp_bounds_delta_global = Dict{Symbol, real(basis)}() + # Note: False sharing causes critical performance issues on multiple threads when using a vector + # of length `Threads.nthreads()`. Initializing a vector of length `n * Threads.nthreads()` + # and then only using every n-th entry, fixes the problem and allows proper scaling. + # Since there are no processors with caches over 128B, we use `n = 128B / size(uEltype)` + stride_size = div(128, sizeof(eltype(basis.nodes))) # = n for key in bound_keys - idp_bounds_delta[key] = zeros(real(basis), 2) + idp_bounds_delta_local[key] = [zero(real(basis)) + for _ in 1:(stride_size * Threads.nthreads())] + idp_bounds_delta_global[key] = zero(real(basis)) end - return (; subcell_limiter_coefficients, idp_bounds_delta) + return (; subcell_limiter_coefficients, idp_bounds_delta_local, + idp_bounds_delta_global) end function (limiter::SubcellLimiterIDP)(u::AbstractArray{<:Any, 4}, semi, dg::DGSEM, t, dt; kwargs...) @unpack alpha = limiter.cache.subcell_limiter_coefficients - alpha .= zero(eltype(alpha)) + # TODO: Do not abuse `reset_du!` but maybe implement a generic `set_zero!` + @trixi_timeit timer() "reset alpha" reset_du!(alpha, dg, semi.cache) if limiter.local_minmax @trixi_timeit timer() "local min/max limiting" idp_local_minmax!(alpha, limiter, From 4b07706f01cc17c7ef6215c21da312e221cb0c00 Mon Sep 17 00:00:00 2001 From: Daniel Doehring Date: Tue, 30 Jan 2024 20:32:24 +0100 Subject: [PATCH 08/63] Do not safe sol (#1820) --- examples/p4est_2d_dgsem/elixir_euler_NACA6412airfoil_mach2.jl | 1 + 1 file changed, 1 insertion(+) diff --git a/examples/p4est_2d_dgsem/elixir_euler_NACA6412airfoil_mach2.jl b/examples/p4est_2d_dgsem/elixir_euler_NACA6412airfoil_mach2.jl index fcd2ca00e10..7e55a259596 100644 --- a/examples/p4est_2d_dgsem/elixir_euler_NACA6412airfoil_mach2.jl +++ b/examples/p4est_2d_dgsem/elixir_euler_NACA6412airfoil_mach2.jl @@ -103,6 +103,7 @@ callbacks = CallbackSet(summary_callback, ############################################################################### sol = solve(ode, SSPRK104(; thread = OrdinaryDiffEq.True()); dt = 1.0, # overwritten by the `stepsize_callback` + save_everystep = false, callback = callbacks); summary_callback() # print the timer summary From 07990295b7ba155669ef4c2953809abe8e3c4880 Mon Sep 17 00:00:00 2001 From: Simon Candelaresi <10759273+SimonCan@users.noreply.github.com> Date: Wed, 31 Jan 2024 13:21:11 +0000 Subject: [PATCH 09/63] Sc/converters coupling (#1558) * Added coupling converters. * Added generic converter_function for structured 2d meshes. * Added example elixir for coupling converters. * Cleaned up converter coupling elixir. * Added equations in coupling converters. * Added converter functions. * Added identity converter function. * Autoformat for converter coupling implementation. * Added coupled converter elixir. * Corrected file name of coupled converters test. * Removed redundant doc string. * Added function signature in doc string. * Removed coverage_override in coupled tests. * Removed old commented code. * Update make.jl Added interface coupling docs to the main menu. * Update make.jl Moved converter coupling section. * Create coupling.md * Update coupling.md Added some documentation on coupling converters. * Removed troublesome AnalysisCallbackCoupled from test. * Chenged coupling converter function. * Changed coupling converter function and updated tests. * Sepcialized coupling function call. * Removed volume coupling from documentation to avoit confusion. * Update src/coupling_converters/coupling_converters.jl Co-authored-by: Hendrik Ranocha * Removed redundant converter function for coupling. * Removed redundant coupling converter file mentioned in some files. * Autoreformatted. * Removed old coupled elixir and replaced it with one using converter functions. * Updated errors for coupled tests. * Corrected test results for coupled equations. * Corrected comment. * Removed coupled test from special tests. * Removed coupled test from specials. * Chaned the coupling function to the identity. * Updated coupling tests. * Updated errors for coupled test. * Added advice about binary compatability for coupled equations in the documentation. * Typo. * Added numerical fluxes. * Corrected rs copy routine. Now loop over this semi's components. * Reformatted equations source file. * Removed problemating include of time_integration.jl. * Removed export of deleted methods. * Reverted to old version of compressible Euler multicomponent with no support for structured grid. * Renamed documentation file for multi-physics coupling. * Renamed doc reference. * Update src/semidiscretization/semidiscretization_coupled.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/src/multi-physics_coupling.md Co-authored-by: Michael Schlottke-Lakemper * Update docs/src/multi-physics_coupling.md Co-authored-by: Michael Schlottke-Lakemper * Update docs/src/multi-physics_coupling.md Co-authored-by: Michael Schlottke-Lakemper * Reinstated structured_2d_dgsem coupled in special tests. * Update examples/structured_2d_dgsem/elixir_advection_coupled.jl Co-authored-by: Michael Schlottke-Lakemper * Renamed CouplingFunction to CouplingConverter. * Update src/semidiscretization/semidiscretization_coupled.jl Co-authored-by: Michael Schlottke-Lakemper * Cleaned the copy of coupled boundary values. * Reduced time span for example coupling elixir. * Removed redundant loop. * Applied formatter. * Removed default coupling covnerter function. * Moved coupling converter function into elixir. * Apply suggestions from code review Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com> * Update docs/make.jl Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com> * Removed coupling_converters.jl from the include. * Corrected introduced issue with coupling boundary copy. The latest change to clean up the boundary copying introduced a bug related to the determination of the wrong node indices. This is now corrected. * Corrected comment on final simulation time. * Updated errors for coupled test to reflect changed final simulation time. * Added miladd. * Corrected coordinate finding in semidiscretization_coupled. * Fixed issued related to memory allocation. * Corrected loop over semidiscretization. * Removed commented out code. * Fixed type instability with loops over semidiscretizations using lispy tuple programming. * Removed obsolete code. * Fixed another typa instability in coupled semidiscretization. * Cleaning up of the coupled semidiscretization. * Autoformatted coupled semidiscretization. * Fixed last type instability in coupling. * Autoformatter on semidiscretization. * Fixed bug in boundary values copy that arose when coupling multiple systems. * aplpied autoformatter on coupled semidiscretization. * Extended the structured 2d example elixir for the coupled advection to 4 semidiscretizations. This hase two purpuses: 1. Users are given an example fro 2d coupling avoiding common pitfalls. 2. This increases the code coverege for the test. * Updated test results for coupled advection in 2d to reflect the 4 semidiscretizations that are now used. * Added correct errors for tests for the coupled adveciton equations in structured 2d. * Update examples/structured_2d_dgsem/elixir_advection_coupled.jl Co-authored-by: Erik Faulhaber <44124897+efaulhaber@users.noreply.github.com> * Update examples/structured_2d_dgsem/elixir_advection_coupled.jl Co-authored-by: Erik Faulhaber <44124897+efaulhaber@users.noreply.github.com> * Update src/semidiscretization/semidiscretization_coupled.jl Co-authored-by: Erik Faulhaber <44124897+efaulhaber@users.noreply.github.com> * Update src/semidiscretization/semidiscretization_coupled.jl Co-authored-by: Erik Faulhaber <44124897+efaulhaber@users.noreply.github.com> * Update src/semidiscretization/semidiscretization_coupled.jl Co-authored-by: Erik Faulhaber <44124897+efaulhaber@users.noreply.github.com> * Update src/semidiscretization/semidiscretization_coupled.jl Co-authored-by: Erik Faulhaber <44124897+efaulhaber@users.noreply.github.com> * Update src/semidiscretization/semidiscretization_coupled.jl Co-authored-by: Erik Faulhaber <44124897+efaulhaber@users.noreply.github.com> * Update src/semidiscretization/semidiscretization_coupled.jl Co-authored-by: Erik Faulhaber <44124897+efaulhaber@users.noreply.github.com> * Update src/semidiscretization/semidiscretization_coupled.jl Co-authored-by: Erik Faulhaber <44124897+efaulhaber@users.noreply.github.com> * Corrected foreach_enumerate implementation. * Fix closing parens * Remove unused recursive rhs! * Pass equations to converter function * Apply formatting * Reverted copy_to_coupled_boundary to previou version to avoid type instability. * Corrected computation of coupled semidiscretizations and fixed memory issue. * Removed redundant nelements function, as it is no longer used. * Applied autoformatter. * Improvements in style and added info about passing equations to coupling functions, as suggested by Andrew and Daniel. * Restored timings in semidiscretization coupled. --------- Co-authored-by: Michael Schlottke-Lakemper Co-authored-by: Hendrik Ranocha Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com> Co-authored-by: Erik Faulhaber <44124897+efaulhaber@users.noreply.github.com> --- docs/make.jl | 1 + docs/src/multi-physics_coupling.md | 46 +++++ .../elixir_advection_coupled.jl | 191 +++++++++++++----- .../semidiscretization_coupled.jl | 191 ++++++++++++------ test/test_structured_2d.jl | 28 ++- 5 files changed, 340 insertions(+), 117 deletions(-) create mode 100644 docs/src/multi-physics_coupling.md diff --git a/docs/make.jl b/docs/make.jl index dee87371bd1..7fce3b31e24 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -108,6 +108,7 @@ makedocs( ], "Time integration" => "time_integration.md", "Callbacks" => "callbacks.md", + "Coupling" => "multi-physics_coupling.md" ], "Advanced topics & developers" => [ "Conventions" =>"conventions.md", diff --git a/docs/src/multi-physics_coupling.md b/docs/src/multi-physics_coupling.md new file mode 100644 index 00000000000..eec92bc21de --- /dev/null +++ b/docs/src/multi-physics_coupling.md @@ -0,0 +1,46 @@ +# [Multi-physics coupling](@id multi-physics-coupling) +A complex simulation can consist of different spatial domains in which +different equations are being solved, different numerical methods being used +or the grid structure is different. +One example would be a fluid in a tank and an extended hot plate attached to it. +We would then like to solve the Navier-Stokes equations in the fluid domain +and the heat conduction equations in the plate. +The coupling would happen at the interface through the exchange of thermal energy. + + +## Converter coupling +It may happen that the two systems to be coupled do not share any variables, but +share some of the physics. +In such a situation, the same physics is just represented in a different form and with +a different set of variables. +This is the case, for instance assuming two domains, if there is a fluid system in one domain +and a Vlasov system in the other domain. +In that case we would have variables representing distribution functions of +the Vlasov system on one side and variables representing the mechanical quantities, like density, +of the fluid system. +To translate the fields from one description to the other one needs to use +converter functions. +These functions need to be hand tailored by the user in the elixir file where each +pair of coupled systems requires two coupling functions, one for each direction. + +In the general case, we have a system $A$ with $m$ variables +$u_{A,i}, \: i = 1, \dots, m$ and another +system $B$ with $n$ variables $u_{B,j}, \: j = 1, \dots, n$. +We then define two coupling functions, one that transforms $u_A$ into $u_B$ +and one that goes the other way. + +In their minimal form they take the position vector $x$, state vector $u$ +and the equations of the two coupled systems +and return the transformed variables. +By passing the equations we can make use of their parameters, if they are required. +Examples can be seen in `examples/structured_2d_dgsem/elixir_advection_coupled.jl`. + + +## Warning about binary compatibility +Currently the coordinate values on the nodes can differ by machine precision when +simulating the mesh and when splitting the mesh in multiple domains. +This is an issue coming from the coordinate interpolation on the nodes. +As a result, running a simulation in a single system and in two coupled domains +may result in a difference of the order of the machine precision. +While this is not an issue for most practical problems, it is best to keep this in mind when comparing test runs. + diff --git a/examples/structured_2d_dgsem/elixir_advection_coupled.jl b/examples/structured_2d_dgsem/elixir_advection_coupled.jl index 2a56d23f4c0..43b68f21b03 100644 --- a/examples/structured_2d_dgsem/elixir_advection_coupled.jl +++ b/examples/structured_2d_dgsem/elixir_advection_coupled.jl @@ -2,31 +2,38 @@ using OrdinaryDiffEq using Trixi ############################################################################### -# Coupled semidiscretization of two linear advection systems, which are connected periodically +# Coupled semidiscretization of four linear advection systems using converter functions such that +# they are also coupled across the domain boundaries to generate a periodic system. # -# In this elixir, we have a square domain that is divided into a left half and a right half. On each -# half of the domain, a completely independent SemidiscretizationHyperbolic is created for the -# linear advection equations. The two systems are coupled in the x-direction and have periodic -# boundaries in the y-direction. For a high-level overview, see also the figure below: +# In this elixir, we have a square domain that is divided into a upper-left, lower-left, +# upper-right and lower-right quarter. On each quarter +# of the domain, a completely independent SemidiscretizationHyperbolic is created for the +# linear advection equations. The four systems are coupled in the x and y-direction. +# For a high-level overview, see also the figure below: # # (-1, 1) ( 1, 1) # ┌────────────────────┬────────────────────┐ -# │ ↑ periodic ↑ │ ↑ periodic ↑ │ -# │ │ │ +# │ ↑ coupled ↑ │ ↑ coupled ↑ │ # │ │ │ # │ ========= │ ========= │ # │ system #1 │ system #2 │ # │ ========= │ ========= │ # │ │ │ +# │<-- coupled │<-- coupled │ +# │ coupled -->│ coupled -->│ # │ │ │ +# │ ↓ coupled ↓ │ ↓ coupled ↓ │ +# ├────────────────────┼────────────────────┤ +# │ ↑ coupled ↑ │ ↑ coupled ↑ │ # │ │ │ +# │ ========= │ ========= │ +# │ system #3 │ system #4 │ +# │ ========= │ ========= │ # │ │ │ -# │ coupled -->│<-- coupled │ -# │ │ │ -# │<-- coupled │ coupled -->│ -# │ │ │ +# │<-- coupled │<-- coupled │ +# │ coupled -->│ coupled -->│ # │ │ │ -# │ ↓ periodic ↓ │ ↓ periodic ↓ │ +# │ ↓ coupled ↓ │ ↓ coupled ↓ │ # └────────────────────┴────────────────────┘ # (-1, -1) ( 1, -1) @@ -36,60 +43,135 @@ equations = LinearScalarAdvectionEquation2D(advection_velocity) # Create DG solver with polynomial degree = 3 and (local) Lax-Friedrichs/Rusanov flux as surface flux solver = DGSEM(polydeg = 3, surface_flux = flux_lax_friedrichs) -# First mesh is the left half of a [-1,1]^2 square -coordinates_min1 = (-1.0, -1.0) # minimum coordinates (min(x), min(y)) +# This will be the number of elements for each quarter/semidiscretization. +cells_per_dimension = (8, 8) + +########### +# system #1 +########### + +coordinates_min1 = (-1.0, 0.0) # minimum coordinates (min(x), min(y)) coordinates_max1 = (0.0, 1.0) # maximum coordinates (max(x), max(y)) -# Define identical resolution as a variable such that it is easier to change from `trixi_include` -cells_per_dimension = (8, 16) +mesh1 = StructuredMesh(cells_per_dimension, coordinates_min1, coordinates_max1) -cells_per_dimension1 = cells_per_dimension +# Define the coupling functions +coupling_function12 = (x, u, equations_other, equations_own) -> u +coupling_function13 = (x, u, equations_other, equations_own) -> u -mesh1 = StructuredMesh(cells_per_dimension1, coordinates_min1, coordinates_max1) +# Define the coupling boundary conditions and the system it is coupled to. +boundary_conditions_x_neg1 = BoundaryConditionCoupled(2, (:end, :i_forward), Float64, + coupling_function12) +boundary_conditions_x_pos1 = BoundaryConditionCoupled(2, (:begin, :i_forward), Float64, + coupling_function12) +boundary_conditions_y_neg1 = BoundaryConditionCoupled(3, (:i_forward, :end), Float64, + coupling_function13) +boundary_conditions_y_pos1 = BoundaryConditionCoupled(3, (:i_forward, :begin), Float64, + coupling_function13) # A semidiscretization collects data structures and functions for the spatial discretization semi1 = SemidiscretizationHyperbolic(mesh1, equations, initial_condition_convergence_test, solver, - boundary_conditions = ( - # Connect left boundary with right boundary of right mesh - x_neg = BoundaryConditionCoupled(2, - (:end, - :i_forward), - Float64), - # Connect right boundary with left boundary of right mesh - x_pos = BoundaryConditionCoupled(2, - (:begin, - :i_forward), - Float64), - y_neg = boundary_condition_periodic, - y_pos = boundary_condition_periodic)) - -# Second mesh is the right half of a [-1,1]^2 square -coordinates_min2 = (0.0, -1.0) # minimum coordinates (min(x), min(y)) + boundary_conditions = (x_neg = boundary_conditions_x_neg1, + x_pos = boundary_conditions_x_pos1, + y_neg = boundary_conditions_y_neg1, + y_pos = boundary_conditions_y_pos1)) + +########### +# system #2 +########### + +coordinates_min2 = (0.0, 0.0) # minimum coordinates (min(x), min(y)) coordinates_max2 = (1.0, 1.0) # maximum coordinates (max(x), max(y)) -cells_per_dimension2 = cells_per_dimension +mesh2 = StructuredMesh(cells_per_dimension, coordinates_min2, coordinates_max2) -mesh2 = StructuredMesh(cells_per_dimension2, coordinates_min2, coordinates_max2) +# Define the coupling functions +coupling_function21 = (x, u, equations_other, equations_own) -> u +coupling_function24 = (x, u, equations_other, equations_own) -> u +# Define the coupling boundary conditions and the system it is coupled to. +boundary_conditions_x_neg2 = BoundaryConditionCoupled(1, (:end, :i_forward), Float64, + coupling_function21) +boundary_conditions_x_pos2 = BoundaryConditionCoupled(1, (:begin, :i_forward), Float64, + coupling_function21) +boundary_conditions_y_neg2 = BoundaryConditionCoupled(4, (:i_forward, :end), Float64, + coupling_function24) +boundary_conditions_y_pos2 = BoundaryConditionCoupled(4, (:i_forward, :begin), Float64, + coupling_function24) + +# A semidiscretization collects data structures and functions for the spatial discretization semi2 = SemidiscretizationHyperbolic(mesh2, equations, initial_condition_convergence_test, solver, - boundary_conditions = ( - # Connect left boundary with right boundary of left mesh - x_neg = BoundaryConditionCoupled(1, - (:end, - :i_forward), - Float64), - # Connect right boundary with left boundary of left mesh - x_pos = BoundaryConditionCoupled(1, - (:begin, - :i_forward), - Float64), - y_neg = boundary_condition_periodic, - y_pos = boundary_condition_periodic)) - -# Create a semidiscretization that bundles semi1 and semi2 -semi = SemidiscretizationCoupled(semi1, semi2) + boundary_conditions = (x_neg = boundary_conditions_x_neg2, + x_pos = boundary_conditions_x_pos2, + y_neg = boundary_conditions_y_neg2, + y_pos = boundary_conditions_y_pos2)) + +########### +# system #3 +########### + +coordinates_min3 = (-1.0, -1.0) # minimum coordinates (min(x), min(y)) +coordinates_max3 = (0.0, 0.0) # maximum coordinates (max(x), max(y)) + +mesh3 = StructuredMesh(cells_per_dimension, coordinates_min3, coordinates_max3) + +# Define the coupling functions +coupling_function34 = (x, u, equations_other, equations_own) -> u +coupling_function31 = (x, u, equations_other, equations_own) -> u + +# Define the coupling boundary conditions and the system it is coupled to. +boundary_conditions_x_neg3 = BoundaryConditionCoupled(4, (:end, :i_forward), Float64, + coupling_function34) +boundary_conditions_x_pos3 = BoundaryConditionCoupled(4, (:begin, :i_forward), Float64, + coupling_function34) +boundary_conditions_y_neg3 = BoundaryConditionCoupled(1, (:i_forward, :end), Float64, + coupling_function31) +boundary_conditions_y_pos3 = BoundaryConditionCoupled(1, (:i_forward, :begin), Float64, + coupling_function31) + +# A semidiscretization collects data structures and functions for the spatial discretization +semi3 = SemidiscretizationHyperbolic(mesh3, equations, initial_condition_convergence_test, + solver, + boundary_conditions = (x_neg = boundary_conditions_x_neg3, + x_pos = boundary_conditions_x_pos3, + y_neg = boundary_conditions_y_neg3, + y_pos = boundary_conditions_y_pos3)) + +########### +# system #4 +########### + +coordinates_min4 = (0.0, -1.0) # minimum coordinates (min(x), min(y)) +coordinates_max4 = (1.0, 0.0) # maximum coordinates (max(x), max(y)) + +mesh4 = StructuredMesh(cells_per_dimension, coordinates_min4, coordinates_max4) + +# Define the coupling functions +coupling_function43 = (x, u, equations_other, equations_own) -> u +coupling_function42 = (x, u, equations_other, equations_own) -> u + +# Define the coupling boundary conditions and the system it is coupled to. +boundary_conditions_x_neg4 = BoundaryConditionCoupled(3, (:end, :i_forward), Float64, + coupling_function43) +boundary_conditions_x_pos4 = BoundaryConditionCoupled(3, (:begin, :i_forward), Float64, + coupling_function43) +boundary_conditions_y_neg4 = BoundaryConditionCoupled(2, (:i_forward, :end), Float64, + coupling_function42) +boundary_conditions_y_pos4 = BoundaryConditionCoupled(2, (:i_forward, :begin), Float64, + coupling_function42) + +# A semidiscretization collects data structures and functions for the spatial discretization +semi4 = SemidiscretizationHyperbolic(mesh4, equations, initial_condition_convergence_test, + solver, + boundary_conditions = (x_neg = boundary_conditions_x_neg4, + x_pos = boundary_conditions_x_pos4, + y_neg = boundary_conditions_y_neg4, + y_pos = boundary_conditions_y_pos4)) + +# Create a semidiscretization that bundles all the semidiscretizations. +semi = SemidiscretizationCoupled(semi1, semi2, semi3, semi4) ############################################################################### # ODE solvers, callbacks etc. @@ -104,7 +186,10 @@ summary_callback = SummaryCallback() # The AnalysisCallback allows to analyse the solution in regular intervals and prints the results analysis_callback1 = AnalysisCallback(semi1, interval = 100) analysis_callback2 = AnalysisCallback(semi2, interval = 100) -analysis_callback = AnalysisCallbackCoupled(semi, analysis_callback1, analysis_callback2) +analysis_callback3 = AnalysisCallback(semi3, interval = 100) +analysis_callback4 = AnalysisCallback(semi4, interval = 100) +analysis_callback = AnalysisCallbackCoupled(semi, analysis_callback1, analysis_callback2, + analysis_callback3, analysis_callback4) # The SaveSolutionCallback allows to save the solution to a file in regular intervals save_solution = SaveSolutionCallback(interval = 100, diff --git a/src/semidiscretization/semidiscretization_coupled.jl b/src/semidiscretization/semidiscretization_coupled.jl index 0941ae6a8ca..dc21dbe9a1e 100644 --- a/src/semidiscretization/semidiscretization_coupled.jl +++ b/src/semidiscretization/semidiscretization_coupled.jl @@ -1,3 +1,10 @@ +# By default, Julia/LLVM does not use fused multiply-add operations (FMAs). +# Since these FMAs can increase the performance of many numerical algorithms, +# we need to opt-in explicitly. +# See https://ranocha.de/blog/Optimizing_EC_Trixi for further details. +@muladd begin +#! format: noindent + """ SemidiscretizationCoupled @@ -65,11 +72,13 @@ function Base.show(io::IO, ::MIME"text/plain", semi::SemidiscretizationCoupled) summary_line(io, "system", i) mesh, equations, solver, _ = mesh_equations_solver_cache(semi.semis[i]) summary_line(increment_indent(io), "mesh", mesh |> typeof |> nameof) - summary_line(increment_indent(io), "equations", equations |> typeof |> nameof) + summary_line(increment_indent(io), "equations", + equations |> typeof |> nameof) summary_line(increment_indent(io), "initial condition", semi.semis[i].initial_condition) # no boundary conditions since that could be too much - summary_line(increment_indent(io), "source terms", semi.semis[i].source_terms) + summary_line(increment_indent(io), "source terms", + semi.semis[i].source_terms) summary_line(increment_indent(io), "solver", solver |> typeof |> nameof) end summary_line(io, "total #DOFs per field", ndofs(semi)) @@ -106,20 +115,14 @@ end @inline Base.real(semi::SemidiscretizationCoupled) = promote_type(real.(semi.semis)...) -@inline Base.eltype(semi::SemidiscretizationCoupled) = promote_type(eltype.(semi.semis)...) +@inline function Base.eltype(semi::SemidiscretizationCoupled) + promote_type(eltype.(semi.semis)...) +end @inline function ndofs(semi::SemidiscretizationCoupled) sum(ndofs, semi.semis) end -@inline function nelements(semi::SemidiscretizationCoupled) - return sum(semi.semis) do semi_ - mesh, equations, solver, cache = mesh_equations_solver_cache(semi_) - - nelements(mesh, solver, cache) - end -end - function compute_coefficients(t, semi::SemidiscretizationCoupled) @unpack u_indices = semi @@ -137,23 +140,40 @@ end @view u_ode[semi.u_indices[index]] end +# Same as `foreach(enumerate(something))`, but without allocations. +# +# Note that compile times may increase if this is used with big tuples. +@inline foreach_enumerate(func, collection) = foreach_enumerate(func, collection, 1) +@inline foreach_enumerate(func, collection::Tuple{}, index) = nothing + +@inline function foreach_enumerate(func, collection, index) + element = first(collection) + remaining_collection = Base.tail(collection) + + func((index, element)) + + # Process remaining collection + foreach_enumerate(func, remaining_collection, index + 1) +end + function rhs!(du_ode, u_ode, semi::SemidiscretizationCoupled, t) @unpack u_indices = semi time_start = time_ns() @trixi_timeit timer() "copy to coupled boundaries" begin - for semi_ in semi.semis - copy_to_coupled_boundary!(semi_.boundary_conditions, u_ode, semi) + foreach(semi.semis) do semi_ + copy_to_coupled_boundary!(semi_.boundary_conditions, u_ode, semi, semi_) end end # Call rhs! for each semidiscretization - for i in eachsystem(semi) - u_loc = get_system_u_ode(u_ode, i, semi) - du_loc = get_system_u_ode(du_ode, i, semi) - - @trixi_timeit timer() "system #$i" rhs!(du_loc, u_loc, semi.semis[i], t) + @trixi_timeit timer() "copy to coupled boundaries" begin + foreach_enumerate(semi.semis) do (i, semi_) + u_loc = get_system_u_ode(u_ode, i, semi) + du_loc = get_system_u_ode(du_ode, i, semi) + rhs!(du_loc, u_loc, semi_, t) + end end runtime = time_ns() - time_start @@ -309,7 +329,8 @@ end for i in eachsystem(semi) u_ode_slice = get_system_u_ode(u_ode, i, semi) - save_solution_file(semis[i], u_ode_slice, solution_callback, integrator, system = i) + save_solution_file(semis[i], u_ode_slice, solution_callback, integrator, + system = i) end end @@ -332,7 +353,7 @@ end ################################################################################ """ - BoundaryConditionCoupled(other_semi_index, indices, uEltype) + BoundaryConditionCoupled(other_semi_index, indices, uEltype, coupling_converter) Boundary condition to glue two meshes together. Solution values at the boundary of another mesh will be used as boundary values. This requires the use @@ -348,32 +369,37 @@ This is currently only implemented for [`StructuredMesh`](@ref). - `indices::Tuple`: node/cell indices at the boundary of the mesh in the other semidiscretization. See examples below. - `uEltype::Type`: element type of solution +- `coupling_converter::CouplingConverter`: function to call for converting the solution + state of one system to the other system # Examples ```julia # Connect the left boundary of mesh 2 to our boundary such that our positive # boundary direction will match the positive y direction of the other boundary -BoundaryConditionCoupled(2, (:begin, :i), Float64) +BoundaryConditionCoupled(2, (:begin, :i), Float64, fun) # Connect the same two boundaries oppositely oriented -BoundaryConditionCoupled(2, (:begin, :i_backwards), Float64) +BoundaryConditionCoupled(2, (:begin, :i_backwards), Float64, fun) # Using this as y_neg boundary will connect `our_cells[i, 1, j]` to `other_cells[j, end-i, end]` -BoundaryConditionCoupled(2, (:j, :i_backwards, :end), Float64) +BoundaryConditionCoupled(2, (:j, :i_backwards, :end), Float64, fun) ``` !!! warning "Experimental code" This is an experimental feature and can change any time. """ -mutable struct BoundaryConditionCoupled{NDIMS, NDIMST2M1, uEltype <: Real, Indices} +mutable struct BoundaryConditionCoupled{NDIMS, NDIMST2M1, uEltype <: Real, Indices, + CouplingConverter} # NDIMST2M1 == NDIMS * 2 - 1 # Buffer for boundary values: [variable, nodes_i, nodes_j, cell_i, cell_j] - u_boundary :: Array{uEltype, NDIMST2M1} # NDIMS * 2 - 1 - other_semi_index :: Int - other_orientation :: Int - indices :: Indices - - function BoundaryConditionCoupled(other_semi_index, indices, uEltype) + u_boundary :: Array{uEltype, NDIMST2M1} # NDIMS * 2 - 1 + other_semi_index :: Int + other_orientation :: Int + indices :: Indices + coupling_converter :: CouplingConverter + + function BoundaryConditionCoupled(other_semi_index, indices, uEltype, + coupling_converter) NDIMS = length(indices) u_boundary = Array{uEltype, NDIMS * 2 - 1}(undef, ntuple(_ -> 0, NDIMS * 2 - 1)) @@ -385,8 +411,10 @@ mutable struct BoundaryConditionCoupled{NDIMS, NDIMST2M1, uEltype <: Real, Indic other_orientation = 3 end - new{NDIMS, NDIMS * 2 - 1, uEltype, typeof(indices)}(u_boundary, other_semi_index, - other_orientation, indices) + new{NDIMS, NDIMS * 2 - 1, uEltype, typeof(indices), + typeof(coupling_converter)}(u_boundary, + other_semi_index, other_orientation, + indices, coupling_converter) end end @@ -395,8 +423,10 @@ function Base.eltype(boundary_condition::BoundaryConditionCoupled) end function (boundary_condition::BoundaryConditionCoupled)(u_inner, orientation, direction, - cell_indices, surface_node_indices, - surface_flux_function, equations) + cell_indices, + surface_node_indices, + surface_flux_function, + equations) # get_node_vars(boundary_condition.u_boundary, equations, solver, surface_node_indices..., cell_indices...), # but we don't have a solver here u_boundary = SVector(ntuple(v -> boundary_condition.u_boundary[v, @@ -421,13 +451,15 @@ function allocate_coupled_boundary_conditions(semi::AbstractSemidiscretization) for direction in 1:n_boundaries boundary_condition = semi.boundary_conditions[direction] - allocate_coupled_boundary_condition(boundary_condition, direction, mesh, equations, + allocate_coupled_boundary_condition(boundary_condition, direction, mesh, + equations, solver) end end # Don't do anything for other BCs than BoundaryConditionCoupled -function allocate_coupled_boundary_condition(boundary_condition, direction, mesh, equations, +function allocate_coupled_boundary_condition(boundary_condition, direction, mesh, + equations, solver) return nothing end @@ -448,43 +480,69 @@ function allocate_coupled_boundary_condition(boundary_condition::BoundaryConditi end # Don't do anything for other BCs than BoundaryConditionCoupled -function copy_to_coupled_boundary!(boundary_condition, u_ode, semi) +function copy_to_coupled_boundary!(boundary_condition, u_ode, semi_coupled, semi) return nothing end +function copy_to_coupled_boundary!(u_ode, semi_coupled, semi, i, n_boundaries, + boundary_condition, boundary_conditions...) + copy_to_coupled_boundary!(boundary_condition, u_ode, semi_coupled, semi) + if i < n_boundaries + copy_to_coupled_boundary!(u_ode, semi_coupled, semi, i + 1, n_boundaries, + boundary_conditions...) + end +end + function copy_to_coupled_boundary!(boundary_conditions::Union{Tuple, NamedTuple}, u_ode, - semi) - for boundary_condition in boundary_conditions - copy_to_coupled_boundary!(boundary_condition, u_ode, semi) + semi_coupled, semi) + copy_to_coupled_boundary!(u_ode, semi_coupled, semi, 1, length(boundary_conditions), + boundary_conditions...) +end + +function mesh_equations_solver_cache(other_semi_index, i, semi_, semi_tuple...) + if i == other_semi_index + return mesh_equations_solver_cache(semi_) + else + # Walk through semidiscretizations until we find `i` + mesh_equations_solver_cache(other_semi_index, i + 1, semi_tuple...) end end # In 2D -function copy_to_coupled_boundary!(boundary_condition::BoundaryConditionCoupled{2}, u_ode, - semi) - @unpack u_indices = semi +function copy_to_coupled_boundary!(boundary_condition::BoundaryConditionCoupled{2}, + u_ode, + semi_coupled, semi) + @unpack u_indices = semi_coupled @unpack other_semi_index, other_orientation, indices = boundary_condition + @unpack coupling_converter, u_boundary = boundary_condition + + mesh_own, equations_own, solver_own, cache_own = mesh_equations_solver_cache(semi) + + mesh_other, equations_other, solver_other, cache_other = mesh_equations_solver_cache(other_semi_index, + 1, + semi_coupled.semis...) - mesh, equations, solver, cache = mesh_equations_solver_cache(semi.semis[other_semi_index]) - u = wrap_array(get_system_u_ode(u_ode, other_semi_index, semi), mesh, equations, solver, - cache) + node_coordinates_other = cache_other.elements.node_coordinates + u_ode_other = get_system_u_ode(u_ode, other_semi_index, semi_coupled) + u_other = wrap_array(u_ode_other, mesh_other, equations_other, solver_other, + cache_other) - linear_indices = LinearIndices(size(mesh)) + linear_indices = LinearIndices(size(mesh_other)) if other_orientation == 1 - cells = axes(mesh, 2) + cells = axes(mesh_other, 2) else # other_orientation == 2 - cells = axes(mesh, 1) + cells = axes(mesh_other, 1) end # Copy solution data to the coupled boundary using "delayed indexing" with # a start value and a step size to get the correct face and orientation. - node_index_range = eachnode(solver) + node_index_range = eachnode(solver_other) i_node_start, i_node_step = index_to_start_step_2d(indices[1], node_index_range) j_node_start, j_node_step = index_to_start_step_2d(indices[2], node_index_range) - i_cell_start, i_cell_step = index_to_start_step_2d(indices[1], axes(mesh, 1)) - j_cell_start, j_cell_step = index_to_start_step_2d(indices[2], axes(mesh, 2)) + i_cell_start, i_cell_step = index_to_start_step_2d(indices[1], axes(mesh_other, 1)) + j_cell_start, j_cell_step = index_to_start_step_2d(indices[2], axes(mesh_other, 2)) i_cell = i_cell_start j_cell = j_cell_start @@ -492,16 +550,26 @@ function copy_to_coupled_boundary!(boundary_condition::BoundaryConditionCoupled{ for cell in cells i_node = i_node_start j_node = j_node_start - - for i in eachnode(solver) - for v in 1:size(u, 1) - boundary_condition.u_boundary[v, i, cell] = u[v, i_node, j_node, - linear_indices[i_cell, - j_cell]] + element_id = linear_indices[i_cell, j_cell] + + for element_id in eachnode(solver_other) + x_other = get_node_coords(node_coordinates_other, equations_other, + solver_other, + i_node, j_node, linear_indices[i_cell, j_cell]) + u_node_other = get_node_vars(u_other, equations_other, solver_other, i_node, + j_node, linear_indices[i_cell, j_cell]) + u_node_converted = coupling_converter(x_other, u_node_other, + equations_other, + equations_own) + + for i in eachindex(u_node_converted) + u_boundary[i, element_id, cell] = u_node_converted[i] end + i_node += i_node_step j_node += j_node_step end + i_cell += i_cell_step j_cell += j_cell_step end @@ -511,7 +579,8 @@ end ### DGSEM/structured ################################################################################ -@inline function calc_boundary_flux_by_direction!(surface_flux_values, u, t, orientation, +@inline function calc_boundary_flux_by_direction!(surface_flux_values, u, t, + orientation, boundary_condition::BoundaryConditionCoupled, mesh::StructuredMesh, equations, surface_integral, dg::DG, cache, @@ -531,7 +600,8 @@ end sign_jacobian = sign(inverse_jacobian[node_indices..., element]) # Contravariant vector Ja^i is the normal vector - normal = sign_jacobian * get_contravariant_vector(orientation, contravariant_vectors, + normal = sign_jacobian * + get_contravariant_vector(orientation, contravariant_vectors, node_indices..., element) # If the mapping is orientation-reversing, the normal vector will be reversed (see above). @@ -608,3 +678,4 @@ function analyze_convergence(errors_coupled, iterations, return eoc_mean_values end +end # @muladd diff --git a/test/test_structured_2d.jl b/test/test_structured_2d.jl index e5d45ebcc07..522510a42e3 100644 --- a/test/test_structured_2d.jl +++ b/test/test_structured_2d.jl @@ -33,14 +33,34 @@ end @trixi_testset "elixir_advection_coupled.jl" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_advection_coupled.jl"), - l2=[7.816742843181738e-6, 7.816742843196112e-6], - linf=[6.314906965543265e-5, 6.314906965410039e-5], + l2=[ + 7.816742843336293e-6, + 7.816742843340186e-6, + 7.816742843025513e-6, + 7.816742843061526e-6, + ], + linf=[ + 6.314906965276812e-5, + 6.314906965187994e-5, + 6.31490696496595e-5, + 6.314906965032563e-5, + ], coverage_override=(maxiters = 10^5,)) @testset "analysis_callback(sol) for AnalysisCallbackCoupled" begin errors = analysis_callback(sol) - @test errors.l2≈[7.816742843181738e-6, 7.816742843196112e-6] rtol=1.0e-4 - @test errors.linf≈[6.314906965543265e-5, 6.314906965410039e-5] rtol=1.0e-4 + @test errors.l2≈[ + 7.816742843336293e-6, + 7.816742843340186e-6, + 7.816742843025513e-6, + 7.816742843061526e-6, + ] rtol=1.0e-4 + @test errors.linf≈[ + 6.314906965276812e-5, + 6.314906965187994e-5, + 6.31490696496595e-5, + 6.314906965032563e-5, + ] rtol=1.0e-4 # Ensure that we do not have excessive memory allocations # (e.g., from type instabilities) let From d53fdb59fe71c1ba956fc758b5874c3914304ddf Mon Sep 17 00:00:00 2001 From: Johannes Markert <10619309+jmark@users.noreply.github.com> Date: Wed, 31 Jan 2024 16:49:35 +0100 Subject: [PATCH 10/63] Feature: T8codeMesh backend with MPI support (#1803) * Initial commit for the new feature using t8code as meshing backend. * Delete t8code_2d_dgsem * Added new examples and tests. Testing updates for T8code.jl. * Worked in the comments. * Fixed spelling. * Update src/auxiliary/auxiliary.jl Co-authored-by: Hendrik Ranocha * Added whitespace in Unions. * Adapted commented out code block reporting the no. of elements per level. * Added dummy save mesh support for . * Added test . * Added to method signature. * Deleted unnecessary comments. * Removed commented out tests. * Fixed Morton ordering bug in 2D at mortar interfaces. * Disabled `save_solution` callbacks and added more tests. * Added more tests. * Updated code according to the review. * Update src/auxiliary/t8code.jl Co-authored-by: Hendrik Ranocha * Update src/auxiliary/t8code.jl Co-authored-by: Hendrik Ranocha * Update src/auxiliary/t8code.jl Co-authored-by: Hendrik Ranocha * Update src/auxiliary/t8code.jl Co-authored-by: Hendrik Ranocha * Update src/meshes/t8code_mesh.jl Co-authored-by: Hendrik Ranocha * Update src/meshes/t8code_mesh.jl Co-authored-by: Hendrik Ranocha * Update src/meshes/t8code_mesh.jl Co-authored-by: Hendrik Ranocha * Update src/meshes/t8code_mesh.jl Co-authored-by: Hendrik Ranocha * Update src/meshes/t8code_mesh.jl Co-authored-by: Hendrik Ranocha * Update src/meshes/t8code_mesh.jl Co-authored-by: Hendrik Ranocha * Update src/solvers/dgsem_t8code/containers_2d.jl Co-authored-by: Hendrik Ranocha * Update src/meshes/t8code_mesh.jl Co-authored-by: Hendrik Ranocha * Code cleanup. * Updated to T8code@0.3.0 * Fixing minor issues. * Fixed typo. * Code cleanup. * Enabled `set_ghost` in examples. * Generalized type info in function signature. * Added namespace qualifier. * Updated comments. * Refactored code and deleted lots of it. * Removed a copy operation. * Initial commit. * Fxinig minor bugs. * Fixed minor typo. * Added first 3d example and fixed segfault. * Added many 3D examples and tests. * Backup. * Fixed merging issues. * Adding more tests. * Fixed some merging issues and formatting. * Fixed spelling. * Fixed spelling and changed assert macro. * Applied automatic formatting. * Applied automatic formatting. * Backup. * Removed superfluous outer constructor for T8codeMesh. * Added return statement for consistency. * Fixed wrong indentation by autoformatter. * Added comments. * Made sure an exception is thrown. * Changed flags for sc_init for t8code initialization. * Updated formatting. * Workaround for error about calling MPI routines after MPI has been finalized. * Upped to T8code v0.4.1. * Added mpi_finailize_hook for proper memory cleanup. * Added t8code to test_threaded.jl * Added a `save_mesh_file` call in order to satisfy code coverage. * Improved finalizer logic for T8coeMesh. * Refined code. * Restructured to do blocks. * Moved save_mesh_file call to test file. * Fixed spelling error. * Made sc_finalize optional. * Fixed spelling. * Cleaned up examples. * Updated and cleaned t8code solver codes. * Updated tests for t8code 3D code. * Fixed spelling. * Update elixir_euler_source_terms_nonconforming_unstructured_curved.jl * Update elixir_euler_source_terms_nonconforming_unstructured_curved.jl * Fixed indentation. * Update src/solvers/dgsem_structured/dg_3d.jl Co-authored-by: Hendrik Ranocha * Update src/solvers/dgsem_t8code/containers_3d.jl Co-authored-by: Andrew Winters * Update src/callbacks_step/amr_dg3d.jl Co-authored-by: Andrew Winters * Update examples/t8code_3d_dgsem/elixir_euler_ec.jl Co-authored-by: Andrew Winters * Update examples/t8code_3d_dgsem/elixir_advection_unstructured_curved.jl Co-authored-by: Andrew Winters * Update examples/t8code_3d_dgsem/elixir_advection_amr_unstructured_curved.jl Co-authored-by: Andrew Winters * Update src/solvers/dgsem_structured/dg_3d.jl Co-authored-by: Hendrik Ranocha * Update src/meshes/t8code_mesh.jl Co-authored-by: Hendrik Ranocha * Update src/callbacks_step/analysis_dg3d.jl Co-authored-by: Hendrik Ranocha * Update examples/t8code_3d_dgsem/elixir_euler_free_stream.jl Co-authored-by: Andrew Winters * Removed NDIMS from T8codeMesh construction in case of p4est/p8est connectivity input. * Aligned T8codeMesh constructur with other mesh constructors. * Update examples/t8code_3d_dgsem/elixir_euler_sedov.jl Co-authored-by: Andrew Winters * Update examples/t8code_3d_dgsem/elixir_euler_sedov.jl Co-authored-by: Andrew Winters * Cleanup up. * Added @allocated test. * Fixed formatting. * Applied formatter. * Added ParallelT8codeMesh to constructor. * Code cleanup. * Extended T8codeMesh backend to support MPI interfaces datastructures. * Update NEWS.md (#1780) * set version to v0.6.5 * set development version to v0.6.6-pre * hotfix: restrict DiffEqBase.jl to let CI pass (#1788) * hotfix: restrict DiffEqBase.jl to let CI pass * restrict DiffEqBase.jl in main Project.toml * Update Project.toml * Parabolic Mortar for AMR `P4estMesh{3}` (#1765) * Clean branch * Un-Comment * un-comment * test coarsen * remove redundancy * Remove support for passive terms * expand resize * comments * format * Avoid code duplication * Update src/callbacks_step/amr_dg1d.jl Co-authored-by: Michael Schlottke-Lakemper * comment * comment & format * Try to increase coverage * Slightly more expressive names * Apply suggestions from code review * add specifier for 1d * Structs for resizing parabolic helpers * check if mortars are present * reuse `reinitialize_containers!` * resize calls for parabolic helpers * update analysis callbacks * Velocities for compr euler * Init container * correct copy-paste error * resize each dim * add dispatch * Add AMR for shear layer * USe only amr shear layer * first steps towards p4est parabolic amr * Add tests * remove plots * Format * remove redundant line * platform independent tests * No need for different flux_viscous comps after adding container_viscous to p4est * Laplace 3d * Longer times to allow converage to hit coarsen! * Increase testing of Laplace 3D * Add tests for velocities * remove comment * add elixir for amr testing * adding commented out mortar routines in 2D * Adding Mortar to 2d dg parabolic term * remove testing snippet * fix comments * add more arguments for dispatch * add some temporary todo notes * some updates for AP and KS * specialize mortar_fluxes_to_elements * BUGFIX: apply_jacobian_parabolic! was incorrect for P4estMesh * fixed rhs_parabolic! for mortars * more changes to elixir * indexing bug * comments * Adding the example for nonperiodic BCs with amr * hopefully this fixes AMR boundaries for parabolic terms * add elixir * Example with non periodic bopundary conditions * remove cruft * 3D parabolic amr * TGV elixir * Creating test for AMR 3D parabolic * Formatting * test formatting * Update src/Trixi.jl * Update src/equations/compressible_euler_1d.jl * Update src/equations/compressible_euler_2d.jl * Update src/equations/compressible_euler_3d.jl * Update src/solvers/dgsem_tree/container_viscous_2d.jl * Update src/solvers/dgsem_tree/container_viscous_2d.jl * Update src/solvers/dgsem_tree/container_viscous_2d.jl * Update src/solvers/dgsem_tree/container_viscous_3d.jl * Update src/solvers/dgsem_tree/container_viscous_3d.jl * Update src/solvers/dgsem_tree/container_viscous_3d.jl * Update src/solvers/dgsem_p4est/dg_2d_parabolic.jl * Update src/solvers/dgsem_p4est/dg_2d_parabolic.jl * Update src/solvers/dgsem_tree/dg_2d_parabolic.jl * Update src/solvers/dgsem_tree/dg_2d_parabolic.jl * Update src/solvers/dgsem_tree/dg_2d_parabolic.jl * Update src/solvers/dgsem_tree/dg_2d_parabolic.jl * Update src/solvers/dgsem_tree/dg_2d_parabolic.jl * Update src/solvers/dgsem_tree/dg_2d_parabolic.jl * Update src/solvers/dgsem_tree/dg_2d_parabolic.jl * Update src/solvers/dgsem_tree/dg_2d_parabolic.jl * Update src/solvers/dgsem_tree/dg_2d_parabolic.jl * Update test/test_parabolic_3d.jl * Update src/solvers/dgsem_tree/dg_3d_parabolic.jl * Update src/solvers/dgsem_tree/dg_3d_parabolic.jl * Update src/solvers/dgsem_tree/dg_3d_parabolic.jl * Update src/solvers/dgsem_tree/dg_3d_parabolic.jl * Update src/solvers/dgsem_tree/dg_3d_parabolic.jl * Update src/solvers/dgsem_tree/dg_3d_parabolic.jl * Update src/solvers/dgsem_tree/dg_3d_parabolic.jl * Update src/solvers/dgsem_tree/dg_3d_parabolic.jl * Update src/solvers/dgsem_p4est/dg_3d_parabolic.jl * Update src/solvers/dgsem_p4est/dg_3d_parabolic.jl * Update src/solvers/dgsem_p4est/dg_3d_parabolic.jl * Update src/solvers/dgsem_p4est/dg_3d_parabolic.jl * Update src/solvers/dgsem_p4est/dg_2d_parabolic.jl * Update src/solvers/dgsem_p4est/dg_2d.jl * Update src/solvers/dgsem_p4est/dg_2d_parabolic.jl * Update src/solvers/dgsem_p4est/dg_2d_parabolic.jl * Update test/test_parabolic_3d.jl * Update test/test_parabolic_3d.jl * Update test/test_parabolic_3d.jl * Update examples/p4est_3d_dgsem/elixir_navierstokes_3d_blast_wave_amr.jl * Update examples/p4est_3d_dgsem/elixir_navierstokes_taylor_green_vortex_amr.jl * Update examples/p4est_3d_dgsem/elixir_navierstokes_3d_blast_wave_amr.jl * Update examples/p4est_3d_dgsem/elixir_navierstokes_taylor_green_vortex_amr.jl * Update examples/p4est_3d_dgsem/elixir_navierstokes_3d_blast_wave_amr.jl * Update examples/p4est_3d_dgsem/elixir_navierstokes_3d_blast_wave_amr.jl * Update examples/p4est_3d_dgsem/elixir_navierstokes_taylor_green_vortex_amr.jl * Update examples/p4est_3d_dgsem/elixir_navierstokes_3d_blast_wave_amr.jl * Update examples/p4est_3d_dgsem/elixir_navierstokes_taylor_green_vortex_amr.jl * Update examples/p4est_3d_dgsem/elixir_navierstokes_3d_blast_wave_amr.jl * Update examples/p4est_3d_dgsem/elixir_navierstokes_taylor_green_vortex_amr.jl * Update dg_3d_parabolic.jl * Update test_parabolic_3d.jl * Update elixir_navierstokes_3d_blast_wave_amr.jl * Update elixir_navierstokes_taylor_green_vortex_amr.jl * Update dg_3d_parabolic.jl * Update test_parabolic_3d.jl * Update test_parabolic_3d.jl * Update examples/p4est_3d_dgsem/elixir_navierstokes_3d_blast_wave_amr.jl * Update elixir_navierstokes_3d_blast_wave_amr.jl * Update elixir_navierstokes_taylor_green_vortex_amr.jl * Update dg_3d_parabolic.jl * Update test_parabolic_3d.jl * Delete examples/p4est_3d_dgsem/elixir_navierstokes_3d_blast_wave_amr.jl * Create elixir_navierstokes_blast_wave_amr.jl * Update test_parabolic_3d.jl * Update NEWS.md * Update NEWS.md * Update src/solvers/dgsem_p4est/dg_3d_parabolic.jl * Update src/solvers/dgsem_p4est/dg_3d_parabolic.jl * Update src/solvers/dgsem_p4est/dg_3d_parabolic.jl * Update src/solvers/dgsem_p4est/dg_3d_parabolic.jl --------- Co-authored-by: Daniel_Doehring Co-authored-by: Daniel Doehring Co-authored-by: Michael Schlottke-Lakemper Co-authored-by: Jesse Chan <1156048+jlchan@users.noreply.github.com> Co-authored-by: Jesse Chan * reset the timer also on non-root MPI processes (#1787) Co-authored-by: Michael Schlottke-Lakemper * Add HLLC flux for non-cartesian meshes to CompressibleEulerEquations{2,3}D (#1790) * add HLLC flux for non-cartesian meshes * add tests for HLLC flux * Add 2D test with HLLC * Update test_p4est_3d.jl * Update test_p4est_2d.jl * Update test_p4est_3d.jl * Update src/equations/compressible_euler_3d.jl Co-authored-by: Hendrik Ranocha * Update src/equations/compressible_euler_2d.jl Co-authored-by: Hendrik Ranocha * Update compressible_euler_2d.jl * Update compressible_euler_3d.jl * Update test_p4est_2d.jl * Update test_p4est_3d.jl * Update compressible_euler_2d.jl * Update compressible_euler_2d.jl --------- Co-authored-by: Daniel Doehring Co-authored-by: Hendrik Ranocha * Bump crate-ci/typos from 1.16.23 to 1.16.26 (#1793) Bumps [crate-ci/typos](https://github.com/crate-ci/typos) from 1.16.23 to 1.16.26. - [Release notes](https://github.com/crate-ci/typos/releases) - [Changelog](https://github.com/crate-ci/typos/blob/master/CHANGELOG.md) - [Commits](https://github.com/crate-ci/typos/compare/v1.16.23...v1.16.26) --- updated-dependencies: - dependency-name: crate-ci/typos dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Extend `CompressibleEulerQuasi1D` and `ShallowWaterQuasi1D` to `DGMulti` (#1797) * adding DGMulti versions of fluxes * remove incorrect factor of 2 * add example and test * formatting * add comment * revert removing factor of 2 * formatting * add SWE quasi-1D test d * enable quasi1D SWE for DGMulti * add docstrings * formatting * Update src/equations/compressible_euler_quasi_1d.jl Co-authored-by: Hendrik Ranocha * adding comments explaining why `normal_direction` is included in 1D * Apply suggestions from code review Co-authored-by: Daniel Doehring --------- Co-authored-by: Hendrik Ranocha Co-authored-by: Daniel Doehring * Fix boundary_condition_slip_wall for SWE (#1798) * fix_wall_bc * add test * apply formatter * adjust some comments * update elixir and test; add topography * comments explaining usage of `ForwardDiff.jacobian` (#1800) * Bump actions/upload-artifact from 3 to 4 (#1795) * Bump actions/upload-artifact from 3 to 4 Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 3 to 4. - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/v3...v4) --- updated-dependencies: - dependency-name: actions/upload-artifact dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] * bump download-artifact to v4 --------- Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Hendrik Ranocha * Code cleanup. * Applied formatter. * Registered mpi t8code tests. * Added load-balancing feature to T8codeMesh. * Applied formatter. * Updated some test values. * Fixed typo. * Removed unused member variable. * Apply suggestions from code review Co-authored-by: Daniel Doehring * suggestions from review * fix format (strange?) * Added comments to help interpreting the source code. * Update src/callbacks_step/amr_dg3d.jl Co-authored-by: Benedict <135045760+bgeihe@users.noreply.github.com> * Adhered to unified mesh constructor calling scheme. * Applied formatter. * Switched to Float64 instead of Cdouble. * Update src/meshes/t8code_mesh.jl Co-authored-by: Daniel Doehring * Refactored negative volume check. * Applied formatter. * Fixed typo resp. bug. * Apply suggestions from code review Co-authored-by: Hendrik Ranocha * add missing allocation checks * Some refactoring. * Deleted msh file. * Fixed a bug. * Code cleanup. * Ignore gmsh files. * Removed adapt! from global namespace. * Added documentation. * Added @test_warn to test. * Applied formatter. * Apply suggestions from code review Co-authored-by: Hendrik Ranocha Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com> * Turned @warn to @info. * Code cleanup and added @deprecated routines in order to avoid breaking release. * Applied formatter. * Added formatter pragmas to avoid ugly formatting. * Applied formatter. * Code cleanup. Documenting. * Applied formatter. * Removed remnants of development. * Removed dubious commented out line. * minors in comments skip ci * Added `retrieve` function which downloads missing mesh file without race conditions in case of MPI environment. * Added Downloads as dependency. * Added missing namespace qualifier. * add compat bound * Apply suggestions from code review Co-authored-by: Daniel Doehring Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com> * use retrieve everywhere for downloading * try to improve formatting * and what julia formatter makes out of it * try to consolidate max_dt computation * format * add default allocation tests * remove left over vtk_write * Revert "try to consolidate max_dt computation" This reverts commit d0e9a2cb2882f426a3966aac03e6ce497e1b720f. * fix variable name * less consolidation * remove unused variables * Update src/auxiliary/auxiliary.jl Co-authored-by: Hendrik Ranocha * Update src/Trixi.jl Co-authored-by: Hendrik Ranocha * revert b068d1183 (manually) * use Trixi.download * Revert "use retrieve everywhere for downloading" This reverts commit a438547e23bc489f12beea625dcc0905a50d18ce. * change to new Trixi.download signature * format * remove merge leftover * format * Code refactor. Applied review comments. * Fixed bug. * Fixed typo. * Update src/auxiliary/auxiliary.jl Co-authored-by: Hendrik Ranocha * Update src/meshes/t8code_mesh.jl Co-authored-by: Hendrik Ranocha * Update src/meshes/t8code_mesh.jl Co-authored-by: Hendrik Ranocha * Applying review comments. * Added return early if there is nothing to do in adapt routines. --------- Signed-off-by: dependabot[bot] Co-authored-by: Johannes Markert Co-authored-by: Hendrik Ranocha Co-authored-by: Andrew Winters Co-authored-by: Jesse Chan <1156048+jlchan@users.noreply.github.com> Co-authored-by: Hendrik Ranocha Co-authored-by: Ahmad Peyvan <115842305+apey236@users.noreply.github.com> Co-authored-by: Daniel_Doehring Co-authored-by: Daniel Doehring Co-authored-by: Michael Schlottke-Lakemper Co-authored-by: Jesse Chan Co-authored-by: Benedict <135045760+bgeihe@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Patrick Ersing <114223904+patrickersing@users.noreply.github.com> Co-authored-by: Benedict Geihe Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com> --- Project.toml | 2 + .../elixir_2d_euler_vortex_unstructured.jl | 9 +- examples/dgmulti_2d/elixir_euler_hohqmesh.jl | 9 +- .../elixir_advection_amr_unstructured_flag.jl | 7 +- .../elixir_advection_unstructured_flag.jl | 7 +- .../elixir_euler_blast_wave_amr.jl | 7 +- .../elixir_euler_double_mach_amr.jl | 8 +- .../elixir_euler_forward_step_amr.jl | 8 +- .../elixir_euler_free_stream.jl | 7 +- ...e_terms_nonconforming_unstructured_flag.jl | 7 +- .../elixir_euler_supersonic_cylinder.jl | 8 +- .../elixir_euler_wall_bc_amr.jl | 8 +- examples/p4est_2d_dgsem/elixir_mhd_rotor.jl | 7 +- ...lixir_advection_amr_unstructured_curved.jl | 7 +- .../elixir_advection_unstructured_curved.jl | 7 +- examples/p4est_3d_dgsem/elixir_euler_ec.jl | 7 +- .../elixir_euler_free_stream.jl | 7 +- .../elixir_euler_free_stream_extruded.jl | 7 +- ...terms_nonconforming_unstructured_curved.jl | 7 +- ...euler_source_terms_nonperiodic_hohqmesh.jl | 8 +- .../elixir_shallowwater_well_balanced.jl | 1 - .../elixir_advection_amr_unstructured_flag.jl | 7 +- .../elixir_advection_unstructured_flag.jl | 7 +- .../elixir_euler_free_stream.jl | 7 +- ...e_terms_nonconforming_unstructured_flag.jl | 7 +- examples/t8code_2d_dgsem/elixir_mhd_rotor.jl | 7 +- ...lixir_advection_amr_unstructured_curved.jl | 9 +- .../elixir_advection_unstructured_curved.jl | 7 +- examples/t8code_3d_dgsem/elixir_euler_ec.jl | 7 +- .../elixir_euler_free_stream.jl | 7 +- .../elixir_euler_free_stream_extruded.jl | 7 +- ...terms_nonconforming_unstructured_curved.jl | 7 +- .../elixir_acoustics_gauss_wall.jl | 8 +- .../elixir_advection_basic.jl | 9 +- .../elixir_euler_basic.jl | 9 +- .../unstructured_2d_dgsem/elixir_euler_ec.jl | 9 +- .../elixir_euler_free_stream.jl | 9 +- .../elixir_euler_periodic.jl | 9 +- .../elixir_euler_sedov.jl | 7 +- .../elixir_euler_wall_bc.jl | 9 +- .../elixir_mhd_alfven_wave.jl | 8 +- .../unstructured_2d_dgsem/elixir_mhd_ec.jl | 8 +- .../elixir_shallowwater_dirichlet.jl | 8 +- .../elixir_shallowwater_ec.jl | 8 +- .../elixir_shallowwater_ec_shockcapturing.jl | 8 +- .../elixir_shallowwater_source_terms.jl | 8 +- ...ixir_shallowwater_three_mound_dam_break.jl | 13 +- ...lixir_shallowwater_twolayer_convergence.jl | 8 +- .../elixir_shallowwater_twolayer_dam_break.jl | 8 +- ...xir_shallowwater_twolayer_well_balanced.jl | 8 +- ...xir_shallowwater_wall_bc_shockcapturing.jl | 9 +- .../elixir_shallowwater_well_balanced.jl | 9 +- .../elixir_advection_basic.jl | 9 +- .../elixir_euler_free_stream.jl | 9 +- .../elixir_euler_source_terms.jl | 9 +- src/Trixi.jl | 1 + src/auxiliary/auxiliary.jl | 23 + src/auxiliary/t8code.jl | 235 +------ src/callbacks_step/amr.jl | 40 +- src/callbacks_step/amr_dg.jl | 11 +- src/callbacks_step/amr_dg2d.jl | 7 +- src/callbacks_step/amr_dg3d.jl | 7 +- src/callbacks_step/analysis_dg2d_parallel.jl | 6 +- src/callbacks_step/analysis_dg3d_parallel.jl | 6 +- src/callbacks_step/stepsize_dg2d.jl | 32 + src/callbacks_step/stepsize_dg3d.jl | 32 + src/meshes/p4est_mesh.jl | 4 + src/meshes/t8code_mesh.jl | 577 +++++++++++++++++- .../dgsem_p4est/containers_parallel.jl | 6 +- src/solvers/dgsem_p4est/dg_2d_parallel.jl | 21 +- src/solvers/dgsem_p4est/dg_3d_parallel.jl | 23 +- src/solvers/dgsem_p4est/dg_parallel.jl | 9 +- src/solvers/dgsem_t8code/containers.jl | 13 +- src/solvers/dgsem_t8code/containers_2d.jl | 3 +- src/solvers/dgsem_t8code/containers_3d.jl | 3 +- .../dgsem_t8code/containers_parallel.jl | 65 ++ src/solvers/dgsem_t8code/dg.jl | 7 +- src/solvers/dgsem_t8code/dg_parallel.jl | 135 ++++ src/solvers/dgsem_tree/dg_2d_parallel.jl | 3 +- test/test_mpi.jl | 4 +- test/test_mpi_p4est_2d.jl | 63 ++ test/test_mpi_p4est_3d.jl | 81 +++ test/test_mpi_t8code_2d.jl | 142 +++++ test/test_mpi_t8code_3d.jl | 180 ++++++ test/test_t8code_2d.jl | 7 +- 85 files changed, 1529 insertions(+), 640 deletions(-) create mode 100644 src/solvers/dgsem_t8code/containers_parallel.jl create mode 100644 src/solvers/dgsem_t8code/dg_parallel.jl create mode 100644 test/test_mpi_t8code_2d.jl create mode 100644 test/test_mpi_t8code_3d.jl diff --git a/Project.toml b/Project.toml index 0bbdec206d8..e99b08e0e81 100644 --- a/Project.toml +++ b/Project.toml @@ -9,6 +9,7 @@ ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9" DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8" DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e" DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def" +Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6" EllipsisNotation = "da5c29d0-fa7d-589e-88eb-ea29b0a81949" FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b" ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" @@ -57,6 +58,7 @@ ConstructionBase = "1.3" DataStructures = "0.18.15" DiffEqBase = "6 - 6.143" DiffEqCallbacks = "2.25" +Downloads = "1.6" EllipsisNotation = "1.0" FillArrays = "0.13.2, 1" ForwardDiff = "0.10.18" diff --git a/benchmark/elixir_2d_euler_vortex_unstructured.jl b/benchmark/elixir_2d_euler_vortex_unstructured.jl index 082b6648abf..43e4b6559de 100644 --- a/benchmark/elixir_2d_euler_vortex_unstructured.jl +++ b/benchmark/elixir_2d_euler_vortex_unstructured.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -49,11 +48,9 @@ end initial_condition = initial_condition_isentropic_vortex solver = DGSEM(polydeg = 3, surface_flux = flux_lax_friedrichs) -default_mesh_file = joinpath(@__DIR__, "mesh_uniform_cartesian.mesh") -isfile(default_mesh_file) || - download("https://gist.githubusercontent.com/ranocha/f4ea19ba3b62348968c971db43d7798b/raw/a506abb9479c020920cf6068c142670fc1a9aadc/mesh_uniform_cartesian.mesh", - default_mesh_file) -mesh_file = default_mesh_file +mesh_file = Trixi.download("https://gist.githubusercontent.com/ranocha/f4ea19ba3b62348968c971db43d7798b/raw/a506abb9479c020920cf6068c142670fc1a9aadc/mesh_uniform_cartesian.mesh", + joinpath(@__DIR__, "mesh_uniform_cartesian.mesh")) + mesh = UnstructuredMesh2D(mesh_file, periodicity = true) semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver) diff --git a/examples/dgmulti_2d/elixir_euler_hohqmesh.jl b/examples/dgmulti_2d/elixir_euler_hohqmesh.jl index f534b5bc8ad..9b14a5c6827 100644 --- a/examples/dgmulti_2d/elixir_euler_hohqmesh.jl +++ b/examples/dgmulti_2d/elixir_euler_hohqmesh.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -30,12 +29,8 @@ dg = DGMulti(polydeg = 8, element_type = Quad(), approximation_type = SBP(), ############################################################################### # Get the curved quad mesh from a file (downloads the file if not available locally) - -default_mesh_file = joinpath(@__DIR__, "mesh_trixi_unstructured_mesh_docs.mesh") -isfile(default_mesh_file) || - download("https://gist.githubusercontent.com/andrewwinters5000/52056f1487853fab63b7f4ed7f171c80/raw/9d573387dfdbb8bce2a55db7246f4207663ac07f/mesh_trixi_unstructured_mesh_docs.mesh", - default_mesh_file) -mesh_file = default_mesh_file +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/52056f1487853fab63b7f4ed7f171c80/raw/9d573387dfdbb8bce2a55db7246f4207663ac07f/mesh_trixi_unstructured_mesh_docs.mesh", + joinpath(@__DIR__, "mesh_trixi_unstructured_mesh_docs.mesh")) mesh = DGMultiMesh(dg, mesh_file) diff --git a/examples/p4est_2d_dgsem/elixir_advection_amr_unstructured_flag.jl b/examples/p4est_2d_dgsem/elixir_advection_amr_unstructured_flag.jl index 0a50b3644f0..4bfb2d3e375 100644 --- a/examples/p4est_2d_dgsem/elixir_advection_amr_unstructured_flag.jl +++ b/examples/p4est_2d_dgsem/elixir_advection_amr_unstructured_flag.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -31,10 +30,8 @@ Trixi.validate_faces(faces) mapping_flag = Trixi.transfinite_mapping(faces) # Unstructured mesh with 24 cells of the square domain [-1, 1]^n -mesh_file = joinpath(@__DIR__, "square_unstructured_2.inp") -isfile(mesh_file) || - download("https://gist.githubusercontent.com/efaulhaber/63ff2ea224409e55ee8423b3a33e316a/raw/7db58af7446d1479753ae718930741c47a3b79b7/square_unstructured_2.inp", - mesh_file) +mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/63ff2ea224409e55ee8423b3a33e316a/raw/7db58af7446d1479753ae718930741c47a3b79b7/square_unstructured_2.inp", + joinpath(@__DIR__, "square_unstructured_2.inp")) mesh = P4estMesh{2}(mesh_file, polydeg = 3, mapping = mapping_flag, diff --git a/examples/p4est_2d_dgsem/elixir_advection_unstructured_flag.jl b/examples/p4est_2d_dgsem/elixir_advection_unstructured_flag.jl index 37fcc547f60..1ab96925fe6 100644 --- a/examples/p4est_2d_dgsem/elixir_advection_unstructured_flag.jl +++ b/examples/p4est_2d_dgsem/elixir_advection_unstructured_flag.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -29,10 +28,8 @@ Trixi.validate_faces(faces) mapping_flag = Trixi.transfinite_mapping(faces) # Unstructured mesh with 24 cells of the square domain [-1, 1]^n -mesh_file = joinpath(@__DIR__, "square_unstructured_2.inp") -isfile(mesh_file) || - download("https://gist.githubusercontent.com/efaulhaber/63ff2ea224409e55ee8423b3a33e316a/raw/7db58af7446d1479753ae718930741c47a3b79b7/square_unstructured_2.inp", - mesh_file) +mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/63ff2ea224409e55ee8423b3a33e316a/raw/7db58af7446d1479753ae718930741c47a3b79b7/square_unstructured_2.inp", + joinpath(@__DIR__, "square_unstructured_2.inp")) mesh = P4estMesh{2}(mesh_file, polydeg = 3, mapping = mapping_flag, diff --git a/examples/p4est_2d_dgsem/elixir_euler_blast_wave_amr.jl b/examples/p4est_2d_dgsem/elixir_euler_blast_wave_amr.jl index 0ca4fdc2eb7..5db5f74a686 100644 --- a/examples/p4est_2d_dgsem/elixir_euler_blast_wave_amr.jl +++ b/examples/p4est_2d_dgsem/elixir_euler_blast_wave_amr.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -50,10 +49,8 @@ volume_integral = VolumeIntegralShockCapturingHG(indicator_sc; solver = DGSEM(basis, surface_flux, volume_integral) # Unstructured mesh with 48 cells of the square domain [-1, 1]^n -mesh_file = joinpath(@__DIR__, "square_unstructured_1.inp") -isfile(mesh_file) || - download("https://gist.githubusercontent.com/efaulhaber/a075f8ec39a67fa9fad8f6f84342cbca/raw/a7206a02ed3a5d3cadacd8d9694ac154f9151db7/square_unstructured_1.inp", - mesh_file) +mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/a075f8ec39a67fa9fad8f6f84342cbca/raw/a7206a02ed3a5d3cadacd8d9694ac154f9151db7/square_unstructured_1.inp", + joinpath(@__DIR__, "square_unstructured_1.inp")) mesh = P4estMesh{2}(mesh_file, polydeg = 3, initial_refinement_level = 1) diff --git a/examples/p4est_2d_dgsem/elixir_euler_double_mach_amr.jl b/examples/p4est_2d_dgsem/elixir_euler_double_mach_amr.jl index 92928146d7b..fbc11e89185 100644 --- a/examples/p4est_2d_dgsem/elixir_euler_double_mach_amr.jl +++ b/examples/p4est_2d_dgsem/elixir_euler_double_mach_amr.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -99,11 +98,8 @@ solver = DGSEM(polydeg = polydeg, surface_flux = surface_flux, volume_integral = volume_integral) # Get the unstructured quad mesh from a file (downloads the file if not available locally) -default_mesh_file = joinpath(@__DIR__, "abaqus_double_mach.inp") -isfile(default_mesh_file) || - download("https://gist.githubusercontent.com/andrewwinters5000/a0806ef0d03cf5ea221af523167b6e32/raw/61ed0eb017eb432d996ed119a52fb041fe363e8c/abaqus_double_mach.inp", - default_mesh_file) -mesh_file = default_mesh_file +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/a0806ef0d03cf5ea221af523167b6e32/raw/61ed0eb017eb432d996ed119a52fb041fe363e8c/abaqus_double_mach.inp", + joinpath(@__DIR__, "abaqus_double_mach.inp")) mesh = P4estMesh{2}(mesh_file) diff --git a/examples/p4est_2d_dgsem/elixir_euler_forward_step_amr.jl b/examples/p4est_2d_dgsem/elixir_euler_forward_step_amr.jl index 0ec9fc222f2..654efd5e209 100644 --- a/examples/p4est_2d_dgsem/elixir_euler_forward_step_amr.jl +++ b/examples/p4est_2d_dgsem/elixir_euler_forward_step_amr.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -104,11 +103,8 @@ solver = DGSEM(polydeg = polydeg, surface_flux = surface_flux, volume_integral = volume_integral) # Get the unstructured quad mesh from a file (downloads the file if not available locally) -default_mesh_file = joinpath(@__DIR__, "abaqus_forward_step.inp") -isfile(default_mesh_file) || - download("https://gist.githubusercontent.com/andrewwinters5000/b346ee6aa5446687f128eab8b37d52a7/raw/cd1e1d43bebd8d2631a07caec45585ec8456ca4c/abaqus_forward_step.inp", - default_mesh_file) -mesh_file = default_mesh_file +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/b346ee6aa5446687f128eab8b37d52a7/raw/cd1e1d43bebd8d2631a07caec45585ec8456ca4c/abaqus_forward_step.inp", + joinpath(@__DIR__, "abaqus_forward_step.inp")) mesh = P4estMesh{2}(mesh_file) diff --git a/examples/p4est_2d_dgsem/elixir_euler_free_stream.jl b/examples/p4est_2d_dgsem/elixir_euler_free_stream.jl index 38307a7d781..ab11dc11567 100644 --- a/examples/p4est_2d_dgsem/elixir_euler_free_stream.jl +++ b/examples/p4est_2d_dgsem/elixir_euler_free_stream.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -31,10 +30,8 @@ end # Get the uncurved mesh from a file (downloads the file if not available locally) # Unstructured mesh with 48 cells of the square domain [-1, 1]^n -mesh_file = joinpath(@__DIR__, "square_unstructured_1.inp") -isfile(mesh_file) || - download("https://gist.githubusercontent.com/efaulhaber/a075f8ec39a67fa9fad8f6f84342cbca/raw/a7206a02ed3a5d3cadacd8d9694ac154f9151db7/square_unstructured_1.inp", - mesh_file) +mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/a075f8ec39a67fa9fad8f6f84342cbca/raw/a7206a02ed3a5d3cadacd8d9694ac154f9151db7/square_unstructured_1.inp", + joinpath(@__DIR__, "square_unstructured_1.inp")) # Map the unstructured mesh with the mapping above mesh = P4estMesh{2}(mesh_file, polydeg = 3, mapping = mapping, initial_refinement_level = 1) diff --git a/examples/p4est_2d_dgsem/elixir_euler_source_terms_nonconforming_unstructured_flag.jl b/examples/p4est_2d_dgsem/elixir_euler_source_terms_nonconforming_unstructured_flag.jl index 09d018309a6..084fd699b8e 100644 --- a/examples/p4est_2d_dgsem/elixir_euler_source_terms_nonconforming_unstructured_flag.jl +++ b/examples/p4est_2d_dgsem/elixir_euler_source_terms_nonconforming_unstructured_flag.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -31,10 +30,8 @@ mapping_flag = Trixi.transfinite_mapping(faces) # Get the uncurved mesh from a file (downloads the file if not available locally) # Unstructured mesh with 24 cells of the square domain [-1, 1]^n -mesh_file = joinpath(@__DIR__, "square_unstructured_2.inp") -isfile(mesh_file) || - download("https://gist.githubusercontent.com/efaulhaber/63ff2ea224409e55ee8423b3a33e316a/raw/7db58af7446d1479753ae718930741c47a3b79b7/square_unstructured_2.inp", - mesh_file) +mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/63ff2ea224409e55ee8423b3a33e316a/raw/7db58af7446d1479753ae718930741c47a3b79b7/square_unstructured_2.inp", + joinpath(@__DIR__, "square_unstructured_2.inp")) mesh = P4estMesh{2}(mesh_file, polydeg = 3, mapping = mapping_flag, diff --git a/examples/p4est_2d_dgsem/elixir_euler_supersonic_cylinder.jl b/examples/p4est_2d_dgsem/elixir_euler_supersonic_cylinder.jl index 36c5624ba97..76ee96d4766 100644 --- a/examples/p4est_2d_dgsem/elixir_euler_supersonic_cylinder.jl +++ b/examples/p4est_2d_dgsem/elixir_euler_supersonic_cylinder.jl @@ -13,7 +13,6 @@ # # Keywords: supersonic flow, shock capturing, AMR, unstructured curved mesh, positivity preservation, compressible Euler, 2D -using Downloads: download using OrdinaryDiffEq using Trixi @@ -82,11 +81,8 @@ solver = DGSEM(polydeg = polydeg, surface_flux = surface_flux, volume_integral = volume_integral) # Get the unstructured quad mesh from a file (downloads the file if not available locally) -default_mesh_file = joinpath(@__DIR__, "abaqus_cylinder_in_channel.inp") -isfile(default_mesh_file) || - download("https://gist.githubusercontent.com/andrewwinters5000/a08f78f6b185b63c3baeff911a63f628/raw/addac716ea0541f588b9d2bd3f92f643eb27b88f/abaqus_cylinder_in_channel.inp", - default_mesh_file) -mesh_file = default_mesh_file +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/a08f78f6b185b63c3baeff911a63f628/raw/addac716ea0541f588b9d2bd3f92f643eb27b88f/abaqus_cylinder_in_channel.inp", + joinpath(@__DIR__, "abaqus_cylinder_in_channel.inp")) mesh = P4estMesh{2}(mesh_file) diff --git a/examples/p4est_2d_dgsem/elixir_euler_wall_bc_amr.jl b/examples/p4est_2d_dgsem/elixir_euler_wall_bc_amr.jl index 8b8d05bade8..75e60d0c78b 100644 --- a/examples/p4est_2d_dgsem/elixir_euler_wall_bc_amr.jl +++ b/examples/p4est_2d_dgsem/elixir_euler_wall_bc_amr.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -39,11 +38,8 @@ solver = DGSEM(polydeg = 5, surface_flux = flux_lax_friedrichs, volume_integral = VolumeIntegralFluxDifferencing(volume_flux)) # Get the unstructured quad mesh from a file (downloads the file if not available locally) -default_mesh_file = joinpath(@__DIR__, "abaqus_gingerbread_man.inp") -isfile(default_mesh_file) || - download("https://gist.githubusercontent.com/andrewwinters5000/0e9e990a04b5105d1d2e3096a6e41272/raw/0d924b1d7e7d3cc1070a6cc22fe1d501687aa6dd/abaqus_gingerbread_man.inp", - default_mesh_file) -mesh_file = default_mesh_file +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/0e9e990a04b5105d1d2e3096a6e41272/raw/0d924b1d7e7d3cc1070a6cc22fe1d501687aa6dd/abaqus_gingerbread_man.inp", + joinpath(@__DIR__, "abaqus_gingerbread_man.inp")) mesh = P4estMesh{2}(mesh_file) diff --git a/examples/p4est_2d_dgsem/elixir_mhd_rotor.jl b/examples/p4est_2d_dgsem/elixir_mhd_rotor.jl index 380db487356..089e82580c9 100644 --- a/examples/p4est_2d_dgsem/elixir_mhd_rotor.jl +++ b/examples/p4est_2d_dgsem/elixir_mhd_rotor.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -69,10 +68,8 @@ function mapping_twist(xi, eta) return SVector(x, y) end -mesh_file = joinpath(@__DIR__, "square_unstructured_2.inp") -isfile(mesh_file) || - download("https://gist.githubusercontent.com/efaulhaber/63ff2ea224409e55ee8423b3a33e316a/raw/7db58af7446d1479753ae718930741c47a3b79b7/square_unstructured_2.inp", - mesh_file) +mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/63ff2ea224409e55ee8423b3a33e316a/raw/7db58af7446d1479753ae718930741c47a3b79b7/square_unstructured_2.inp", + joinpath(@__DIR__, "square_unstructured_2.inp")) mesh = P4estMesh{2}(mesh_file, polydeg = 4, diff --git a/examples/p4est_3d_dgsem/elixir_advection_amr_unstructured_curved.jl b/examples/p4est_3d_dgsem/elixir_advection_amr_unstructured_curved.jl index cd280cf5bf6..33afd2e030e 100644 --- a/examples/p4est_3d_dgsem/elixir_advection_amr_unstructured_curved.jl +++ b/examples/p4est_3d_dgsem/elixir_advection_amr_unstructured_curved.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -49,10 +48,8 @@ function mapping(xi, eta, zeta) end # Unstructured mesh with 48 cells of the cube domain [-1, 1]^3 -mesh_file = joinpath(@__DIR__, "cube_unstructured_2.inp") -isfile(mesh_file) || - download("https://gist.githubusercontent.com/efaulhaber/b8df0033798e4926dec515fc045e8c2c/raw/b9254cde1d1fb64b6acc8416bc5ccdd77a240227/cube_unstructured_2.inp", - mesh_file) +mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/b8df0033798e4926dec515fc045e8c2c/raw/b9254cde1d1fb64b6acc8416bc5ccdd77a240227/cube_unstructured_2.inp", + joinpath(@__DIR__, "cube_unstructured_2.inp")) # Mesh polydeg of 2 (half the solver polydeg) to ensure FSP (see above). mesh = P4estMesh{3}(mesh_file, polydeg = 2, diff --git a/examples/p4est_3d_dgsem/elixir_advection_unstructured_curved.jl b/examples/p4est_3d_dgsem/elixir_advection_unstructured_curved.jl index 6df9ac0b16a..83adcbf6a63 100644 --- a/examples/p4est_3d_dgsem/elixir_advection_unstructured_curved.jl +++ b/examples/p4est_3d_dgsem/elixir_advection_unstructured_curved.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -46,10 +45,8 @@ function mapping(xi, eta, zeta) end # Unstructured mesh with 68 cells of the cube domain [-1, 1]^3 -mesh_file = joinpath(@__DIR__, "cube_unstructured_1.inp") -isfile(mesh_file) || - download("https://gist.githubusercontent.com/efaulhaber/d45c8ac1e248618885fa7cc31a50ab40/raw/37fba24890ab37cfa49c39eae98b44faf4502882/cube_unstructured_1.inp", - mesh_file) +mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/d45c8ac1e248618885fa7cc31a50ab40/raw/37fba24890ab37cfa49c39eae98b44faf4502882/cube_unstructured_1.inp", + joinpath(@__DIR__, "cube_unstructured_1.inp")) mesh = P4estMesh{3}(mesh_file, polydeg = 3, mapping = mapping, diff --git a/examples/p4est_3d_dgsem/elixir_euler_ec.jl b/examples/p4est_3d_dgsem/elixir_euler_ec.jl index d9d774a7ffc..91698545052 100644 --- a/examples/p4est_3d_dgsem/elixir_euler_ec.jl +++ b/examples/p4est_3d_dgsem/elixir_euler_ec.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -46,10 +45,8 @@ function mapping(xi_, eta_, zeta_) end # Unstructured mesh with 48 cells of the cube domain [-1, 1]^3 -mesh_file = joinpath(@__DIR__, "cube_unstructured_2.inp") -isfile(mesh_file) || - download("https://gist.githubusercontent.com/efaulhaber/b8df0033798e4926dec515fc045e8c2c/raw/b9254cde1d1fb64b6acc8416bc5ccdd77a240227/cube_unstructured_2.inp", - mesh_file) +mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/b8df0033798e4926dec515fc045e8c2c/raw/b9254cde1d1fb64b6acc8416bc5ccdd77a240227/cube_unstructured_2.inp", + joinpath(@__DIR__, "cube_unstructured_2.inp")) mesh = P4estMesh{3}(mesh_file, polydeg = 5, mapping = mapping, diff --git a/examples/p4est_3d_dgsem/elixir_euler_free_stream.jl b/examples/p4est_3d_dgsem/elixir_euler_free_stream.jl index 24a781ca59e..6406a38186b 100644 --- a/examples/p4est_3d_dgsem/elixir_euler_free_stream.jl +++ b/examples/p4est_3d_dgsem/elixir_euler_free_stream.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -47,10 +46,8 @@ function mapping(xi_, eta_, zeta_) end # Unstructured mesh with 68 cells of the cube domain [-1, 1]^3 -mesh_file = joinpath(@__DIR__, "cube_unstructured_1.inp") -isfile(mesh_file) || - download("https://gist.githubusercontent.com/efaulhaber/d45c8ac1e248618885fa7cc31a50ab40/raw/37fba24890ab37cfa49c39eae98b44faf4502882/cube_unstructured_1.inp", - mesh_file) +mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/d45c8ac1e248618885fa7cc31a50ab40/raw/37fba24890ab37cfa49c39eae98b44faf4502882/cube_unstructured_1.inp", + joinpath(@__DIR__, "cube_unstructured_1.inp")) # Mesh polydeg of 2 (half the solver polydeg) to ensure FSP (see above). mesh = P4estMesh{3}(mesh_file, polydeg = 2, diff --git a/examples/p4est_3d_dgsem/elixir_euler_free_stream_extruded.jl b/examples/p4est_3d_dgsem/elixir_euler_free_stream_extruded.jl index f56fe3a429d..08307a449a7 100644 --- a/examples/p4est_3d_dgsem/elixir_euler_free_stream_extruded.jl +++ b/examples/p4est_3d_dgsem/elixir_euler_free_stream_extruded.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -36,10 +35,8 @@ function mapping(xi, eta_, zeta_) end # Unstructured mesh with 48 cells of the cube domain [-1, 1]^3 -mesh_file = joinpath(@__DIR__, "cube_unstructured_2.inp") -isfile(mesh_file) || - download("https://gist.githubusercontent.com/efaulhaber/b8df0033798e4926dec515fc045e8c2c/raw/b9254cde1d1fb64b6acc8416bc5ccdd77a240227/cube_unstructured_2.inp", - mesh_file) +mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/b8df0033798e4926dec515fc045e8c2c/raw/b9254cde1d1fb64b6acc8416bc5ccdd77a240227/cube_unstructured_2.inp", + joinpath(@__DIR__, "cube_unstructured_2.inp")) mesh = P4estMesh{3}(mesh_file, polydeg = 3, mapping = mapping, diff --git a/examples/p4est_3d_dgsem/elixir_euler_source_terms_nonconforming_unstructured_curved.jl b/examples/p4est_3d_dgsem/elixir_euler_source_terms_nonconforming_unstructured_curved.jl index 0de22eaea40..e7ca0cad4ba 100644 --- a/examples/p4est_3d_dgsem/elixir_euler_source_terms_nonconforming_unstructured_curved.jl +++ b/examples/p4est_3d_dgsem/elixir_euler_source_terms_nonconforming_unstructured_curved.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -49,10 +48,8 @@ function mapping(xi, eta, zeta) end # Unstructured mesh with 68 cells of the cube domain [-1, 1]^3 -mesh_file = joinpath(@__DIR__, "cube_unstructured_1.inp") -isfile(mesh_file) || - download("https://gist.githubusercontent.com/efaulhaber/d45c8ac1e248618885fa7cc31a50ab40/raw/37fba24890ab37cfa49c39eae98b44faf4502882/cube_unstructured_1.inp", - mesh_file) +mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/d45c8ac1e248618885fa7cc31a50ab40/raw/37fba24890ab37cfa49c39eae98b44faf4502882/cube_unstructured_1.inp", + joinpath(@__DIR__, "cube_unstructured_1.inp")) # Mesh polydeg of 2 (half the solver polydeg) to ensure FSP (see above). mesh = P4estMesh{3}(mesh_file, polydeg = 2, diff --git a/examples/p4est_3d_dgsem/elixir_euler_source_terms_nonperiodic_hohqmesh.jl b/examples/p4est_3d_dgsem/elixir_euler_source_terms_nonperiodic_hohqmesh.jl index 0fa3a28fe8b..7d81d6739bf 100644 --- a/examples/p4est_3d_dgsem/elixir_euler_source_terms_nonperiodic_hohqmesh.jl +++ b/examples/p4est_3d_dgsem/elixir_euler_source_terms_nonperiodic_hohqmesh.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -19,11 +18,8 @@ boundary_conditions = Dict(:Bottom => boundary_condition, solver = DGSEM(polydeg = 4, surface_flux = flux_lax_friedrichs) # Unstructured 3D half circle mesh from HOHQMesh -default_mesh_file = joinpath(@__DIR__, "abaqus_half_circle_3d.inp") -isfile(default_mesh_file) || - download("https://gist.githubusercontent.com/andrewwinters5000/11461efbfb02c42e06aca338b3d0b645/raw/81deeb1ebc4945952c30af5bb75fe222a18d975c/abaqus_half_circle_3d.inp", - default_mesh_file) -mesh_file = default_mesh_file +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/11461efbfb02c42e06aca338b3d0b645/raw/81deeb1ebc4945952c30af5bb75fe222a18d975c/abaqus_half_circle_3d.inp", + joinpath(@__DIR__, "abaqus_half_circle_3d.inp")) mesh = P4estMesh{3}(mesh_file, initial_refinement_level = 0) diff --git a/examples/structured_2d_dgsem/elixir_shallowwater_well_balanced.jl b/examples/structured_2d_dgsem/elixir_shallowwater_well_balanced.jl index 61dd252fd83..a6a56aa807c 100644 --- a/examples/structured_2d_dgsem/elixir_shallowwater_well_balanced.jl +++ b/examples/structured_2d_dgsem/elixir_shallowwater_well_balanced.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi diff --git a/examples/t8code_2d_dgsem/elixir_advection_amr_unstructured_flag.jl b/examples/t8code_2d_dgsem/elixir_advection_amr_unstructured_flag.jl index f285d24fc6c..0923e328487 100644 --- a/examples/t8code_2d_dgsem/elixir_advection_amr_unstructured_flag.jl +++ b/examples/t8code_2d_dgsem/elixir_advection_amr_unstructured_flag.jl @@ -1,4 +1,3 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -31,10 +30,8 @@ Trixi.validate_faces(faces) mapping_flag = Trixi.transfinite_mapping(faces) # Unstructured mesh with 24 cells of the square domain [-1, 1]^n -mesh_file = joinpath(@__DIR__, "square_unstructured_2.inp") -isfile(mesh_file) || - download("https://gist.githubusercontent.com/efaulhaber/63ff2ea224409e55ee8423b3a33e316a/raw/7db58af7446d1479753ae718930741c47a3b79b7/square_unstructured_2.inp", - mesh_file) +mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/63ff2ea224409e55ee8423b3a33e316a/raw/7db58af7446d1479753ae718930741c47a3b79b7/square_unstructured_2.inp", + joinpath(@__DIR__, "square_unstructured_2.inp")) # INP mesh files are only support by p4est. Hence, we # create a p4est connecvity object first from which diff --git a/examples/t8code_2d_dgsem/elixir_advection_unstructured_flag.jl b/examples/t8code_2d_dgsem/elixir_advection_unstructured_flag.jl index 5ba1ab15489..ba8f1b59b80 100644 --- a/examples/t8code_2d_dgsem/elixir_advection_unstructured_flag.jl +++ b/examples/t8code_2d_dgsem/elixir_advection_unstructured_flag.jl @@ -1,4 +1,3 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -28,10 +27,8 @@ Trixi.validate_faces(faces) mapping_flag = Trixi.transfinite_mapping(faces) # Unstructured mesh with 24 cells of the square domain [-1, 1]^n. -mesh_file = joinpath(@__DIR__, "square_unstructured_2.inp") -isfile(mesh_file) || - download("https://gist.githubusercontent.com/efaulhaber/63ff2ea224409e55ee8423b3a33e316a/raw/7db58af7446d1479753ae718930741c47a3b79b7/square_unstructured_2.inp", - mesh_file) +mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/63ff2ea224409e55ee8423b3a33e316a/raw/7db58af7446d1479753ae718930741c47a3b79b7/square_unstructured_2.inp", + joinpath(@__DIR__, "square_unstructured_2.inp")) # INP mesh files are only support by p4est. Hence, we # create a p4est connecvity object first from which diff --git a/examples/t8code_2d_dgsem/elixir_euler_free_stream.jl b/examples/t8code_2d_dgsem/elixir_euler_free_stream.jl index 37d15f38566..5e6c4193c50 100644 --- a/examples/t8code_2d_dgsem/elixir_euler_free_stream.jl +++ b/examples/t8code_2d_dgsem/elixir_euler_free_stream.jl @@ -1,4 +1,3 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -30,10 +29,8 @@ end # Get the uncurved mesh from a file (downloads the file if not available locally) # Unstructured mesh with 48 cells of the square domain [-1, 1]^n -mesh_file = joinpath(@__DIR__, "square_unstructured_1.inp") -isfile(mesh_file) || - download("https://gist.githubusercontent.com/efaulhaber/a075f8ec39a67fa9fad8f6f84342cbca/raw/a7206a02ed3a5d3cadacd8d9694ac154f9151db7/square_unstructured_1.inp", - mesh_file) +mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/a075f8ec39a67fa9fad8f6f84342cbca/raw/a7206a02ed3a5d3cadacd8d9694ac154f9151db7/square_unstructured_1.inp", + joinpath(@__DIR__, "square_unstructured_1.inp")) # INP mesh files are only support by p4est. Hence, we # create a p4est connecvity object first from which diff --git a/examples/t8code_2d_dgsem/elixir_euler_source_terms_nonconforming_unstructured_flag.jl b/examples/t8code_2d_dgsem/elixir_euler_source_terms_nonconforming_unstructured_flag.jl index bcc1abc560e..e496eb76729 100644 --- a/examples/t8code_2d_dgsem/elixir_euler_source_terms_nonconforming_unstructured_flag.jl +++ b/examples/t8code_2d_dgsem/elixir_euler_source_terms_nonconforming_unstructured_flag.jl @@ -1,4 +1,3 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -30,10 +29,8 @@ mapping_flag = Trixi.transfinite_mapping(faces) # Get the uncurved mesh from a file (downloads the file if not available locally) # Unstructured mesh with 24 cells of the square domain [-1, 1]^n -mesh_file = joinpath(@__DIR__, "square_unstructured_2.inp") -isfile(mesh_file) || - download("https://gist.githubusercontent.com/efaulhaber/63ff2ea224409e55ee8423b3a33e316a/raw/7db58af7446d1479753ae718930741c47a3b79b7/square_unstructured_2.inp", - mesh_file) +mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/63ff2ea224409e55ee8423b3a33e316a/raw/7db58af7446d1479753ae718930741c47a3b79b7/square_unstructured_2.inp", + joinpath(@__DIR__, "square_unstructured_2.inp")) # INP mesh files are only support by p4est. Hence, we # create a p4est connecvity object first from which diff --git a/examples/t8code_2d_dgsem/elixir_mhd_rotor.jl b/examples/t8code_2d_dgsem/elixir_mhd_rotor.jl index adb154948fb..ff2e40ae607 100644 --- a/examples/t8code_2d_dgsem/elixir_mhd_rotor.jl +++ b/examples/t8code_2d_dgsem/elixir_mhd_rotor.jl @@ -1,4 +1,3 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -68,10 +67,8 @@ function mapping_twist(xi, eta) return SVector(x, y) end -mesh_file = joinpath(@__DIR__, "square_unstructured_2.inp") -isfile(mesh_file) || - download("https://gist.githubusercontent.com/efaulhaber/63ff2ea224409e55ee8423b3a33e316a/raw/7db58af7446d1479753ae718930741c47a3b79b7/square_unstructured_2.inp", - mesh_file) +mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/63ff2ea224409e55ee8423b3a33e316a/raw/7db58af7446d1479753ae718930741c47a3b79b7/square_unstructured_2.inp", + joinpath(@__DIR__, "square_unstructured_2.inp")) # INP mesh files are only support by p4est. Hence, we # create a p4est connecvity object first from which diff --git a/examples/t8code_3d_dgsem/elixir_advection_amr_unstructured_curved.jl b/examples/t8code_3d_dgsem/elixir_advection_amr_unstructured_curved.jl index 617736afbdd..e7c0f4b7318 100644 --- a/examples/t8code_3d_dgsem/elixir_advection_amr_unstructured_curved.jl +++ b/examples/t8code_3d_dgsem/elixir_advection_amr_unstructured_curved.jl @@ -1,4 +1,3 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -47,11 +46,9 @@ function mapping(xi, eta, zeta) return SVector(5 * x, 5 * y, 5 * z) end -# Unstructured mesh with 48 cells of the cube domain [-1, 1]^3 -mesh_file = joinpath(@__DIR__, "cube_unstructured_2.inp") -isfile(mesh_file) || - download("https://gist.githubusercontent.com/efaulhaber/b8df0033798e4926dec515fc045e8c2c/raw/b9254cde1d1fb64b6acc8416bc5ccdd77a240227/cube_unstructured_2.inp", - mesh_file) +# Unstructured mesh with 48 cells of the cube domain [-1, 1]^3. +mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/b8df0033798e4926dec515fc045e8c2c/raw/b9254cde1d1fb64b6acc8416bc5ccdd77a240227/cube_unstructured_2.inp", + joinpath(@__DIR__, "cube_unstructured_2.inp")) # INP mesh files are only support by p4est. Hence, we # create a p4est connectivity object first from which diff --git a/examples/t8code_3d_dgsem/elixir_advection_unstructured_curved.jl b/examples/t8code_3d_dgsem/elixir_advection_unstructured_curved.jl index df358435c9a..ee27ee117fe 100644 --- a/examples/t8code_3d_dgsem/elixir_advection_unstructured_curved.jl +++ b/examples/t8code_3d_dgsem/elixir_advection_unstructured_curved.jl @@ -1,4 +1,3 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -45,10 +44,8 @@ function mapping(xi, eta, zeta) end # Unstructured mesh with 68 cells of the cube domain [-1, 1]^3 -mesh_file = joinpath(@__DIR__, "cube_unstructured_1.inp") -isfile(mesh_file) || - download("https://gist.githubusercontent.com/efaulhaber/d45c8ac1e248618885fa7cc31a50ab40/raw/37fba24890ab37cfa49c39eae98b44faf4502882/cube_unstructured_1.inp", - mesh_file) +mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/d45c8ac1e248618885fa7cc31a50ab40/raw/37fba24890ab37cfa49c39eae98b44faf4502882/cube_unstructured_1.inp", + joinpath(@__DIR__, "cube_unstructured_1.inp")) # INP mesh files are only support by p4est. Hence, we # create a p4est connectivity object first from which diff --git a/examples/t8code_3d_dgsem/elixir_euler_ec.jl b/examples/t8code_3d_dgsem/elixir_euler_ec.jl index 07745c3ac56..b720bfcd375 100644 --- a/examples/t8code_3d_dgsem/elixir_euler_ec.jl +++ b/examples/t8code_3d_dgsem/elixir_euler_ec.jl @@ -1,4 +1,3 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -45,10 +44,8 @@ function mapping(xi_, eta_, zeta_) end # Unstructured mesh with 48 cells of the cube domain [-1, 1]^3 -mesh_file = joinpath(@__DIR__, "cube_unstructured_2.inp") -isfile(mesh_file) || - download("https://gist.githubusercontent.com/efaulhaber/b8df0033798e4926dec515fc045e8c2c/raw/b9254cde1d1fb64b6acc8416bc5ccdd77a240227/cube_unstructured_2.inp", - mesh_file) +mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/b8df0033798e4926dec515fc045e8c2c/raw/b9254cde1d1fb64b6acc8416bc5ccdd77a240227/cube_unstructured_2.inp", + joinpath(@__DIR__, "cube_unstructured_2.inp")) # INP mesh files are only support by p4est. Hence, we # create a p4est connectivity object first from which diff --git a/examples/t8code_3d_dgsem/elixir_euler_free_stream.jl b/examples/t8code_3d_dgsem/elixir_euler_free_stream.jl index e135d464810..b70a6091adf 100644 --- a/examples/t8code_3d_dgsem/elixir_euler_free_stream.jl +++ b/examples/t8code_3d_dgsem/elixir_euler_free_stream.jl @@ -1,4 +1,3 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -46,10 +45,8 @@ function mapping(xi_, eta_, zeta_) end # Unstructured mesh with 68 cells of the cube domain [-1, 1]^3 -mesh_file = joinpath(@__DIR__, "cube_unstructured_1.inp") -isfile(mesh_file) || - download("https://gist.githubusercontent.com/efaulhaber/d45c8ac1e248618885fa7cc31a50ab40/raw/37fba24890ab37cfa49c39eae98b44faf4502882/cube_unstructured_1.inp", - mesh_file) +mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/d45c8ac1e248618885fa7cc31a50ab40/raw/37fba24890ab37cfa49c39eae98b44faf4502882/cube_unstructured_1.inp", + joinpath(@__DIR__, "cube_unstructured_1.inp")) # INP mesh files are only support by p4est. Hence, we # create a p4est connectivity object first from which diff --git a/examples/t8code_3d_dgsem/elixir_euler_free_stream_extruded.jl b/examples/t8code_3d_dgsem/elixir_euler_free_stream_extruded.jl index d129b59826e..6ae38d20b5a 100644 --- a/examples/t8code_3d_dgsem/elixir_euler_free_stream_extruded.jl +++ b/examples/t8code_3d_dgsem/elixir_euler_free_stream_extruded.jl @@ -1,4 +1,3 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -35,10 +34,8 @@ function mapping(xi, eta_, zeta_) end # Unstructured mesh with 48 cells of the cube domain [-1, 1]^3 -mesh_file = joinpath(@__DIR__, "cube_unstructured_2.inp") -isfile(mesh_file) || - download("https://gist.githubusercontent.com/efaulhaber/b8df0033798e4926dec515fc045e8c2c/raw/b9254cde1d1fb64b6acc8416bc5ccdd77a240227/cube_unstructured_2.inp", - mesh_file) +mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/b8df0033798e4926dec515fc045e8c2c/raw/b9254cde1d1fb64b6acc8416bc5ccdd77a240227/cube_unstructured_2.inp", + joinpath(@__DIR__, "cube_unstructured_2.inp")) # INP mesh files are only support by p4est. Hence, we # create a p4est connecvity object first from which diff --git a/examples/t8code_3d_dgsem/elixir_euler_source_terms_nonconforming_unstructured_curved.jl b/examples/t8code_3d_dgsem/elixir_euler_source_terms_nonconforming_unstructured_curved.jl index d4664522bea..6856be36ea1 100644 --- a/examples/t8code_3d_dgsem/elixir_euler_source_terms_nonconforming_unstructured_curved.jl +++ b/examples/t8code_3d_dgsem/elixir_euler_source_terms_nonconforming_unstructured_curved.jl @@ -1,4 +1,3 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -48,10 +47,8 @@ function mapping(xi, eta, zeta) end # Unstructured mesh with 68 cells of the cube domain [-1, 1]^3 -mesh_file = joinpath(@__DIR__, "cube_unstructured_1.inp") -isfile(mesh_file) || - download("https://gist.githubusercontent.com/efaulhaber/d45c8ac1e248618885fa7cc31a50ab40/raw/37fba24890ab37cfa49c39eae98b44faf4502882/cube_unstructured_1.inp", - mesh_file) +mesh_file = Trixi.download("https://gist.githubusercontent.com/efaulhaber/d45c8ac1e248618885fa7cc31a50ab40/raw/37fba24890ab37cfa49c39eae98b44faf4502882/cube_unstructured_1.inp", + joinpath(@__DIR__, "cube_unstructured_1.inp")) # INP mesh files are only support by p4est. Hence, we # create a p4est connecvity object first from which diff --git a/examples/unstructured_2d_dgsem/elixir_acoustics_gauss_wall.jl b/examples/unstructured_2d_dgsem/elixir_acoustics_gauss_wall.jl index 8f8e867dca8..9741430d11c 100644 --- a/examples/unstructured_2d_dgsem/elixir_acoustics_gauss_wall.jl +++ b/examples/unstructured_2d_dgsem/elixir_acoustics_gauss_wall.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -14,11 +13,8 @@ equations = AcousticPerturbationEquations2D(v_mean_global = (0.0, -0.5), solver = DGSEM(polydeg = 4, surface_flux = flux_lax_friedrichs) # Create unstructured quadrilateral mesh from a file -default_mesh_file = joinpath(@__DIR__, "mesh_five_circles_in_circle.mesh") -isfile(default_mesh_file) || - download("https://gist.githubusercontent.com/andrewwinters5000/3c79baad6b4d73bb26ec6420b5d16f45/raw/22aefc4ec2107cf0bffc40e81dfbc52240c625b1/mesh_five_circles_in_circle.mesh", - default_mesh_file) -mesh_file = default_mesh_file +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/3c79baad6b4d73bb26ec6420b5d16f45/raw/22aefc4ec2107cf0bffc40e81dfbc52240c625b1/mesh_five_circles_in_circle.mesh", + joinpath(@__DIR__, "mesh_five_circles_in_circle.mesh")) mesh = UnstructuredMesh2D(mesh_file) diff --git a/examples/unstructured_2d_dgsem/elixir_advection_basic.jl b/examples/unstructured_2d_dgsem/elixir_advection_basic.jl index afef6c2c38f..c0ee453344d 100644 --- a/examples/unstructured_2d_dgsem/elixir_advection_basic.jl +++ b/examples/unstructured_2d_dgsem/elixir_advection_basic.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -16,12 +15,8 @@ solver = DGSEM(polydeg = 6, surface_flux = flux_lax_friedrichs) ############################################################################### # Get the curved quad mesh from a file (downloads the file if not available locally) - -default_mesh_file = joinpath(@__DIR__, "mesh_periodic_square_with_twist.mesh") -isfile(default_mesh_file) || - download("https://gist.githubusercontent.com/andrewwinters5000/12ce661d7c354c3d94c74b964b0f1c96/raw/8275b9a60c6e7ebbdea5fc4b4f091c47af3d5273/mesh_periodic_square_with_twist.mesh", - default_mesh_file) -mesh_file = default_mesh_file +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/12ce661d7c354c3d94c74b964b0f1c96/raw/8275b9a60c6e7ebbdea5fc4b4f091c47af3d5273/mesh_periodic_square_with_twist.mesh", + joinpath(@__DIR__, "mesh_periodic_square_with_twist.mesh")) mesh = UnstructuredMesh2D(mesh_file, periodicity = true) diff --git a/examples/unstructured_2d_dgsem/elixir_euler_basic.jl b/examples/unstructured_2d_dgsem/elixir_euler_basic.jl index cd6a1995757..f8976120d53 100644 --- a/examples/unstructured_2d_dgsem/elixir_euler_basic.jl +++ b/examples/unstructured_2d_dgsem/elixir_euler_basic.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -25,12 +24,8 @@ solver = DGSEM(polydeg = 8, surface_flux = flux_lax_friedrichs) ############################################################################### # Get the curved quad mesh from a file (downloads the file if not available locally) - -default_mesh_file = joinpath(@__DIR__, "mesh_trixi_unstructured_mesh_docs.mesh") -isfile(default_mesh_file) || - download("https://gist.githubusercontent.com/andrewwinters5000/52056f1487853fab63b7f4ed7f171c80/raw/9d573387dfdbb8bce2a55db7246f4207663ac07f/mesh_trixi_unstructured_mesh_docs.mesh", - default_mesh_file) -mesh_file = default_mesh_file +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/52056f1487853fab63b7f4ed7f171c80/raw/9d573387dfdbb8bce2a55db7246f4207663ac07f/mesh_trixi_unstructured_mesh_docs.mesh", + joinpath(@__DIR__, "mesh_trixi_unstructured_mesh_docs.mesh")) mesh = UnstructuredMesh2D(mesh_file) diff --git a/examples/unstructured_2d_dgsem/elixir_euler_ec.jl b/examples/unstructured_2d_dgsem/elixir_euler_ec.jl index 0f53aa62a18..58b4d9a1dd2 100644 --- a/examples/unstructured_2d_dgsem/elixir_euler_ec.jl +++ b/examples/unstructured_2d_dgsem/elixir_euler_ec.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -19,12 +18,8 @@ solver = DGSEM(polydeg = 6, surface_flux = flux_ranocha, ############################################################################### # Get the curved quad mesh from a file - -default_mesh_file = joinpath(@__DIR__, "mesh_periodic_square_with_twist.mesh") -isfile(default_mesh_file) || - download("https://gist.githubusercontent.com/andrewwinters5000/12ce661d7c354c3d94c74b964b0f1c96/raw/8275b9a60c6e7ebbdea5fc4b4f091c47af3d5273/mesh_periodic_square_with_twist.mesh", - default_mesh_file) -mesh_file = default_mesh_file +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/12ce661d7c354c3d94c74b964b0f1c96/raw/8275b9a60c6e7ebbdea5fc4b4f091c47af3d5273/mesh_periodic_square_with_twist.mesh", + joinpath(@__DIR__, "mesh_periodic_square_with_twist.mesh")) mesh = UnstructuredMesh2D(mesh_file, periodicity = true) diff --git a/examples/unstructured_2d_dgsem/elixir_euler_free_stream.jl b/examples/unstructured_2d_dgsem/elixir_euler_free_stream.jl index a2fec1a320a..f266a3de0b2 100644 --- a/examples/unstructured_2d_dgsem/elixir_euler_free_stream.jl +++ b/examples/unstructured_2d_dgsem/elixir_euler_free_stream.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -26,12 +25,8 @@ solver = DGSEM(polydeg = 6, surface_flux = flux_hll) ############################################################################### # Get the curved quad mesh from a file (downloads the file if not available locally) - -default_mesh_file = joinpath(@__DIR__, "mesh_gingerbread_man.mesh") -isfile(default_mesh_file) || - download("https://gist.githubusercontent.com/andrewwinters5000/2c6440b5f8a57db131061ad7aa78ee2b/raw/1f89fdf2c874ff678c78afb6fe8dc784bdfd421f/mesh_gingerbread_man.mesh", - default_mesh_file) -mesh_file = default_mesh_file +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/2c6440b5f8a57db131061ad7aa78ee2b/raw/1f89fdf2c874ff678c78afb6fe8dc784bdfd421f/mesh_gingerbread_man.mesh", + joinpath(@__DIR__, "mesh_gingerbread_man.mesh")) mesh = UnstructuredMesh2D(mesh_file) diff --git a/examples/unstructured_2d_dgsem/elixir_euler_periodic.jl b/examples/unstructured_2d_dgsem/elixir_euler_periodic.jl index afd177f0740..e640001ad7f 100644 --- a/examples/unstructured_2d_dgsem/elixir_euler_periodic.jl +++ b/examples/unstructured_2d_dgsem/elixir_euler_periodic.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -19,12 +18,8 @@ solver = DGSEM(polydeg = 6, surface_flux = FluxRotated(flux_hll)) ############################################################################### # Get the curved quad mesh from a file (downloads the file if not available locally) - -default_mesh_file = joinpath(@__DIR__, "mesh_periodic_square_with_twist.mesh") -isfile(default_mesh_file) || - download("https://gist.githubusercontent.com/andrewwinters5000/12ce661d7c354c3d94c74b964b0f1c96/raw/8275b9a60c6e7ebbdea5fc4b4f091c47af3d5273/mesh_periodic_square_with_twist.mesh", - default_mesh_file) -mesh_file = default_mesh_file +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/12ce661d7c354c3d94c74b964b0f1c96/raw/8275b9a60c6e7ebbdea5fc4b4f091c47af3d5273/mesh_periodic_square_with_twist.mesh", + joinpath(@__DIR__, "mesh_periodic_square_with_twist.mesh")) mesh = UnstructuredMesh2D(mesh_file, periodicity = true) diff --git a/examples/unstructured_2d_dgsem/elixir_euler_sedov.jl b/examples/unstructured_2d_dgsem/elixir_euler_sedov.jl index e1cc0932969..06053273b74 100644 --- a/examples/unstructured_2d_dgsem/elixir_euler_sedov.jl +++ b/examples/unstructured_2d_dgsem/elixir_euler_sedov.jl @@ -55,11 +55,8 @@ solver = DGSEM(polydeg = polydeg, surface_flux = surface_flux, volume_integral = volume_integral) # Get the curved quad mesh from a file -default_mesh_file = joinpath(@__DIR__, "mesh_periodic_square_with_twist.mesh") -isfile(default_mesh_file) || - download("https://gist.githubusercontent.com/andrewwinters5000/12ce661d7c354c3d94c74b964b0f1c96/raw/8275b9a60c6e7ebbdea5fc4b4f091c47af3d5273/mesh_periodic_square_with_twist.mesh", - default_mesh_file) -mesh_file = default_mesh_file +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/12ce661d7c354c3d94c74b964b0f1c96/raw/8275b9a60c6e7ebbdea5fc4b4f091c47af3d5273/mesh_periodic_square_with_twist.mesh", + joinpath(@__DIR__, "mesh_periodic_square_with_twist.mesh")) mesh = UnstructuredMesh2D(mesh_file, periodicity = true) diff --git a/examples/unstructured_2d_dgsem/elixir_euler_wall_bc.jl b/examples/unstructured_2d_dgsem/elixir_euler_wall_bc.jl index b2abefe7eeb..65e5eb51ce6 100644 --- a/examples/unstructured_2d_dgsem/elixir_euler_wall_bc.jl +++ b/examples/unstructured_2d_dgsem/elixir_euler_wall_bc.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -40,12 +39,8 @@ solver = DGSEM(polydeg = 4, surface_flux = flux_hll) ############################################################################### # Get the curved quad mesh from a file - -default_mesh_file = joinpath(@__DIR__, "mesh_box_around_circle.mesh") -isfile(default_mesh_file) || - download("https://gist.githubusercontent.com/andrewwinters5000/8b9b11a1eedfa54b215c122c3d17b271/raw/0d2b5d98c87e67a6f384693a8b8e54b4c9fcbf3d/mesh_box_around_circle.mesh", - default_mesh_file) -mesh_file = default_mesh_file +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/8b9b11a1eedfa54b215c122c3d17b271/raw/0d2b5d98c87e67a6f384693a8b8e54b4c9fcbf3d/mesh_box_around_circle.mesh", + joinpath(@__DIR__, "mesh_box_around_circle.mesh")) mesh = UnstructuredMesh2D(mesh_file) diff --git a/examples/unstructured_2d_dgsem/elixir_mhd_alfven_wave.jl b/examples/unstructured_2d_dgsem/elixir_mhd_alfven_wave.jl index 3ed3e828ca8..0c7152a6ea0 100644 --- a/examples/unstructured_2d_dgsem/elixir_mhd_alfven_wave.jl +++ b/examples/unstructured_2d_dgsem/elixir_mhd_alfven_wave.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -17,12 +16,9 @@ solver = DGSEM(polydeg = 7, volume_integral = VolumeIntegralFluxDifferencing(volume_flux)) # Get the unstructured quad mesh from a file (downloads the file if not available locally) -default_mesh_file = joinpath(@__DIR__, "mesh_alfven_wave_with_twist_and_flip.mesh") -isfile(default_mesh_file) || - download("https://gist.githubusercontent.com/andrewwinters5000/8f8cd23df27fcd494553f2a89f3c1ba4/raw/85e3c8d976bbe57ca3d559d653087b0889535295/mesh_alfven_wave_with_twist_and_flip.mesh", - default_mesh_file) +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/8f8cd23df27fcd494553f2a89f3c1ba4/raw/85e3c8d976bbe57ca3d559d653087b0889535295/mesh_alfven_wave_with_twist_and_flip.mesh", + joinpath(@__DIR__, "mesh_alfven_wave_with_twist_and_flip.mesh")) -mesh_file = default_mesh_file mesh = UnstructuredMesh2D(mesh_file, periodicity = true) semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver) diff --git a/examples/unstructured_2d_dgsem/elixir_mhd_ec.jl b/examples/unstructured_2d_dgsem/elixir_mhd_ec.jl index a40f92cac02..805934e305d 100644 --- a/examples/unstructured_2d_dgsem/elixir_mhd_ec.jl +++ b/examples/unstructured_2d_dgsem/elixir_mhd_ec.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -35,11 +34,8 @@ solver = DGSEM(polydeg = 6, volume_integral = VolumeIntegralFluxDifferencing(volume_flux)) # Get the unstructured quad mesh from a file (downloads the file if not available locally) -default_mesh_file = joinpath(@__DIR__, "mesh_alfven_wave_with_twist_and_flip.mesh") -isfile(default_mesh_file) || - download("https://gist.githubusercontent.com/andrewwinters5000/8f8cd23df27fcd494553f2a89f3c1ba4/raw/85e3c8d976bbe57ca3d559d653087b0889535295/mesh_alfven_wave_with_twist_and_flip.mesh", - default_mesh_file) -mesh_file = default_mesh_file +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/8f8cd23df27fcd494553f2a89f3c1ba4/raw/85e3c8d976bbe57ca3d559d653087b0889535295/mesh_alfven_wave_with_twist_and_flip.mesh", + joinpath(@__DIR__, "mesh_alfven_wave_with_twist_and_flip.mesh")) mesh = UnstructuredMesh2D(mesh_file, periodicity = true) diff --git a/examples/unstructured_2d_dgsem/elixir_shallowwater_dirichlet.jl b/examples/unstructured_2d_dgsem/elixir_shallowwater_dirichlet.jl index 1148f25fae3..df1a69192ce 100644 --- a/examples/unstructured_2d_dgsem/elixir_shallowwater_dirichlet.jl +++ b/examples/unstructured_2d_dgsem/elixir_shallowwater_dirichlet.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -38,11 +37,8 @@ solver = DGSEM(polydeg = 4, surface_flux = (flux_hll, flux_nonconservative_fjord # This setup is for the curved, split form well-balancedness testing # Get the unstructured quad mesh from a file (downloads the file if not available locally) -default_mesh_file = joinpath(@__DIR__, "mesh_outer_circle.mesh") -isfile(default_mesh_file) || - download("https://gist.githubusercontent.com/andrewwinters5000/9beddd9cd00e2a0a15865129eeb24928/raw/be71e67fa48bc4e1e97f5f6cd77c3ed34c6ba9be/mesh_outer_circle.mesh", - default_mesh_file) -mesh_file = default_mesh_file +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/9beddd9cd00e2a0a15865129eeb24928/raw/be71e67fa48bc4e1e97f5f6cd77c3ed34c6ba9be/mesh_outer_circle.mesh", + joinpath(@__DIR__, "mesh_outer_circle.mesh")) mesh = UnstructuredMesh2D(mesh_file) diff --git a/examples/unstructured_2d_dgsem/elixir_shallowwater_ec.jl b/examples/unstructured_2d_dgsem/elixir_shallowwater_ec.jl index 8e9d396d826..9122fb8287d 100644 --- a/examples/unstructured_2d_dgsem/elixir_shallowwater_ec.jl +++ b/examples/unstructured_2d_dgsem/elixir_shallowwater_ec.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -25,11 +24,8 @@ solver = DGSEM(polydeg = 6, # This setup is for the curved, split form entropy conservation testing (needs periodic BCs) # Get the unstructured quad mesh from a file (downloads the file if not available locally) -default_mesh_file = joinpath(@__DIR__, "mesh_alfven_wave_with_twist_and_flip.mesh") -isfile(default_mesh_file) || - download("https://gist.githubusercontent.com/andrewwinters5000/8f8cd23df27fcd494553f2a89f3c1ba4/raw/85e3c8d976bbe57ca3d559d653087b0889535295/mesh_alfven_wave_with_twist_and_flip.mesh", - default_mesh_file) -mesh_file = default_mesh_file +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/8f8cd23df27fcd494553f2a89f3c1ba4/raw/85e3c8d976bbe57ca3d559d653087b0889535295/mesh_alfven_wave_with_twist_and_flip.mesh", + joinpath(@__DIR__, "mesh_alfven_wave_with_twist_and_flip.mesh")) mesh = UnstructuredMesh2D(mesh_file, periodicity = true) diff --git a/examples/unstructured_2d_dgsem/elixir_shallowwater_ec_shockcapturing.jl b/examples/unstructured_2d_dgsem/elixir_shallowwater_ec_shockcapturing.jl index 94202b81df0..98408db5a78 100644 --- a/examples/unstructured_2d_dgsem/elixir_shallowwater_ec_shockcapturing.jl +++ b/examples/unstructured_2d_dgsem/elixir_shallowwater_ec_shockcapturing.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -34,11 +33,8 @@ solver = DGSEM(basis, surface_flux, volume_integral) # This setup is for the curved, split form entropy conservation testing (needs periodic BCs) # Get the unstructured quad mesh from a file (downloads the file if not available locally) -default_mesh_file = joinpath(@__DIR__, "mesh_alfven_wave_with_twist_and_flip.mesh") -isfile(default_mesh_file) || - download("https://gist.githubusercontent.com/andrewwinters5000/8f8cd23df27fcd494553f2a89f3c1ba4/raw/85e3c8d976bbe57ca3d559d653087b0889535295/mesh_alfven_wave_with_twist_and_flip.mesh", - default_mesh_file) -mesh_file = default_mesh_file +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/8f8cd23df27fcd494553f2a89f3c1ba4/raw/85e3c8d976bbe57ca3d559d653087b0889535295/mesh_alfven_wave_with_twist_and_flip.mesh", + joinpath(@__DIR__, "mesh_alfven_wave_with_twist_and_flip.mesh")) mesh = UnstructuredMesh2D(mesh_file, periodicity = true) diff --git a/examples/unstructured_2d_dgsem/elixir_shallowwater_source_terms.jl b/examples/unstructured_2d_dgsem/elixir_shallowwater_source_terms.jl index 07668688406..a7aa5808955 100644 --- a/examples/unstructured_2d_dgsem/elixir_shallowwater_source_terms.jl +++ b/examples/unstructured_2d_dgsem/elixir_shallowwater_source_terms.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -23,11 +22,8 @@ solver = DGSEM(polydeg = 6, surface_flux = surface_flux, # This setup is for the curved, split form convergence test on a periodic domain # Get the unstructured quad mesh from a file (downloads the file if not available locally) -default_mesh_file = joinpath(@__DIR__, "mesh_alfven_wave_with_twist_and_flip.mesh") -isfile(default_mesh_file) || - download("https://gist.githubusercontent.com/andrewwinters5000/8f8cd23df27fcd494553f2a89f3c1ba4/raw/85e3c8d976bbe57ca3d559d653087b0889535295/mesh_alfven_wave_with_twist_and_flip.mesh", - default_mesh_file) -mesh_file = default_mesh_file +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/8f8cd23df27fcd494553f2a89f3c1ba4/raw/85e3c8d976bbe57ca3d559d653087b0889535295/mesh_alfven_wave_with_twist_and_flip.mesh", + joinpath(@__DIR__, "mesh_alfven_wave_with_twist_and_flip.mesh")) mesh = UnstructuredMesh2D(mesh_file, periodicity = true) diff --git a/examples/unstructured_2d_dgsem/elixir_shallowwater_three_mound_dam_break.jl b/examples/unstructured_2d_dgsem/elixir_shallowwater_three_mound_dam_break.jl index 6164f9d4a55..df321aad267 100644 --- a/examples/unstructured_2d_dgsem/elixir_shallowwater_three_mound_dam_break.jl +++ b/examples/unstructured_2d_dgsem/elixir_shallowwater_three_mound_dam_break.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -93,16 +92,10 @@ solver = DGSEM(basis, surface_flux, volume_integral) ############################################################################### # Get the unstructured quad mesh from a file (downloads the file if not available locally) +mesh_file = Trixi.download("https://gist.githubusercontent.com/svengoldberg/c3c87fecb3fc6e46be7f0d1c7cb35f83/raw/e817ecd9e6c4686581d63c46128f9b6468d396d3/mesh_three_mound.mesh", + joinpath(@__DIR__, "mesh_three_mound.mesh")) -default_meshfile = joinpath(@__DIR__, "mesh_three_mound.mesh") - -isfile(default_meshfile) || - download("https://gist.githubusercontent.com/svengoldberg/c3c87fecb3fc6e46be7f0d1c7cb35f83/raw/e817ecd9e6c4686581d63c46128f9b6468d396d3/mesh_three_mound.mesh", - default_meshfile) - -meshfile = default_meshfile - -mesh = UnstructuredMesh2D(meshfile) +mesh = UnstructuredMesh2D(mesh_file) # Create the semi discretization object semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver; diff --git a/examples/unstructured_2d_dgsem/elixir_shallowwater_twolayer_convergence.jl b/examples/unstructured_2d_dgsem/elixir_shallowwater_twolayer_convergence.jl index 0b86095663a..fcc08b6f991 100644 --- a/examples/unstructured_2d_dgsem/elixir_shallowwater_twolayer_convergence.jl +++ b/examples/unstructured_2d_dgsem/elixir_shallowwater_twolayer_convergence.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -24,11 +23,8 @@ solver = DGSEM(polydeg = 6, surface_flux = surface_flux, # This setup is for the curved, split form convergence test on a periodic domain # Get the unstructured quad mesh from a file (downloads the file if not available locally) -default_mesh_file = joinpath(@__DIR__, "mesh_alfven_wave_with_twist_and_flip.mesh") -isfile(default_mesh_file) || - download("https://gist.githubusercontent.com/andrewwinters5000/8f8cd23df27fcd494553f2a89f3c1ba4/raw/85e3c8d976bbe57ca3d559d653087b0889535295/mesh_alfven_wave_with_twist_and_flip.mesh", - default_mesh_file) -mesh_file = default_mesh_file +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/8f8cd23df27fcd494553f2a89f3c1ba4/raw/85e3c8d976bbe57ca3d559d653087b0889535295/mesh_alfven_wave_with_twist_and_flip.mesh", + joinpath(@__DIR__, "mesh_alfven_wave_with_twist_and_flip.mesh")) mesh = UnstructuredMesh2D(mesh_file, periodicity = true) diff --git a/examples/unstructured_2d_dgsem/elixir_shallowwater_twolayer_dam_break.jl b/examples/unstructured_2d_dgsem/elixir_shallowwater_twolayer_dam_break.jl index 4ad5f7e3201..821f31c52ac 100644 --- a/examples/unstructured_2d_dgsem/elixir_shallowwater_twolayer_dam_break.jl +++ b/examples/unstructured_2d_dgsem/elixir_shallowwater_twolayer_dam_break.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -48,11 +47,8 @@ solver = DGSEM(polydeg = 6, surface_flux = surface_flux, ############################################################################### # Get the unstructured quad mesh from a file (downloads the file if not available locally) -default_mesh_file = joinpath(@__DIR__, "mesh_alfven_wave_with_twist_and_flip.mesh") -isfile(default_mesh_file) || - download("https://gist.githubusercontent.com/andrewwinters5000/8f8cd23df27fcd494553f2a89f3c1ba4/raw/85e3c8d976bbe57ca3d559d653087b0889535295/mesh_alfven_wave_with_twist_and_flip.mesh", - default_mesh_file) -mesh_file = default_mesh_file +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/8f8cd23df27fcd494553f2a89f3c1ba4/raw/85e3c8d976bbe57ca3d559d653087b0889535295/mesh_alfven_wave_with_twist_and_flip.mesh", + joinpath(@__DIR__, "mesh_alfven_wave_with_twist_and_flip.mesh")) mesh = UnstructuredMesh2D(mesh_file, periodicity = false) diff --git a/examples/unstructured_2d_dgsem/elixir_shallowwater_twolayer_well_balanced.jl b/examples/unstructured_2d_dgsem/elixir_shallowwater_twolayer_well_balanced.jl index 6a727df2502..ca1f54595bb 100644 --- a/examples/unstructured_2d_dgsem/elixir_shallowwater_twolayer_well_balanced.jl +++ b/examples/unstructured_2d_dgsem/elixir_shallowwater_twolayer_well_balanced.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -42,11 +41,8 @@ solver = DGSEM(polydeg = 6, surface_flux = surface_flux, # This setup is for the curved, split form well-balancedness testing # Get the unstructured quad mesh from a file (downloads the file if not available locally) -default_mesh_file = joinpath(@__DIR__, "mesh_alfven_wave_with_twist_and_flip.mesh") -isfile(default_mesh_file) || - download("https://gist.githubusercontent.com/andrewwinters5000/8f8cd23df27fcd494553f2a89f3c1ba4/raw/85e3c8d976bbe57ca3d559d653087b0889535295/mesh_alfven_wave_with_twist_and_flip.mesh", - default_mesh_file) -mesh_file = default_mesh_file +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/8f8cd23df27fcd494553f2a89f3c1ba4/raw/85e3c8d976bbe57ca3d559d653087b0889535295/mesh_alfven_wave_with_twist_and_flip.mesh", + joinpath(@__DIR__, "mesh_alfven_wave_with_twist_and_flip.mesh")) mesh = UnstructuredMesh2D(mesh_file, periodicity = true) diff --git a/examples/unstructured_2d_dgsem/elixir_shallowwater_wall_bc_shockcapturing.jl b/examples/unstructured_2d_dgsem/elixir_shallowwater_wall_bc_shockcapturing.jl index 76b9642d595..f115113ed27 100644 --- a/examples/unstructured_2d_dgsem/elixir_shallowwater_wall_bc_shockcapturing.jl +++ b/examples/unstructured_2d_dgsem/elixir_shallowwater_wall_bc_shockcapturing.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -55,12 +54,8 @@ solver = DGSEM(polydeg = polydeg, surface_flux = surface_flux, ############################################################################### # Get the unstructured quad mesh from a file (downloads the file if not available locally) - -default_mesh_file = joinpath(@__DIR__, "mesh_outer_circle.mesh") -isfile(default_mesh_file) || - download("https://gist.githubusercontent.com/andrewwinters5000/9beddd9cd00e2a0a15865129eeb24928/raw/be71e67fa48bc4e1e97f5f6cd77c3ed34c6ba9be/mesh_outer_circle.mesh", - default_mesh_file) -mesh_file = default_mesh_file +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/9beddd9cd00e2a0a15865129eeb24928/raw/be71e67fa48bc4e1e97f5f6cd77c3ed34c6ba9be/mesh_outer_circle.mesh", + joinpath(@__DIR__, "mesh_outer_circle.mesh")) mesh = UnstructuredMesh2D(mesh_file) diff --git a/examples/unstructured_2d_dgsem/elixir_shallowwater_well_balanced.jl b/examples/unstructured_2d_dgsem/elixir_shallowwater_well_balanced.jl index bf4d0be682a..6bad3a77f03 100644 --- a/examples/unstructured_2d_dgsem/elixir_shallowwater_well_balanced.jl +++ b/examples/unstructured_2d_dgsem/elixir_shallowwater_well_balanced.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -36,13 +35,9 @@ solver = DGSEM(polydeg = 6, surface_flux = surface_flux, ############################################################################### # This setup is for the curved, split form well-balancedness testing - # Get the unstructured quad mesh from a file (downloads the file if not available locally) -default_mesh_file = joinpath(@__DIR__, "mesh_alfven_wave_with_twist_and_flip.mesh") -isfile(default_mesh_file) || - download("https://gist.githubusercontent.com/andrewwinters5000/8f8cd23df27fcd494553f2a89f3c1ba4/raw/85e3c8d976bbe57ca3d559d653087b0889535295/mesh_alfven_wave_with_twist_and_flip.mesh", - default_mesh_file) -mesh_file = default_mesh_file +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/8f8cd23df27fcd494553f2a89f3c1ba4/raw/85e3c8d976bbe57ca3d559d653087b0889535295/mesh_alfven_wave_with_twist_and_flip.mesh", + joinpath(@__DIR__, "mesh_alfven_wave_with_twist_and_flip.mesh")) mesh = UnstructuredMesh2D(mesh_file, periodicity = true) diff --git a/examples/unstructured_2d_fdsbp/elixir_advection_basic.jl b/examples/unstructured_2d_fdsbp/elixir_advection_basic.jl index c181203e7a4..fe7e708f3b3 100644 --- a/examples/unstructured_2d_fdsbp/elixir_advection_basic.jl +++ b/examples/unstructured_2d_fdsbp/elixir_advection_basic.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -21,12 +20,8 @@ solver = FDSBP(D_SBP, ############################################################################### # Get the curved quad mesh from a file (downloads the file if not available locally) - -default_mesh_file = joinpath(@__DIR__, "mesh_periodic_square_with_twist.mesh") -isfile(default_mesh_file) || - download("https://gist.githubusercontent.com/andrewwinters5000/12ce661d7c354c3d94c74b964b0f1c96/raw/8275b9a60c6e7ebbdea5fc4b4f091c47af3d5273/mesh_periodic_square_with_twist.mesh", - default_mesh_file) -mesh_file = default_mesh_file +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/12ce661d7c354c3d94c74b964b0f1c96/raw/8275b9a60c6e7ebbdea5fc4b4f091c47af3d5273/mesh_periodic_square_with_twist.mesh", + joinpath(@__DIR__, "mesh_periodic_square_with_twist.mesh")) mesh = UnstructuredMesh2D(mesh_file, periodicity = true) diff --git a/examples/unstructured_2d_fdsbp/elixir_euler_free_stream.jl b/examples/unstructured_2d_fdsbp/elixir_euler_free_stream.jl index 7ada50c0c65..25a81c16bf9 100644 --- a/examples/unstructured_2d_fdsbp/elixir_euler_free_stream.jl +++ b/examples/unstructured_2d_fdsbp/elixir_euler_free_stream.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -33,12 +32,8 @@ solver = FDSBP(D_SBP, ############################################################################### # Get the curved quad mesh from a file (downloads the file if not available locally) - -default_mesh_file = joinpath(@__DIR__, "mesh_gingerbread_man.mesh") -isfile(default_mesh_file) || - download("https://gist.githubusercontent.com/andrewwinters5000/2c6440b5f8a57db131061ad7aa78ee2b/raw/1f89fdf2c874ff678c78afb6fe8dc784bdfd421f/mesh_gingerbread_man.mesh", - default_mesh_file) -mesh_file = default_mesh_file +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/2c6440b5f8a57db131061ad7aa78ee2b/raw/1f89fdf2c874ff678c78afb6fe8dc784bdfd421f/mesh_gingerbread_man.mesh", + joinpath(@__DIR__, "mesh_gingerbread_man.mesh")) mesh = UnstructuredMesh2D(mesh_file) diff --git a/examples/unstructured_2d_fdsbp/elixir_euler_source_terms.jl b/examples/unstructured_2d_fdsbp/elixir_euler_source_terms.jl index edcd221bf59..5f11d41ad5c 100644 --- a/examples/unstructured_2d_fdsbp/elixir_euler_source_terms.jl +++ b/examples/unstructured_2d_fdsbp/elixir_euler_source_terms.jl @@ -1,5 +1,4 @@ -using Downloads: download using OrdinaryDiffEq using Trixi @@ -22,12 +21,8 @@ solver = FDSBP(D_SBP, ############################################################################### # Get the curved quad mesh from a file (downloads the file if not available locally) - -default_mesh_file = joinpath(@__DIR__, "mesh_periodic_square_with_twist.mesh") -isfile(default_mesh_file) || - download("https://gist.githubusercontent.com/andrewwinters5000/12ce661d7c354c3d94c74b964b0f1c96/raw/8275b9a60c6e7ebbdea5fc4b4f091c47af3d5273/mesh_periodic_square_with_twist.mesh", - default_mesh_file) -mesh_file = default_mesh_file +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/12ce661d7c354c3d94c74b964b0f1c96/raw/8275b9a60c6e7ebbdea5fc4b4f091c47af3d5273/mesh_periodic_square_with_twist.mesh", + joinpath(@__DIR__, "mesh_periodic_square_with_twist.mesh")) mesh = UnstructuredMesh2D(mesh_file, periodicity = true) diff --git a/src/Trixi.jl b/src/Trixi.jl index e18b2f6415c..8d74fbc9736 100644 --- a/src/Trixi.jl +++ b/src/Trixi.jl @@ -39,6 +39,7 @@ import SciMLBase: get_du, get_tmp_cache, u_modified!, get_proposed_dt, set_proposed_dt!, terminate!, remake, add_tstop!, has_tstop, first_tstop +using Downloads: Downloads using CodeTracking: CodeTracking using ConstructionBase: ConstructionBase using DiffEqCallbacks: PeriodicCallback, PeriodicCallbackAffect diff --git a/src/auxiliary/auxiliary.jl b/src/auxiliary/auxiliary.jl index 1f7d30d6aa8..92da9a5ba8b 100644 --- a/src/auxiliary/auxiliary.jl +++ b/src/auxiliary/auxiliary.jl @@ -345,4 +345,27 @@ function register_error_hints() return nothing end + +""" + Trixi.download(src_url, file_path) + +Download a file from given `src_url` to given `file_path` if +`file_path` is not already a file. This function just returns +`file_path`. +This is a small wrapper of `Downloads.download(src_url, file_path)` +that avoids race conditions when multiple MPI ranks are used. +""" +function download(src_url, file_path) + # Note that `mpi_isroot()` is also `true` if running + # in serial (without MPI). + if mpi_isroot() + isfile(file_path) || Downloads.download(src_url, file_path) + end + + if mpi_isparallel() + MPI.Barrier(mpi_comm()) + end + + return file_path +end end # @muladd diff --git a/src/auxiliary/t8code.jl b/src/auxiliary/t8code.jl index db01476bb86..7c1399fc803 100644 --- a/src/auxiliary/t8code.jl +++ b/src/auxiliary/t8code.jl @@ -46,230 +46,6 @@ function init_t8code() return nothing end -function trixi_t8_unref_forest(forest) - t8_forest_unref(Ref(forest)) -end - -function t8_free(ptr) - T8code.Libt8.sc_free(t8_get_package_id(), ptr) -end - -function trixi_t8_count_interfaces(forest) - # Check that forest is a committed, that is valid and usable, forest. - @assert t8_forest_is_committed(forest) != 0 - - # Get the number of local elements of forest. - num_local_elements = t8_forest_get_local_num_elements(forest) - # Get the number of ghost elements of forest. - num_ghost_elements = t8_forest_get_num_ghosts(forest) - # Get the number of trees that have elements of this process. - num_local_trees = t8_forest_get_num_local_trees(forest) - - current_index = t8_locidx_t(0) - - local_num_conform = 0 - local_num_mortars = 0 - local_num_boundary = 0 - - for itree in 0:(num_local_trees - 1) - tree_class = t8_forest_get_tree_class(forest, itree) - eclass_scheme = t8_forest_get_eclass_scheme(forest, tree_class) - - # Get the number of elements of this tree. - num_elements_in_tree = t8_forest_get_tree_num_elements(forest, itree) - - for ielement in 0:(num_elements_in_tree - 1) - element = t8_forest_get_element_in_tree(forest, itree, ielement) - - level = t8_element_level(eclass_scheme, element) - - num_faces = t8_element_num_faces(eclass_scheme, element) - - for iface in 0:(num_faces - 1) - pelement_indices_ref = Ref{Ptr{t8_locidx_t}}() - pneighbor_leafs_ref = Ref{Ptr{Ptr{t8_element}}}() - pneigh_scheme_ref = Ref{Ptr{t8_eclass_scheme}}() - - dual_faces_ref = Ref{Ptr{Cint}}() - num_neighbors_ref = Ref{Cint}() - - forest_is_balanced = Cint(1) - - t8_forest_leaf_face_neighbors(forest, itree, element, - pneighbor_leafs_ref, iface, dual_faces_ref, - num_neighbors_ref, - pelement_indices_ref, pneigh_scheme_ref, - forest_is_balanced) - - num_neighbors = num_neighbors_ref[] - neighbor_ielements = unsafe_wrap(Array, pelement_indices_ref[], - num_neighbors) - neighbor_leafs = unsafe_wrap(Array, pneighbor_leafs_ref[], num_neighbors) - neighbor_scheme = pneigh_scheme_ref[] - - if num_neighbors > 0 - neighbor_level = t8_element_level(neighbor_scheme, neighbor_leafs[1]) - - # Conforming interface: The second condition ensures we only visit the interface once. - if level == neighbor_level && current_index <= neighbor_ielements[1] - local_num_conform += 1 - elseif level < neighbor_level - local_num_mortars += 1 - end - else - local_num_boundary += 1 - end - - t8_free(dual_faces_ref[]) - t8_free(pneighbor_leafs_ref[]) - t8_free(pelement_indices_ref[]) - end # for - - current_index += 1 - end # for - end # for - - return (interfaces = local_num_conform, - mortars = local_num_mortars, - boundaries = local_num_boundary) -end - -function trixi_t8_fill_mesh_info(forest, elements, interfaces, mortars, boundaries, - boundary_names) - # Check that forest is a committed, that is valid and usable, forest. - @assert t8_forest_is_committed(forest) != 0 - - # Get the number of local elements of forest. - num_local_elements = t8_forest_get_local_num_elements(forest) - # Get the number of ghost elements of forest. - num_ghost_elements = t8_forest_get_num_ghosts(forest) - # Get the number of trees that have elements of this process. - num_local_trees = t8_forest_get_num_local_trees(forest) - - current_index = t8_locidx_t(0) - - local_num_conform = 0 - local_num_mortars = 0 - local_num_boundary = 0 - - for itree in 0:(num_local_trees - 1) - tree_class = t8_forest_get_tree_class(forest, itree) - eclass_scheme = t8_forest_get_eclass_scheme(forest, tree_class) - - # Get the number of elements of this tree. - num_elements_in_tree = t8_forest_get_tree_num_elements(forest, itree) - - for ielement in 0:(num_elements_in_tree - 1) - element = t8_forest_get_element_in_tree(forest, itree, ielement) - - level = t8_element_level(eclass_scheme, element) - - num_faces = t8_element_num_faces(eclass_scheme, element) - - for iface in 0:(num_faces - 1) - - # Compute the `orientation` of the touching faces. - if t8_element_is_root_boundary(eclass_scheme, element, iface) == 1 - cmesh = t8_forest_get_cmesh(forest) - itree_in_cmesh = t8_forest_ltreeid_to_cmesh_ltreeid(forest, itree) - iface_in_tree = t8_element_tree_face(eclass_scheme, element, iface) - orientation_ref = Ref{Cint}() - - t8_cmesh_get_face_neighbor(cmesh, itree_in_cmesh, iface_in_tree, C_NULL, - orientation_ref) - orientation = orientation_ref[] - else - orientation = zero(Cint) - end - - pelement_indices_ref = Ref{Ptr{t8_locidx_t}}() - pneighbor_leafs_ref = Ref{Ptr{Ptr{t8_element}}}() - pneigh_scheme_ref = Ref{Ptr{t8_eclass_scheme}}() - - dual_faces_ref = Ref{Ptr{Cint}}() - num_neighbors_ref = Ref{Cint}() - - forest_is_balanced = Cint(1) - - t8_forest_leaf_face_neighbors(forest, itree, element, - pneighbor_leafs_ref, iface, dual_faces_ref, - num_neighbors_ref, - pelement_indices_ref, pneigh_scheme_ref, - forest_is_balanced) - - num_neighbors = num_neighbors_ref[] - dual_faces = unsafe_wrap(Array, dual_faces_ref[], num_neighbors) - neighbor_ielements = unsafe_wrap(Array, pelement_indices_ref[], - num_neighbors) - neighbor_leafs = unsafe_wrap(Array, pneighbor_leafs_ref[], num_neighbors) - neighbor_scheme = pneigh_scheme_ref[] - - if num_neighbors > 0 - neighbor_level = t8_element_level(neighbor_scheme, neighbor_leafs[1]) - - # Conforming interface: The second condition ensures we only visit the interface once. - if level == neighbor_level && current_index <= neighbor_ielements[1] - local_num_conform += 1 - - faces = (iface, dual_faces[1]) - interface_id = local_num_conform - - # Write data to interfaces container. - interfaces.neighbor_ids[1, interface_id] = current_index + 1 - interfaces.neighbor_ids[2, interface_id] = neighbor_ielements[1] + 1 - - # Save interfaces.node_indices dimension specific in containers_3d.jl. - init_interface_node_indices!(interfaces, faces, orientation, - interface_id) - # Non-conforming interface. - elseif level < neighbor_level - local_num_mortars += 1 - - faces = (dual_faces[1], iface) - - mortar_id = local_num_mortars - - # Last entry is the large element. - mortars.neighbor_ids[end, mortar_id] = current_index + 1 - - # Fill in the `mortars.neighbor_ids` array and reorder if necessary. - init_mortar_neighbor_ids!(mortars, faces[2], faces[1], - orientation, neighbor_ielements, - mortar_id) - - # Fill in the `mortars.node_indices` array. - init_mortar_node_indices!(mortars, faces, orientation, mortar_id) - - # else: "level > neighbor_level" is skipped since we visit the mortar interface only once. - end - - # Domain boundary. - else - local_num_boundary += 1 - boundary_id = local_num_boundary - - boundaries.neighbor_ids[boundary_id] = current_index + 1 - - init_boundary_node_indices!(boundaries, iface, boundary_id) - - # One-based indexing. - boundaries.name[boundary_id] = boundary_names[iface + 1, itree + 1] - end - - t8_free(dual_faces_ref[]) - t8_free(pneighbor_leafs_ref[]) - t8_free(pelement_indices_ref[]) - end # for iface = ... - - current_index += 1 - end # for - end # for - - return (interfaces = local_num_conform, - mortars = local_num_mortars, - boundaries = local_num_boundary) -end - function trixi_t8_get_local_element_levels(forest) # Check that forest is a committed, that is valid and usable, forest. @assert t8_forest_is_committed(forest) != 0 @@ -341,23 +117,16 @@ function adapt_callback(forest, end function trixi_t8_adapt_new(old_forest, indicators) - # Check that forest is a committed, that is valid and usable, forest. - @assert t8_forest_is_committed(old_forest) != 0 - - # Init new forest. new_forest_ref = Ref{t8_forest_t}() t8_forest_init(new_forest_ref) new_forest = new_forest_ref[] - let set_from = C_NULL, recursive = 0, set_for_coarsening = 0, no_repartition = 0, - do_ghost = 1 - + let set_from = C_NULL, recursive = 0, no_repartition = 1, do_ghost = 1 t8_forest_set_user_data(new_forest, pointer(indicators)) t8_forest_set_adapt(new_forest, old_forest, @t8_adapt_callback(adapt_callback), recursive) t8_forest_set_balance(new_forest, set_from, no_repartition) - t8_forest_set_partition(new_forest, set_from, set_for_coarsening) - t8_forest_set_ghost(new_forest, do_ghost, T8_GHOST_FACES) # Note: MPI support not available yet so it is a dummy call. + t8_forest_set_ghost(new_forest, do_ghost, T8_GHOST_FACES) t8_forest_commit(new_forest) end diff --git a/src/callbacks_step/amr.jl b/src/callbacks_step/amr.jl index 5854c8617c3..6f57d6647fc 100644 --- a/src/callbacks_step/amr.jl +++ b/src/callbacks_step/amr.jl @@ -726,7 +726,7 @@ function (amr_callback::AMRCallback)(u_ode::AbstractVector, mesh::P4estMesh, return has_changed end -function (amr_callback::AMRCallback)(u_ode::AbstractVector, mesh::SerialT8codeMesh, +function (amr_callback::AMRCallback)(u_ode::AbstractVector, mesh::T8codeMesh, equations, dg::DG, cache, semi, t, iter; only_refine = false, only_coarsen = false, @@ -754,29 +754,29 @@ function (amr_callback::AMRCallback)(u_ode::AbstractVector, mesh::SerialT8codeMe @trixi_timeit timer() "adapt" begin difference = @trixi_timeit timer() "mesh" trixi_t8_adapt!(mesh, indicators) - @trixi_timeit timer() "solver" adapt!(u_ode, adaptor, mesh, equations, dg, - cache, difference) - end + # Store whether there were any cells coarsened or refined and perform load balancing. + has_changed = any(difference .!= 0) - # Store whether there were any cells coarsened or refined and perform load balancing. - has_changed = any(difference .!= 0) + # Check if mesh changed on other processes + if mpi_isparallel() + has_changed = MPI.Allreduce!(Ref(has_changed), |, mpi_comm())[] + end - # TODO: T8codeMesh for MPI not implemented yet. - # Check if mesh changed on other processes - # if mpi_isparallel() - # has_changed = MPI.Allreduce!(Ref(has_changed), |, mpi_comm())[] - # end + if has_changed + @trixi_timeit timer() "solver" adapt!(u_ode, adaptor, mesh, equations, dg, + cache, difference) + end + end if has_changed - # TODO: T8codeMesh for MPI not implemented yet. - # if mpi_isparallel() && amr_callback.dynamic_load_balancing - # @trixi_timeit timer() "dynamic load balancing" begin - # global_first_quadrant = unsafe_wrap(Array, mesh.p4est.global_first_quadrant, mpi_nranks() + 1) - # old_global_first_quadrant = copy(global_first_quadrant) - # partition!(mesh) - # rebalance_solver!(u_ode, mesh, equations, dg, cache, old_global_first_quadrant) - # end - # end + if mpi_isparallel() && amr_callback.dynamic_load_balancing + @trixi_timeit timer() "dynamic load balancing" begin + old_global_first_element_ids = get_global_first_element_ids(mesh) + partition!(mesh) + rebalance_solver!(u_ode, mesh, equations, dg, cache, + old_global_first_element_ids) + end + end reinitialize_boundaries!(semi.boundary_conditions, cache) end diff --git a/src/callbacks_step/amr_dg.jl b/src/callbacks_step/amr_dg.jl index 1dcfdccdea8..0a7055af409 100644 --- a/src/callbacks_step/amr_dg.jl +++ b/src/callbacks_step/amr_dg.jl @@ -6,11 +6,14 @@ #! format: noindent # Redistribute data for load balancing after partitioning the mesh -function rebalance_solver!(u_ode::AbstractVector, mesh::ParallelP4estMesh, equations, +function rebalance_solver!(u_ode::AbstractVector, + mesh::Union{ParallelP4estMesh, ParallelT8codeMesh}, + equations, dg::DGSEM, cache, old_global_first_quadrant) - # mpi ranks are 0-based, this array uses 1-based indices - global_first_quadrant = unsafe_wrap(Array, mesh.p4est.global_first_quadrant, - mpi_nranks() + 1) + + # MPI ranks are 0-based. This array uses 1-based indices. + global_first_quadrant = get_global_first_element_ids(mesh) + if global_first_quadrant[mpi_rank() + 1] == old_global_first_quadrant[mpi_rank() + 1] && global_first_quadrant[mpi_rank() + 2] == diff --git a/src/callbacks_step/amr_dg2d.jl b/src/callbacks_step/amr_dg2d.jl index b816bc06e65..94524b23a3a 100644 --- a/src/callbacks_step/amr_dg2d.jl +++ b/src/callbacks_step/amr_dg2d.jl @@ -385,7 +385,12 @@ function adapt!(u_ode::AbstractVector, adaptor, mesh::T8codeMesh{2}, equations, # Return early if there is nothing to do. if !any(difference .!= 0) - return nothing + if mpi_isparallel() + # MPICache init uses all-to-all communication -> reinitialize even if there is nothing to do + # locally (there still might be other MPI ranks that have refined elements) + reinitialize_containers!(mesh, equations, dg, cache) + end + return end # Number of (local) cells/elements. diff --git a/src/callbacks_step/amr_dg3d.jl b/src/callbacks_step/amr_dg3d.jl index 392cbba9e28..3f67951bafe 100644 --- a/src/callbacks_step/amr_dg3d.jl +++ b/src/callbacks_step/amr_dg3d.jl @@ -316,7 +316,12 @@ function adapt!(u_ode::AbstractVector, adaptor, mesh::T8codeMesh{3}, equations, # Return early if there is nothing to do. if !any(difference .!= 0) - return nothing + if mpi_isparallel() + # MPICache init uses all-to-all communication -> reinitialize even if there is nothing to do + # locally (there still might be other MPI ranks that have refined elements) + reinitialize_containers!(mesh, equations, dg, cache) + end + return end # Number of (local) cells/elements. diff --git a/src/callbacks_step/analysis_dg2d_parallel.jl b/src/callbacks_step/analysis_dg2d_parallel.jl index a04bf732604..000daa015dc 100644 --- a/src/callbacks_step/analysis_dg2d_parallel.jl +++ b/src/callbacks_step/analysis_dg2d_parallel.jl @@ -91,7 +91,8 @@ function calc_error_norms_per_element(func, u, t, analyzer, end function calc_error_norms(func, u, t, analyzer, - mesh::ParallelP4estMesh{2}, equations, + mesh::Union{ParallelP4estMesh{2}, ParallelT8codeMesh{2}}, + equations, initial_condition, dg::DGSEM, cache, cache_analysis) @unpack vandermonde, weights = analyzer @unpack node_coordinates, inverse_jacobian = cache.elements @@ -171,7 +172,8 @@ function integrate_via_indices(func::Func, u, end function integrate_via_indices(func::Func, u, - mesh::ParallelP4estMesh{2}, equations, + mesh::Union{ParallelP4estMesh{2}, ParallelT8codeMesh{2}}, + equations, dg::DGSEM, cache, args...; normalize = true) where {Func} @unpack weights = dg.basis diff --git a/src/callbacks_step/analysis_dg3d_parallel.jl b/src/callbacks_step/analysis_dg3d_parallel.jl index d8756d91c9d..de777be406d 100644 --- a/src/callbacks_step/analysis_dg3d_parallel.jl +++ b/src/callbacks_step/analysis_dg3d_parallel.jl @@ -6,7 +6,8 @@ #! format: noindent function calc_error_norms(func, u, t, analyzer, - mesh::ParallelP4estMesh{3}, equations, + mesh::Union{ParallelP4estMesh{3}, ParallelT8codeMesh{3}}, + equations, initial_condition, dg::DGSEM, cache, cache_analysis) @unpack vandermonde, weights = analyzer @unpack node_coordinates, inverse_jacobian = cache.elements @@ -64,7 +65,8 @@ function calc_error_norms(func, u, t, analyzer, end function integrate_via_indices(func::Func, u, - mesh::ParallelP4estMesh{3}, equations, + mesh::Union{ParallelP4estMesh{3}, ParallelT8codeMesh{3}}, + equations, dg::DGSEM, cache, args...; normalize = true) where {Func} @unpack weights = dg.basis diff --git a/src/callbacks_step/stepsize_dg2d.jl b/src/callbacks_step/stepsize_dg2d.jl index 673c3ba6aa6..c6d32c0f6dc 100644 --- a/src/callbacks_step/stepsize_dg2d.jl +++ b/src/callbacks_step/stepsize_dg2d.jl @@ -174,4 +174,36 @@ function max_dt(u, t, mesh::ParallelP4estMesh{2}, return dt end + +function max_dt(u, t, mesh::ParallelT8codeMesh{2}, + constant_speed::False, equations, dg::DG, cache) + # call the method accepting a general `mesh::T8codeMesh{2}` + # TODO: MPI, we should improve this; maybe we should dispatch on `u` + # and create some MPI array type, overloading broadcasting and mapreduce etc. + # Then, this specific array type should also work well with DiffEq etc. + dt = invoke(max_dt, + Tuple{typeof(u), typeof(t), T8codeMesh{2}, + typeof(constant_speed), typeof(equations), typeof(dg), + typeof(cache)}, + u, t, mesh, constant_speed, equations, dg, cache) + dt = MPI.Allreduce!(Ref(dt), min, mpi_comm())[] + + return dt +end + +function max_dt(u, t, mesh::ParallelT8codeMesh{2}, + constant_speed::True, equations, dg::DG, cache) + # call the method accepting a general `mesh::T8codeMesh{2}` + # TODO: MPI, we should improve this; maybe we should dispatch on `u` + # and create some MPI array type, overloading broadcasting and mapreduce etc. + # Then, this specific array type should also work well with DiffEq etc. + dt = invoke(max_dt, + Tuple{typeof(u), typeof(t), T8codeMesh{2}, + typeof(constant_speed), typeof(equations), typeof(dg), + typeof(cache)}, + u, t, mesh, constant_speed, equations, dg, cache) + dt = MPI.Allreduce!(Ref(dt), min, mpi_comm())[] + + return dt +end end # @muladd diff --git a/src/callbacks_step/stepsize_dg3d.jl b/src/callbacks_step/stepsize_dg3d.jl index 822ab2f87ec..664596f989e 100644 --- a/src/callbacks_step/stepsize_dg3d.jl +++ b/src/callbacks_step/stepsize_dg3d.jl @@ -150,4 +150,36 @@ function max_dt(u, t, mesh::ParallelP4estMesh{3}, return dt end + +function max_dt(u, t, mesh::ParallelT8codeMesh{3}, + constant_speed::False, equations, dg::DG, cache) + # call the method accepting a general `mesh::T8codeMesh{3}` + # TODO: MPI, we should improve this; maybe we should dispatch on `u` + # and create some MPI array type, overloading broadcasting and mapreduce etc. + # Then, this specific array type should also work well with DiffEq etc. + dt = invoke(max_dt, + Tuple{typeof(u), typeof(t), T8codeMesh{3}, + typeof(constant_speed), typeof(equations), typeof(dg), + typeof(cache)}, + u, t, mesh, constant_speed, equations, dg, cache) + dt = MPI.Allreduce!(Ref(dt), min, mpi_comm())[] + + return dt +end + +function max_dt(u, t, mesh::ParallelT8codeMesh{3}, + constant_speed::True, equations, dg::DG, cache) + # call the method accepting a general `mesh::T8codeMesh{3}` + # TODO: MPI, we should improve this; maybe we should dispatch on `u` + # and create some MPI array type, overloading broadcasting and mapreduce etc. + # Then, this specific array type should also work well with DiffEq etc. + dt = invoke(max_dt, + Tuple{typeof(u), typeof(t), T8codeMesh{3}, + typeof(constant_speed), typeof(equations), typeof(dg), + typeof(cache)}, + u, t, mesh, constant_speed, equations, dg, cache) + dt = MPI.Allreduce!(Ref(dt), min, mpi_comm())[] + + return dt +end end # @muladd diff --git a/src/meshes/p4est_mesh.jl b/src/meshes/p4est_mesh.jl index c5d39ef00c0..abe9d9345b5 100644 --- a/src/meshes/p4est_mesh.jl +++ b/src/meshes/p4est_mesh.jl @@ -1700,6 +1700,10 @@ function bilinear_interpolation!(coordinate, face_vertices, u, v) end end +function get_global_first_element_ids(mesh::P4estMesh) + return unsafe_wrap(Array, mesh.p4est.global_first_quadrant, mpi_nranks() + 1) +end + function balance!(mesh::P4estMesh{2}, init_fn = C_NULL) p4est_balance(mesh.p4est, P4EST_CONNECT_FACE, init_fn) # Due to a bug in `p4est`, the forest needs to be rebalanced twice sometimes diff --git a/src/meshes/t8code_mesh.jl b/src/meshes/t8code_mesh.jl index c9665a22af9..6fb4d861d10 100644 --- a/src/meshes/t8code_mesh.jl +++ b/src/meshes/t8code_mesh.jl @@ -7,8 +7,6 @@ to manage trees and mesh refinement. """ mutable struct T8codeMesh{NDIMS, RealT <: Real, IsParallel, NDIMSP2, NNODES} <: AbstractMesh{NDIMS} - cmesh :: Ptr{t8_cmesh} # cpointer to coarse mesh - scheme :: Ptr{t8_eclass_scheme} # cpointer to element scheme forest :: Ptr{t8_forest} # cpointer to forest is_parallel :: IsParallel @@ -25,14 +23,15 @@ mutable struct T8codeMesh{NDIMS, RealT <: Real, IsParallel, NDIMSP2, NNODES} <: nmortars :: Int nboundaries :: Int - function T8codeMesh{NDIMS}(cmesh, scheme, forest, tree_node_coordinates, nodes, + nmpiinterfaces :: Int + nmpimortars :: Int + + function T8codeMesh{NDIMS}(forest, tree_node_coordinates, nodes, boundary_names, current_filename) where {NDIMS} - is_parallel = False() + is_parallel = mpi_isparallel() ? True() : False() - mesh = new{NDIMS, Float64, typeof(is_parallel), NDIMS + 2, length(nodes)}(cmesh, - scheme, - forest, + mesh = new{NDIMS, Float64, typeof(is_parallel), NDIMS + 2, length(nodes)}(forest, is_parallel) mesh.nodes = nodes @@ -52,7 +51,7 @@ mutable struct T8codeMesh{NDIMS, RealT <: Real, IsParallel, NDIMSP2, NNODES} <: # further down. However, this might cause a pile-up of `mesh` # objects during long-running sessions. if !MPI.Finalized() - trixi_t8_unref_forest(mesh.forest) + t8_forest_unref(Ref(mesh.forest)) end end @@ -63,7 +62,7 @@ mutable struct T8codeMesh{NDIMS, RealT <: Real, IsParallel, NDIMSP2, NNODES} <: # more information. if haskey(ENV, "TRIXI_T8CODE_SC_FINALIZE") MPI.add_finalize_hook!() do - trixi_t8_unref_forest(mesh.forest) + t8_forest_unref(Ref(mesh.forest)) end end @@ -72,16 +71,15 @@ mutable struct T8codeMesh{NDIMS, RealT <: Real, IsParallel, NDIMSP2, NNODES} <: end const SerialT8codeMesh{NDIMS} = T8codeMesh{NDIMS, <:Real, <:False} +const ParallelT8codeMesh{NDIMS} = T8codeMesh{NDIMS, <:Real, <:True} @inline mpi_parallel(mesh::SerialT8codeMesh) = False() +@inline mpi_parallel(mesh::ParallelT8codeMesh) = True() @inline Base.ndims(::T8codeMesh{NDIMS}) where {NDIMS} = NDIMS @inline Base.real(::T8codeMesh{NDIMS, RealT}) where {NDIMS, RealT} = RealT -@inline ntrees(mesh::T8codeMesh) = Int(t8_forest_get_num_local_trees(mesh.forest)) +@inline ntrees(mesh::T8codeMesh) = size(mesh.tree_node_coordinates)[end] @inline ncells(mesh::T8codeMesh) = Int(t8_forest_get_local_num_elements(mesh.forest)) -@inline ninterfaces(mesh::T8codeMesh) = mesh.ninterfaces -@inline nmortars(mesh::T8codeMesh) = mesh.nmortars -@inline nboundaries(mesh::T8codeMesh) = mesh.nboundaries function Base.show(io::IO, mesh::T8codeMesh) print(io, "T8codeMesh{", ndims(mesh), ", ", real(mesh), "}") @@ -184,21 +182,23 @@ function T8codeMesh(trees_per_dimension; polydeg = 1, T8code.Libt8.p8est_connectivity_destroy(conn) end + do_face_ghost = mpi_isparallel() scheme = t8_scheme_new_default_cxx() - forest = t8_forest_new_uniform(cmesh, scheme, initial_refinement_level, 0, mpi_comm()) + forest = t8_forest_new_uniform(cmesh, scheme, initial_refinement_level, do_face_ghost, + mpi_comm()) basis = LobattoLegendreBasis(RealT, polydeg) nodes = basis.nodes + num_trees = t8_cmesh_get_num_trees(cmesh) + tree_node_coordinates = Array{RealT, NDIMS + 2}(undef, NDIMS, ntuple(_ -> length(nodes), NDIMS)..., - prod(trees_per_dimension)) + num_trees) # Get cell length in reference mesh: Omega_ref = [-1,1]^NDIMS. dx = [2 / n for n in trees_per_dimension] - num_local_trees = t8_cmesh_get_num_local_trees(cmesh) - # Non-periodic boundaries. boundary_names = fill(Symbol("---"), 2 * NDIMS, prod(trees_per_dimension)) @@ -208,7 +208,7 @@ function T8codeMesh(trees_per_dimension; polydeg = 1, mapping_ = mapping end - for itree in 1:num_local_trees + for itree in 1:num_trees veptr = t8_cmesh_get_tree_vertices(cmesh, itree - 1) verts = unsafe_wrap(Array, veptr, (3, 1 << NDIMS)) @@ -256,7 +256,7 @@ function T8codeMesh(trees_per_dimension; polydeg = 1, end end - return T8codeMesh{NDIMS}(cmesh, scheme, forest, tree_node_coordinates, nodes, + return T8codeMesh{NDIMS}(forest, tree_node_coordinates, nodes, boundary_names, "") end @@ -290,21 +290,25 @@ function T8codeMesh(cmesh::Ptr{t8_cmesh}; @assert (NDIMS == 2||NDIMS == 3) "NDIMS should be 2 or 3." + do_face_ghost = mpi_isparallel() scheme = t8_scheme_new_default_cxx() - forest = t8_forest_new_uniform(cmesh, scheme, initial_refinement_level, 0, mpi_comm()) + forest = t8_forest_new_uniform(cmesh, scheme, initial_refinement_level, do_face_ghost, + mpi_comm()) basis = LobattoLegendreBasis(RealT, polydeg) nodes = basis.nodes - num_local_trees = t8_cmesh_get_num_local_trees(cmesh) + num_trees = t8_cmesh_get_num_trees(cmesh) tree_node_coordinates = Array{RealT, NDIMS + 2}(undef, NDIMS, ntuple(_ -> length(nodes), NDIMS)..., - num_local_trees) + num_trees) nodes_in = [-1.0, 1.0] matrix = polynomial_interpolation_matrix(nodes_in, nodes) + num_local_trees = t8_cmesh_get_num_local_trees(cmesh) + if NDIMS == 2 data_in = Array{RealT, 3}(undef, 2, 2, 2) tmp1 = zeros(RealT, 2, length(nodes), length(nodes_in)) @@ -353,7 +357,7 @@ function T8codeMesh(cmesh::Ptr{t8_cmesh}; tmp1 = zeros(RealT, 3, length(nodes), length(nodes_in), length(nodes_in)) verts = zeros(3, 8) - for itree in 0:(num_local_trees - 1) + for itree in 0:(num_trees - 1) veptr = t8_cmesh_get_tree_vertices(cmesh, itree) # Note, `verts = unsafe_wrap(Array, veptr, (3, 1 << NDIMS))` @@ -387,9 +391,9 @@ function T8codeMesh(cmesh::Ptr{t8_cmesh}; map_node_coordinates!(tree_node_coordinates, mapping) # There's no simple and generic way to distinguish boundaries. Name all of them :all. - boundary_names = fill(:all, 2 * NDIMS, num_local_trees) + boundary_names = fill(:all, 2 * NDIMS, num_trees) - return T8codeMesh{NDIMS}(cmesh, scheme, forest, tree_node_coordinates, nodes, + return T8codeMesh{NDIMS}(forest, tree_node_coordinates, nodes, boundary_names, "") end @@ -442,7 +446,7 @@ function T8codeMesh(conn::Ptr{p8est_connectivity}; kwargs...) end """ - T8codeMesh{NDIMS}(meshfile::String; kwargs...) + T8codeMesh(meshfile::String, ndims; kwargs...) Main mesh constructor for the `T8codeMesh` that imports an unstructured, conforming mesh from a Gmsh mesh file (`.msh`). @@ -461,7 +465,6 @@ mesh from a Gmsh mesh file (`.msh`). - `initial_refinement_level::Integer`: refine the mesh uniformly to this level before the simulation starts. """ function T8codeMesh(meshfile::String, ndims; kwargs...) - # Prevent `t8code` from crashing Julia if the file doesn't exist. @assert isfile(meshfile) @@ -586,13 +589,525 @@ function adapt!(mesh::T8codeMesh, adapt_callback; recursive = true, balance = tr return nothing end -# TODO: Just a placeholder. Will be implemented later when MPI is supported. -function balance!(mesh::T8codeMesh, init_fn = C_NULL) +""" + Trixi.balance!(mesh::T8codeMesh) + +Balance a `T8codeMesh` to ensure 2^(NDIMS-1):1 face neighbors. +""" +function balance!(mesh::T8codeMesh) + new_forest_ref = Ref{t8_forest_t}() + t8_forest_init(new_forest_ref) + new_forest = new_forest_ref[] + + let set_from = mesh.forest, no_repartition = 1, do_ghost = 1 + t8_forest_set_balance(new_forest, set_from, no_repartition) + t8_forest_set_ghost(new_forest, do_ghost, T8_GHOST_FACES) + t8_forest_commit(new_forest) + end + + mesh.forest = new_forest + + return nothing +end + +""" + Trixi.partition!(mesh::T8codeMesh) + +Partition a `T8codeMesh` in order to redistribute elements evenly among MPI ranks. + +# Arguments +- `mesh::T8codeMesh`: Initialized mesh object. +""" +function partition!(mesh::T8codeMesh) + new_forest_ref = Ref{t8_forest_t}() + t8_forest_init(new_forest_ref) + new_forest = new_forest_ref[] + + let set_from = mesh.forest, do_ghost = 1, allow_for_coarsening = 1 + t8_forest_set_partition(new_forest, set_from, allow_for_coarsening) + t8_forest_set_ghost(new_forest, do_ghost, T8_GHOST_FACES) + t8_forest_commit(new_forest) + end + + mesh.forest = new_forest + return nothing end -# TODO: Just a placeholder. Will be implemented later when MPI is supported. -function partition!(mesh::T8codeMesh; allow_coarsening = true, weight_fn = C_NULL) +# Compute the global ids (zero-indexed) of first element in each MPI rank. +function get_global_first_element_ids(mesh::T8codeMesh) + n_elements_local = Int(t8_forest_get_local_num_elements(mesh.forest)) + n_elements_by_rank = Vector{Int}(undef, mpi_nranks()) + n_elements_by_rank[mpi_rank() + 1] = n_elements_local + MPI.Allgather!(MPI.UBuffer(n_elements_by_rank, 1), mpi_comm()) + return [sum(n_elements_by_rank[1:(rank - 1)]) for rank in 1:(mpi_nranks() + 1)] +end + +function count_interfaces(mesh::T8codeMesh) + @assert t8_forest_is_committed(mesh.forest) != 0 + + num_local_elements = t8_forest_get_local_num_elements(mesh.forest) + num_local_trees = t8_forest_get_num_local_trees(mesh.forest) + + current_index = t8_locidx_t(0) + + local_num_conform = 0 + local_num_mortars = 0 + local_num_boundary = 0 + + local_num_mpi_conform = 0 + local_num_mpi_mortars = 0 + + visited_global_mortar_ids = Set{UInt64}([]) + + max_level = t8_forest_get_maxlevel(mesh.forest) #UInt64 + max_tree_num_elements = UInt64(2^ndims(mesh))^max_level + + if mpi_isparallel() + ghost_num_trees = t8_forest_ghost_num_trees(mesh.forest) + + ghost_tree_element_offsets = [num_local_elements + + t8_forest_ghost_get_tree_element_offset(mesh.forest, + itree) + for itree in 0:(ghost_num_trees - 1)] + ghost_global_treeids = [t8_forest_ghost_get_global_treeid(mesh.forest, itree) + for itree in 0:(ghost_num_trees - 1)] + end + + for itree in 0:(num_local_trees - 1) + tree_class = t8_forest_get_tree_class(mesh.forest, itree) + eclass_scheme = t8_forest_get_eclass_scheme(mesh.forest, tree_class) + + num_elements_in_tree = t8_forest_get_tree_num_elements(mesh.forest, itree) + + global_itree = t8_forest_global_tree_id(mesh.forest, itree) + + for ielement in 0:(num_elements_in_tree - 1) + element = t8_forest_get_element_in_tree(mesh.forest, itree, ielement) + + level = t8_element_level(eclass_scheme, element) + + num_faces = t8_element_num_faces(eclass_scheme, element) + + # Note: This works only for forests of one element class. + current_linear_id = global_itree * max_tree_num_elements + + t8_element_get_linear_id(eclass_scheme, element, max_level) + + for iface in 0:(num_faces - 1) + pelement_indices_ref = Ref{Ptr{t8_locidx_t}}() + pneighbor_leafs_ref = Ref{Ptr{Ptr{t8_element}}}() + pneigh_scheme_ref = Ref{Ptr{t8_eclass_scheme}}() + + dual_faces_ref = Ref{Ptr{Cint}}() + num_neighbors_ref = Ref{Cint}() + + forest_is_balanced = Cint(1) + + t8_forest_leaf_face_neighbors(mesh.forest, itree, element, + pneighbor_leafs_ref, iface, dual_faces_ref, + num_neighbors_ref, + pelement_indices_ref, pneigh_scheme_ref, + forest_is_balanced) + + num_neighbors = num_neighbors_ref[] + dual_faces = unsafe_wrap(Array, dual_faces_ref[], num_neighbors) + neighbor_ielements = unsafe_wrap(Array, pelement_indices_ref[], + num_neighbors) + neighbor_leafs = unsafe_wrap(Array, pneighbor_leafs_ref[], num_neighbors) + neighbor_scheme = pneigh_scheme_ref[] + + if num_neighbors == 0 + local_num_boundary += 1 + else + neighbor_level = t8_element_level(neighbor_scheme, neighbor_leafs[1]) + + if all(neighbor_ielements .< num_local_elements) + # Conforming interface: The second condition ensures we + # only visit the interface once. + if level == neighbor_level && current_index <= neighbor_ielements[1] + local_num_conform += 1 + elseif level < neighbor_level + local_num_mortars += 1 + # `else level > neighbor_level` is ignored since we + # only want to count the mortar interface once. + end + else + if level == neighbor_level + local_num_mpi_conform += 1 + elseif level < neighbor_level + local_num_mpi_mortars += 1 + + global_mortar_id = 2 * ndims(mesh) * current_linear_id + iface + + else # level > neighbor_level + neighbor_global_ghost_itree = ghost_global_treeids[findlast(ghost_tree_element_offsets .<= + neighbor_ielements[1])] + neighbor_linear_id = neighbor_global_ghost_itree * + max_tree_num_elements + + t8_element_get_linear_id(neighbor_scheme, + neighbor_leafs[1], + max_level) + global_mortar_id = 2 * ndims(mesh) * neighbor_linear_id + + dual_faces[1] + + if !(global_mortar_id in visited_global_mortar_ids) + push!(visited_global_mortar_ids, global_mortar_id) + local_num_mpi_mortars += 1 + end + end + end + end + + t8_free(dual_faces_ref[]) + t8_free(pneighbor_leafs_ref[]) + t8_free(pelement_indices_ref[]) + end # for + + current_index += 1 + end # for + end # for + + return (interfaces = local_num_conform, + mortars = local_num_mortars, + boundaries = local_num_boundary, + mpi_interfaces = local_num_mpi_conform, + mpi_mortars = local_num_mpi_mortars) +end + +# I know this routine is an unmaintainable behemoth. However, I see no real +# and elegant way to refactor this into, for example, smaller parts. The +# `t8_forest_leaf_face_neighbors` routine is as of now rather costly and it +# makes sense to query it only once per face per element and extract all the +# information needed at once in order to fill the connectivity information. +# Instead, I opted for good documentation. +function fill_mesh_info!(mesh::T8codeMesh, interfaces, mortars, boundaries, + boundary_names; mpi_mesh_info = nothing) + @assert t8_forest_is_committed(mesh.forest) != 0 + + num_local_elements = t8_forest_get_local_num_elements(mesh.forest) + num_local_trees = t8_forest_get_num_local_trees(mesh.forest) + + if !isnothing(mpi_mesh_info) + #! format: off + remotes = t8_forest_ghost_get_remotes(mesh.forest) + ghost_num_trees = t8_forest_ghost_num_trees(mesh.forest) + + ghost_remote_first_elem = [num_local_elements + + t8_forest_ghost_remote_first_elem(mesh.forest, remote) + for remote in remotes] + + ghost_tree_element_offsets = [num_local_elements + + t8_forest_ghost_get_tree_element_offset(mesh.forest, itree) + for itree in 0:(ghost_num_trees - 1)] + + ghost_global_treeids = [t8_forest_ghost_get_global_treeid(mesh.forest, itree) + for itree in 0:(ghost_num_trees - 1)] + #! format: on + end + + # Process-local index of the current element in the space-filling curve. + current_index = t8_locidx_t(0) + + # Increment counters for the different interface/mortar/boundary types. + local_num_conform = 0 + local_num_mortars = 0 + local_num_boundary = 0 + + local_num_mpi_conform = 0 + local_num_mpi_mortars = 0 + + # Works for quads and hexs only. This mapping is needed in the MPI mortar + # sections below. + map_iface_to_ichild_to_position = [ + # 0 1 2 3 4 5 6 7 ichild/iface + [1, 0, 2, 0, 3, 0, 4, 0], # 0 + [0, 1, 0, 2, 0, 3, 0, 4], # 1 + [1, 2, 0, 0, 3, 4, 0, 0], # 2 + [0, 0, 1, 2, 0, 0, 3, 4], # 3 + [1, 2, 3, 4, 0, 0, 0, 0], # 4 + [0, 0, 0, 0, 1, 2, 3, 4], # 5 + ] + + # Helper variables to compute unique global MPI interface/mortar ids. + max_level = t8_forest_get_maxlevel(mesh.forest) #UInt64 + max_tree_num_elements = UInt64(2^ndims(mesh))^max_level + + # These two variables help to ensure that we count MPI mortars from smaller + # elements point of view only once. + visited_global_mortar_ids = Set{UInt64}([]) + global_mortar_id_to_local = Dict{UInt64, Int}([]) + + # Loop over all local trees. + for itree in 0:(num_local_trees - 1) + tree_class = t8_forest_get_tree_class(mesh.forest, itree) + eclass_scheme = t8_forest_get_eclass_scheme(mesh.forest, tree_class) + + num_elements_in_tree = t8_forest_get_tree_num_elements(mesh.forest, itree) + + global_itree = t8_forest_global_tree_id(mesh.forest, itree) + + # Loop over all local elements of the current local tree. + for ielement in 0:(num_elements_in_tree - 1) + element = t8_forest_get_element_in_tree(mesh.forest, itree, ielement) + + level = t8_element_level(eclass_scheme, element) + + num_faces = t8_element_num_faces(eclass_scheme, element) + + # Note: This works only for forests of one element class. + current_linear_id = global_itree * max_tree_num_elements + + t8_element_get_linear_id(eclass_scheme, element, max_level) + + # Loop over all faces of the current local element. + for iface in 0:(num_faces - 1) + # Compute the `orientation` of the touching faces. + if t8_element_is_root_boundary(eclass_scheme, element, iface) == 1 + cmesh = t8_forest_get_cmesh(mesh.forest) + itree_in_cmesh = t8_forest_ltreeid_to_cmesh_ltreeid(mesh.forest, itree) + iface_in_tree = t8_element_tree_face(eclass_scheme, element, iface) + orientation_ref = Ref{Cint}() + + t8_cmesh_get_face_neighbor(cmesh, itree_in_cmesh, iface_in_tree, C_NULL, + orientation_ref) + orientation = orientation_ref[] + else + orientation = zero(Cint) + end + + pelement_indices_ref = Ref{Ptr{t8_locidx_t}}() + pneighbor_leafs_ref = Ref{Ptr{Ptr{t8_element}}}() + pneigh_scheme_ref = Ref{Ptr{t8_eclass_scheme}}() + + dual_faces_ref = Ref{Ptr{Cint}}() + num_neighbors_ref = Ref{Cint}() + + forest_is_balanced = Cint(1) + + # Query neighbor information from t8code. + t8_forest_leaf_face_neighbors(mesh.forest, itree, element, + pneighbor_leafs_ref, iface, dual_faces_ref, + num_neighbors_ref, + pelement_indices_ref, pneigh_scheme_ref, + forest_is_balanced) + + num_neighbors = num_neighbors_ref[] + dual_faces = unsafe_wrap(Array, dual_faces_ref[], num_neighbors) + neighbor_ielements = unsafe_wrap(Array, pelement_indices_ref[], + num_neighbors) + neighbor_leafs = unsafe_wrap(Array, pneighbor_leafs_ref[], num_neighbors) + neighbor_scheme = pneigh_scheme_ref[] + + # Now we check for the different cases. The nested if-structure is as follows: + # + # if `boundary`: + # + # + # else: // It must be an interface or mortar. + # + # if `all neighbors are local elements`: + # + # if `local interface`: + # + # elseif `local mortar from larger element point of view`: + # + # else: // `local mortar from smaller elements point of view` + # // We only count local mortars once. + # + # else: // It must be either a MPI interface or a MPI mortar. + # + # if `MPI interface`: + # + # elseif `MPI mortar from larger element point of view`: + # + # else: // `MPI mortar from smaller elements point of view` + # + # + # // end + + # Domain boundary. + if num_neighbors == 0 + local_num_boundary += 1 + boundary_id = local_num_boundary + + boundaries.neighbor_ids[boundary_id] = current_index + 1 + + init_boundary_node_indices!(boundaries, iface, boundary_id) + + # One-based indexing. + boundaries.name[boundary_id] = boundary_names[iface + 1, itree + 1] + + # Interface or mortar. + else + neighbor_level = t8_element_level(neighbor_scheme, neighbor_leafs[1]) + + # Local interface or mortar. + if all(neighbor_ielements .< num_local_elements) + + # Local interface: The second condition ensures we only visit the interface once. + if level == neighbor_level && current_index <= neighbor_ielements[1] + local_num_conform += 1 + + interfaces.neighbor_ids[1, local_num_conform] = current_index + + 1 + interfaces.neighbor_ids[2, local_num_conform] = neighbor_ielements[1] + + 1 + + init_interface_node_indices!(interfaces, (iface, dual_faces[1]), + orientation, + local_num_conform) + # Local mortar. + elseif level < neighbor_level + local_num_mortars += 1 + + # Last entry is the large element. + mortars.neighbor_ids[end, local_num_mortars] = current_index + 1 + + init_mortar_neighbor_ids!(mortars, iface, dual_faces[1], + orientation, neighbor_ielements, + local_num_mortars) + + init_mortar_node_indices!(mortars, (dual_faces[1], iface), + orientation, local_num_mortars) + + # else: `level > neighbor_level` is skipped since we visit the mortar interface only once. + end + + # MPI interface or MPI mortar. + else + + # MPI interface. + if level == neighbor_level + local_num_mpi_conform += 1 + + neighbor_global_ghost_itree = ghost_global_treeids[findlast(ghost_tree_element_offsets .<= + neighbor_ielements[1])] + + neighbor_linear_id = neighbor_global_ghost_itree * + max_tree_num_elements + + t8_element_get_linear_id(neighbor_scheme, + neighbor_leafs[1], + max_level) + + if current_linear_id < neighbor_linear_id + local_side = 1 + smaller_iface = iface + smaller_linear_id = current_linear_id + faces = (iface, dual_faces[1]) + else + local_side = 2 + smaller_iface = dual_faces[1] + smaller_linear_id = neighbor_linear_id + faces = (dual_faces[1], iface) + end + + global_interface_id = 2 * ndims(mesh) * smaller_linear_id + + smaller_iface + + mpi_mesh_info.mpi_interfaces.local_neighbor_ids[local_num_mpi_conform] = current_index + + 1 + mpi_mesh_info.mpi_interfaces.local_sides[local_num_mpi_conform] = local_side + + init_mpi_interface_node_indices!(mpi_mesh_info.mpi_interfaces, + faces, local_side, orientation, + local_num_mpi_conform) + + neighbor_rank = remotes[findlast(ghost_remote_first_elem .<= + neighbor_ielements[1])] + mpi_mesh_info.neighbor_ranks_interface[local_num_mpi_conform] = neighbor_rank + + mpi_mesh_info.global_interface_ids[local_num_mpi_conform] = global_interface_id + + # MPI Mortar: from larger element point of view + elseif level < neighbor_level + local_num_mpi_mortars += 1 + + global_mortar_id = 2 * ndims(mesh) * current_linear_id + iface + + neighbor_ids = neighbor_ielements .+ 1 + + local_neighbor_positions = findall(neighbor_ids .<= + num_local_elements) + local_neighbor_ids = [neighbor_ids[i] + for i in local_neighbor_positions] + local_neighbor_positions = [map_iface_to_ichild_to_position[dual_faces[1] + 1][t8_element_child_id(neighbor_scheme, neighbor_leafs[i]) + 1] + for i in local_neighbor_positions] + + # Last entry is the large element. + push!(local_neighbor_ids, current_index + 1) + push!(local_neighbor_positions, 2^(ndims(mesh) - 1) + 1) + + mpi_mesh_info.mpi_mortars.local_neighbor_ids[local_num_mpi_mortars] = local_neighbor_ids + mpi_mesh_info.mpi_mortars.local_neighbor_positions[local_num_mpi_mortars] = local_neighbor_positions + + init_mortar_node_indices!(mpi_mesh_info.mpi_mortars, + (dual_faces[1], iface), orientation, + local_num_mpi_mortars) + + neighbor_ranks = [remotes[findlast(ghost_remote_first_elem .<= + ineighbor_ghost)] + for ineighbor_ghost in filter(x -> x >= + num_local_elements, + neighbor_ielements)] + mpi_mesh_info.neighbor_ranks_mortar[local_num_mpi_mortars] = neighbor_ranks + + mpi_mesh_info.global_mortar_ids[local_num_mpi_mortars] = global_mortar_id + + # MPI Mortar: from smaller elements point of view + else + neighbor_global_ghost_itree = ghost_global_treeids[findlast(ghost_tree_element_offsets .<= + neighbor_ielements[1])] + neighbor_linear_id = neighbor_global_ghost_itree * + max_tree_num_elements + + t8_element_get_linear_id(neighbor_scheme, + neighbor_leafs[1], + max_level) + global_mortar_id = 2 * ndims(mesh) * neighbor_linear_id + + dual_faces[1] + + if global_mortar_id in visited_global_mortar_ids + local_mpi_mortar_id = global_mortar_id_to_local[global_mortar_id] + + push!(mpi_mesh_info.mpi_mortars.local_neighbor_ids[local_mpi_mortar_id], + current_index + 1) + push!(mpi_mesh_info.mpi_mortars.local_neighbor_positions[local_mpi_mortar_id], + map_iface_to_ichild_to_position[iface + 1][t8_element_child_id(eclass_scheme, element) + 1]) + else + local_num_mpi_mortars += 1 + local_mpi_mortar_id = local_num_mpi_mortars + push!(visited_global_mortar_ids, global_mortar_id) + global_mortar_id_to_local[global_mortar_id] = local_mpi_mortar_id + + mpi_mesh_info.mpi_mortars.local_neighbor_ids[local_mpi_mortar_id] = [ + current_index + 1, + ] + mpi_mesh_info.mpi_mortars.local_neighbor_positions[local_mpi_mortar_id] = [ + map_iface_to_ichild_to_position[iface + 1][t8_element_child_id(eclass_scheme, element) + 1], + ] + init_mortar_node_indices!(mpi_mesh_info.mpi_mortars, + (iface, dual_faces[1]), + orientation, local_mpi_mortar_id) + + neighbor_ranks = [ + remotes[findlast(ghost_remote_first_elem .<= + neighbor_ielements[1])], + ] + mpi_mesh_info.neighbor_ranks_mortar[local_mpi_mortar_id] = neighbor_ranks + + mpi_mesh_info.global_mortar_ids[local_mpi_mortar_id] = global_mortar_id + end + end + end + end + + t8_free(dual_faces_ref[]) + t8_free(pneighbor_leafs_ref[]) + t8_free(pelement_indices_ref[]) + end # for iface + + current_index += 1 + end # for ielement + end # for itree + return nothing end diff --git a/src/solvers/dgsem_p4est/containers_parallel.jl b/src/solvers/dgsem_p4est/containers_parallel.jl index 7c7bd868457..fd2749155bb 100644 --- a/src/solvers/dgsem_p4est/containers_parallel.jl +++ b/src/solvers/dgsem_p4est/containers_parallel.jl @@ -43,7 +43,8 @@ function Base.resize!(mpi_interfaces::P4estMPIInterfaceContainer, capacity) end # Create MPI interface container and initialize interface data -function init_mpi_interfaces(mesh::ParallelP4estMesh, equations, basis, elements) +function init_mpi_interfaces(mesh::Union{ParallelP4estMesh, ParallelT8codeMesh}, + equations, basis, elements) NDIMS = ndims(elements) uEltype = eltype(elements) @@ -133,7 +134,8 @@ function Base.resize!(mpi_mortars::P4estMPIMortarContainer, capacity) end # Create MPI mortar container and initialize MPI mortar data -function init_mpi_mortars(mesh::ParallelP4estMesh, equations, basis, elements) +function init_mpi_mortars(mesh::Union{ParallelP4estMesh, ParallelT8codeMesh}, equations, + basis, elements) NDIMS = ndims(mesh) RealT = real(mesh) uEltype = eltype(elements) diff --git a/src/solvers/dgsem_p4est/dg_2d_parallel.jl b/src/solvers/dgsem_p4est/dg_2d_parallel.jl index a8887351c46..3bf0cd0cab5 100644 --- a/src/solvers/dgsem_p4est/dg_2d_parallel.jl +++ b/src/solvers/dgsem_p4est/dg_2d_parallel.jl @@ -6,7 +6,8 @@ #! format: noindent function prolong2mpiinterfaces!(cache, u, - mesh::ParallelP4estMesh{2}, + mesh::Union{ParallelP4estMesh{2}, + ParallelT8codeMesh{2}}, equations, surface_integral, dg::DG) @unpack mpi_interfaces = cache index_range = eachnode(dg) @@ -43,7 +44,8 @@ function prolong2mpiinterfaces!(cache, u, end function calc_mpi_interface_flux!(surface_flux_values, - mesh::ParallelP4estMesh{2}, + mesh::Union{ParallelP4estMesh{2}, + ParallelT8codeMesh{2}}, nonconservative_terms, equations, surface_integral, dg::DG, cache) @unpack local_neighbor_ids, node_indices, local_sides = cache.mpi_interfaces @@ -106,7 +108,8 @@ end # Inlined version of the interface flux computation for conservation laws @inline function calc_mpi_interface_flux!(surface_flux_values, - mesh::P4estMesh{2}, + mesh::Union{ParallelP4estMesh{2}, + ParallelT8codeMesh{2}}, nonconservative_terms::False, equations, surface_integral, dg::DG, cache, interface_index, normal_direction, @@ -131,7 +134,8 @@ end end function prolong2mpimortars!(cache, u, - mesh::ParallelP4estMesh{2}, equations, + mesh::Union{ParallelP4estMesh{2}, ParallelT8codeMesh{2}}, + equations, mortar_l2::LobattoLegendreMortarL2, surface_integral, dg::DGSEM) @unpack node_indices = cache.mpi_mortars @@ -199,7 +203,7 @@ function prolong2mpimortars!(cache, u, end function calc_mpi_mortar_flux!(surface_flux_values, - mesh::ParallelP4estMesh{2}, + mesh::Union{ParallelP4estMesh{2}, ParallelT8codeMesh{2}}, nonconservative_terms, equations, mortar_l2::LobattoLegendreMortarL2, surface_integral, dg::DG, cache) @@ -253,7 +257,8 @@ end # Inlined version of the mortar flux computation on small elements for conservation laws @inline function calc_mpi_mortar_flux!(fstar, - mesh::ParallelP4estMesh{2}, + mesh::Union{ParallelP4estMesh{2}, + ParallelT8codeMesh{2}}, nonconservative_terms::False, equations, surface_integral, dg::DG, cache, mortar_index, position_index, normal_direction, @@ -271,7 +276,9 @@ end end @inline function mpi_mortar_fluxes_to_elements!(surface_flux_values, - mesh::ParallelP4estMesh{2}, equations, + mesh::Union{ParallelP4estMesh{2}, + ParallelT8codeMesh{2}}, + equations, mortar_l2::LobattoLegendreMortarL2, dg::DGSEM, cache, mortar, fstar, u_buffer) diff --git a/src/solvers/dgsem_p4est/dg_3d_parallel.jl b/src/solvers/dgsem_p4est/dg_3d_parallel.jl index 13bf2a1a2eb..e504e06d2c4 100644 --- a/src/solvers/dgsem_p4est/dg_3d_parallel.jl +++ b/src/solvers/dgsem_p4est/dg_3d_parallel.jl @@ -6,7 +6,7 @@ #! format: noindent function rhs!(du, u, t, - mesh::ParallelP4estMesh{3}, equations, + mesh::Union{ParallelP4estMesh{3}, ParallelT8codeMesh{3}}, equations, initial_condition, boundary_conditions, source_terms::Source, dg::DG, cache) where {Source} # Start to receive MPI data @@ -113,7 +113,8 @@ function rhs!(du, u, t, end function prolong2mpiinterfaces!(cache, u, - mesh::ParallelP4estMesh{3}, + mesh::Union{ParallelP4estMesh{3}, + ParallelT8codeMesh{3}}, equations, surface_integral, dg::DG) @unpack mpi_interfaces = cache index_range = eachnode(dg) @@ -160,7 +161,8 @@ function prolong2mpiinterfaces!(cache, u, end function calc_mpi_interface_flux!(surface_flux_values, - mesh::ParallelP4estMesh{3}, + mesh::Union{ParallelP4estMesh{3}, + ParallelT8codeMesh{3}}, nonconservative_terms, equations, surface_integral, dg::DG, cache) @unpack local_neighbor_ids, node_indices, local_sides = cache.mpi_interfaces @@ -237,7 +239,8 @@ end # Inlined version of the interface flux computation for conservation laws @inline function calc_mpi_interface_flux!(surface_flux_values, - mesh::P4estMesh{3}, + mesh::Union{ParallelP4estMesh{3}, + ParallelT8codeMesh{3}}, nonconservative_terms::False, equations, surface_integral, dg::DG, cache, interface_index, normal_direction, @@ -265,7 +268,8 @@ end end function prolong2mpimortars!(cache, u, - mesh::ParallelP4estMesh{3}, equations, + mesh::Union{ParallelP4estMesh{3}, ParallelT8codeMesh{3}}, + equations, mortar_l2::LobattoLegendreMortarL2, surface_integral, dg::DGSEM) @unpack node_indices = cache.mpi_mortars @@ -374,7 +378,7 @@ function prolong2mpimortars!(cache, u, end function calc_mpi_mortar_flux!(surface_flux_values, - mesh::ParallelP4estMesh{3}, + mesh::Union{ParallelP4estMesh{3}, ParallelT8codeMesh{3}}, nonconservative_terms, equations, mortar_l2::LobattoLegendreMortarL2, surface_integral, dg::DG, cache) @@ -437,7 +441,8 @@ end # Inlined version of the mortar flux computation on small elements for conservation laws @inline function calc_mpi_mortar_flux!(fstar, - mesh::ParallelP4estMesh{3}, + mesh::Union{ParallelP4estMesh{3}, + ParallelT8codeMesh{3}}, nonconservative_terms::False, equations, surface_integral, dg::DG, cache, mortar_index, position_index, normal_direction, @@ -456,7 +461,9 @@ end end @inline function mpi_mortar_fluxes_to_elements!(surface_flux_values, - mesh::ParallelP4estMesh{3}, equations, + mesh::Union{ParallelP4estMesh{3}, + ParallelT8codeMesh{3}}, + equations, mortar_l2::LobattoLegendreMortarL2, dg::DGSEM, cache, mortar, fstar, u_buffer, fstar_tmp) diff --git a/src/solvers/dgsem_p4est/dg_parallel.jl b/src/solvers/dgsem_p4est/dg_parallel.jl index 712ede2bfce..eaa6ab5cee2 100644 --- a/src/solvers/dgsem_p4est/dg_parallel.jl +++ b/src/solvers/dgsem_p4est/dg_parallel.jl @@ -166,7 +166,8 @@ end # at `index_base`+1 in the MPI buffer. `data_size` is the data size associated with each small # position (i.e. position 1 or 2). The data corresponding to the large side (i.e. position 3) has # size `2 * data_size`. -@inline function buffer_mortar_indices(mesh::ParallelP4estMesh{2}, index_base, +@inline function buffer_mortar_indices(mesh::Union{ParallelP4estMesh{2}, + ParallelT8codeMesh{2}}, index_base, data_size) return ( # first, last for local element in position 1 (small element) @@ -185,7 +186,8 @@ end # at `index_base`+1 in the MPI buffer. `data_size` is the data size associated with each small # position (i.e. position 1 to 4). The data corresponding to the large side (i.e. position 5) has # size `4 * data_size`. -@inline function buffer_mortar_indices(mesh::ParallelP4estMesh{3}, index_base, +@inline function buffer_mortar_indices(mesh::Union{ParallelP4estMesh{3}, + ParallelT8codeMesh{3}}, index_base, data_size) return ( # first, last for local element in position 1 (small element) @@ -491,7 +493,8 @@ end # Exchange normal directions of small elements of the MPI mortars. They are needed on all involved # MPI ranks to calculate the mortar fluxes. -function exchange_normal_directions!(mpi_mortars, mpi_cache, mesh::ParallelP4estMesh, +function exchange_normal_directions!(mpi_mortars, mpi_cache, + mesh::Union{ParallelP4estMesh, ParallelT8codeMesh}, n_nodes) RealT = real(mesh) n_dims = ndims(mesh) diff --git a/src/solvers/dgsem_t8code/containers.jl b/src/solvers/dgsem_t8code/containers.jl index 093feb2985a..d7ff79fbf2f 100644 --- a/src/solvers/dgsem_t8code/containers.jl +++ b/src/solvers/dgsem_t8code/containers.jl @@ -18,19 +18,22 @@ function reinitialize_containers!(mesh::T8codeMesh, equations, dg::DGSEM, cache) @unpack boundaries = cache resize!(boundaries, mesh.nboundaries) - trixi_t8_fill_mesh_info(mesh.forest, elements, interfaces, mortars, boundaries, - mesh.boundary_names) + fill_mesh_info!(mesh, interfaces, mortars, boundaries, + mesh.boundary_names) return nothing end function count_required_surfaces!(mesh::T8codeMesh) - counts = trixi_t8_count_interfaces(mesh.forest) + counts = count_interfaces(mesh) mesh.nmortars = counts.mortars mesh.ninterfaces = counts.interfaces mesh.nboundaries = counts.boundaries + mesh.nmpimortars = counts.mpi_mortars + mesh.nmpiinterfaces = counts.mpi_interfaces + return counts end @@ -38,7 +41,9 @@ end function count_required_surfaces(mesh::T8codeMesh) return (interfaces = mesh.ninterfaces, mortars = mesh.nmortars, - boundaries = mesh.nboundaries) + boundaries = mesh.nboundaries, + mpi_interfaces = mesh.nmpiinterfaces, + mpi_mortars = mesh.nmpimortars) end # Compatibility to `dgsem_p4est/containers.jl`. diff --git a/src/solvers/dgsem_t8code/containers_2d.jl b/src/solvers/dgsem_t8code/containers_2d.jl index bf77826a34b..ce525bfdf65 100644 --- a/src/solvers/dgsem_t8code/containers_2d.jl +++ b/src/solvers/dgsem_t8code/containers_2d.jl @@ -26,6 +26,7 @@ function calc_node_coordinates!(node_coordinates, tree_class = t8_forest_get_tree_class(mesh.forest, itree) eclass_scheme = t8_forest_get_eclass_scheme(mesh.forest, tree_class) num_elements_in_tree = t8_forest_get_tree_num_elements(mesh.forest, itree) + global_itree = t8_forest_global_tree_id(mesh.forest, itree) for ielement in 0:(num_elements_in_tree - 1) element = t8_forest_get_element_in_tree(mesh.forest, itree, ielement) @@ -55,7 +56,7 @@ function calc_node_coordinates!(node_coordinates, multiply_dimensionwise!(view(node_coordinates, :, :, :, current_index += 1), matrix1, matrix2, view(mesh.tree_node_coordinates, :, :, :, - itree + 1), + global_itree + 1), tmp1) end end diff --git a/src/solvers/dgsem_t8code/containers_3d.jl b/src/solvers/dgsem_t8code/containers_3d.jl index f2d54ff07da..4d56bc734aa 100644 --- a/src/solvers/dgsem_t8code/containers_3d.jl +++ b/src/solvers/dgsem_t8code/containers_3d.jl @@ -28,6 +28,7 @@ function calc_node_coordinates!(node_coordinates, tree_class = t8_forest_get_tree_class(mesh.forest, itree) eclass_scheme = t8_forest_get_eclass_scheme(mesh.forest, tree_class) num_elements_in_tree = t8_forest_get_tree_num_elements(mesh.forest, itree) + global_itree = t8_forest_global_tree_id(mesh.forest, itree) for ielement in 0:(num_elements_in_tree - 1) element = t8_forest_get_element_in_tree(mesh.forest, itree, ielement) @@ -63,7 +64,7 @@ function calc_node_coordinates!(node_coordinates, current_index += 1), matrix1, matrix2, matrix3, view(mesh.tree_node_coordinates, :, :, :, :, - itree + 1), + global_itree + 1), tmp1) end end diff --git a/src/solvers/dgsem_t8code/containers_parallel.jl b/src/solvers/dgsem_t8code/containers_parallel.jl new file mode 100644 index 00000000000..0cb3f5887a0 --- /dev/null +++ b/src/solvers/dgsem_t8code/containers_parallel.jl @@ -0,0 +1,65 @@ +function reinitialize_containers!(mesh::ParallelT8codeMesh, equations, dg::DGSEM, cache) + @unpack elements, interfaces, boundaries, mortars, mpi_interfaces, mpi_mortars, + mpi_cache = cache + resize!(elements, ncells(mesh)) + init_elements!(elements, mesh, dg.basis) + + count_required_surfaces!(mesh) + required = count_required_surfaces(mesh) + + resize!(interfaces, required.interfaces) + + resize!(boundaries, required.boundaries) + + resize!(mortars, required.mortars) + + resize!(mpi_interfaces, required.mpi_interfaces) + + resize!(mpi_mortars, required.mpi_mortars) + + mpi_mesh_info = (mpi_mortars = mpi_mortars, + mpi_interfaces = mpi_interfaces, + + # Temporary arrays for updating `mpi_cache`. + global_mortar_ids = fill(UInt64(0), nmpimortars(mpi_mortars)), + global_interface_ids = fill(UInt64(0), nmpiinterfaces(mpi_interfaces)), + neighbor_ranks_mortar = Vector{Vector{Int}}(undef, + nmpimortars(mpi_mortars)), + neighbor_ranks_interface = fill(-1, nmpiinterfaces(mpi_interfaces))) + + fill_mesh_info!(mesh, interfaces, mortars, boundaries, + mesh.boundary_names; mpi_mesh_info = mpi_mesh_info) + + init_mpi_cache!(mpi_cache, mesh, mpi_mesh_info, nvariables(equations), nnodes(dg), + eltype(elements)) + + empty!(mpi_mesh_info.global_mortar_ids) + empty!(mpi_mesh_info.global_interface_ids) + empty!(mpi_mesh_info.neighbor_ranks_mortar) + empty!(mpi_mesh_info.neighbor_ranks_interface) + + # Re-initialize and distribute normal directions of MPI mortars; requires + # MPI communication, so the MPI cache must be re-initialized beforehand. + init_normal_directions!(mpi_mortars, dg.basis, elements) + exchange_normal_directions!(mpi_mortars, mpi_cache, mesh, nnodes(dg)) + + return nothing +end + +# Compatibility to `dgsem_p4est/containers.jl`. +function init_mpi_interfaces!(interfaces, mesh::ParallelT8codeMesh) + # Do nothing. + return nothing +end + +# Compatibility to `dgsem_p4est/containers.jl`. +function init_mpi_mortars!(mortars, mesh::ParallelT8codeMesh) + # Do nothing. + return nothing +end + +# Compatibility to `dgsem_p4est/containers_parallel.jl`. +function init_mpi_mortars!(mpi_mortars, mesh::ParallelT8codeMesh, basis, elements) + # Do nothing. + return nothing +end diff --git a/src/solvers/dgsem_t8code/dg.jl b/src/solvers/dgsem_t8code/dg.jl index 6e9660c917d..e01b12e0f80 100644 --- a/src/solvers/dgsem_t8code/dg.jl +++ b/src/solvers/dgsem_t8code/dg.jl @@ -13,8 +13,8 @@ function create_cache(mesh::T8codeMesh, equations::AbstractEquations, dg::DG, :: boundaries = init_boundaries(mesh, equations, dg.basis, elements) mortars = init_mortars(mesh, equations, dg.basis, elements) - trixi_t8_fill_mesh_info(mesh.forest, elements, interfaces, mortars, boundaries, - mesh.boundary_names) + fill_mesh_info!(mesh, interfaces, mortars, boundaries, + mesh.boundary_names) cache = (; elements, interfaces, boundaries, mortars) @@ -29,4 +29,7 @@ end include("containers.jl") include("containers_2d.jl") include("containers_3d.jl") + +include("containers_parallel.jl") +include("dg_parallel.jl") end # @muladd diff --git a/src/solvers/dgsem_t8code/dg_parallel.jl b/src/solvers/dgsem_t8code/dg_parallel.jl new file mode 100644 index 00000000000..ece614b7d75 --- /dev/null +++ b/src/solvers/dgsem_t8code/dg_parallel.jl @@ -0,0 +1,135 @@ +@muladd begin +#! format: noindent + +# This method is called when a `SemidiscretizationHyperbolic` is constructed. +# It constructs the basic `cache` used throughout the simulation to compute +# the RHS etc. +function create_cache(mesh::ParallelT8codeMesh, equations::AbstractEquations, dg::DG, + ::Any, + ::Type{uEltype}) where {uEltype <: Real} + # Make sure to balance and partition the forest before creating any + # containers in case someone has tampered with forest after creating the + # mesh. + balance!(mesh) + partition!(mesh) + + count_required_surfaces!(mesh) + + elements = init_elements(mesh, equations, dg.basis, uEltype) + mortars = init_mortars(mesh, equations, dg.basis, elements) + interfaces = init_interfaces(mesh, equations, dg.basis, elements) + boundaries = init_boundaries(mesh, equations, dg.basis, elements) + + mpi_mortars = init_mpi_mortars(mesh, equations, dg.basis, elements) + mpi_interfaces = init_mpi_interfaces(mesh, equations, dg.basis, elements) + + mpi_mesh_info = (mpi_mortars = mpi_mortars, + mpi_interfaces = mpi_interfaces, + global_mortar_ids = fill(UInt64(0), nmpimortars(mpi_mortars)), + global_interface_ids = fill(UInt64(0), + nmpiinterfaces(mpi_interfaces)), + neighbor_ranks_mortar = Vector{Vector{Int}}(undef, + nmpimortars(mpi_mortars)), + neighbor_ranks_interface = fill(-1, + nmpiinterfaces(mpi_interfaces))) + + fill_mesh_info!(mesh, interfaces, mortars, boundaries, + mesh.boundary_names; mpi_mesh_info = mpi_mesh_info) + + mpi_cache = init_mpi_cache(mesh, mpi_mesh_info, nvariables(equations), nnodes(dg), + uEltype) + + empty!(mpi_mesh_info.global_mortar_ids) + empty!(mpi_mesh_info.global_interface_ids) + empty!(mpi_mesh_info.neighbor_ranks_mortar) + empty!(mpi_mesh_info.neighbor_ranks_interface) + + init_normal_directions!(mpi_mortars, dg.basis, elements) + exchange_normal_directions!(mpi_mortars, mpi_cache, mesh, nnodes(dg)) + + cache = (; elements, interfaces, mpi_interfaces, boundaries, mortars, mpi_mortars, + mpi_cache) + + # Add specialized parts of the cache required to compute the volume integral etc. + cache = (; cache..., + create_cache(mesh, equations, dg.volume_integral, dg, uEltype)...) + cache = (; cache..., create_cache(mesh, equations, dg.mortar, uEltype)...) + + return cache +end + +function init_mpi_cache(mesh::ParallelT8codeMesh, mpi_mesh_info, nvars, nnodes, uEltype) + mpi_cache = P4estMPICache(uEltype) + init_mpi_cache!(mpi_cache, mesh, mpi_mesh_info, nvars, nnodes, uEltype) + return mpi_cache +end + +function init_mpi_cache!(mpi_cache::P4estMPICache, mesh::ParallelT8codeMesh, + mpi_mesh_info, nvars, nnodes, uEltype) + mpi_neighbor_ranks, mpi_neighbor_interfaces, mpi_neighbor_mortars = init_mpi_neighbor_connectivity(mpi_mesh_info, + mesh) + + mpi_send_buffers, mpi_recv_buffers, mpi_send_requests, mpi_recv_requests = init_mpi_data_structures(mpi_neighbor_interfaces, + mpi_neighbor_mortars, + ndims(mesh), + nvars, + nnodes, + uEltype) + + n_elements_global = Int(t8_forest_get_global_num_elements(mesh.forest)) + n_elements_local = Int(t8_forest_get_local_num_elements(mesh.forest)) + + n_elements_by_rank = Vector{Int}(undef, mpi_nranks()) + n_elements_by_rank[mpi_rank() + 1] = n_elements_local + + MPI.Allgather!(MPI.UBuffer(n_elements_by_rank, 1), mpi_comm()) + + n_elements_by_rank = OffsetArray(n_elements_by_rank, 0:(mpi_nranks() - 1)) + + # Account for 1-based indexing in Julia. + first_element_global_id = sum(n_elements_by_rank[0:(mpi_rank() - 1)]) + 1 + + @assert n_elements_global==sum(n_elements_by_rank) "error in total number of elements" + + @pack! mpi_cache = mpi_neighbor_ranks, mpi_neighbor_interfaces, + mpi_neighbor_mortars, + mpi_send_buffers, mpi_recv_buffers, + mpi_send_requests, mpi_recv_requests, + n_elements_by_rank, n_elements_global, + first_element_global_id + + return mpi_cache +end + +function init_mpi_neighbor_connectivity(mpi_mesh_info, mesh::ParallelT8codeMesh) + @unpack mpi_interfaces, mpi_mortars, global_interface_ids, neighbor_ranks_interface, global_mortar_ids, neighbor_ranks_mortar = mpi_mesh_info + + mpi_neighbor_ranks = vcat(neighbor_ranks_interface, neighbor_ranks_mortar...) |> + sort |> unique + + p = sortperm(global_interface_ids) + + neighbor_ranks_interface .= neighbor_ranks_interface[p] + interface_ids = collect(1:nmpiinterfaces(mpi_interfaces))[p] + + p = sortperm(global_mortar_ids) + neighbor_ranks_mortar .= neighbor_ranks_mortar[p] + mortar_ids = collect(1:nmpimortars(mpi_mortars))[p] + + # For each neighbor rank, init connectivity data structures + mpi_neighbor_interfaces = Vector{Vector{Int}}(undef, length(mpi_neighbor_ranks)) + mpi_neighbor_mortars = Vector{Vector{Int}}(undef, length(mpi_neighbor_ranks)) + for (index, d) in enumerate(mpi_neighbor_ranks) + mpi_neighbor_interfaces[index] = interface_ids[findall(==(d), + neighbor_ranks_interface)] + mpi_neighbor_mortars[index] = mortar_ids[findall(x -> (d in x), + neighbor_ranks_mortar)] + end + + # Check that all interfaces were counted exactly once + @assert mapreduce(length, +, mpi_neighbor_interfaces; init = 0) == + nmpiinterfaces(mpi_interfaces) + + return mpi_neighbor_ranks, mpi_neighbor_interfaces, mpi_neighbor_mortars +end +end # @muladd diff --git a/src/solvers/dgsem_tree/dg_2d_parallel.jl b/src/solvers/dgsem_tree/dg_2d_parallel.jl index 8095dae123a..157d462aa2f 100644 --- a/src/solvers/dgsem_tree/dg_2d_parallel.jl +++ b/src/solvers/dgsem_tree/dg_2d_parallel.jl @@ -446,7 +446,8 @@ function init_mpi_neighbor_connectivity(elements, mpi_interfaces, mpi_mortars, end function rhs!(du, u, t, - mesh::Union{ParallelTreeMesh{2}, ParallelP4estMesh{2}}, equations, + mesh::Union{ParallelTreeMesh{2}, ParallelP4estMesh{2}, + ParallelT8codeMesh{2}}, equations, initial_condition, boundary_conditions, source_terms::Source, dg::DG, cache) where {Source} # Start to receive MPI data diff --git a/test/test_mpi.jl b/test/test_mpi.jl index ad1ba4e835d..1ab1282b891 100644 --- a/test/test_mpi.jl +++ b/test/test_mpi.jl @@ -19,10 +19,12 @@ CI_ON_WINDOWS = (get(ENV, "GITHUB_ACTIONS", false) == "true") && Sys.iswindows() # TreeMesh tests include("test_mpi_tree.jl") - # P4estMesh tests + # P4estMesh and T8codeMesh tests include("test_mpi_p4est_2d.jl") + include("test_mpi_t8code_2d.jl") if !CI_ON_WINDOWS # see comment on `CI_ON_WINDOWS` above include("test_mpi_p4est_3d.jl") + include("test_mpi_t8code_3d.jl") end end # MPI diff --git a/test/test_mpi_p4est_2d.jl b/test/test_mpi_p4est_2d.jl index da90537fcfd..6d66bc68a26 100644 --- a/test/test_mpi_p4est_2d.jl +++ b/test/test_mpi_p4est_2d.jl @@ -33,6 +33,15 @@ const EXAMPLES_DIR = pkgdir(Trixi, "examples", "p4est_2d_dgsem") @test errors.linf≈[0.00011787417954578494] rtol=1.0e-4 end end + + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end end @trixi_testset "elixir_advection_nonconforming_flag.jl" begin @@ -40,6 +49,15 @@ const EXAMPLES_DIR = pkgdir(Trixi, "examples", "p4est_2d_dgsem") "elixir_advection_nonconforming_flag.jl"), l2=[3.198940059144588e-5], linf=[0.00030636069494005547]) + + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end end @trixi_testset "elixir_advection_unstructured_flag.jl" begin @@ -47,6 +65,15 @@ const EXAMPLES_DIR = pkgdir(Trixi, "examples", "p4est_2d_dgsem") "elixir_advection_unstructured_flag.jl"), l2=[0.0005379687442422346], linf=[0.007438525029884735]) + + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end end @trixi_testset "elixir_advection_amr_solution_independent.jl" begin @@ -56,6 +83,15 @@ const EXAMPLES_DIR = pkgdir(Trixi, "examples", "p4est_2d_dgsem") l2=[4.949660644033807e-5], linf=[0.0004867846262313763], coverage_override=(maxiters = 6,)) + + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end end @trixi_testset "elixir_advection_amr_unstructured_flag.jl" begin @@ -64,6 +100,15 @@ const EXAMPLES_DIR = pkgdir(Trixi, "examples", "p4est_2d_dgsem") l2=[0.0012766060609964525], linf=[0.01750280631586159], coverage_override=(maxiters = 6,)) + + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end end @trixi_testset "elixir_advection_restart.jl" begin @@ -73,6 +118,15 @@ const EXAMPLES_DIR = pkgdir(Trixi, "examples", "p4est_2d_dgsem") # With the default `maxiters = 1` in coverage tests, # there would be no time steps after the restart. coverage_override=(maxiters = 100_000,)) + + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end end @trixi_testset "elixir_euler_source_terms_nonconforming_unstructured_flag.jl" begin @@ -90,6 +144,15 @@ const EXAMPLES_DIR = pkgdir(Trixi, "examples", "p4est_2d_dgsem") 0.03759938693042297, 0.08039824959535657, ]) + + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end end end end # P4estMesh MPI diff --git a/test/test_mpi_p4est_3d.jl b/test/test_mpi_p4est_3d.jl index 75f43650082..cca9093ec51 100644 --- a/test/test_mpi_p4est_3d.jl +++ b/test/test_mpi_p4est_3d.jl @@ -33,6 +33,15 @@ const EXAMPLES_DIR = pkgdir(Trixi, "examples", "p4est_3d_dgsem") @test errors.linf≈[0.0014548839020096516] rtol=1.0e-4 end end + + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end end @trixi_testset "elixir_advection_amr.jl" begin @@ -46,6 +55,15 @@ const EXAMPLES_DIR = pkgdir(Trixi, "examples", "p4est_3d_dgsem") initial_refinement_level = 2, base_level = 2, med_level = 3, max_level = 4)) + + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end end @trixi_testset "elixir_advection_amr_unstructured_curved.jl" begin @@ -58,6 +76,15 @@ const EXAMPLES_DIR = pkgdir(Trixi, "examples", "p4est_3d_dgsem") initial_refinement_level = 0, base_level = 0, med_level = 1, max_level = 2)) + + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end end @trixi_testset "elixir_advection_restart.jl" begin @@ -67,12 +94,30 @@ const EXAMPLES_DIR = pkgdir(Trixi, "examples", "p4est_3d_dgsem") # With the default `maxiters = 1` in coverage tests, # there would be no time steps after the restart. coverage_override=(maxiters = 100_000,)) + + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end end @trixi_testset "elixir_advection_cubed_sphere.jl" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_advection_cubed_sphere.jl"), l2=[0.002006918015656413], linf=[0.027655117058380085]) + + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end end # Compressible Euler @@ -94,6 +139,15 @@ const EXAMPLES_DIR = pkgdir(Trixi, "examples", "p4est_3d_dgsem") 0.008526972236273522, ], tspan=(0.0, 0.01)) + + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end end @trixi_testset "elixir_euler_source_terms_nonperiodic.jl" begin @@ -114,6 +168,15 @@ const EXAMPLES_DIR = pkgdir(Trixi, "examples", "p4est_3d_dgsem") 0.01562861968368434, ], tspan=(0.0, 1.0)) + + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end end @trixi_testset "elixir_euler_ec.jl" begin @@ -134,6 +197,15 @@ const EXAMPLES_DIR = pkgdir(Trixi, "examples", "p4est_3d_dgsem") ], tspan=(0.0, 0.2), coverage_override=(polydeg = 3,)) # Prevent long compile time in CI + + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end end @trixi_testset "elixir_euler_source_terms_nonperiodic_hohqmesh.jl" begin @@ -153,6 +225,15 @@ const EXAMPLES_DIR = pkgdir(Trixi, "examples", "p4est_3d_dgsem") 0.048396544302230504, 0.1154589758186293, ]) + + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end end end end # P4estMesh MPI diff --git a/test/test_mpi_t8code_2d.jl b/test/test_mpi_t8code_2d.jl new file mode 100644 index 00000000000..7c7fc03898c --- /dev/null +++ b/test/test_mpi_t8code_2d.jl @@ -0,0 +1,142 @@ +module TestExamplesMPIT8codeMesh2D + +using Test +using Trixi + +include("test_trixi.jl") + +const EXAMPLES_DIR = pkgdir(Trixi, "examples", "t8code_2d_dgsem") + +@testset "T8codeMesh MPI 2D" begin +#! format: noindent + +# Run basic tests +@testset "Examples 2D" begin + # Linear scalar advection + @trixi_testset "elixir_advection_basic.jl" begin + @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_advection_basic.jl"), + # Expected errors are exactly the same as with TreeMesh! + l2=[8.311947673061856e-6], + linf=[6.627000273229378e-5]) + + @testset "error-based step size control" begin + Trixi.mpi_isroot() && println("-"^100) + Trixi.mpi_isroot() && + println("elixir_advection_basic.jl with error-based step size control") + + sol = solve(ode, RDPK3SpFSAL35(); abstol = 1.0e-4, reltol = 1.0e-4, + ode_default_options()..., callback = callbacks) + summary_callback() + errors = analysis_callback(sol) + if Trixi.mpi_isroot() + @test errors.l2≈[3.3022040342579066e-5] rtol=1.0e-4 + @test errors.linf≈[0.00011787417954578494] rtol=1.0e-4 + end + end + + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end + end + + @trixi_testset "elixir_advection_nonconforming_flag.jl" begin + @test_trixi_include(joinpath(EXAMPLES_DIR, + "elixir_advection_nonconforming_flag.jl"), + l2=[3.198940059144588e-5], + linf=[0.00030636069494005547]) + + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end + end + + @trixi_testset "elixir_advection_unstructured_flag.jl" begin + @test_trixi_include(joinpath(EXAMPLES_DIR, + "elixir_advection_unstructured_flag.jl"), + l2=[0.0005379687442422346], + linf=[0.007438525029884735]) + + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end + end + + @trixi_testset "elixir_advection_amr_solution_independent.jl" begin + @test_trixi_include(joinpath(EXAMPLES_DIR, + "elixir_advection_amr_solution_independent.jl"), + # Expected errors are exactly the same as with TreeMesh! + l2=[4.933027431215839e-5], + linf=[0.00048678461161243136], + coverage_override=(maxiters = 6,)) + + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end + end + + @trixi_testset "elixir_advection_amr_unstructured_flag.jl" begin + @test_trixi_include(joinpath(EXAMPLES_DIR, + "elixir_advection_amr_unstructured_flag.jl"), + l2=[0.001980652042312077], + linf=[0.0328882442132265], + coverage_override=(maxiters = 6,)) + + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end + end + + @trixi_testset "elixir_euler_source_terms_nonconforming_unstructured_flag.jl" begin + @test_trixi_include(joinpath(EXAMPLES_DIR, + "elixir_euler_source_terms_nonconforming_unstructured_flag.jl"), + l2=[ + 0.0034516244508588046, + 0.0023420334036925493, + 0.0024261923964557187, + 0.004731710454271893, + ], + linf=[ + 0.04155789011775046, + 0.024772109862748914, + 0.03759938693042297, + 0.08039824959535657, + ]) + + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end + end +end +end # T8codeMesh MPI + +end # module diff --git a/test/test_mpi_t8code_3d.jl b/test/test_mpi_t8code_3d.jl new file mode 100644 index 00000000000..a15690a7629 --- /dev/null +++ b/test/test_mpi_t8code_3d.jl @@ -0,0 +1,180 @@ +module TestExamplesMPIT8codeMesh3D + +using Test +using Trixi + +include("test_trixi.jl") + +const EXAMPLES_DIR = pkgdir(Trixi, "examples", "t8code_3d_dgsem") + +@testset "T8codeMesh MPI 3D" begin +#! format: noindent + +# Run basic tests +@testset "Examples 3D" begin + # Linear scalar advection + @trixi_testset "elixir_advection_basic.jl" begin + @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_advection_basic.jl"), + # Expected errors are exactly the same as with TreeMesh! + l2=[0.00016263963870641478], + linf=[0.0014537194925779984]) + + @testset "error-based step size control" begin + Trixi.mpi_isroot() && println("-"^100) + Trixi.mpi_isroot() && + println("elixir_advection_basic.jl with error-based step size control") + + sol = solve(ode, RDPK3SpFSAL35(); abstol = 1.0e-4, reltol = 1.0e-4, + ode_default_options()..., callback = callbacks) + summary_callback() + errors = analysis_callback(sol) + if Trixi.mpi_isroot() + @test errors.l2≈[0.00016800412839949264] rtol=1.0e-4 + @test errors.linf≈[0.0014548839020096516] rtol=1.0e-4 + end + end + + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end + end + + @trixi_testset "elixir_advection_amr.jl" begin + @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_advection_amr.jl"), + # Expected errors are exactly the same as with TreeMesh! + l2=[1.1302812803902801e-5], + linf=[0.0007889950196294793], + # override values are different from the serial tests to ensure each process holds at least + # one element, otherwise OrdinaryDiffEq fails during initialization + coverage_override=(maxiters = 6, + initial_refinement_level = 2, + base_level = 2, med_level = 3, + max_level = 4)) + + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end + end + + @trixi_testset "elixir_advection_amr_unstructured_curved.jl" begin + @test_trixi_include(joinpath(EXAMPLES_DIR, + "elixir_advection_amr_unstructured_curved.jl"), + l2=[2.0556575425846923e-5], + linf=[0.00105682693484822], + tspan=(0.0, 1.0), + coverage_override=(maxiters = 6, + initial_refinement_level = 0, + base_level = 0, med_level = 1, + max_level = 2)) + + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end + end + + # Compressible Euler + @trixi_testset "elixir_euler_source_terms_nonconforming_unstructured_curved.jl" begin + @test_trixi_include(joinpath(EXAMPLES_DIR, + "elixir_euler_source_terms_nonconforming_unstructured_curved.jl"), + l2=[ + 4.070355207909268e-5, + 4.4993257426833716e-5, + 5.10588457841744e-5, + 5.102840924036687e-5, + 0.00019986264001630542, + ], + linf=[ + 0.0016987332417202072, + 0.003622956808262634, + 0.002029576258317789, + 0.0024206977281964193, + 0.008526972236273522, + ], + tspan=(0.0, 0.01)) + + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end + end + + @trixi_testset "elixir_euler_source_terms_nonperiodic.jl" begin + @test_trixi_include(joinpath(EXAMPLES_DIR, + "elixir_euler_source_terms_nonperiodic.jl"), + l2=[ + 0.0015106060984283647, + 0.0014733349038567685, + 0.00147333490385685, + 0.001473334903856929, + 0.0028149479453087093, + ], + linf=[ + 0.008070806335238156, + 0.009007245083113125, + 0.009007245083121784, + 0.009007245083102688, + 0.01562861968368434, + ], + tspan=(0.0, 1.0)) + + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end + end + + @trixi_testset "elixir_euler_ec.jl" begin + @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_ec.jl"), + l2=[ + 0.010380390326164493, + 0.006192950051354618, + 0.005970674274073704, + 0.005965831290564327, + 0.02628875593094754, + ], + linf=[ + 0.3326911600075694, + 0.2824952141320467, + 0.41401037398065543, + 0.45574161423218573, + 0.8099577682187109, + ], + tspan=(0.0, 0.2), + coverage_override=(polydeg = 3,)) # Prevent long compile time in CI + + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end + end +end +end # T8codeMesh MPI + +end # module diff --git a/test/test_t8code_2d.jl b/test/test_t8code_2d.jl index ab95e068d02..d536a6dd73a 100644 --- a/test/test_t8code_2d.jl +++ b/test/test_t8code_2d.jl @@ -33,10 +33,9 @@ end @trixi_testset "test check_for_negative_volumes" begin @test_warn "Discovered negative volumes" begin # Unstructured mesh with six cells which have left-handed node ordering. - mesh_file = joinpath(EXAMPLES_DIR, "rectangle_with_negative_volumes.msh") - isfile(mesh_file) || - download("https://gist.githubusercontent.com/jmark/bfe0d45f8e369298d6cc637733819013/raw/cecf86edecc736e8b3e06e354c494b2052d41f7a/rectangle_with_negative_volumes.msh", - mesh_file) + mesh_file = Trixi.download("https://gist.githubusercontent.com/jmark/bfe0d45f8e369298d6cc637733819013/raw/cecf86edecc736e8b3e06e354c494b2052d41f7a/rectangle_with_negative_volumes.msh", + joinpath(EXAMPLES_DIR, + "rectangle_with_negative_volumes.msh")) # This call should throw a warning about negative volumes detected. mesh = T8codeMesh(mesh_file, 2) From c7cee980f56835e9c396424e742efe85da465042 Mon Sep 17 00:00:00 2001 From: Andrew Winters Date: Wed, 31 Jan 2024 19:09:15 +0100 Subject: [PATCH 11/63] Remove race condition in mpi testing (#1821) * remove race condition in mpi testing * add additional barriers --- test/test_mpi.jl | 2 ++ test/test_mpi_tree.jl | 3 ++- test/test_threaded.jl | 2 ++ 3 files changed, 6 insertions(+), 1 deletion(-) diff --git a/test/test_mpi.jl b/test/test_mpi.jl index 1ab1282b891..001d9bff86e 100644 --- a/test/test_mpi.jl +++ b/test/test_mpi.jl @@ -8,6 +8,7 @@ include("test_trixi.jl") # Start with a clean environment: remove Trixi.jl output directory if it exists outdir = "out" Trixi.mpi_isroot() && isdir(outdir) && rm(outdir, recursive = true) +Trixi.MPI.Barrier(Trixi.mpi_comm()) # CI with MPI and some tests fails often on Windows. Thus, we check whether this # is the case here. We use GitHub Actions, so we can check whether we run CI @@ -45,5 +46,6 @@ end # MPI supporting functionality # Clean up afterwards: delete Trixi.jl output directory Trixi.mpi_isroot() && @test_nowarn rm(outdir, recursive = true) +Trixi.MPI.Barrier(Trixi.mpi_comm()) end # module diff --git a/test/test_mpi_tree.jl b/test/test_mpi_tree.jl index 0831f6a1313..6351a405b5d 100644 --- a/test/test_mpi_tree.jl +++ b/test/test_mpi_tree.jl @@ -76,7 +76,8 @@ CI_ON_WINDOWS = (get(ENV, "GITHUB_ACTIONS", false) == "true") && Sys.iswindows() # Here, we also test that SaveSolutionCallback prints multiple mesh files with AMR # Start with a clean environment: remove Trixi.jl output directory if it exists outdir = "out" - isdir(outdir) && rm(outdir, recursive = true) + Trixi.mpi_isroot() && isdir(outdir) && rm(outdir, recursive = true) + Trixi.MPI.Barrier(Trixi.mpi_comm()) @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_advection_amr_refine_twice.jl"), l2=[0.00020547512522578292], diff --git a/test/test_threaded.jl b/test/test_threaded.jl index dbbcbf4c7ce..a8a1b1b425a 100644 --- a/test/test_threaded.jl +++ b/test/test_threaded.jl @@ -8,6 +8,7 @@ include("test_trixi.jl") # Start with a clean environment: remove Trixi.jl output directory if it exists outdir = "out" Trixi.mpi_isroot() && isdir(outdir) && rm(outdir, recursive = true) +Trixi.MPI.Barrier(Trixi.mpi_comm()) @testset "Threaded tests" begin #! format: noindent @@ -471,5 +472,6 @@ end # Clean up afterwards: delete Trixi.jl output directory Trixi.mpi_isroot() && isdir(outdir) && @test_nowarn rm(outdir, recursive = true) +Trixi.MPI.Barrier(Trixi.mpi_comm()) end # module From dfd632e69631ff4dbb42215966d4f7a546b92816 Mon Sep 17 00:00:00 2001 From: Benjamin Bolm <74359358+bennibolm@users.noreply.github.com> Date: Wed, 31 Jan 2024 21:50:27 +0100 Subject: [PATCH 12/63] Add subcell positivity limiting of non-linear variables (#1738) * Add positivity limiting of non-linear variables * Revise derivative function call; Add default derivative version * Adapt test to actually test pos limiter for nonlinear variables * Add unit test to test default implementation of variable_derivative * Clean up comments and code * Rename Newton-bisection variables * Implement suggestions * Relocate functions * Implement suggestions * Change error message for negative value with low-order method * Add changes from main to new limiter * Update NEWS.md * Rename is_valid_state and gradient_u --------- Co-authored-by: Michael Schlottke-Lakemper --- NEWS.md | 1 + ...kelvin_helmholtz_instability_sc_subcell.jl | 91 ++++++++ .../elixir_mhd_shockcapturing_subcell.jl | 7 +- src/callbacks_stage/subcell_bounds_check.jl | 8 + .../subcell_bounds_check_2d.jl | 18 ++ src/equations/compressible_euler_2d.jl | 21 ++ src/equations/equations.jl | 6 + src/equations/ideal_glm_mhd_2d.jl | 23 ++ src/solvers/dgsem_tree/subcell_limiters.jl | 60 +++-- src/solvers/dgsem_tree/subcell_limiters_2d.jl | 215 +++++++++++++++++- test/test_tree_2d_euler.jl | 26 +++ test/test_tree_2d_mhd.jl | 32 +-- test/test_unit.jl | 23 +- 13 files changed, 496 insertions(+), 35 deletions(-) create mode 100644 examples/tree_2d_dgsem/elixir_euler_kelvin_helmholtz_instability_sc_subcell.jl diff --git a/NEWS.md b/NEWS.md index 3a3a504a911..02a723fca45 100644 --- a/NEWS.md +++ b/NEWS.md @@ -11,6 +11,7 @@ for human readability. - `flux_hllc` on non-cartesian meshes for `CompressibleEulerEquations{2,3}D` - Different boundary conditions for quad/hex meshes in Abaqus format, even if not generated by HOHQMesh, can now be digested by Trixi in 2D and 3D. +- Subcell (positivity) limiting support for nonlinear variables in 2D for `TreeMesh` ## Changes when updating to v0.6 from v0.5.x diff --git a/examples/tree_2d_dgsem/elixir_euler_kelvin_helmholtz_instability_sc_subcell.jl b/examples/tree_2d_dgsem/elixir_euler_kelvin_helmholtz_instability_sc_subcell.jl new file mode 100644 index 00000000000..1817672778a --- /dev/null +++ b/examples/tree_2d_dgsem/elixir_euler_kelvin_helmholtz_instability_sc_subcell.jl @@ -0,0 +1,91 @@ + +using OrdinaryDiffEq +using Trixi + +############################################################################### +# semidiscretization of the compressible Euler equations +gamma = 1.4 +equations = CompressibleEulerEquations2D(gamma) + +""" + initial_condition_kelvin_helmholtz_instability(x, t, equations::CompressibleEulerEquations2D) + +A version of the classical Kelvin-Helmholtz instability based on +- Andrés M. Rueda-Ramírez, Gregor J. Gassner (2021) + A Subcell Finite Volume Positivity-Preserving Limiter for DGSEM Discretizations + of the Euler Equations + [arXiv: 2102.06017](https://arxiv.org/abs/2102.06017) +""" +function initial_condition_kelvin_helmholtz_instability(x, t, + equations::CompressibleEulerEquations2D) + # change discontinuity to tanh + # typical resolution 128^2, 256^2 + # domain size is [-1,+1]^2 + slope = 15 + amplitude = 0.02 + B = tanh(slope * x[2] + 7.5) - tanh(slope * x[2] - 7.5) + rho = 0.5 + 0.75 * B + v1 = 0.5 * (B - 1) + v2 = 0.1 * sin(2 * pi * x[1]) + p = 1.0 + return prim2cons(SVector(rho, v1, v2, p), equations) +end +initial_condition = initial_condition_kelvin_helmholtz_instability + +surface_flux = flux_lax_friedrichs +volume_flux = flux_ranocha +polydeg = 3 +basis = LobattoLegendreBasis(polydeg) + +limiter_idp = SubcellLimiterIDP(equations, basis; + positivity_variables_cons = ["rho"], + positivity_variables_nonlinear = [pressure]) +volume_integral = VolumeIntegralSubcellLimiting(limiter_idp; + volume_flux_dg = volume_flux, + volume_flux_fv = surface_flux) +solver = DGSEM(basis, surface_flux, volume_integral) + +coordinates_min = (-1.0, -1.0) +coordinates_max = (1.0, 1.0) +mesh = TreeMesh(coordinates_min, coordinates_max, + initial_refinement_level = 5, + n_cells_max = 100_000) +semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver) + +############################################################################### +# ODE solvers, callbacks etc. + +tspan = (0.0, 3.7) +ode = semidiscretize(semi, tspan) + +summary_callback = SummaryCallback() + +analysis_interval = 1000 +analysis_callback = AnalysisCallback(semi, interval = analysis_interval) + +alive_callback = AliveCallback(analysis_interval = analysis_interval) + +save_solution = SaveSolutionCallback(interval = 100, + save_initial_solution = true, + save_final_solution = true, + solution_variables = cons2prim) + +save_restart = SaveRestartCallback(interval = 1000, + save_final_restart = true) + +stepsize_callback = StepsizeCallback(cfl = 0.7) + +callbacks = CallbackSet(summary_callback, + analysis_callback, alive_callback, + stepsize_callback, + save_restart, save_solution) + +############################################################################### +# run the simulation + +stage_callbacks = (SubcellLimiterIDPCorrection(), BoundsCheckCallback(save_errors = false)) + +sol = Trixi.solve(ode, Trixi.SimpleSSPRK33(stage_callbacks = stage_callbacks); + dt = 1.0, # solve needs some value here but it will be overwritten by the stepsize_callback + callback = callbacks); +summary_callback() # print the timer summary diff --git a/examples/tree_2d_dgsem/elixir_mhd_shockcapturing_subcell.jl b/examples/tree_2d_dgsem/elixir_mhd_shockcapturing_subcell.jl index fe9ad92467f..74d0370647a 100644 --- a/examples/tree_2d_dgsem/elixir_mhd_shockcapturing_subcell.jl +++ b/examples/tree_2d_dgsem/elixir_mhd_shockcapturing_subcell.jl @@ -22,7 +22,7 @@ function initial_condition_blast_wave(x, t, equations::IdealGlmMhdEquations2D) r = sqrt(x[1]^2 + x[2]^2) pmax = 10.0 - pmin = 1.0 + pmin = 0.01 rhomax = 1.0 rhomin = 0.01 if r <= 0.09 @@ -52,7 +52,8 @@ basis = LobattoLegendreBasis(3) limiter_idp = SubcellLimiterIDP(equations, basis; positivity_variables_cons = ["rho"], - positivity_correction_factor = 0.5) + positivity_variables_nonlinear = [pressure], + positivity_correction_factor = 0.1) volume_integral = VolumeIntegralSubcellLimiting(limiter_idp; volume_flux_dg = volume_flux, volume_flux_fv = surface_flux) @@ -84,7 +85,7 @@ save_solution = SaveSolutionCallback(interval = 100, save_final_solution = true, solution_variables = cons2prim) -cfl = 0.5 +cfl = 0.4 stepsize_callback = StepsizeCallback(cfl = cfl) glm_speed_callback = GlmSpeedCallback(glm_scale = 0.5, cfl = cfl) diff --git a/src/callbacks_stage/subcell_bounds_check.jl b/src/callbacks_stage/subcell_bounds_check.jl index 9f34a6b3b4b..4dbf44d29c4 100644 --- a/src/callbacks_stage/subcell_bounds_check.jl +++ b/src/callbacks_stage/subcell_bounds_check.jl @@ -97,6 +97,9 @@ function init_callback(callback::BoundsCheckCallback, semi, limiter::SubcellLimi end print(f, ", " * string(variables[v]) * "_min") end + for variable in limiter.positivity_variables_nonlinear + print(f, ", " * string(variable) * "_min") + end end println(f) end @@ -142,6 +145,11 @@ end println(string(variables[v]) * ":\n- positivity: ", idp_bounds_delta_global[Symbol(string(v), "_min")]) end + for variable in limiter.positivity_variables_nonlinear + variable_string = string(variable) + println(variable_string * ":\n- positivity: ", + idp_bounds_delta_global[Symbol(variable_string, "_min")]) + end end println("─"^100 * "\n") diff --git a/src/callbacks_stage/subcell_bounds_check_2d.jl b/src/callbacks_stage/subcell_bounds_check_2d.jl index 545d19b5136..19d73968c9a 100644 --- a/src/callbacks_stage/subcell_bounds_check_2d.jl +++ b/src/callbacks_stage/subcell_bounds_check_2d.jl @@ -60,6 +60,20 @@ deviation_threaded[stride_size * Threads.threadid()] = deviation end end + for variable in limiter.positivity_variables_nonlinear + key = Symbol(string(variable), "_min") + deviation_threaded = idp_bounds_delta_local[key] + @threaded for element in eachelement(solver, cache) + deviation = deviation_threaded[stride_size * Threads.threadid()] + for j in eachnode(solver), i in eachnode(solver) + var = variable(get_node_vars(u, equations, solver, i, j, element), + equations) + deviation = max(deviation, + variable_bounds[key][i, j, element] - var) + end + deviation_threaded[stride_size * Threads.threadid()] = deviation + end + end end for (key, _) in idp_bounds_delta_local @@ -92,6 +106,10 @@ print(f, ", ", idp_bounds_delta_local[Symbol(string(v), "_min")][stride_size]) end + for variable in limiter.positivity_variables_nonlinear + print(f, ", ", + idp_bounds_delta_local[Symbol(string(variable), "_min")][stride_size]) + end end println(f) end diff --git a/src/equations/compressible_euler_2d.jl b/src/equations/compressible_euler_2d.jl index 3c6f759db2b..f5a632723cf 100644 --- a/src/equations/compressible_euler_2d.jl +++ b/src/equations/compressible_euler_2d.jl @@ -1632,6 +1632,18 @@ end return p end +# Transformation from conservative variables u to d(p)/d(u) +@inline function gradient_conservative(::typeof(pressure), + u, equations::CompressibleEulerEquations2D) + rho, rho_v1, rho_v2, rho_e = u + + v1 = rho_v1 / rho + v2 = rho_v2 / rho + v_square = v1^2 + v2^2 + + return (equations.gamma - 1.0) * SVector(0.5 * v_square, -v1, -v2, 1.0) +end + @inline function density_pressure(u, equations::CompressibleEulerEquations2D) rho, rho_v1, rho_v2, rho_e = u rho_times_p = (equations.gamma - 1) * (rho * rho_e - 0.5 * (rho_v1^2 + rho_v2^2)) @@ -1699,4 +1711,13 @@ end @inline function energy_internal(cons, equations::CompressibleEulerEquations2D) return energy_total(cons, equations) - energy_kinetic(cons, equations) end + +# State validation for Newton-bisection method of subcell IDP limiting +@inline function Base.isvalid(u, equations::CompressibleEulerEquations2D) + p = pressure(u, equations) + if u[1] <= 0.0 || p <= 0.0 + return false + end + return true +end end # @muladd diff --git a/src/equations/equations.jl b/src/equations/equations.jl index 7a3c326984d..c041bf117ba 100644 --- a/src/equations/equations.jl +++ b/src/equations/equations.jl @@ -376,6 +376,12 @@ of the correct length `nvariables(equations)`. """ function energy_internal end +# Default implementation of gradient for `variable`. Used for subcell limiting. +# Implementing a gradient function for a specific variable improves the performance. +@inline function gradient_conservative(variable, u, equations) + return ForwardDiff.gradient(x -> variable(x, equations), u) +end + #################################################################################################### # Include files with actual implementations for different systems of equations. diff --git a/src/equations/ideal_glm_mhd_2d.jl b/src/equations/ideal_glm_mhd_2d.jl index 43d1991e34b..4366cd32f08 100644 --- a/src/equations/ideal_glm_mhd_2d.jl +++ b/src/equations/ideal_glm_mhd_2d.jl @@ -1118,6 +1118,20 @@ end return p end +# Transformation from conservative variables u to d(p)/d(u) +@inline function gradient_conservative(::typeof(pressure), + u, equations::IdealGlmMhdEquations2D) + rho, rho_v1, rho_v2, rho_v3, rho_e, B1, B2, B3, psi = u + + v1 = rho_v1 / rho + v2 = rho_v2 / rho + v3 = rho_v3 / rho + v_square = v1^2 + v2^2 + v3^2 + + return (equations.gamma - 1.0) * + SVector(0.5 * v_square, -v1, -v2, -v3, 1.0, -B1, -B2, -B3, -psi) +end + @inline function density_pressure(u, equations::IdealGlmMhdEquations2D) rho, rho_v1, rho_v2, rho_v3, rho_e, B1, B2, B3, psi = u p = (equations.gamma - 1) * (rho_e - 0.5 * (rho_v1^2 + rho_v2^2 + rho_v3^2) / rho @@ -1384,6 +1398,15 @@ end cons[9]^2 / 2) end +# State validation for Newton-bisection method of subcell IDP limiting +@inline function Base.isvalid(u, equations::IdealGlmMhdEquations2D) + p = pressure(u, equations) + if u[1] <= 0.0 || p <= 0.0 + return false + end + return true +end + # Calculate the cross helicity (\vec{v}⋅\vec{B}) for a conservative state `cons' @inline function cross_helicity(cons, ::IdealGlmMhdEquations2D) return (cons[2] * cons[6] + cons[3] * cons[7] + cons[4] * cons[8]) / cons[1] diff --git a/src/solvers/dgsem_tree/subcell_limiters.jl b/src/solvers/dgsem_tree/subcell_limiters.jl index 055e7ce24a4..e433c953779 100644 --- a/src/solvers/dgsem_tree/subcell_limiters.jl +++ b/src/solvers/dgsem_tree/subcell_limiters.jl @@ -16,18 +16,28 @@ end SubcellLimiterIDP(equations::AbstractEquations, basis; local_minmax_variables_cons = String[], positivity_variables_cons = String[], - positivity_correction_factor = 0.1) + positivity_variables_nonlinear = [], + positivity_correction_factor = 0.1, + max_iterations_newton = 10, + newton_tolerances = (1.0e-12, 1.0e-14), + gamma_constant_newton = 2 * ndims(equations)) Subcell invariant domain preserving (IDP) limiting used with [`VolumeIntegralSubcellLimiting`](@ref) including: - Local maximum/minimum Zalesak-type limiting for conservative variables (`local_minmax_variables_cons`) -- Positivity limiting for conservative variables (`positivity_variables_cons`) +- Positivity limiting for conservative variables (`positivity_variables_cons`) and nonlinear variables +(`positivity_variables_nonlinear`) Conservative variables to be limited are passed as a vector of strings, e.g. `local_minmax_variables_cons = ["rho"]` -and `positivity_variables_cons = ["rho"]`. +and `positivity_variables_cons = ["rho"]`. For nonlinear variables the specific functions are +passed in a vector, e.g. `positivity_variables_nonlinear = [pressure]`. The bounds are calculated using the low-order FV solution. The positivity limiter uses `positivity_correction_factor` such that `u^new >= positivity_correction_factor * u^FV`. +The limiting of nonlinear variables uses a Newton-bisection method with a maximum of +`max_iterations_newton` iterations, relative and absolute tolerances of `newton_tolerances` +and a provisional update constant `gamma_constant_newton` (`gamma_constant_newton>=2*d`, +where `d = #dimensions`). See equation (20) of Pazner (2020) and equation (30) of Rueda-Ramírez et al. (2022). !!! note This limiter and the correction callback [`SubcellLimiterIDPCorrection`](@ref) only work together. @@ -45,22 +55,32 @@ The bounds are calculated using the low-order FV solution. The positivity limite !!! warning "Experimental implementation" This is an experimental feature and may change in future releases. """ -struct SubcellLimiterIDP{RealT <: Real, Cache} <: AbstractSubcellLimiter +struct SubcellLimiterIDP{RealT <: Real, LimitingVariablesNonlinear, Cache} <: + AbstractSubcellLimiter local_minmax::Bool local_minmax_variables_cons::Vector{Int} # Local mininum/maximum principles for conservative variables positivity::Bool positivity_variables_cons::Vector{Int} # Positivity for conservative variables + positivity_variables_nonlinear::LimitingVariablesNonlinear # Positivity for nonlinear variables positivity_correction_factor::RealT cache::Cache + max_iterations_newton::Int + newton_tolerances::Tuple{RealT, RealT} # Relative and absolute tolerances for Newton's method + gamma_constant_newton::RealT # Constant for the subcell limiting of convex (nonlinear) constraints end # this method is used when the limiter is constructed as for shock-capturing volume integrals function SubcellLimiterIDP(equations::AbstractEquations, basis; local_minmax_variables_cons = String[], positivity_variables_cons = String[], - positivity_correction_factor = 0.1) + positivity_variables_nonlinear = [], + positivity_correction_factor = 0.1, + max_iterations_newton = 10, + newton_tolerances = (1.0e-12, 1.0e-14), + gamma_constant_newton = 2 * ndims(equations)) local_minmax = (length(local_minmax_variables_cons) > 0) - positivity = (length(positivity_variables_cons) > 0) + positivity = (length(positivity_variables_cons) + + length(positivity_variables_nonlinear) > 0) local_minmax_variables_cons_ = get_variable_index.(local_minmax_variables_cons, equations) @@ -80,13 +100,20 @@ function SubcellLimiterIDP(equations::AbstractEquations, basis; bound_keys = (bound_keys..., Symbol(string(v), "_min")) end end + for variable in positivity_variables_nonlinear + bound_keys = (bound_keys..., Symbol(string(variable), "_min")) + end cache = create_cache(SubcellLimiterIDP, equations, basis, bound_keys) SubcellLimiterIDP{typeof(positivity_correction_factor), + typeof(positivity_variables_nonlinear), typeof(cache)}(local_minmax, local_minmax_variables_cons_, positivity, positivity_variables_cons_, - positivity_correction_factor, cache) + positivity_variables_nonlinear, + positivity_correction_factor, cache, + max_iterations_newton, newton_tolerances, + gamma_constant_newton) end function Base.show(io::IO, limiter::SubcellLimiterIDP) @@ -97,10 +124,15 @@ function Base.show(io::IO, limiter::SubcellLimiterIDP) if !(local_minmax || positivity) print(io, "No limiter selected => pure DG method") else - print(io, "limiter=(") - local_minmax && print(io, "min/max limiting, ") - positivity && print(io, "positivity") - print(io, "), ") + features = String[] + if local_minmax + push!(features, "local min/max") + end + if positivity + push!(features, "positivity") + end + join(io, features, ", ") + print(io, "Limiter=($features), ") end print(io, "Local bounds with FV solution") print(io, ")") @@ -120,15 +152,15 @@ function Base.show(io::IO, ::MIME"text/plain", limiter::SubcellLimiterIDP) if local_minmax setup = [ setup..., - "" => "local maximum/minimum bounds for conservative variables $(limiter.local_minmax_variables_cons)", + "" => "Local maximum/minimum limiting for conservative variables $(limiter.local_minmax_variables_cons)", ] end if positivity - string = "positivity for conservative variables $(limiter.positivity_variables_cons)" + string = "Positivity limiting for conservative variables $(limiter.positivity_variables_cons) and $(limiter.positivity_variables_nonlinear)" setup = [setup..., "" => string] setup = [ setup..., - "" => " positivity correction factor = $(limiter.positivity_correction_factor)", + "" => "- with positivity correction factor = $(limiter.positivity_correction_factor)", ] end setup = [ diff --git a/src/solvers/dgsem_tree/subcell_limiters_2d.jl b/src/solvers/dgsem_tree/subcell_limiters_2d.jl index 3d272359fe4..3f7954c8958 100644 --- a/src/solvers/dgsem_tree/subcell_limiters_2d.jl +++ b/src/solvers/dgsem_tree/subcell_limiters_2d.jl @@ -5,6 +5,10 @@ @muladd begin #! format: noindent +############################################################################### +# IDP Limiting +############################################################################### + # this method is used when the limiter is constructed as for shock-capturing volume integrals function create_cache(limiter::Type{SubcellLimiterIDP}, equations::AbstractEquations{2}, basis::LobattoLegendreBasis, bound_keys) @@ -66,6 +70,9 @@ function (limiter::SubcellLimiterIDP)(u::AbstractArray{<:Any, 4}, semi, dg::DGSE return nothing end +############################################################################### +# Calculation of local bounds using low-order FV solution + @inline function calc_bounds_twosided!(var_min, var_max, variable, u, t, semi) mesh, equations, dg, cache = mesh_equations_solver_cache(semi) # Calc bounds inside elements @@ -164,6 +171,9 @@ end return nothing end +############################################################################### +# Local minimum/maximum limiting + @inline function idp_local_minmax!(alpha, limiter, u, t, dt, semi) for variable in limiter.local_minmax_variables_cons idp_local_minmax!(alpha, limiter, u, t, dt, semi, variable) @@ -233,16 +243,36 @@ end return nothing end +############################################################################### +# Global positivity limiting + @inline function idp_positivity!(alpha, limiter, u, dt, semi) # Conservative variables for variable in limiter.positivity_variables_cons - idp_positivity!(alpha, limiter, u, dt, semi, variable) + @trixi_timeit timer() "conservative variables" idp_positivity_conservative!(alpha, + limiter, + u, + dt, + semi, + variable) + end + + # Nonlinear variables + for variable in limiter.positivity_variables_nonlinear + @trixi_timeit timer() "nonlinear variables" idp_positivity_nonlinear!(alpha, + limiter, + u, dt, + semi, + variable) end return nothing end -@inline function idp_positivity!(alpha, limiter, u, dt, semi, variable) +############################################################################### +# Global positivity limiting of conservative variables + +@inline function idp_positivity_conservative!(alpha, limiter, u, dt, semi, variable) mesh, equations, dg, cache = mesh_equations_solver_cache(semi) (; antidiffusive_flux1_L, antidiffusive_flux2_L, antidiffusive_flux1_R, antidiffusive_flux2_R) = cache.antidiffusive_fluxes (; inverse_weights) = dg.basis @@ -256,7 +286,7 @@ end for j in eachnode(dg), i in eachnode(dg) var = u[variable, i, j, element] if var < 0 - error("Safe $variable is not safe. element=$element, node: $i $j, value=$var") + error("Safe low-order method produces negative value for conservative variable $variable. Try a smaller time step.") end # Compute bound @@ -302,4 +332,183 @@ end return nothing end + +@inline function idp_positivity_nonlinear!(alpha, limiter, u, dt, semi, variable) + _, equations, dg, cache = mesh_equations_solver_cache(semi) + (; positivity_correction_factor) = limiter + + (; variable_bounds) = limiter.cache.subcell_limiter_coefficients + var_min = variable_bounds[Symbol(string(variable), "_min")] + + @threaded for element in eachelement(dg, semi.cache) + inverse_jacobian = cache.elements.inverse_jacobian[element] + for j in eachnode(dg), i in eachnode(dg) + # Compute bound + u_local = get_node_vars(u, equations, dg, i, j, element) + var = variable(u_local, equations) + if var < 0 + error("Safe low-order method produces negative value for variable $variable. Try a smaller time step.") + end + var_min[i, j, element] = positivity_correction_factor * var + + # Perform Newton's bisection method to find new alpha + newton_loops_alpha!(alpha, var_min[i, j, element], u_local, i, j, element, + variable, initial_check_nonnegative_newton_idp, + final_check_nonnegative_newton_idp, inverse_jacobian, + dt, equations, dg, cache, limiter) + end + end + + return nothing +end + +@inline function newton_loops_alpha!(alpha, bound, u, i, j, element, variable, + initial_check, final_check, inverse_jacobian, dt, + equations, dg, cache, limiter) + (; inverse_weights) = dg.basis + (; antidiffusive_flux1_L, antidiffusive_flux2_L, antidiffusive_flux1_R, antidiffusive_flux2_R) = cache.antidiffusive_fluxes + + (; gamma_constant_newton) = limiter + + # negative xi direction + antidiffusive_flux = gamma_constant_newton * inverse_jacobian * inverse_weights[i] * + get_node_vars(antidiffusive_flux1_R, equations, dg, i, j, + element) + newton_loop!(alpha, bound, u, i, j, element, variable, initial_check, final_check, + equations, dt, limiter, antidiffusive_flux) + + # positive xi direction + antidiffusive_flux = -gamma_constant_newton * inverse_jacobian * + inverse_weights[i] * + get_node_vars(antidiffusive_flux1_L, equations, dg, i + 1, j, + element) + newton_loop!(alpha, bound, u, i, j, element, variable, initial_check, final_check, + equations, dt, limiter, antidiffusive_flux) + + # negative eta direction + antidiffusive_flux = gamma_constant_newton * inverse_jacobian * inverse_weights[j] * + get_node_vars(antidiffusive_flux2_R, equations, dg, i, j, + element) + newton_loop!(alpha, bound, u, i, j, element, variable, initial_check, final_check, + equations, dt, limiter, antidiffusive_flux) + + # positive eta direction + antidiffusive_flux = -gamma_constant_newton * inverse_jacobian * + inverse_weights[j] * + get_node_vars(antidiffusive_flux2_L, equations, dg, i, j + 1, + element) + newton_loop!(alpha, bound, u, i, j, element, variable, initial_check, final_check, + equations, dt, limiter, antidiffusive_flux) + + return nothing +end + +@inline function newton_loop!(alpha, bound, u, i, j, element, variable, initial_check, + final_check, equations, dt, limiter, antidiffusive_flux) + newton_reltol, newton_abstol = limiter.newton_tolerances + + beta = 1 - alpha[i, j, element] + + beta_L = 0 # alpha = 1 + beta_R = beta # No higher beta (lower alpha) than the current one + + u_curr = u + beta * dt * antidiffusive_flux + + # If state is valid, perform initial check and return if correction is not needed + if isvalid(u_curr, equations) + goal = goal_function_newton_idp(variable, bound, u_curr, equations) + + initial_check(bound, goal, newton_abstol) && return nothing + end + + # Newton iterations + for iter in 1:(limiter.max_iterations_newton) + beta_old = beta + + # If the state is valid, evaluate d(goal)/d(beta) + if isvalid(u_curr, equations) + dgoal_dbeta = dgoal_function_newton_idp(variable, u_curr, dt, + antidiffusive_flux, equations) + else # Otherwise, perform a bisection step + dgoal_dbeta = 0 + end + + if dgoal_dbeta != 0 + # Update beta with Newton's method + beta = beta - goal / dgoal_dbeta + end + + # Check bounds + if (beta < beta_L) || (beta > beta_R) || (dgoal_dbeta == 0) || isnan(beta) + # Out of bounds, do a bisection step + beta = 0.5 * (beta_L + beta_R) + # Get new u + u_curr = u + beta * dt * antidiffusive_flux + + # If the state is invalid, finish bisection step without checking tolerance and iterate further + if !isvalid(u_curr, equations) + beta_R = beta + continue + end + + # Check new beta for condition and update bounds + goal = goal_function_newton_idp(variable, bound, u_curr, equations) + if initial_check(bound, goal, newton_abstol) + # New beta fulfills condition + beta_L = beta + else + # New beta does not fulfill condition + beta_R = beta + end + else + # Get new u + u_curr = u + beta * dt * antidiffusive_flux + + # If the state is invalid, redefine right bound without checking tolerance and iterate further + if !isvalid(u_curr, equations) + beta_R = beta + continue + end + + # Evaluate goal function + goal = goal_function_newton_idp(variable, bound, u_curr, equations) + end + + # Check relative tolerance + if abs(beta_old - beta) <= newton_reltol + break + end + + # Check absolute tolerance + if final_check(bound, goal, newton_abstol) + break + end + end + + new_alpha = 1 - beta + if alpha[i, j, element] > new_alpha + newton_abstol + error("Alpha is getting smaller. old: $(alpha[i, j, element]), new: $new_alpha") + else + alpha[i, j, element] = new_alpha + end + + return nothing +end + +### Auxiliary routines for Newton's bisection method ### +# Initial checks +@inline initial_check_nonnegative_newton_idp(bound, goal, newton_abstol) = goal <= 0 + +# Goal and d(Goal)d(u) function +@inline goal_function_newton_idp(variable, bound, u, equations) = bound - + variable(u, equations) +@inline function dgoal_function_newton_idp(variable, u, dt, antidiffusive_flux, + equations) + -dot(gradient_conservative(variable, u, equations), dt * antidiffusive_flux) +end + +# Final checks +@inline function final_check_nonnegative_newton_idp(bound, goal, newton_abstol) + (goal <= eps()) && (goal > -max(newton_abstol, abs(bound) * newton_abstol)) +end end # @muladd diff --git a/test/test_tree_2d_euler.jl b/test/test_tree_2d_euler.jl index 61b5c54b5e9..b937abe92c0 100644 --- a/test/test_tree_2d_euler.jl +++ b/test/test_tree_2d_euler.jl @@ -581,6 +581,32 @@ end end end +@trixi_testset "elixir_euler_kelvin_helmholtz_instability_sc_subcell.jl" begin + @test_trixi_include(joinpath(EXAMPLES_DIR, + "elixir_euler_kelvin_helmholtz_instability_sc_subcell.jl"), + l2=[ + 0.42185634563805724, + 0.1686471269704017, + 0.18240674916968103, + 0.17858250604280654, + ], + linf=[ + 1.7012978064377158, + 0.7149714986746726, + 0.5822547982757897, + 0.7300051017382696, + ], + tspan=(0.0, 2.0)) + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 15000 + end +end + @trixi_testset "elixir_euler_colliding_flow.jl" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_colliding_flow.jl"), l2=[ diff --git a/test/test_tree_2d_mhd.jl b/test/test_tree_2d_mhd.jl index 953c077c0a3..1f8458075aa 100644 --- a/test/test_tree_2d_mhd.jl +++ b/test/test_tree_2d_mhd.jl @@ -332,24 +332,28 @@ end @trixi_testset "elixir_mhd_shockcapturing_subcell.jl" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_mhd_shockcapturing_subcell.jl"), - l2=[2.9974425783503109e-02, - 7.2849646345685956e-02, - 7.2488477174662239e-02, + l2=[ + 3.2064026219236076e-02, + 7.2461094392606618e-02, + 7.2380202888062711e-02, 0.0000000000000000e+00, - 1.2507971380965512e+00, - 1.8929505145499678e-02, - 1.2218606317164420e-02, + 8.6293936673145932e-01, + 8.4091669534557805e-03, + 5.2156364913231732e-03, 0.0000000000000000e+00, - 3.0154796910479838e-03], - linf=[3.2147382412340830e-01, - 1.3709471664007811e+00, - 1.3465154685288383e+00, + 2.0786952301129021e-04, + ], + linf=[ + 3.8778760255775635e-01, + 9.4666683953698927e-01, + 9.4618924645661928e-01, 0.0000000000000000e+00, - 1.6051257523415284e+01, - 3.0564266749926644e-01, - 2.3908016329805595e-01, + 1.0980297261521951e+01, + 1.0264404591009069e-01, + 1.0655686942176350e-01, 0.0000000000000000e+00, - 1.3711262178549158e-01], + 6.1013422157115546e-03, + ], tspan=(0.0, 0.003)) # Ensure that we do not have excessive memory allocations # (e.g., from type instabilities) diff --git a/test/test_unit.jl b/test/test_unit.jl index e8a8effbe29..7943d952f71 100644 --- a/test/test_unit.jl +++ b/test/test_unit.jl @@ -416,7 +416,8 @@ end indicator_hg = IndicatorHennemannGassner(1.0, 0.0, true, "variable", "cache") @test_nowarn show(stdout, indicator_hg) - limiter_idp = SubcellLimiterIDP(true, [1], true, [1], 0.1, "cache") + limiter_idp = SubcellLimiterIDP(true, [1], true, [1], ["variable"], 0.1, "cache", 1, + (1.0, 1.0), 1.0) @test_nowarn show(stdout, limiter_idp) # TODO: TrixiShallowWater: move unit test @@ -1220,6 +1221,26 @@ end end end +@testset "Consistency check for `gradient_conservative` routine" begin + # Set up conservative variables, equations + u = [ + 0.5011914484393387, + 0.8829127712445113, + 0.43024132987932817, + 0.7560616633050348, + ] + + equations = CompressibleEulerEquations2D(1.4) + + # Define wrapper function for pressure in order to call default implementation + function pressure_test(u, equations) + return pressure(u, equations) + end + + @test Trixi.gradient_conservative(pressure_test, u, equations) ≈ + Trixi.gradient_conservative(pressure, u, equations) +end + @testset "Equivalent Fluxes" begin # Set up equations and dummy conservative variables state # Burgers' Equation From e2c92f32457e22d6f8b766bf1ecd7a25d413cc6e Mon Sep 17 00:00:00 2001 From: Daniel Doehring Date: Thu, 1 Feb 2024 09:35:16 +0100 Subject: [PATCH 13/63] Move Jacobian for para P4est to respective files, add muladd (#1807) * Move Jacobian for para P4est to respective files, add muladd * fmt * compare checks without muladd * update test val for muladd * test vals --------- Co-authored-by: Jesse Chan <1156048+jlchan@users.noreply.github.com> --- src/solvers/dgsem_p4est/dg_2d_parabolic.jl | 176 +++++++++++++++------ src/solvers/dgsem_p4est/dg_3d_parabolic.jl | 137 +++++++++++----- src/solvers/dgsem_tree/dg_2d_parabolic.jl | 18 --- src/solvers/dgsem_tree/dg_3d_parabolic.jl | 18 --- test/test_parabolic_2d.jl | 4 +- 5 files changed, 228 insertions(+), 125 deletions(-) diff --git a/src/solvers/dgsem_p4est/dg_2d_parabolic.jl b/src/solvers/dgsem_p4est/dg_2d_parabolic.jl index 299f2f6140a..ed21f371449 100644 --- a/src/solvers/dgsem_p4est/dg_2d_parabolic.jl +++ b/src/solvers/dgsem_p4est/dg_2d_parabolic.jl @@ -1,7 +1,15 @@ +# By default, Julia/LLVM does not use fused multiply-add operations (FMAs). +# Since these FMAs can increase the performance of many numerical algorithms, +# we need to opt-in explicitly. +# See https://ranocha.de/blog/Optimizing_EC_Trixi for further details. +@muladd begin +#! format: noindent + # This method is called when a SemidiscretizationHyperbolicParabolic is constructed. # It constructs the basic `cache` used throughout the simulation to compute # the RHS etc. -function create_cache_parabolic(mesh::P4estMesh{2}, equations_hyperbolic::AbstractEquations, +function create_cache_parabolic(mesh::P4estMesh{2}, + equations_hyperbolic::AbstractEquations, equations_parabolic::AbstractEquationsParabolic, dg::DG, parabolic_scheme, RealT, uEltype) balance!(mesh) @@ -167,12 +175,14 @@ function calc_gradient!(gradients, u_transformed, t, element) for ii in eachnode(dg) - multiply_add_to_node_vars!(gradients_x, derivative_dhat[ii, i], u_node, + multiply_add_to_node_vars!(gradients_x, derivative_dhat[ii, i], + u_node, equations_parabolic, dg, ii, j, element) end for jj in eachnode(dg) - multiply_add_to_node_vars!(gradients_y, derivative_dhat[jj, j], u_node, + multiply_add_to_node_vars!(gradients_y, derivative_dhat[jj, j], + u_node, equations_parabolic, dg, i, jj, element) end end @@ -185,9 +195,11 @@ function calc_gradient!(gradients, u_transformed, t, Ja21, Ja22 = get_contravariant_vector(2, contravariant_vectors, i, j, element) - gradients_reference_1 = get_node_vars(gradients_x, equations_parabolic, dg, + gradients_reference_1 = get_node_vars(gradients_x, equations_parabolic, + dg, i, j, element) - gradients_reference_2 = get_node_vars(gradients_y, equations_parabolic, dg, + gradients_reference_2 = get_node_vars(gradients_y, equations_parabolic, + dg, i, j, element) # note that the contravariant vectors are transposed compared with computations of flux @@ -199,9 +211,11 @@ function calc_gradient!(gradients, u_transformed, t, gradient_y_node = Ja12 * gradients_reference_1 + Ja22 * gradients_reference_2 - set_node_vars!(gradients_x, gradient_x_node, equations_parabolic, dg, i, j, + set_node_vars!(gradients_x, gradient_x_node, equations_parabolic, dg, i, + j, element) - set_node_vars!(gradients_y, gradient_y_node, equations_parabolic, dg, i, j, + set_node_vars!(gradients_y, gradient_y_node, equations_parabolic, dg, i, + j, element) end end @@ -219,7 +233,8 @@ function calc_gradient!(gradients, u_transformed, t, @trixi_timeit timer() "interface flux" begin calc_interface_flux!(cache_parabolic.elements.surface_flux_values, mesh, False(), # False() = no nonconservative terms - equations_parabolic, dg.surface_integral, dg, cache_parabolic) + equations_parabolic, dg.surface_integral, dg, + cache_parabolic) end # Prolong solution to boundaries @@ -231,7 +246,8 @@ function calc_gradient!(gradients, u_transformed, t, # Calculate boundary fluxes @trixi_timeit timer() "boundary flux" begin calc_boundary_flux_gradients!(cache_parabolic, t, boundary_conditions_parabolic, - mesh, equations_parabolic, dg.surface_integral, dg) + mesh, equations_parabolic, dg.surface_integral, + dg) end # Prolong solution to mortars. This resues the hyperbolic version of `prolong2mortars` @@ -268,70 +284,94 @@ function calc_gradient!(gradients, u_transformed, t, # Compute x-component of gradients # surface at -x - normal_direction_x, _ = get_normal_direction(1, contravariant_vectors, + normal_direction_x, _ = get_normal_direction(1, + contravariant_vectors, 1, l, element) gradients_x[v, 1, l, element] = (gradients_x[v, 1, l, element] + - surface_flux_values[v, l, 1, element] * + surface_flux_values[v, l, 1, + element] * factor_1 * normal_direction_x) # surface at +x - normal_direction_x, _ = get_normal_direction(2, contravariant_vectors, + normal_direction_x, _ = get_normal_direction(2, + contravariant_vectors, nnodes(dg), l, element) - gradients_x[v, nnodes(dg), l, element] = (gradients_x[v, nnodes(dg), l, + gradients_x[v, nnodes(dg), l, element] = (gradients_x[v, nnodes(dg), + l, element] + - surface_flux_values[v, l, 2, + surface_flux_values[v, l, + 2, element] * - factor_2 * normal_direction_x) + factor_2 * + normal_direction_x) # surface at -y - normal_direction_x, _ = get_normal_direction(3, contravariant_vectors, + normal_direction_x, _ = get_normal_direction(3, + contravariant_vectors, l, 1, element) gradients_x[v, l, 1, element] = (gradients_x[v, l, 1, element] + - surface_flux_values[v, l, 3, element] * + surface_flux_values[v, l, 3, + element] * factor_1 * normal_direction_x) # surface at +y - normal_direction_x, _ = get_normal_direction(4, contravariant_vectors, + normal_direction_x, _ = get_normal_direction(4, + contravariant_vectors, l, nnodes(dg), element) - gradients_x[v, l, nnodes(dg), element] = (gradients_x[v, l, nnodes(dg), + gradients_x[v, l, nnodes(dg), element] = (gradients_x[v, l, + nnodes(dg), element] + - surface_flux_values[v, l, 4, + surface_flux_values[v, l, + 4, element] * - factor_2 * normal_direction_x) + factor_2 * + normal_direction_x) # Compute y-component of gradients # surface at -x - _, normal_direction_y = get_normal_direction(1, contravariant_vectors, + _, normal_direction_y = get_normal_direction(1, + contravariant_vectors, 1, l, element) gradients_y[v, 1, l, element] = (gradients_y[v, 1, l, element] + - surface_flux_values[v, l, 1, element] * + surface_flux_values[v, l, 1, + element] * factor_1 * normal_direction_y) # surface at +x - _, normal_direction_y = get_normal_direction(2, contravariant_vectors, + _, normal_direction_y = get_normal_direction(2, + contravariant_vectors, nnodes(dg), l, element) - gradients_y[v, nnodes(dg), l, element] = (gradients_y[v, nnodes(dg), l, + gradients_y[v, nnodes(dg), l, element] = (gradients_y[v, nnodes(dg), + l, element] + - surface_flux_values[v, l, 2, + surface_flux_values[v, l, + 2, element] * - factor_2 * normal_direction_y) + factor_2 * + normal_direction_y) # surface at -y - _, normal_direction_y = get_normal_direction(3, contravariant_vectors, + _, normal_direction_y = get_normal_direction(3, + contravariant_vectors, l, 1, element) gradients_y[v, l, 1, element] = (gradients_y[v, l, 1, element] + - surface_flux_values[v, l, 3, element] * + surface_flux_values[v, l, 3, + element] * factor_1 * normal_direction_y) # surface at +y - _, normal_direction_y = get_normal_direction(4, contravariant_vectors, + _, normal_direction_y = get_normal_direction(4, + contravariant_vectors, l, nnodes(dg), element) - gradients_y[v, l, nnodes(dg), element] = (gradients_y[v, l, nnodes(dg), + gradients_y[v, l, nnodes(dg), element] = (gradients_y[v, l, + nnodes(dg), element] + - surface_flux_values[v, l, 4, + surface_flux_values[v, l, + 4, element] * - factor_2 * normal_direction_y) + factor_2 * + normal_direction_y) end end end @@ -444,24 +484,30 @@ function calc_volume_integral!(du, flux_viscous, @threaded for element in eachelement(dg, cache) # Calculate volume terms in one element for j in eachnode(dg), i in eachnode(dg) - flux1 = get_node_vars(flux_viscous_x, equations_parabolic, dg, i, j, element) - flux2 = get_node_vars(flux_viscous_y, equations_parabolic, dg, i, j, element) + flux1 = get_node_vars(flux_viscous_x, equations_parabolic, dg, i, j, + element) + flux2 = get_node_vars(flux_viscous_y, equations_parabolic, dg, i, j, + element) # Compute the contravariant flux by taking the scalar product of the # first contravariant vector Ja^1 and the flux vector - Ja11, Ja12 = get_contravariant_vector(1, contravariant_vectors, i, j, element) + Ja11, Ja12 = get_contravariant_vector(1, contravariant_vectors, i, j, + element) contravariant_flux1 = Ja11 * flux1 + Ja12 * flux2 for ii in eachnode(dg) - multiply_add_to_node_vars!(du, derivative_dhat[ii, i], contravariant_flux1, + multiply_add_to_node_vars!(du, derivative_dhat[ii, i], + contravariant_flux1, equations_parabolic, dg, ii, j, element) end # Compute the contravariant flux by taking the scalar product of the # second contravariant vector Ja^2 and the flux vector - Ja21, Ja22 = get_contravariant_vector(2, contravariant_vectors, i, j, element) + Ja21, Ja22 = get_contravariant_vector(2, contravariant_vectors, i, j, + element) contravariant_flux2 = Ja21 * flux1 + Ja22 * flux2 for jj in eachnode(dg) - multiply_add_to_node_vars!(du, derivative_dhat[jj, j], contravariant_flux2, + multiply_add_to_node_vars!(du, derivative_dhat[jj, j], + contravariant_flux2, equations_parabolic, dg, i, jj, element) end end @@ -503,7 +549,8 @@ function prolong2interfaces!(cache_parabolic, flux_viscous, # this is the outward normal direction on the primary element normal_direction = get_normal_direction(primary_direction, contravariant_vectors, - i_primary, j_primary, primary_element) + i_primary, j_primary, + primary_element) for v in eachvariable(equations_parabolic) # OBS! `interfaces.u` stores the interpolated *fluxes* and *not the solution*! @@ -602,7 +649,8 @@ function calc_interface_flux!(surface_flux_values, # primary element. We assume a BR-1 type of flux. viscous_flux_normal_ll, viscous_flux_normal_rr = get_surface_node_vars(cache_parabolic.interfaces.u, equations_parabolic, - dg, node, + dg, + node, interface) flux = 0.5 * (viscous_flux_normal_ll + viscous_flux_normal_rr) @@ -624,9 +672,11 @@ function calc_interface_flux!(surface_flux_values, end function prolong2mortars_divergence!(cache, flux_viscous::Vector{Array{uEltype, 4}}, - mesh::Union{P4estMesh{2}, T8codeMesh{2}}, equations, + mesh::Union{P4estMesh{2}, T8codeMesh{2}}, + equations, mortar_l2::LobattoLegendreMortarL2, - surface_integral, dg::DGSEM) where {uEltype <: Real} + surface_integral, + dg::DGSEM) where {uEltype <: Real} @unpack neighbor_ids, node_indices = cache.mortars @unpack contravariant_vectors = cache.elements index_range = eachnode(dg) @@ -683,7 +733,8 @@ function prolong2mortars_divergence!(cache, flux_viscous::Vector{Array{uEltype, j_large = j_large_start element = neighbor_ids[3, mortar] for i in eachnode(dg) - normal_direction = get_normal_direction(direction_index, contravariant_vectors, + normal_direction = get_normal_direction(direction_index, + contravariant_vectors, i_large, j_large, element) for v in eachvariable(equations) @@ -732,8 +783,10 @@ function calc_mortar_flux_divergence!(surface_flux_values, for position in 1:2 for node in eachnode(dg) for v in eachvariable(equations) - viscous_flux_normal_ll = cache.mortars.u[1, v, position, node, mortar] - viscous_flux_normal_rr = cache.mortars.u[2, v, position, node, mortar] + viscous_flux_normal_ll = cache.mortars.u[1, v, position, node, + mortar] + viscous_flux_normal_rr = cache.mortars.u[2, v, position, node, + mortar] # TODO: parabolic; only BR1 at the moment fstar[position][v, node] = 0.5 * (viscous_flux_normal_ll + @@ -824,7 +877,8 @@ end function calc_boundary_flux_gradients!(cache, t, boundary_condition::Union{BoundaryConditionPeriodic, BoundaryConditionDoNothing}, - mesh::P4estMesh, equations, surface_integral, dg::DG) + mesh::P4estMesh, equations, surface_integral, + dg::DG) @assert isempty(eachboundary(dg, cache)) end @@ -913,7 +967,8 @@ function calc_boundary_flux!(cache, t, boundary_index) # Outward-pointing normal direction (not normalized) - normal_direction = get_normal_direction(direction_index, contravariant_vectors, + normal_direction = get_normal_direction(direction_index, + contravariant_vectors, i_node, j_node, element) # TODO: revisit if we want more general boundary treatments. @@ -922,11 +977,13 @@ function calc_boundary_flux!(cache, t, flux_inner = u_inner # Coordinates at boundary node - x = get_node_coords(node_coordinates, equations_parabolic, dg, i_node, j_node, + x = get_node_coords(node_coordinates, equations_parabolic, dg, i_node, + j_node, element) flux_ = boundary_condition_parabolic(flux_inner, u_inner, normal_direction, - x, t, operator_type, equations_parabolic) + x, t, operator_type, + equations_parabolic) # Copy flux to element storage in the correct orientation for v in eachvariable(equations_parabolic) @@ -938,3 +995,22 @@ function calc_boundary_flux!(cache, t, end end end + +function apply_jacobian_parabolic!(du, mesh::P4estMesh{2}, + equations::AbstractEquationsParabolic, + dg::DG, cache) + @unpack inverse_jacobian = cache.elements + + @threaded for element in eachelement(dg, cache) + for j in eachnode(dg), i in eachnode(dg) + factor = inverse_jacobian[i, j, element] + + for v in eachvariable(equations) + du[v, i, j, element] *= factor + end + end + end + + return nothing +end +end # @muladd diff --git a/src/solvers/dgsem_p4est/dg_3d_parabolic.jl b/src/solvers/dgsem_p4est/dg_3d_parabolic.jl index 83d663809a7..63d431d35d5 100644 --- a/src/solvers/dgsem_p4est/dg_3d_parabolic.jl +++ b/src/solvers/dgsem_p4est/dg_3d_parabolic.jl @@ -1,7 +1,15 @@ +# By default, Julia/LLVM does not use fused multiply-add operations (FMAs). +# Since these FMAs can increase the performance of many numerical algorithms, +# we need to opt-in explicitly. +# See https://ranocha.de/blog/Optimizing_EC_Trixi for further details. +@muladd begin +#! format: noindent + # This method is called when a SemidiscretizationHyperbolicParabolic is constructed. # It constructs the basic `cache` used throughout the simulation to compute # the RHS etc. -function create_cache_parabolic(mesh::P4estMesh{3}, equations_hyperbolic::AbstractEquations, +function create_cache_parabolic(mesh::P4estMesh{3}, + equations_hyperbolic::AbstractEquations, equations_parabolic::AbstractEquationsParabolic, dg::DG, parabolic_scheme, RealT, uEltype) balance!(mesh) @@ -73,11 +81,14 @@ function calc_gradient!(gradients, u_transformed, t, Ja31, Ja32, Ja33 = get_contravariant_vector(3, contravariant_vectors, i, j, k, element) - gradients_reference_1 = get_node_vars(gradients_x, equations_parabolic, dg, + gradients_reference_1 = get_node_vars(gradients_x, equations_parabolic, + dg, i, j, k, element) - gradients_reference_2 = get_node_vars(gradients_y, equations_parabolic, dg, + gradients_reference_2 = get_node_vars(gradients_y, equations_parabolic, + dg, i, j, k, element) - gradients_reference_3 = get_node_vars(gradients_z, equations_parabolic, dg, + gradients_reference_3 = get_node_vars(gradients_z, equations_parabolic, + dg, i, j, k, element) # note that the contravariant vectors are transposed compared with computations of flux @@ -115,7 +126,8 @@ function calc_gradient!(gradients, u_transformed, t, @trixi_timeit timer() "interface flux" begin calc_interface_flux!(cache_parabolic.elements.surface_flux_values, mesh, False(), # False() = no nonconservative terms - equations_parabolic, dg.surface_integral, dg, cache_parabolic) + equations_parabolic, dg.surface_integral, dg, + cache_parabolic) end # Prolong solution to boundaries @@ -127,7 +139,8 @@ function calc_gradient!(gradients, u_transformed, t, # Calculate boundary fluxes @trixi_timeit timer() "boundary flux" begin calc_boundary_flux_gradients!(cache_parabolic, t, boundary_conditions_parabolic, - mesh, equations_parabolic, dg.surface_integral, dg) + mesh, equations_parabolic, dg.surface_integral, + dg) end # Prolong solution to mortars. These should reuse the hyperbolic version of `prolong2mortars` @@ -165,7 +178,8 @@ function calc_gradient!(gradients, u_transformed, t, for dim in 1:3 grad = gradients[dim] # surface at -x - normal_direction = get_normal_direction(1, contravariant_vectors, + normal_direction = get_normal_direction(1, + contravariant_vectors, 1, l, m, element) grad[v, 1, l, m, element] = (grad[v, 1, l, m, element] + surface_flux_values[v, l, m, 1, @@ -173,18 +187,22 @@ function calc_gradient!(gradients, u_transformed, t, factor_1 * normal_direction[dim]) # surface at +x - normal_direction = get_normal_direction(2, contravariant_vectors, - nnodes(dg), l, m, element) + normal_direction = get_normal_direction(2, + contravariant_vectors, + nnodes(dg), l, m, + element) grad[v, nnodes(dg), l, m, element] = (grad[v, nnodes(dg), l, m, element] + - surface_flux_values[v, l, m, + surface_flux_values[v, l, + m, 2, element] * factor_2 * normal_direction[dim]) # surface at -y - normal_direction = get_normal_direction(3, contravariant_vectors, + normal_direction = get_normal_direction(3, + contravariant_vectors, l, m, 1, element) grad[v, l, 1, m, element] = (grad[v, l, 1, m, element] + surface_flux_values[v, l, m, 3, @@ -192,18 +210,22 @@ function calc_gradient!(gradients, u_transformed, t, factor_1 * normal_direction[dim]) # surface at +y - normal_direction = get_normal_direction(4, contravariant_vectors, - l, nnodes(dg), m, element) + normal_direction = get_normal_direction(4, + contravariant_vectors, + l, nnodes(dg), m, + element) grad[v, l, nnodes(dg), m, element] = (grad[v, l, nnodes(dg), m, element] + - surface_flux_values[v, l, m, + surface_flux_values[v, l, + m, 4, element] * factor_2 * normal_direction[dim]) # surface at -z - normal_direction = get_normal_direction(5, contravariant_vectors, + normal_direction = get_normal_direction(5, + contravariant_vectors, l, m, 1, element) grad[v, l, m, 1, element] = (grad[v, l, m, 1, element] + surface_flux_values[v, l, m, 5, @@ -211,11 +233,14 @@ function calc_gradient!(gradients, u_transformed, t, factor_1 * normal_direction[dim]) # surface at +z - normal_direction = get_normal_direction(6, contravariant_vectors, - l, m, nnodes(dg), element) + normal_direction = get_normal_direction(6, + contravariant_vectors, + l, m, nnodes(dg), + element) grad[v, l, m, nnodes(dg), element] = (grad[v, l, m, nnodes(dg), element] + - surface_flux_values[v, l, m, + surface_flux_values[v, l, + m, 6, element] * factor_2 * @@ -366,37 +391,46 @@ function calc_volume_integral!(du, flux_viscous, @threaded for element in eachelement(dg, cache) # Calculate volume terms in one element for k in eachnode(dg), j in eachnode(dg), i in eachnode(dg) - flux1 = get_node_vars(flux_viscous_x, equations_parabolic, dg, i, j, k, element) - flux2 = get_node_vars(flux_viscous_y, equations_parabolic, dg, i, j, k, element) - flux3 = get_node_vars(flux_viscous_z, equations_parabolic, dg, i, j, k, element) + flux1 = get_node_vars(flux_viscous_x, equations_parabolic, dg, i, j, k, + element) + flux2 = get_node_vars(flux_viscous_y, equations_parabolic, dg, i, j, k, + element) + flux3 = get_node_vars(flux_viscous_z, equations_parabolic, dg, i, j, k, + element) # Compute the contravariant flux by taking the scalar product of the # first contravariant vector Ja^1 and the flux vector - Ja11, Ja12, Ja13 = get_contravariant_vector(1, contravariant_vectors, i, j, k, + Ja11, Ja12, Ja13 = get_contravariant_vector(1, contravariant_vectors, i, j, + k, element) contravariant_flux1 = Ja11 * flux1 + Ja12 * flux2 + Ja13 * flux3 for ii in eachnode(dg) - multiply_add_to_node_vars!(du, derivative_dhat[ii, i], contravariant_flux1, + multiply_add_to_node_vars!(du, derivative_dhat[ii, i], + contravariant_flux1, equations_parabolic, dg, ii, j, k, element) end # Compute the contravariant flux by taking the scalar product of the # second contravariant vector Ja^2 and the flux vector - Ja21, Ja22, Ja23 = get_contravariant_vector(2, contravariant_vectors, i, j, k, + Ja21, Ja22, Ja23 = get_contravariant_vector(2, contravariant_vectors, i, j, + k, element) contravariant_flux2 = Ja21 * flux1 + Ja22 * flux2 + Ja23 * flux3 for jj in eachnode(dg) - multiply_add_to_node_vars!(du, derivative_dhat[jj, j], contravariant_flux2, + multiply_add_to_node_vars!(du, derivative_dhat[jj, j], + contravariant_flux2, equations_parabolic, dg, i, jj, k, element) end # Compute the contravariant flux by taking the scalar product of the # second contravariant vector Ja^2 and the flux vector - Ja31, Ja32, Ja33 = get_contravariant_vector(3, contravariant_vectors, i, j, k, + Ja31, Ja32, Ja33 = get_contravariant_vector(3, contravariant_vectors, i, j, + k, element) contravariant_flux3 = Ja31 * flux1 + Ja32 * flux2 + Ja33 * flux3 for kk in eachnode(dg) - multiply_add_to_node_vars!(du, derivative_dhat[kk, k], contravariant_flux3, + multiply_add_to_node_vars!(du, derivative_dhat[kk, k], + contravariant_flux3, equations_parabolic, dg, i, j, kk, element) end end @@ -574,7 +608,8 @@ function calc_interface_flux!(surface_flux_values, viscous_flux_normal_ll, viscous_flux_normal_rr = get_surface_node_vars(cache_parabolic.interfaces.u, equations_parabolic, dg, - i, j, + i, + j, interface) flux = 0.5 * (viscous_flux_normal_ll + viscous_flux_normal_rr) @@ -606,7 +641,8 @@ function calc_interface_flux!(surface_flux_values, end function prolong2mortars_divergence!(cache, flux_viscous, - mesh::Union{P4estMesh{3}, T8codeMesh{3}}, equations, + mesh::Union{P4estMesh{3}, T8codeMesh{3}}, + equations, mortar_l2::LobattoLegendreMortarL2, surface_integral, dg::DGSEM) @unpack neighbor_ids, node_indices = cache.mortars @@ -642,11 +678,14 @@ function prolong2mortars_divergence!(cache, flux_viscous, element) for v in eachvariable(equations) - flux_viscous = SVector(flux_viscous_x[v, i_small, j_small, k_small, + flux_viscous = SVector(flux_viscous_x[v, i_small, j_small, + k_small, element], - flux_viscous_y[v, i_small, j_small, k_small, + flux_viscous_y[v, i_small, j_small, + k_small, element], - flux_viscous_z[v, i_small, j_small, k_small, + flux_viscous_z[v, i_small, j_small, + k_small, element]) cache.mortars.u[1, v, position, i, j, mortar] = dot(flux_viscous, @@ -688,7 +727,8 @@ function prolong2mortars_divergence!(cache, flux_viscous, for i in eachnode(dg) normal_direction = get_normal_direction(direction_index, contravariant_vectors, - i_large, j_large, k_large, element) + i_large, j_large, k_large, + element) for v in eachvariable(equations) flux_viscous = SVector(flux_viscous_x[v, i_large, j_large, k_large, @@ -827,7 +867,8 @@ end # TODO: parabolic; only BR1 at the moment flux_ = 0.5 * (u_ll + u_rr) # Copy flux to buffer - set_node_vars!(fstar, flux_, equations, dg, i_node_index, j_node_index, position_index) + set_node_vars!(fstar, flux_, equations, dg, i_node_index, j_node_index, + position_index) end # TODO: parabolic, finish implementing `calc_boundary_flux_gradients!` and `calc_boundary_flux_divergence!` @@ -862,7 +903,8 @@ function prolong2boundaries!(cache_parabolic, flux_viscous, for j in eachnode(dg) for i in eachnode(dg) # this is the outward normal direction on the primary element - normal_direction = get_normal_direction(direction, contravariant_vectors, + normal_direction = get_normal_direction(direction, + contravariant_vectors, i_node, j_node, k_node, element) for v in eachvariable(equations_parabolic) @@ -873,7 +915,8 @@ function prolong2boundaries!(cache_parabolic, flux_viscous, flux_viscous_z[v, i_node, j_node, k_node, element]) - boundaries.u[v, i, j, boundary] = dot(flux_viscous, normal_direction) + boundaries.u[v, i, j, boundary] = dot(flux_viscous, + normal_direction) end i_node += i_node_step_i j_node += j_node_step_i @@ -940,7 +983,8 @@ function calc_boundary_flux!(cache, t, j_node, k_node, element) - flux_ = boundary_condition_parabolic(flux_inner, u_inner, normal_direction, + flux_ = boundary_condition_parabolic(flux_inner, u_inner, + normal_direction, x, t, operator_type, equations_parabolic) @@ -959,3 +1003,22 @@ function calc_boundary_flux!(cache, t, end end end + +function apply_jacobian_parabolic!(du, mesh::P4estMesh{3}, + equations::AbstractEquationsParabolic, + dg::DG, cache) + @unpack inverse_jacobian = cache.elements + + @threaded for element in eachelement(dg, cache) + for k in eachnode(dg), j in eachnode(dg), i in eachnode(dg) + factor = inverse_jacobian[i, j, k, element] + + for v in eachvariable(equations) + du[v, i, j, k, element] *= factor + end + end + end + + return nothing +end +end # @muladd diff --git a/src/solvers/dgsem_tree/dg_2d_parabolic.jl b/src/solvers/dgsem_tree/dg_2d_parabolic.jl index b1c27343999..a6c962e03cd 100644 --- a/src/solvers/dgsem_tree/dg_2d_parabolic.jl +++ b/src/solvers/dgsem_tree/dg_2d_parabolic.jl @@ -951,22 +951,4 @@ function apply_jacobian_parabolic!(du, mesh::TreeMesh{2}, return nothing end - -function apply_jacobian_parabolic!(du, mesh::P4estMesh{2}, - equations::AbstractEquationsParabolic, - dg::DG, cache) - @unpack inverse_jacobian = cache.elements - - @threaded for element in eachelement(dg, cache) - for j in eachnode(dg), i in eachnode(dg) - factor = inverse_jacobian[i, j, element] - - for v in eachvariable(equations) - du[v, i, j, element] *= factor - end - end - end - - return nothing -end end # @muladd diff --git a/src/solvers/dgsem_tree/dg_3d_parabolic.jl b/src/solvers/dgsem_tree/dg_3d_parabolic.jl index ee0e7c6b069..d5504744742 100644 --- a/src/solvers/dgsem_tree/dg_3d_parabolic.jl +++ b/src/solvers/dgsem_tree/dg_3d_parabolic.jl @@ -1033,22 +1033,4 @@ function apply_jacobian_parabolic!(du, mesh::TreeMesh{3}, return nothing end - -function apply_jacobian_parabolic!(du, mesh::P4estMesh{3}, - equations::AbstractEquationsParabolic, - dg::DG, cache) - @unpack inverse_jacobian = cache.elements - - @threaded for element in eachelement(dg, cache) - for k in eachnode(dg), j in eachnode(dg), i in eachnode(dg) - factor = inverse_jacobian[i, j, k, element] - - for v in eachvariable(equations) - du[v, i, j, k, element] *= factor - end - end - end - - return nothing -end end # @muladd diff --git a/test/test_parabolic_2d.jl b/test/test_parabolic_2d.jl index 6632cd0bb27..f7185a1a904 100644 --- a/test/test_parabolic_2d.jl +++ b/test/test_parabolic_2d.jl @@ -561,8 +561,8 @@ end @test_trixi_include(joinpath(examples_dir(), "p4est_2d_dgsem", "elixir_advection_diffusion_nonperiodic_amr.jl"), tspan=(0.0, 0.01), - l2=[0.00793438523666649], - linf=[0.11030633127144573]) + l2=[0.007933791324450538], + linf=[0.11029480573492567]) # Ensure that we do not have excessive memory allocations # (e.g., from type instabilities) let From 3ed62fb4e3bbd034b49fa452e4034c909b3a549b Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Thu, 1 Feb 2024 18:01:29 +0100 Subject: [PATCH 14/63] Bump actions/cache from 3 to 4 (#1828) Bumps [actions/cache](https://github.com/actions/cache) from 3 to 4. - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](https://github.com/actions/cache/compare/v3...v4) --- updated-dependencies: - dependency-name: actions/cache dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/benchmark.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/benchmark.yml b/.github/workflows/benchmark.yml index 6aa4809c1c2..4531c3aee0a 100644 --- a/.github/workflows/benchmark.yml +++ b/.github/workflows/benchmark.yml @@ -26,7 +26,7 @@ jobs: version: ${{ matrix.version }} arch: ${{ matrix.arch }} show-versioninfo: true - - uses: actions/cache@v3 + - uses: actions/cache@v4 env: cache-name: cache-artifacts with: From db1d7054b7832cb56dddda1076921dfd0476a2b2 Mon Sep 17 00:00:00 2001 From: Hendrik Ranocha Date: Fri, 2 Feb 2024 08:46:49 +0100 Subject: [PATCH 15/63] fix typo leafs -> leaves --- src/meshes/t8code_mesh.jl | 38 +++++++++++++++++++------------------- test/test_parabolic_2d.jl | 12 ++++++------ test/test_parabolic_3d.jl | 28 ++++++++++++++-------------- 3 files changed, 39 insertions(+), 39 deletions(-) diff --git a/src/meshes/t8code_mesh.jl b/src/meshes/t8code_mesh.jl index 6fb4d861d10..cb2ac787e14 100644 --- a/src/meshes/t8code_mesh.jl +++ b/src/meshes/t8code_mesh.jl @@ -1,7 +1,7 @@ """ T8codeMesh{NDIMS} <: AbstractMesh{NDIMS} -An unstructured curved mesh based on trees that uses the C library +An unstructured curved mesh based on trees that uses the C library ['t8code'](https://github.com/DLR-AMR/t8code) to manage trees and mesh refinement. """ @@ -485,7 +485,7 @@ end # form a family and we decide whether this family should be coarsened # or only the first element should be refined. # Otherwise `is_family` must equal zero and we consider the first entry -# of the element array for refinement. +# of the element array for refinement. # Entries of the element array beyond the first `num_elements` are undefined. # \param [in] forest the forest to which the new elements belong # \param [in] forest_from the forest that is adapted. @@ -542,8 +542,8 @@ Adapt a `T8codeMesh` according to a user-defined `adapt_callback`. 0 : Stay unchanged. 1 : Refine element. -- `kwargs`: - - `recursive = true`: Adapt the forest recursively. If true the caller must ensure that the callback +- `kwargs`: + - `recursive = true`: Adapt the forest recursively. If true the caller must ensure that the callback returns 0 for every analyzed element at some point to stop the recursion. - `balance = true`: Make sure the adapted forest is 2^(NDIMS-1):1 balanced. - `partition = true`: Partition the forest to redistribute elements evenly among MPI ranks. @@ -695,7 +695,7 @@ function count_interfaces(mesh::T8codeMesh) for iface in 0:(num_faces - 1) pelement_indices_ref = Ref{Ptr{t8_locidx_t}}() - pneighbor_leafs_ref = Ref{Ptr{Ptr{t8_element}}}() + pneighbor_leaves_ref = Ref{Ptr{Ptr{t8_element}}}() pneigh_scheme_ref = Ref{Ptr{t8_eclass_scheme}}() dual_faces_ref = Ref{Ptr{Cint}}() @@ -704,7 +704,7 @@ function count_interfaces(mesh::T8codeMesh) forest_is_balanced = Cint(1) t8_forest_leaf_face_neighbors(mesh.forest, itree, element, - pneighbor_leafs_ref, iface, dual_faces_ref, + pneighbor_leaves_ref, iface, dual_faces_ref, num_neighbors_ref, pelement_indices_ref, pneigh_scheme_ref, forest_is_balanced) @@ -713,13 +713,13 @@ function count_interfaces(mesh::T8codeMesh) dual_faces = unsafe_wrap(Array, dual_faces_ref[], num_neighbors) neighbor_ielements = unsafe_wrap(Array, pelement_indices_ref[], num_neighbors) - neighbor_leafs = unsafe_wrap(Array, pneighbor_leafs_ref[], num_neighbors) + neighbor_leaves = unsafe_wrap(Array, pneighbor_leaves_ref[], num_neighbors) neighbor_scheme = pneigh_scheme_ref[] if num_neighbors == 0 local_num_boundary += 1 else - neighbor_level = t8_element_level(neighbor_scheme, neighbor_leafs[1]) + neighbor_level = t8_element_level(neighbor_scheme, neighbor_leaves[1]) if all(neighbor_ielements .< num_local_elements) # Conforming interface: The second condition ensures we @@ -745,7 +745,7 @@ function count_interfaces(mesh::T8codeMesh) neighbor_linear_id = neighbor_global_ghost_itree * max_tree_num_elements + t8_element_get_linear_id(neighbor_scheme, - neighbor_leafs[1], + neighbor_leaves[1], max_level) global_mortar_id = 2 * ndims(mesh) * neighbor_linear_id + dual_faces[1] @@ -759,7 +759,7 @@ function count_interfaces(mesh::T8codeMesh) end t8_free(dual_faces_ref[]) - t8_free(pneighbor_leafs_ref[]) + t8_free(pneighbor_leaves_ref[]) t8_free(pelement_indices_ref[]) end # for @@ -875,7 +875,7 @@ function fill_mesh_info!(mesh::T8codeMesh, interfaces, mortars, boundaries, end pelement_indices_ref = Ref{Ptr{t8_locidx_t}}() - pneighbor_leafs_ref = Ref{Ptr{Ptr{t8_element}}}() + pneighbor_leaves_ref = Ref{Ptr{Ptr{t8_element}}}() pneigh_scheme_ref = Ref{Ptr{t8_eclass_scheme}}() dual_faces_ref = Ref{Ptr{Cint}}() @@ -885,7 +885,7 @@ function fill_mesh_info!(mesh::T8codeMesh, interfaces, mortars, boundaries, # Query neighbor information from t8code. t8_forest_leaf_face_neighbors(mesh.forest, itree, element, - pneighbor_leafs_ref, iface, dual_faces_ref, + pneighbor_leaves_ref, iface, dual_faces_ref, num_neighbors_ref, pelement_indices_ref, pneigh_scheme_ref, forest_is_balanced) @@ -894,7 +894,7 @@ function fill_mesh_info!(mesh::T8codeMesh, interfaces, mortars, boundaries, dual_faces = unsafe_wrap(Array, dual_faces_ref[], num_neighbors) neighbor_ielements = unsafe_wrap(Array, pelement_indices_ref[], num_neighbors) - neighbor_leafs = unsafe_wrap(Array, pneighbor_leafs_ref[], num_neighbors) + neighbor_leaves = unsafe_wrap(Array, pneighbor_leaves_ref[], num_neighbors) neighbor_scheme = pneigh_scheme_ref[] # Now we check for the different cases. The nested if-structure is as follows: @@ -913,7 +913,7 @@ function fill_mesh_info!(mesh::T8codeMesh, interfaces, mortars, boundaries, # else: // `local mortar from smaller elements point of view` # // We only count local mortars once. # - # else: // It must be either a MPI interface or a MPI mortar. + # else: // It must be either a MPI interface or a MPI mortar. # # if `MPI interface`: # @@ -938,7 +938,7 @@ function fill_mesh_info!(mesh::T8codeMesh, interfaces, mortars, boundaries, # Interface or mortar. else - neighbor_level = t8_element_level(neighbor_scheme, neighbor_leafs[1]) + neighbor_level = t8_element_level(neighbor_scheme, neighbor_leaves[1]) # Local interface or mortar. if all(neighbor_ielements .< num_local_elements) @@ -985,7 +985,7 @@ function fill_mesh_info!(mesh::T8codeMesh, interfaces, mortars, boundaries, neighbor_linear_id = neighbor_global_ghost_itree * max_tree_num_elements + t8_element_get_linear_id(neighbor_scheme, - neighbor_leafs[1], + neighbor_leaves[1], max_level) if current_linear_id < neighbor_linear_id @@ -1029,7 +1029,7 @@ function fill_mesh_info!(mesh::T8codeMesh, interfaces, mortars, boundaries, num_local_elements) local_neighbor_ids = [neighbor_ids[i] for i in local_neighbor_positions] - local_neighbor_positions = [map_iface_to_ichild_to_position[dual_faces[1] + 1][t8_element_child_id(neighbor_scheme, neighbor_leafs[i]) + 1] + local_neighbor_positions = [map_iface_to_ichild_to_position[dual_faces[1] + 1][t8_element_child_id(neighbor_scheme, neighbor_leaves[i]) + 1] for i in local_neighbor_positions] # Last entry is the large element. @@ -1059,7 +1059,7 @@ function fill_mesh_info!(mesh::T8codeMesh, interfaces, mortars, boundaries, neighbor_linear_id = neighbor_global_ghost_itree * max_tree_num_elements + t8_element_get_linear_id(neighbor_scheme, - neighbor_leafs[1], + neighbor_leaves[1], max_level) global_mortar_id = 2 * ndims(mesh) * neighbor_linear_id + dual_faces[1] @@ -1100,7 +1100,7 @@ function fill_mesh_info!(mesh::T8codeMesh, interfaces, mortars, boundaries, end t8_free(dual_faces_ref[]) - t8_free(pneighbor_leafs_ref[]) + t8_free(pneighbor_leaves_ref[]) t8_free(pelement_indices_ref[]) end # for iface diff --git a/test/test_parabolic_2d.jl b/test/test_parabolic_2d.jl index f7185a1a904..9f1382caa62 100644 --- a/test/test_parabolic_2d.jl +++ b/test/test_parabolic_2d.jl @@ -218,9 +218,9 @@ end "elixir_advection_diffusion.jl"), tspan=(0.0, 0.0)) LLID = Trixi.local_leaf_cells(mesh.tree) - num_leafs = length(LLID) - @assert num_leafs % 8 == 0 - Trixi.refine!(mesh.tree, LLID[1:Int(num_leafs / 8)]) + num_leaves = length(LLID) + @assert num_leaves % 8 == 0 + Trixi.refine!(mesh.tree, LLID[1:Int(num_leaves / 8)]) tspan = (0.0, 1.5) semi = SemidiscretizationHyperbolicParabolic(mesh, (equations, equations_parabolic), @@ -414,9 +414,9 @@ end "elixir_navierstokes_convergence.jl"), tspan=(0.0, 0.0), initial_refinement_level=3) LLID = Trixi.local_leaf_cells(mesh.tree) - num_leafs = length(LLID) - @assert num_leafs % 4 == 0 - Trixi.refine!(mesh.tree, LLID[1:Int(num_leafs / 4)]) + num_leaves = length(LLID) + @assert num_leaves % 4 == 0 + Trixi.refine!(mesh.tree, LLID[1:Int(num_leaves / 4)]) tspan = (0.0, 0.5) semi = SemidiscretizationHyperbolicParabolic(mesh, (equations, equations_parabolic), initial_condition, solver; diff --git a/test/test_parabolic_3d.jl b/test/test_parabolic_3d.jl index 6fbfb8259d4..1eaa9f51a56 100644 --- a/test/test_parabolic_3d.jl +++ b/test/test_parabolic_3d.jl @@ -252,9 +252,9 @@ end "elixir_navierstokes_convergence.jl"), tspan=(0.0, 0.0)) LLID = Trixi.local_leaf_cells(mesh.tree) - num_leafs = length(LLID) - @assert num_leafs % 16 == 0 - Trixi.refine!(mesh.tree, LLID[1:Int(num_leafs / 16)]) + num_leaves = length(LLID) + @assert num_leaves % 16 == 0 + Trixi.refine!(mesh.tree, LLID[1:Int(num_leaves / 16)]) tspan = (0.0, 0.25) semi = SemidiscretizationHyperbolicParabolic(mesh, (equations, equations_parabolic), initial_condition, solver; @@ -325,9 +325,9 @@ end "elixir_navierstokes_taylor_green_vortex.jl"), tspan=(0.0, 0.0)) LLID = Trixi.local_leaf_cells(mesh.tree) - num_leafs = length(LLID) - @assert num_leafs % 32 == 0 - Trixi.refine!(mesh.tree, LLID[1:Int(num_leafs / 32)]) + num_leaves = length(LLID) + @assert num_leaves % 32 == 0 + Trixi.refine!(mesh.tree, LLID[1:Int(num_leaves / 32)]) tspan = (0.0, 0.1) semi = SemidiscretizationHyperbolicParabolic(mesh, (equations, equations_parabolic), initial_condition, solver) @@ -429,8 +429,8 @@ end "elixir_advection_diffusion_amr.jl"), l2=[0.000355780485397024], linf=[0.0010810770271614256]) - # Ensure that we do not have excessive memory allocations - # (e.g., from type instabilities) + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) let t = sol.t[end] u_ode = sol.u[end] @@ -444,8 +444,8 @@ end "elixir_advection_diffusion_nonperiodic.jl"), l2=[0.0009808996243280868], linf=[0.01732621559135459]) - # Ensure that we do not have excessive memory allocations - # (e.g., from type instabilities) + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) let t = sol.t[end] u_ode = sol.u[end] @@ -472,8 +472,8 @@ end 0.12129218723807476, 0.8433893297612087, ]) - # Ensure that we do not have excessive memory allocations - # (e.g., from type instabilities) + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) let t = sol.t[end] u_ode = sol.u[end] @@ -495,8 +495,8 @@ end 0.6782397526873181, 0.17663702154066238, 0.17663702154066266, 0.17663702154066238, 1.7327849844825238, ]) - # Ensure that we do not have excessive memory allocations - # (e.g., from type instabilities) + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) let t = sol.t[end] u_ode = sol.u[end] From 7f7f058d0721bc1634e9fee69a8d136b9ea57bc7 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 2 Feb 2024 08:47:41 +0100 Subject: [PATCH 16/63] Bump crate-ci/typos from 1.16.26 to 1.18.0 (#1826) Bumps [crate-ci/typos](https://github.com/crate-ci/typos) from 1.16.26 to 1.18.0. - [Release notes](https://github.com/crate-ci/typos/releases) - [Changelog](https://github.com/crate-ci/typos/blob/master/CHANGELOG.md) - [Commits](https://github.com/crate-ci/typos/compare/v1.16.26...v1.18.0) --- updated-dependencies: - dependency-name: crate-ci/typos dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Hendrik Ranocha --- .github/workflows/SpellCheck.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/SpellCheck.yml b/.github/workflows/SpellCheck.yml index a780e975155..b242b6e811e 100644 --- a/.github/workflows/SpellCheck.yml +++ b/.github/workflows/SpellCheck.yml @@ -10,4 +10,4 @@ jobs: - name: Checkout Actions Repository uses: actions/checkout@v4 - name: Check spelling - uses: crate-ci/typos@v1.16.26 + uses: crate-ci/typos@v1.18.0 From fa129aa3be558df6246b7339ce2bc966d76bcc6a Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 2 Feb 2024 14:47:13 +0100 Subject: [PATCH 17/63] Bump codecov/codecov-action from 3 to 4 (#1827) Bumps [codecov/codecov-action](https://github.com/codecov/codecov-action) from 3 to 4. - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/v3...v4) --- updated-dependencies: - dependency-name: codecov/codecov-action dependency-type: direct:production update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index f287cc5feb2..2e388366fc8 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -129,7 +129,7 @@ jobs: - uses: julia-actions/julia-processcoverage@v1 with: directories: src,examples,ext - - uses: codecov/codecov-action@v3 + - uses: codecov/codecov-action@v4 with: file: ./lcov.info flags: unittests From ea61e26ff330e720b011a85a2f4b9040e54da870 Mon Sep 17 00:00:00 2001 From: Benjamin Bolm <74359358+bennibolm@users.noreply.github.com> Date: Mon, 5 Feb 2024 11:50:25 +0100 Subject: [PATCH 18/63] Add section about false sharing problems to documentation (#1819) * Add section to docs about false sharing * Fix typos * Fix typo * Implement suggestions --- docs/src/performance.md | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/docs/src/performance.md b/docs/src/performance.md index df66f451b79..82d7f501f63 100644 --- a/docs/src/performance.md +++ b/docs/src/performance.md @@ -267,3 +267,14 @@ requires. It can thus be seen as a proxy for "energy used" and, as an extension, timing result, you need to set the analysis interval such that the `AnalysisCallback` is invoked at least once during the course of the simulation and discard the first PID value. + +## Performance issues with multi-threaded reductions +[False sharing](https://en.wikipedia.org/wiki/False_sharing) is a known performance issue +for systems with distributed caches. It also occurred for the implementation of a thread +parallel bounds checking routine for the subcell IDP limiting +in [PR #1736](https://github.com/trixi-framework/Trixi.jl/pull/1736). +After some [testing and discussion](https://github.com/trixi-framework/Trixi.jl/pull/1736#discussion_r1423881895), +it turned out that initializing a vector of length `n * Threads.nthreads()` and only using every +n-th entry instead of a vector of length `Threads.nthreads()` fixes the problem. +Since there are no processors with caches over 128B, we use `n = 128B / size(uEltype)`. +Now, the bounds checking routine of the IDP limiting scales as hoped. From 14151e636ef654cb5421b3a7e498a9d76ed46a64 Mon Sep 17 00:00:00 2001 From: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com> Date: Mon, 5 Feb 2024 12:49:51 +0100 Subject: [PATCH 19/63] Add entry for gmsh tutorial in introduction (#1829) * add entry for gmsh tutorial in introduction * Update docs/literate/src/files/index.jl --------- Co-authored-by: Daniel Doehring Co-authored-by: Daniel Doehring --- docs/literate/src/files/index.jl | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/docs/literate/src/files/index.jl b/docs/literate/src/files/index.jl index e259d25fb2f..26637e5b24b 100644 --- a/docs/literate/src/files/index.jl +++ b/docs/literate/src/files/index.jl @@ -108,20 +108,26 @@ # software in the Trixi.jl ecosystem, and then run a simulation using Trixi.jl on said mesh. # In the end, the tutorial briefly explains how to simulate an example using AMR via `P4estMesh`. -# ### [15 Explicit time stepping](@ref time_stepping) +# ### [15 P4est mesh from gmsh](@ref p4est_from_gmsh) +#- +# This tutorial describes how to obtain a [`P4estMesh`](@ref) from an existing mesh generated +# by [`gmsh`](https://gmsh.info/) or any other meshing software that can export to the Abaqus +# input `.inp` format. The tutorial demonstrates how edges/faces can be associated with boundary conditions based on the physical nodesets. + +# ### [16 Explicit time stepping](@ref time_stepping) #- # This tutorial is about time integration using [OrdinaryDiffEq.jl](https://github.com/SciML/OrdinaryDiffEq.jl). # It explains how to use their algorithms and presents two types of time step choices - with error-based # and CFL-based adaptive step size control. -# ### [16 Differentiable programming](@ref differentiable_programming) +# ### [17 Differentiable programming](@ref differentiable_programming) #- # This part deals with some basic differentiable programming topics. For example, a Jacobian, its # eigenvalues and a curve of total energy (through the simulation) are calculated and plotted for # a few semidiscretizations. Moreover, we calculate an example for propagating errors with Measurement.jl # at the end. -# ### [17 Custom semidiscretization](@ref custom_semidiscretization) +# ### [18 Custom semidiscretization](@ref custom_semidiscretization) #- # This tutorial describes the [semidiscretiations](@ref overview-semidiscretizations) of Trixi.jl # and explains how to extend them for custom tasks. From 5fec7f42121be7d01d8645fc91fe0da8567f3946 Mon Sep 17 00:00:00 2001 From: ArseniyKholod <119304909+ArseniyKholod@users.noreply.github.com> Date: Tue, 6 Feb 2024 20:52:50 +0100 Subject: [PATCH 20/63] Getting started with trixi (#1343) * 0th tutorial v1 * 0th tutorial v2 * 0th tutorial v3 (topic for developers) * 0th tutorial v4 * 0th tutorial v5 * 0th tutorial v6 * 0th tutorial v6.1 * 0th tutorial v6.2 * 0th tutorial v7 (new example) * 0th tutorial v8 * 0th tutorial v8.1 * 0th tutorial v9 New structure + new usage example * 0th tutorial v9.1 * 0th tutorial v9.2 * Revert "0th tutorial v9.2" This reverts commit e2da5c24c71ec5ebb86ead4da9e6dc33f8b2cf7f. * 0th tutorial v9.3 (test) * Revert "0th tutorial v9.3 (test)" This reverts commit 05d3d1c22729fc65f6a85bc224e0376bf7cc79ac. * 0th tutorial v9.3 (test) * 0th tutorial v9.3 (test checks without diff. prog.) * 0th tutorial v9.3 (test new diff. prog.) * 0th tutorial v9.3 (test new diff. prog. v2) * 0th tutorial v9.3 (test update of packages) * 0th tutorial v9.3 (test update of packages v2) * 0th tutorial v9.3 (downgrade Measurements.jl) * 0th tutorial v9.4 * 0th tutorial v9.5 * 0th tutorial review * 0th tutorial review 2 * 0th tutorial v9.6 * delete test files * Revert "rename into getting_started.jl" This reverts commit 6605ece69240d8bc850c6ef0b14b94beaac5eee6. * Update docs/make.jl Co-authored-by: Michael Schlottke-Lakemper * Update Project.toml Co-authored-by: Michael Schlottke-Lakemper * Update Project.toml Co-authored-by: Michael Schlottke-Lakemper * Update docs/make.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/getting_started_with_Trixi.jl Co-authored-by: Michael Schlottke-Lakemper * rename into getting_started.jl * Update docs/literate/src/files/getting_started_with_Trixi.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/getting_started_with_Trixi.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/getting_started_with_Trixi.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/getting_started_with_Trixi.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/getting_started_with_Trixi.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/getting_started_with_Trixi.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/getting_started_with_Trixi.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/getting_started_with_Trixi.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/getting_started_with_Trixi.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/getting_started_with_Trixi.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/getting_started_with_Trixi.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/getting_started_with_Trixi.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/getting_started_with_Trixi.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/getting_started_with_Trixi.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/getting_started_with_Trixi.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/getting_started_with_Trixi.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/getting_started_with_Trixi.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/getting_started_with_Trixi.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/getting_started_with_Trixi.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/getting_started_with_Trixi.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/getting_started_with_Trixi.jl Co-authored-by: Michael Schlottke-Lakemper * correction of spelling errors * cleaning out directory * Correction according to the comments above * Trixi installation for Linux * Update getting_started.jl * cross-referencing correction * spelling * Update .gitignore Co-authored-by: Michael Schlottke-Lakemper * Update docs/make.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/getting_started.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/getting_started.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/getting_started.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/getting_started.jl Co-authored-by: Michael Schlottke-Lakemper * Update .gitignore * Update docs/literate/src/files/getting_started.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/getting_started.jl Co-authored-by: Michael 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Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com> * Update docs/literate/src/files/first_steps/changing_trixi.jl Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com> * Update docs/literate/src/files/first_steps/changing_trixi.jl Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com> * Update docs/literate/src/files/first_steps/changing_trixi.jl Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com> * Update docs/literate/src/files/first_steps/changing_trixi.jl Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com> * Update docs/literate/src/files/first_steps/changing_trixi.jl Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com> * spelling * delete julia, tabs * add juliaup * add intro * rm * Apply suggestions from code review Co-authored-by: Daniel Doehring * Apply suggestions from code review Co-authored-by: Daniel Doehring * Update docs/literate/src/files/first_steps/getting_started.jl * Update docs/literate/src/files/first_steps/changing_trixi.jl Co-authored-by: Andrew Winters * Update docs/literate/src/files/first_steps/changing_trixi.jl Co-authored-by: Andrew Winters * Update docs/literate/src/files/first_steps/create_first_setup.jl Co-authored-by: Andrew Winters * Update docs/literate/src/files/first_steps/create_first_setup.jl Co-authored-by: Andrew Winters * add save solution dt --------- Co-authored-by: Michael Schlottke-Lakemper Co-authored-by: Simon Candelaresi <10759273+SimonCan@users.noreply.github.com> Co-authored-by: Benedict <135045760+bgeihe@users.noreply.github.com> Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com> Co-authored-by: Daniel Doehring Co-authored-by: Andrew Winters --- .../src/files/first_steps/changing_trixi.jl | 77 +++++ .../files/first_steps/create_first_setup.jl | 268 ++++++++++++++++++ .../src/files/first_steps/getting_started.jl | 242 ++++++++++++++++ docs/literate/src/files/index.jl | 43 +-- docs/make.jl | 6 + 5 files changed, 618 insertions(+), 18 deletions(-) create mode 100644 docs/literate/src/files/first_steps/changing_trixi.jl create mode 100644 docs/literate/src/files/first_steps/create_first_setup.jl create mode 100644 docs/literate/src/files/first_steps/getting_started.jl diff --git a/docs/literate/src/files/first_steps/changing_trixi.jl b/docs/literate/src/files/first_steps/changing_trixi.jl new file mode 100644 index 00000000000..551377a6a71 --- /dev/null +++ b/docs/literate/src/files/first_steps/changing_trixi.jl @@ -0,0 +1,77 @@ +#src # Changing Trixi.jl itself + +# If you plan on editing Trixi.jl itself, you can download Trixi.jl locally and run it from +# the cloned directory. + + +# ## Cloning Trixi.jl + + +# ### Windows + +# If you are using Windows, you can clone Trixi.jl by using the GitHub Desktop tool: +# - If you do not have a GitHub account yet, create it on +# the [GitHub website](https://github.com/join). +# - Download and install [GitHub Desktop](https://desktop.github.com/) and then log in to +# your account. +# - Open GitHub Desktop, press `Ctrl+Shift+O`. +# - In the opened window, paste `trixi-framework/Trixi.jl` and choose the path to the folder where +# you want to save Trixi.jl. Then click `Clone` and Trixi.jl will be cloned to your computer. + +# Now you cloned Trixi.jl and only need to tell Julia to use the local clone as the package sources: +# - Open a terminal using `Win+r` and `cmd`. Navigate to the folder with the cloned Trixi.jl using `cd`. +# - Create a new directory `run`, enter it, and start Julia with the `--project=.` flag: +# ```shell +# mkdir run +# cd run +# julia --project=. +# ``` +# - Now run the following commands to install all relevant packages: +# ```julia +# using Pkg; Pkg.develop(PackageSpec(path="..")) # Tell Julia to use the local Trixi.jl clone +# Pkg.add(["OrdinaryDiffEq", "Plots"]) # Install additional packages +# ``` + +# Now you already installed Trixi.jl from your local clone. Note that if you installed Trixi.jl +# this way, you always have to start Julia with the `--project` flag set to your `run` directory, +# e.g., +# ```shell +# julia --project=. +# ``` +# if already inside the `run` directory. + + +# ### Linux + +# You can clone Trixi.jl to your computer by executing the following commands: +# ```shell +# git clone git@github.com:trixi-framework/Trixi.jl.git +# # If an error occurs, try the following: +# # git clone https://github.com/trixi-framework/Trixi.jl +# cd Trixi.jl +# mkdir run +# cd run +# julia --project=. -e 'using Pkg; Pkg.develop(PackageSpec(path=".."))' # Tell Julia to use the local Trixi.jl clone +# julia --project=. -e 'using Pkg; Pkg.add(["OrdinaryDiffEq", "Plots"])' # Install additional packages +# ``` +# Note that if you installed Trixi.jl this way, +# you always have to start Julia with the `--project` flag set to your `run` directory, e.g., +# ```shell +# julia --project=. +# ``` +# if already inside the `run` directory. + + +# ## Additional reading + +# To further delve into Trixi.jl, you may have a look at the following introductory tutorials. +# - [Introduction to DG methods](@ref scalar_linear_advection_1d) will teach you how to set up a +# simple way to approximate the solution of a hyperbolic partial differential equation. It will +# be especially useful to learn about the +# [Discontinuous Galerkin method](https://en.wikipedia.org/wiki/Discontinuous_Galerkin_method) +# and the way it is implemented in Trixi.jl. +# - [Adding a new scalar conservation law](@ref adding_new_scalar_equations) and +# [Adding a non-conservative equation](@ref adding_nonconservative_equation) +# describe how to add new physics models that are not yet included in Trixi.jl. +# - [Callbacks](@ref callbacks-id) gives an overview of how to regularly execute specific actions +# during a simulation, e.g., to store the solution or adapt the mesh. diff --git a/docs/literate/src/files/first_steps/create_first_setup.jl b/docs/literate/src/files/first_steps/create_first_setup.jl new file mode 100644 index 00000000000..906a6f93461 --- /dev/null +++ b/docs/literate/src/files/first_steps/create_first_setup.jl @@ -0,0 +1,268 @@ +#src # Create first setup + +# In this part of the introductory guide, we will create a first Trixi.jl setup as an extension of +# [`elixir_advection_basic.jl`](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/tree_2d_dgsem/elixir_advection_basic.jl). +# Since Trixi.jl has a common basic structure for the setups, you can create your own by extending +# and modifying the following example. + +# Let's consider the linear advection equation for a state ``u = u(x, y, t)`` on the two-dimensional spatial domain +# ``[-1, 1] \times [-1, 1]`` with a source term +# ```math +# \frac{\partial}{\partial t}u + \frac{\partial}{\partial x} (0.2 u) - \frac{\partial}{\partial y} (0.7 u) = - 2 e^{-t} +# \sin\bigl(2 \pi (x - t) \bigr) \sin\bigl(2 \pi (y - t) \bigr), +# ``` +# with the initial condition +# ```math +# u(x, y, 0) = \sin\bigl(\pi x \bigr) \sin\bigl(\pi y \bigr), +# ``` +# and periodic boundary conditions. + +# The first step is to create and open a file with the .jl extension. You can do this with your +# favorite text editor (if you do not have one, we recommend [VS Code](https://code.visualstudio.com/)). +# In this file you will create your setup. + +# To be able to use functionalities of Trixi.jl, you always need to load Trixi.jl itself +# and the [OrdinaryDiffEq.jl](https://github.com/SciML/OrdinaryDiffEq.jl) package. + +using Trixi +using OrdinaryDiffEq + +# The next thing to do is to choose an equation that is suitable for your problem. To see all the +# currently implemented equations, take a look at +# [`src/equations`](https://github.com/trixi-framework/Trixi.jl/tree/main/src/equations). +# If you are interested in adding a new physics model that has not yet been implemented in +# Trixi.jl, take a look at the tutorials +# [Adding a new scalar conservation law](@ref adding_new_scalar_equations) or +# [Adding a non-conservative equation](@ref adding_nonconservative_equation). + +# The linear scalar advection equation in two spatial dimensions +# ```math +# \frac{\partial}{\partial t}u + \frac{\partial}{\partial x} (a_1 u) + \frac{\partial}{\partial y} (a_2 u) = 0 +# ``` +# is already implemented in Trixi.jl as +# [`LinearScalarAdvectionEquation2D`](@ref), for which we need to define a two-dimensional parameter +# `advection_velocity` describing the parameters ``a_1`` and ``a_2``. Appropriate for our problem is `(0.2, -0.7)`. + +advection_velocity = (0.2, -0.7) +equations = LinearScalarAdvectionEquation2D(advection_velocity) + +# To solve our problem numerically using Trixi.jl, we have to discretize the spatial +# domain, for which we set up a mesh. One of the most used meshes in Trixi.jl is the +# [`TreeMesh`](@ref). The spatial domain used is ``[-1, 1] \times [-1, 1]``. We set an initial number +# of elements in the mesh using `initial_refinement_level`, which describes the initial number of +# hierarchical refinements. In this simple case, the total number of elements is `2^initial_refinement_level` +# throughout the simulation. The variable `n_cells_max` is used to limit the number of elements in the mesh, +# which cannot be exceeded when using [adaptive mesh refinement](@ref Adaptive-mesh-refinement). + +# All minimum and all maximum coordinates must be combined into `Tuples`. + +coordinates_min = (-1.0, -1.0) +coordinates_max = ( 1.0, 1.0) +mesh = TreeMesh(coordinates_min, coordinates_max, + initial_refinement_level = 4, + n_cells_max = 30_000) + +# To approximate the solution of the defined model, we create a [`DGSEM`](@ref) solver. +# The solution in each of the recently defined mesh elements will be approximated by a polynomial +# of degree `polydeg`. For more information about discontinuous Galerkin methods, +# check out the [Introduction to DG methods](@ref scalar_linear_advection_1d) tutorial. + +solver = DGSEM(polydeg=3) + +# Now we need to define an initial condition for our problem. All the already implemented +# initial conditions for [`LinearScalarAdvectionEquation2D`](@ref) can be found in +# [`src/equations/linear_scalar_advection_2d.jl`](https://github.com/trixi-framework/Trixi.jl/blob/main/src/equations/linear_scalar_advection_2d.jl). +# If you want to use, for example, a Gaussian pulse, it can be used as follows: +# ```julia +# initial_conditions = initial_condition_gauss +# ``` +# But to show you how an arbitrary initial condition can be implemented in a way suitable for +# Trixi.jl, we define our own initial conditions. +# ```math +# u(x, y, 0) = \sin\bigl(\pi x \bigr) \sin\bigl(\pi y \bigr). +# ``` +# The initial conditions function must take spatial coordinates, time and equation as arguments +# and returns an initial condition as a statically sized vector `SVector`. Following the same structure, you +# can define your own initial conditions. The time variable `t` can be unused in the initial +# condition, but might also be used to describe an analytical solution if known. If you use the +# initial condition as analytical solution, you can analyze your numerical solution by computing +# the error, see also the +# [section about analyzing the solution](https://trixi-framework.github.io/Trixi.jl/stable/callbacks/#Analyzing-the-numerical-solution). + +function initial_condition_sinpi(x, t, equations::LinearScalarAdvectionEquation2D) + scalar = sinpi(x[1]) * sinpi(x[2]) + return SVector(scalar) +end +initial_condition = initial_condition_sinpi + +# The next step is to define a function of the source term corresponding to our problem. +# ```math +# f(u, x, y, t) = - 2 e^{-t} \sin\bigl(2 \pi (x - t) \bigr) \sin\bigl(2 \pi (y - t) \bigr) +# ``` +# This function must take the state variable, the spatial coordinates, the time and the +# equation itself as arguments and returns the source term as a static vector `SVector`. + +function source_term_exp_sinpi(u, x, t, equations::LinearScalarAdvectionEquation2D) + scalar = - 2 * exp(-t) * sinpi(2*(x[1] - t)) * sinpi(2*(x[2] - t)) + return SVector(scalar) +end + +# Now we collect all the information that is necessary to define a spatial discretization, +# which leaves us with an ODE problem in time with a span from 0.0 to 1.0. +# This approach is commonly referred to as the method of lines. + +semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver; + source_terms = source_term_exp_sinpi) +tspan = (0.0, 1.0) +ode = semidiscretize(semi, tspan); + +# At this point, our problem is defined. We will use the `solve` function defined in +# [OrdinaryDiffEq.jl](https://github.com/SciML/OrdinaryDiffEq.jl) to get the solution. +# OrdinaryDiffEq.jl gives us the ability to customize the solver +# using callbacks without actually modifying it. Trixi.jl already has some implemented +# [Callbacks](@ref callbacks-id). The most widely used callbacks in Trixi.jl are +# [step control callbacks](https://docs.sciml.ai/DiffEqCallbacks/stable/step_control/) that are +# activated at the end of each time step to perform some actions, e.g. to print statistics. +# We will show you how to use some of the common callbacks. + +# To print a summary of the simulation setup at the beginning +# and to reset timers we use the [`SummaryCallback`](@ref). +# When the returned callback is executed directly, the current timer values are shown. + +summary_callback = SummaryCallback() + +# We also want to analyze the current state of the solution in regular intervals. +# The [`AnalysisCallback`](@ref) outputs some useful statistical information during the solving process +# every `interval` time steps. + +analysis_callback = AnalysisCallback(semi, interval = 5) + +# It is also possible to control the time step size using the [`StepsizeCallback`](@ref) if the time +# integration method isn't adaptive itself. To get more details, look at +# [CFL based step size control](@ref CFL-based-step-size-control). + +stepsize_callback = StepsizeCallback(cfl = 1.6) + +# To save the current solution in regular intervals we use the [`SaveSolutionCallback`](@ref). +# We would like to save the initial and final solutions as well. The data +# will be saved as HDF5 files located in the `out` folder. Afterwards it is possible to visualize +# a solution from saved files using Trixi2Vtk.jl and ParaView, which is described below in the +# section [Visualize the solution](@ref Visualize-the-solution). + +save_solution = SaveSolutionCallback(interval = 5, + save_initial_solution = true, + save_final_solution = true) + +# Alternatively, we have the option to print solution files at fixed time intervals. +# ```julua +# save_solution = SaveSolutionCallback(dt = 0.1, +# save_initial_solution = true, +# save_final_solution = true) +# ``` + +# Another useful callback is the [`SaveRestartCallback`](@ref). It saves information for restarting +# in regular intervals. We are interested in saving a restart file for the final solution as +# well. To perform a restart, you need to configure the restart setup in a special way, which is +# described in the section [Restart simulation](@ref restart). + +save_restart = SaveRestartCallback(interval = 100, save_final_restart = true) + +# Create a `CallbackSet` to collect all callbacks so that they can be passed to the `solve` +# function. + +callbacks = CallbackSet(summary_callback, analysis_callback, stepsize_callback, save_solution, + save_restart) + +# The last step is to choose the time integration method. OrdinaryDiffEq.jl defines a wide range of +# [ODE solvers](https://docs.sciml.ai/DiffEqDocs/latest/solvers/ode_solve/), e.g. +# `CarpenterKennedy2N54(williamson_condition = false)`. We will pass the ODE +# problem, the ODE solver and the callbacks to the `solve` function. Also, to use +# `StepsizeCallback`, we must explicitly specify the initial trial time step `dt`, the selected +# value is not important, because it will be overwritten by the `StepsizeCallback`. And there is no +# need to save every step of the solution, we are only interested in the final result. + +sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false), dt = 1.0, + save_everystep = false, callback = callbacks); + +# Finally, we print the timer summary. + +summary_callback() + +# Now you can plot the solution as shown below, analyze it and improve the stability, accuracy or +# efficiency of your setup. + + +# ## Visualize the solution + +# In the previous part of the tutorial, we calculated the final solution of the given problem, now we want +# to visualize it. A more detailed explanation of visualization methods can be found in the section +# [Visualization](@ref visualization). + + +# ### Using Plots.jl + +# The first option is to use the [Plots.jl](https://github.com/JuliaPlots/Plots.jl) package +# directly after calculations, when the solution is saved in the `sol` variable. We load the +# package and use the `plot` function. + +using Plots +plot(sol) + +# To show the mesh on the plot, we need to extract the visualization data from the solution as +# a [`PlotData2D`](@ref) object. Mesh extraction is possible using the [`getmesh`](@ref) function. +# Plots.jl has the `plot!` function that allows you to modify an already built graph. + +pd = PlotData2D(sol) +plot!(getmesh(pd)) + + +# ### Using Trixi2Vtk.jl + +# Another way to visualize a solution is to extract it from a saved HDF5 file. After we used the +# `solve` function with [`SaveSolutionCallback`](@ref) there is a file with the final solution. +# It is located in the `out` folder and is named as follows: `solution_index.h5`. The `index` +# is the final time step of the solution that is padded to 6 digits with zeros from the beginning. +# With [Trixi2Vtk](@ref) you can convert the HDF5 output file generated by Trixi.jl into a VTK file. +# This can be used in visualization tools such as [ParaView](https://www.paraview.org) or +# [VisIt](https://visit.llnl.gov) to plot the solution. The important thing is that currently +# Trixi2Vtk.jl supports conversion only for solutions in 2D and 3D spatial domains. + +# If you haven't added Trixi2Vtk.jl to your project yet, you can add it as follows. +# ```julia +# import Pkg +# Pkg.add(["Trixi2Vtk"]) +# ``` +# Now we load the Trixi2Vtk.jl package and convert the file `out/solution_000018.h5` with +# the final solution using the [`trixi2vtk`](@ref) function saving the resulting file in the +# `out` folder. + +using Trixi2Vtk +trixi2vtk(joinpath("out", "solution_000018.h5"), output_directory="out") + +# Now two files `solution_000018.vtu` and `solution_000018_celldata.vtu` have been generated in the +# `out` folder. The first one contains all the information for visualizing the solution, the +# second one contains all the cell-based or discretization-based information. + +# Now let's visualize the solution from the generated files in ParaView. Follow this short +# instruction to get the visualization. +# - Download, install and open [ParaView](https://www.paraview.org/download/). +# - Press `Ctrl+O` and select the generated files `solution_000018.vtu` and +# `solution_000018_celldata.vtu` from the `out` folder. +# - In the upper-left corner in the Pipeline Browser window, left-click on the eye-icon near +# `solution_000018.vtu`. +# - In the lower-left corner in the Properties window, change the Coloring from Solid Color to +# scalar. This already generates the visualization of the final solution. +# - Now let's add the mesh to the visualization. In the upper-left corner in the +# Pipeline Browser window, left-click on the eye-icon near `solution_000018_celldata.vtu`. +# - In the lower-left corner in the Properties window, change the Representation from Surface +# to Wireframe. Then a white grid should appear on the visualization. +# Now, if you followed the instructions exactly, you should get a similar image as shown in the +# section [Using Plots.jl](@ref Using-Plots.jl): + +# ![paraview_trixi2vtk_example](https://github.com/trixi-framework/Trixi.jl/assets/119304909/0c29139b-6c5d-4d5c-86e1-f4ebc95aca7e) + +# After completing this tutorial you are able to set up your own simulations with +# Trixi.jl. If you have an interest in contributing to Trixi.jl as a developer, refer to the third +# part of the introduction titled [Changing Trixi.jl itself](@ref changing_trixi). + +Sys.rm("out"; recursive=true, force=true) #hide #md \ No newline at end of file diff --git a/docs/literate/src/files/first_steps/getting_started.jl b/docs/literate/src/files/first_steps/getting_started.jl new file mode 100644 index 00000000000..2bfaf33b5fc --- /dev/null +++ b/docs/literate/src/files/first_steps/getting_started.jl @@ -0,0 +1,242 @@ +#src # Getting started + +# Trixi.jl is a numerical simulation framework for conservation laws and +# is written in the [Julia programming language](https://julialang.org/). +# This tutorial is intended for beginners in Julia and Trixi.jl. +# After reading it, you will know how to install Julia and Trixi.jl on your computer, +# and you will be able to download setup files from our GitHub repository, modify them, +# and run simulations. + +# The contents of this tutorial: +# - [Julia installation](@ref Julia-installation) +# - [Trixi.jl installation](@ref Trixi.jl-installation) +# - [Running a simulation](@ref Running-a-simulation) +# - [Getting an existing setup file](@ref Getting-an-existing-setup-file) +# - [Modifying an existing setup](@ref Modifying-an-existing-setup) + + +# ## Julia installation + +# Trixi.jl is compatible with the latest stable release of Julia. Additional details regarding Julia +# support can be found in the [`README.md`](https://github.com/trixi-framework/Trixi.jl#installation) +# file. The current default Julia installation is managed through `juliaup`. You may follow our +# concise installation guidelines for Windows, Linux, and MacOS provided below. In the event of any +# issues during the installation process, please consult the official +# [Julia installation instruction](https://julialang.org/downloads/). + + +# ### Windows + +# - Open a terminal by pressing `Win+r` and entering `cmd` in the opened window. +# - To install Julia, execute the following command in the terminal: +# ```shell +# winget install julia -s msstore +# ``` +# - Verify the successful installation of Julia by executing the following command in the terminal: +# ```shell +# julia +# ``` +# To exit Julia, execute `exit()` or press `Ctrl+d`. + + +# ### Linux and MacOS + +# - To install Julia, run the following command in a terminal: +# ```shell +# curl -fsSL https://install.julialang.org | sh +# ``` +# Follow the instructions displayed in the terminal during the installation process. +# - If an error occurs during the execution of the previous command, you may need to install +# `curl`. On Ubuntu-type systems, you can use the following command: +# ```shell +# sudo apt install curl +# ``` +# After installing `curl`, repeat the first step once more to proceed with Julia installation. +# - Verify the successful installation of Julia by executing the following command in the terminal: +# ```shell +# julia +# ``` +# To exit Julia, execute `exit()` or press `Ctrl+d`. + + +# ## Trixi.jl installation + +# Trixi.jl and its related tools are registered Julia packages, thus their installation +# happens inside Julia. +# For a smooth workflow experience with Trixi.jl, you need to install +# [Trixi.jl](https://github.com/trixi-framework/Trixi.jl), +# [OrdinaryDiffEq.jl](https://github.com/SciML/OrdinaryDiffEq.jl), and +# [Plots.jl](https://github.com/JuliaPlots/Plots.jl). + +# - Open a terminal and start Julia. +# - Execute following commands: +# ```julia +# import Pkg +# Pkg.add(["OrdinaryDiffEq", "Plots", "Trixi"]) +# ``` + +# Now you have installed all these +# packages. [OrdinaryDiffEq.jl](https://github.com/SciML/OrdinaryDiffEq.jl) provides time +# integration schemes used by Trixi.jl and [Plots.jl](https://github.com/JuliaPlots/Plots.jl) +# can be used to directly visualize Trixi.jl results from the Julia REPL. + + +# ## Usage + + +# ### Running a simulation + +# To get you started, Trixi.jl has a large set +# of [example setups](https://github.com/trixi-framework/Trixi.jl/tree/main/examples), that can be +# taken as a basis for your future investigations. In Trixi.jl, we call these setup files +# "elixirs", since they contain Julia code that takes parts of Trixi.jl and combines them into +# something new. + +# Any of the examples can be executed using the [`trixi_include`](@ref) +# function. `trixi_include(...)` expects +# a single string argument with a path to a file containing Julia code. +# For convenience, the [`examples_dir`](@ref) function returns a path to the +# [`examples`](https://github.com/trixi-framework/Trixi.jl/tree/main/examples) +# folder, which has been locally downloaded while installing Trixi.jl. +# `joinpath(...)` can be used to join path components into a full path. + +# Let's execute a short two-dimensional problem setup. It approximates the solution of +# the compressible Euler equations in 2D for an ideal gas ([`CompressibleEulerEquations2D`](@ref)) +# with a weak blast wave as the initial condition. + +# Start Julia in a terminal and execute the following code: + +# ```julia +# using Trixi, OrdinaryDiffEq +# trixi_include(joinpath(examples_dir(), "tree_2d_dgsem", "elixir_euler_ec.jl")) +# ``` +using Trixi, OrdinaryDiffEq #hide #md +trixi_include(@__MODULE__,joinpath(examples_dir(), "tree_2d_dgsem", "elixir_euler_ec.jl")) #hide #md + +# To analyze the result of the computation, we can use the Plots.jl package and the function +# `plot(...)`, which creates a graphical representation of the solution. `sol` is a variable +# defined in the executed example and it contains the solution at the final moment of the simulation. + +using Plots +plot(sol) + +# To obtain a list of all Trixi.jl elixirs execute +# [`get_examples`](@ref). It returns the paths to all example setups. + +get_examples() + +# Editing an existing elixir is the best way to start your first own investigation using Trixi.jl. + + +# ### Getting an existing setup file + +# To edit an existing elixir, you first have to find a suitable one and then copy it to a local +# folder. Let's have a look at how to download the `elixir_euler_ec.jl` elixir used in the previous +# section from the [Trixi.jl GitHub repository](https://github.com/trixi-framework/Trixi.jl). + +# - All examples are located inside +# the [`examples`](https://github.com/trixi-framework/Trixi.jl/tree/main/examples) folder. +# - Navigate to the +# file [`elixir_euler_ec.jl`](https://github.com/trixi-framework/Trixi.jl/blob/main/examples/tree_2d_dgsem/elixir_euler_ec.jl). +# - Right-click the `Raw` button on the right side of the webpage and choose `Save as...` +# (or `Save Link As...`). +# - Choose a folder and save the file. + + +# ### Modifying an existing setup + +# As an example, we will change the initial condition for calculations that occur in +# `elixir_euler_ec.jl`. In this example we consider the compressible Euler equations in two spatial +# dimensions, +# ```math +# \frac{\partial}{\partial t} +# \begin{pmatrix} +# \rho \\ \rho v_1 \\ \rho v_2 \\ \rho e +# \end{pmatrix} +# + +# \frac{\partial}{\partial x} +# \begin{pmatrix} +# \rho v_1 \\ \rho v_1^2 + p \\ \rho v_1 v_2 \\ (\rho e + p) v_1 +# \end{pmatrix} +# + +# \frac{\partial}{\partial y} +# \begin{pmatrix} +# \rho v_2 \\ \rho v_1 v_2 \\ \rho v_2^2 + p \\ (\rho e + p) v_2 +# \end{pmatrix} +# = +# \begin{pmatrix} +# 0 \\ 0 \\ 0 \\ 0 +# \end{pmatrix}, +# ``` +# for an ideal gas with the specific heat ratio ``\gamma``. +# Here, ``\rho`` is the density, ``v_1`` and ``v_2`` are the velocities, ``e`` is the specific +# total energy, and +# ```math +# p = (\gamma - 1) \left( \rho e - \frac{1}{2} \rho (v_1^2 + v_2^2) \right) +# ``` +# is the pressure. +# Initial conditions consist of initial values for ``\rho``, ``\rho v_1``, +# ``\rho v_2`` and ``\rho e``. +# One of the common initial conditions for the compressible Euler equations is a simple density +# wave. Let's implement it. + +# - Open the downloaded file `elixir_euler_ec.jl` with a text editor. +# - Go to the line with the following code: +# ```julia +# initial_condition = initial_condition_weak_blast_wave +# ``` +# Here, [`initial_condition_weak_blast_wave`](@ref) is used as the initial condition. +# - Comment out the line using the `#` symbol: +# ```julia +# # initial_condition = initial_condition_weak_blast_wave +# ``` +# - Now you can create your own initial conditions. Add the following code after the +# commented line: + +function initial_condition_density_waves(x, t, equations::CompressibleEulerEquations2D) + v1 = 0.1 # velocity along x-axis + v2 = 0.2 # velocity along y-axis + rho = 1.0 + 0.98 * sinpi(sum(x) - t * (v1 + v2)) # density wave profile + p = 20 # pressure + rho_e = p / (equations.gamma - 1) + 1/2 * rho * (v1^2 + v2^2) + return SVector(rho, rho*v1, rho*v2, rho_e) +end +initial_condition = initial_condition_density_waves + +# - Execute the following code one more time, but instead of `path/to/file` paste the path to the +# `elixir_euler_ec.jl` file that you just edited. +# ```julia +# using Trixi +# trixi_include(path/to/file) +# using Plots +# plot(sol) +# ``` +# Then you will obtain a new solution from running the simulation with a different initial +# condition. + +trixi_include(@__MODULE__,joinpath(examples_dir(), "tree_2d_dgsem", "elixir_euler_ec.jl"), #hide #md + initial_condition=initial_condition) #hide #md +pd = PlotData2D(sol) #hide #md +p1 = plot(pd["rho"]) #hide #md +p2 = plot(pd["v1"], clim=(0.05, 0.15)) #hide #md +p3 = plot(pd["v2"], clim=(0.15, 0.25)) #hide #md +p4 = plot(pd["p"], clim=(10, 30)) #hide #md +plot(p1, p2, p3, p4) #hide #md + +# To get exactly the same picture execute the following. +# ```julia +# pd = PlotData2D(sol) +# p1 = plot(pd["rho"]) +# p2 = plot(pd["v1"], clim=(0.05, 0.15)) +# p3 = plot(pd["v2"], clim=(0.15, 0.25)) +# p4 = plot(pd["p"], clim=(10, 30)) +# plot(p1, p2, p3, p4) +# ``` + +# Feel free to make further changes to the initial condition to observe different solutions. + +# Now you are able to download, modify and execute simulation setups for Trixi.jl. To explore +# further details on setting up a new simulation with Trixi.jl, refer to the second part of +# the introduction titled [Create first setup](@ref create_first_setup). + +Sys.rm("out"; recursive=true, force=true) #hide #md \ No newline at end of file diff --git a/docs/literate/src/files/index.jl b/docs/literate/src/files/index.jl index 26637e5b24b..1fc025d84da 100644 --- a/docs/literate/src/files/index.jl +++ b/docs/literate/src/files/index.jl @@ -14,20 +14,27 @@ # There are tutorials for the following topics: -# ### [1 Introduction to DG methods](@ref scalar_linear_advection_1d) +# ### [1 First steps in Trixi.jl](@ref getting_started) +#- +# This tutorial provides guidance for getting started with Trixi.jl, and Julia as well. It outlines +# the installation procedures for both Julia and Trixi.jl, the execution of Trixi.jl elixirs, the +# fundamental structure of a Trixi.jl setup, the visualization of results, and the development +# process for Trixi.jl. + +# ### [2 Introduction to DG methods](@ref scalar_linear_advection_1d) #- # This tutorial gives an introduction to discontinuous Galerkin (DG) methods with the example of the # scalar linear advection equation in 1D. Starting with some theoretical explanations, we first implement # a raw version of a discontinuous Galerkin spectral element method (DGSEM). Then, we will show how # to use features of Trixi.jl to achieve the same result. -# ### [2 DGSEM with flux differencing](@ref DGSEM_FluxDiff) +# ### [3 DGSEM with flux differencing](@ref DGSEM_FluxDiff) #- # To improve stability often the flux differencing formulation of the DGSEM (split form) is used. # We want to present the idea and formulation on a basic 1D level. Then, we show how this formulation # can be implemented in Trixi.jl and analyse entropy conservation for two different flux combinations. -# ### [3 Shock capturing with flux differencing and stage limiter](@ref shock_capturing) +# ### [4 Shock capturing with flux differencing and stage limiter](@ref shock_capturing) #- # Using the flux differencing formulation, a simple procedure to capture shocks is a hybrid blending # of a high-order DG method and a low-order subcell finite volume (FV) method. We present the idea on a @@ -35,20 +42,20 @@ # explained and added to an exemplary simulation of the Sedov blast wave with the 2D compressible Euler # equations. -# ### [4 Non-periodic boundary conditions](@ref non_periodic_boundaries) +# ### [5 Non-periodic boundary conditions](@ref non_periodic_boundaries) #- # Thus far, all examples used periodic boundaries. In Trixi.jl, you can also set up a simulation with # non-periodic boundaries. This tutorial presents the implementation of the classical Dirichlet # boundary condition with a following example. Then, other non-periodic boundaries are mentioned. -# ### [5 DG schemes via `DGMulti` solver](@ref DGMulti_1) +# ### [6 DG schemes via `DGMulti` solver](@ref DGMulti_1) #- # This tutorial is about the more general DG solver [`DGMulti`](@ref), introduced [here](@ref DGMulti). # We are showing some examples for this solver, for instance with discretization nodes by Gauss or # triangular elements. Moreover, we present a simple way to include pre-defined triangulate meshes for # non-Cartesian domains using the package [StartUpDG.jl](https://github.com/jlchan/StartUpDG.jl). -# ### [6 Other SBP schemes (FD, CGSEM) via `DGMulti` solver](@ref DGMulti_2) +# ### [7 Other SBP schemes (FD, CGSEM) via `DGMulti` solver](@ref DGMulti_2) #- # Supplementary to the previous tutorial about DG schemes via the `DGMulti` solver we now present # the possibility for `DGMulti` to use other SBP schemes via the package @@ -56,7 +63,7 @@ # For instance, we show how to set up a finite differences (FD) scheme and a continuous Galerkin # (CGSEM) method. -# ### [7 Upwind FD SBP schemes](@ref upwind_fdsbp) +# ### [8 Upwind FD SBP schemes](@ref upwind_fdsbp) #- # General SBP schemes can not only be used via the [`DGMulti`](@ref) solver but # also with a general `DG` solver. In particular, upwind finite difference SBP @@ -64,42 +71,42 @@ # schemes in the `DGMulti` framework, the interface is based on the package # [SummationByPartsOperators.jl](https://github.com/ranocha/SummationByPartsOperators.jl). -# ### [8 Adding a new scalar conservation law](@ref adding_new_scalar_equations) +# ### [9 Adding a new scalar conservation law](@ref adding_new_scalar_equations) #- # This tutorial explains how to add a new physics model using the example of the cubic conservation # law. First, we define the equation using a `struct` `CubicEquation` and the physical flux. Then, # the corresponding standard setup in Trixi.jl (`mesh`, `solver`, `semi` and `ode`) is implemented # and the ODE problem is solved by OrdinaryDiffEq's `solve` method. -# ### [9 Adding a non-conservative equation](@ref adding_nonconservative_equation) +# ### [10 Adding a non-conservative equation](@ref adding_nonconservative_equation) #- # In this part, another physics model is implemented, the nonconservative linear advection equation. # We run two different simulations with different levels of refinement and compare the resulting errors. -# ### [10 Parabolic terms](@ref parabolic_terms) +# ### [11 Parabolic terms](@ref parabolic_terms) #- # This tutorial describes how parabolic terms are implemented in Trixi.jl, e.g., # to solve the advection-diffusion equation. -# ### [11 Adding new parabolic terms](@ref adding_new_parabolic_terms) +# ### [12 Adding new parabolic terms](@ref adding_new_parabolic_terms) #- # This tutorial describes how new parabolic terms can be implemented using Trixi.jl. -# ### [12 Adaptive mesh refinement](@ref adaptive_mesh_refinement) +# ### [13 Adaptive mesh refinement](@ref adaptive_mesh_refinement) #- # Adaptive mesh refinement (AMR) helps to increase the accuracy in sensitive or turbolent regions while # not wasting resources for less interesting parts of the domain. This leads to much more efficient # simulations. This tutorial presents the implementation strategy of AMR in Trixi.jl, including the use of # different indicators and controllers. -# ### [13 Structured mesh with curvilinear mapping](@ref structured_mesh_mapping) +# ### [14 Structured mesh with curvilinear mapping](@ref structured_mesh_mapping) #- # In this tutorial, the use of Trixi.jl's structured curved mesh type [`StructuredMesh`](@ref) is explained. # We present the two basic option to initialize such a mesh. First, the curved domain boundaries # of a circular cylinder are set by explicit boundary functions. Then, a fully curved mesh is # defined by passing the transformation mapping. -# ### [14 Unstructured meshes with HOHQMesh.jl](@ref hohqmesh_tutorial) +# ### [15 Unstructured meshes with HOHQMesh.jl](@ref hohqmesh_tutorial) #- # The purpose of this tutorial is to demonstrate how to use the [`UnstructuredMesh2D`](@ref) # functionality of Trixi.jl. This begins by running and visualizing an available unstructured @@ -108,26 +115,26 @@ # software in the Trixi.jl ecosystem, and then run a simulation using Trixi.jl on said mesh. # In the end, the tutorial briefly explains how to simulate an example using AMR via `P4estMesh`. -# ### [15 P4est mesh from gmsh](@ref p4est_from_gmsh) +# ### [16 P4est mesh from gmsh](@ref p4est_from_gmsh) #- # This tutorial describes how to obtain a [`P4estMesh`](@ref) from an existing mesh generated # by [`gmsh`](https://gmsh.info/) or any other meshing software that can export to the Abaqus # input `.inp` format. The tutorial demonstrates how edges/faces can be associated with boundary conditions based on the physical nodesets. -# ### [16 Explicit time stepping](@ref time_stepping) +# ### [17 Explicit time stepping](@ref time_stepping) #- # This tutorial is about time integration using [OrdinaryDiffEq.jl](https://github.com/SciML/OrdinaryDiffEq.jl). # It explains how to use their algorithms and presents two types of time step choices - with error-based # and CFL-based adaptive step size control. -# ### [17 Differentiable programming](@ref differentiable_programming) +# ### [18 Differentiable programming](@ref differentiable_programming) #- # This part deals with some basic differentiable programming topics. For example, a Jacobian, its # eigenvalues and a curve of total energy (through the simulation) are calculated and plotted for # a few semidiscretizations. Moreover, we calculate an example for propagating errors with Measurement.jl # at the end. -# ### [18 Custom semidiscretization](@ref custom_semidiscretization) +# ### [19 Custom semidiscretization](@ref custom_semidiscretization) #- # This tutorial describes the [semidiscretiations](@ref overview-semidiscretizations) of Trixi.jl # and explains how to extend them for custom tasks. diff --git a/docs/make.jl b/docs/make.jl index 7fce3b31e24..584f151b5f3 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -48,6 +48,12 @@ end # "title" => ["subtitle 1" => ("folder 1", "filename 1.jl"), # "subtitle 2" => ("folder 2", "filename 2.jl")] files = [ + # Topic: introduction + "First steps in Trixi.jl" => [ + "Getting started" => ("first_steps", "getting_started.jl"), + "Create first setup" => ("first_steps", "create_first_setup.jl"), + "Changing Trixi.jl itself" => ("first_steps", "changing_trixi.jl"), + ], # Topic: DG semidiscretizations "Introduction to DG methods" => "scalar_linear_advection_1d.jl", "DGSEM with flux differencing" => "DGSEM_FluxDiff.jl", From fa18c8bab4c6855a989691ede7f8947c5e3ea945 Mon Sep 17 00:00:00 2001 From: Hendrik Ranocha Date: Wed, 7 Feb 2024 07:19:49 +0100 Subject: [PATCH 21/63] fix benchmarks configuration (#1837) --- benchmark/benchmarks.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/benchmark/benchmarks.jl b/benchmark/benchmarks.jl index a3f7d1d2569..15d1d96c05f 100644 --- a/benchmark/benchmarks.jl +++ b/benchmark/benchmarks.jl @@ -55,5 +55,5 @@ let SUITE["latency"]["euler_2d"] = @benchmarkable run( `$(Base.julia_cmd()) -e 'using Trixi; trixi_include(joinpath(examples_dir(), "tree_2d_dgsem", "elixir_euler_kelvin_helmholtz_instability.jl"), tspan=(0.0, 1.0e-10), save_restart=TrivialCallback(), save_solution=TrivialCallback())'`) seconds=60 SUITE["latency"]["mhd_2d"] = @benchmarkable run( - `$(Base.julia_cmd()) -e 'using Trixi; trixi_include(joinpath(examples_dir(), "tree_2d_dgsem", "elixir_mhd_blast_wave.jl"), tspan=(0.0, 1.0e-10), save_restart=TrivialCallback(), save_solution=TrivialCallback())'`) seconds=60 + `$(Base.julia_cmd()) -e 'using Trixi; trixi_include(joinpath(examples_dir(), "tree_2d_dgsem", "elixir_mhd_blast_wave.jl"), tspan=(0.0, 1.0e-10), save_solution=TrivialCallback())'`) seconds=60 end From 8c6d9bc727219e470f56f3317997f17eb5615842 Mon Sep 17 00:00:00 2001 From: Hendrik Ranocha Date: Wed, 7 Feb 2024 07:27:40 +0100 Subject: [PATCH 22/63] Make CI fail if Codecov fails (#1834) --- .github/workflows/ci.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 2e388366fc8..86bd3f836e5 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -134,7 +134,8 @@ jobs: file: ./lcov.info flags: unittests name: codecov-umbrella - fail_ci_if_error: false + fail_ci_if_error: true + verbose: true token: ${{ secrets.CODECOV_TOKEN }} # The standard setup of Coveralls is just annoying for parallel builds, see, e.g., # https://github.com/trixi-framework/Trixi.jl/issues/691 From 4fb8160c397df922e8fc4906a5c8f92225c21ecd Mon Sep 17 00:00:00 2001 From: Michael Schlottke-Lakemper Date: Wed, 7 Feb 2024 08:43:50 +0100 Subject: [PATCH 23/63] Update compat bounds for Makie, CairoMakie (#1836) --- Project.toml | 2 +- docs/Project.toml | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Project.toml b/Project.toml index e99b08e0e81..9b624c7733c 100644 --- a/Project.toml +++ b/Project.toml @@ -68,7 +68,7 @@ LinearAlgebra = "1" LinearMaps = "2.7, 3.0" LoopVectorization = "0.12.118" MPI = "0.20" -Makie = "0.19" +Makie = "0.19, 0.20" MuladdMacro = "0.2.2" Octavian = "0.3.5" OffsetArrays = "1.3" diff --git a/docs/Project.toml b/docs/Project.toml index 3a091f5b4f1..cc48aeb8ed9 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -12,7 +12,7 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" Trixi2Vtk = "bc1476a1-1ca6-4cc3-950b-c312b255ff95" [compat] -CairoMakie = "0.6, 0.7, 0.8, 0.9, 0.10" +CairoMakie = "0.6, 0.7, 0.8, 0.9, 0.10, 0.11" Documenter = "1" ForwardDiff = "0.10" HOHQMesh = "0.1, 0.2" From 3e6872bd486a4cfcc94bd2c31b2fe8510670a7a2 Mon Sep 17 00:00:00 2001 From: Michael Schlottke-Lakemper Date: Wed, 7 Feb 2024 09:06:07 +0100 Subject: [PATCH 24/63] Enable CI testing on Apple Silicon (#1830) * Enable CI testing on Apple Silicon * Use `threaded` instead of `threaded_legacy` --- .github/workflows/ci.yml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 86bd3f836e5..9d398f187b3 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -101,6 +101,10 @@ jobs: os: windows-latest arch: x64 trixi_test: threaded + - version: '1.9' + os: macos-14 + arch: arm64 + trixi_test: threaded steps: - uses: actions/checkout@v4 - uses: julia-actions/setup-julia@v1 From fe6a5276e1ea92a23d4897ca33a057288f277e8f Mon Sep 17 00:00:00 2001 From: Hendrik Ranocha Date: Wed, 7 Feb 2024 10:37:22 +0100 Subject: [PATCH 25/63] coverallsapp at v2 (#1777) Co-authored-by: Michael Schlottke-Lakemper --- .github/workflows/ci.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 9d398f187b3..a7dfe033a90 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -200,7 +200,7 @@ jobs: coverage = merge_coverage_counts(coverage) @show covered_lines, total_lines = get_summary(coverage) LCOV.writefile("./lcov.info", coverage) - - uses: coverallsapp/github-action@master + - uses: coverallsapp/github-action@v2 with: github-token: ${{ secrets.GITHUB_TOKEN }} path-to-lcov: ./lcov.info From 4369c1c00b3e44de43bba95adeedfb37fd09551c Mon Sep 17 00:00:00 2001 From: Hendrik Ranocha Date: Wed, 14 Feb 2024 07:56:08 +0100 Subject: [PATCH 26/63] Fix formatter to older version (#1843) * Fix formatter to older version * fix JuliaFormatter version also in utils folder * Update utils/trixi-format-file.jl Co-authored-by: Arpit Babbar * Update utils/trixi-format.jl Co-authored-by: Arpit Babbar * Apply suggestions from code review Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com> * format --------- Co-authored-by: Arpit Babbar Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com> --- .github/workflows/FormatCheck.yml | 2 +- utils/trixi-format-file.jl | 3 ++- utils/trixi-format.jl | 3 ++- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.github/workflows/FormatCheck.yml b/.github/workflows/FormatCheck.yml index a733cb7cc21..7297f1c3ff5 100644 --- a/.github/workflows/FormatCheck.yml +++ b/.github/workflows/FormatCheck.yml @@ -29,7 +29,7 @@ jobs: # TODO: Change the call below to # format(".") run: | - julia -e 'using Pkg; Pkg.add(PackageSpec(name = "JuliaFormatter"))' + julia -e 'using Pkg; Pkg.add(PackageSpec(name = "JuliaFormatter", version="1.0.45"))' julia -e 'using JuliaFormatter; format(["benchmark", "examples", "ext", "src", "test", "utils"])' - name: Format check run: | diff --git a/utils/trixi-format-file.jl b/utils/trixi-format-file.jl index c4d8e7c9032..9b9a0e4949c 100755 --- a/utils/trixi-format-file.jl +++ b/utils/trixi-format-file.jl @@ -2,7 +2,8 @@ using Pkg Pkg.activate(; temp = true, io = devnull) -Pkg.add("JuliaFormatter"; preserve = PRESERVE_ALL, io = devnull) +Pkg.add(PackageSpec(name = "JuliaFormatter", version = "1.0.45"); preserve = PRESERVE_ALL, + io = devnull) using JuliaFormatter: format_file diff --git a/utils/trixi-format.jl b/utils/trixi-format.jl index d1e7efa656a..63f14078807 100755 --- a/utils/trixi-format.jl +++ b/utils/trixi-format.jl @@ -2,7 +2,8 @@ using Pkg Pkg.activate(; temp = true, io = devnull) -Pkg.add("JuliaFormatter"; preserve = PRESERVE_ALL, io = devnull) +Pkg.add(PackageSpec(name = "JuliaFormatter", version = "1.0.45"); preserve = PRESERVE_ALL, + io = devnull) using JuliaFormatter: format From 4f33837e3c95b5af21057850c30ef603a9191d86 Mon Sep 17 00:00:00 2001 From: Erik Faulhaber <44124897+efaulhaber@users.noreply.github.com> Date: Thu, 15 Feb 2024 08:50:30 +0100 Subject: [PATCH 27/63] Use `trixi_include` from TrixiBase.jl (#1832) * Use `trixi_include` from TrixiBase.jl * Add compat entry for TrixiBase.jl * Remove unused functions * Use `TrixiBase.walkexpr` * Fix docs * Add TrixiBase.jl API reference * Add TrixiBase to docs dependencies * Import `TrixiBase` * Remove `find_assignment` * Add TrixiBase to makedocs modules * Apply suggestions from code review Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com> --------- Co-authored-by: Hendrik Ranocha Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com> --- Project.toml | 2 + docs/Project.toml | 2 + docs/make.jl | 4 +- docs/src/conventions.md | 10 +- docs/src/reference-trixibase.md | 9 ++ src/Trixi.jl | 3 +- src/auxiliary/precompile.jl | 3 - src/auxiliary/special_elixirs.jl | 158 +------------------------------ src/callbacks_step/trivial.jl | 4 +- test/test_unit.jl | 97 ------------------- 10 files changed, 31 insertions(+), 261 deletions(-) create mode 100644 docs/src/reference-trixibase.md diff --git a/Project.toml b/Project.toml index 9b624c7733c..b4a06a70688 100644 --- a/Project.toml +++ b/Project.toml @@ -45,6 +45,7 @@ TimerOutputs = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f" Triangulate = "f7e6ffb2-c36d-4f8f-a77e-16e897189344" TriplotBase = "981d1d27-644d-49a2-9326-4793e63143c3" TriplotRecipes = "808ab39a-a642-4abf-81ff-4cb34ebbffa3" +TrixiBase = "9a0f1c46-06d5-4909-a5a3-ce25d3fa3284" [weakdeps] Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" @@ -95,6 +96,7 @@ TimerOutputs = "0.5.7" Triangulate = "2.0" TriplotBase = "0.1" TriplotRecipes = "0.1" +TrixiBase = "0.1.1" julia = "1.8" [extras] diff --git a/docs/Project.toml b/docs/Project.toml index cc48aeb8ed9..3b8d169fdb8 100644 --- a/docs/Project.toml +++ b/docs/Project.toml @@ -10,6 +10,7 @@ OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed" Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" Trixi2Vtk = "bc1476a1-1ca6-4cc3-950b-c312b255ff95" +TrixiBase = "9a0f1c46-06d5-4909-a5a3-ce25d3fa3284" [compat] CairoMakie = "0.6, 0.7, 0.8, 0.9, 0.10, 0.11" @@ -23,3 +24,4 @@ OrdinaryDiffEq = "6.49.1" Plots = "1.9" Test = "1" Trixi2Vtk = "0.3" +TrixiBase = "0.1.1" diff --git a/docs/make.jl b/docs/make.jl index 584f151b5f3..946b803b71e 100644 --- a/docs/make.jl +++ b/docs/make.jl @@ -8,6 +8,7 @@ end using Trixi using Trixi2Vtk +using TrixiBase # Get Trixi.jl root directory trixi_root_dir = dirname(@__DIR__) @@ -82,7 +83,7 @@ tutorials = create_tutorials(files) # Make documentation makedocs( # Specify modules for which docstrings should be shown - modules = [Trixi, Trixi2Vtk], + modules = [Trixi, TrixiBase, Trixi2Vtk], # Set sitename to Trixi.jl sitename = "Trixi.jl", # Provide additional formatting options @@ -128,6 +129,7 @@ makedocs( "Troubleshooting and FAQ" => "troubleshooting.md", "Reference" => [ "Trixi.jl" => "reference-trixi.md", + "TrixiBase.jl" => "reference-trixibase.md", "Trixi2Vtk.jl" => "reference-trixi2vtk.md" ], "Authors" => "authors.md", diff --git a/docs/src/conventions.md b/docs/src/conventions.md index dab1b8533a5..4f9e0ec4e67 100644 --- a/docs/src/conventions.md +++ b/docs/src/conventions.md @@ -47,10 +47,12 @@ Trixi.jl is distributed with several examples in the form of elixirs, small Julia scripts containing everything to set up and run a simulation. Working interactively from the Julia REPL with these scripts can be quite convenient while for exploratory research and development of Trixi.jl. For example, you -can use the convenience function [`trixi_include`](@ref) to `include` an elixir -with some modified arguments. To enable this, it is helpful to use a consistent -naming scheme in elixirs, since [`trixi_include`](@ref) can only perform simple -replacements. Some standard variables names are +can use the convenience function +[`trixi_include`](@ref) +to `include` an elixir with some modified arguments. To enable this, it is +helpful to use a consistent naming scheme in elixirs, since +[`trixi_include`](@ref) +can only perform simple replacements. Some standard variables names are - `polydeg` for the polynomial degree of a solver - `surface_flux` for the numerical flux at surfaces diff --git a/docs/src/reference-trixibase.md b/docs/src/reference-trixibase.md new file mode 100644 index 00000000000..c7a970f88ec --- /dev/null +++ b/docs/src/reference-trixibase.md @@ -0,0 +1,9 @@ +# TrixiBase.jl API + +```@meta +CurrentModule = TrixiBase +``` + +```@autodocs +Modules = [TrixiBase] +``` diff --git a/src/Trixi.jl b/src/Trixi.jl index 8d74fbc9736..ea72fbc915f 100644 --- a/src/Trixi.jl +++ b/src/Trixi.jl @@ -70,6 +70,7 @@ using Triangulate: Triangulate, TriangulateIO, triangulate export TriangulateIO # for type parameter in DGMultiMesh using TriplotBase: TriplotBase using TriplotRecipes: DGTriPseudocolor +@reexport using TrixiBase: TrixiBase, trixi_include @reexport using SimpleUnPack: @unpack using SimpleUnPack: @pack! using DataStructures: BinaryHeap, FasterForward, extract_all! @@ -129,7 +130,7 @@ include("callbacks_step/callbacks_step.jl") include("callbacks_stage/callbacks_stage.jl") include("semidiscretization/semidiscretization_euler_gravity.jl") -# `trixi_include` and special elixirs such as `convergence_test` +# Special elixirs such as `convergence_test` include("auxiliary/special_elixirs.jl") # Plot recipes and conversion functions to visualize results with Plots.jl diff --git a/src/auxiliary/precompile.jl b/src/auxiliary/precompile.jl index 9cec502f6cb..4d5399b5ba3 100644 --- a/src/auxiliary/precompile.jl +++ b/src/auxiliary/precompile.jl @@ -577,9 +577,6 @@ function _precompile_manual_() @assert Base.precompile(Tuple{typeof(show), Base.TTY, lbm_collision_callback_type}) @assert Base.precompile(Tuple{typeof(show), IOContext{Base.TTY}, MIME"text/plain", lbm_collision_callback_type}) - - # infrastructure, special elixirs - @assert Base.precompile(Tuple{typeof(trixi_include), String}) end @assert Base.precompile(Tuple{typeof(init_mpi)}) diff --git a/src/auxiliary/special_elixirs.jl b/src/auxiliary/special_elixirs.jl index 5fdd9aea0c5..d71a27aa96a 100644 --- a/src/auxiliary/special_elixirs.jl +++ b/src/auxiliary/special_elixirs.jl @@ -5,58 +5,6 @@ @muladd begin #! format: noindent -# Note: We can't call the method below `Trixi.include` since that is created automatically -# inside `module Trixi` to `include` source files and evaluate them within the global scope -# of `Trixi`. However, users will want to evaluate in the global scope of `Main` or something -# similar to manage dependencies on their own. -""" - trixi_include([mod::Module=Main,] elixir::AbstractString; kwargs...) - -`include` the file `elixir` and evaluate its content in the global scope of module `mod`. -You can override specific assignments in `elixir` by supplying keyword arguments. -It's basic purpose is to make it easier to modify some parameters while running Trixi.jl from the -REPL. Additionally, this is used in tests to reduce the computational burden for CI while still -providing examples with sensible default values for users. - -Before replacing assignments in `elixir`, the keyword argument `maxiters` is inserted -into calls to `solve` and `Trixi.solve` with it's default value used in the SciML ecosystem -for ODEs, see the "Miscellaneous" section of the -[documentation](https://docs.sciml.ai/DiffEqDocs/stable/basics/common_solver_opts/). - -# Examples - -```jldoctest -julia> redirect_stdout(devnull) do - trixi_include(@__MODULE__, joinpath(examples_dir(), "tree_1d_dgsem", "elixir_advection_extended.jl"), - tspan=(0.0, 0.1)) - sol.t[end] - end -[ Info: You just called `trixi_include`. Julia may now compile the code, please be patient. -0.1 -``` -""" -function trixi_include(mod::Module, elixir::AbstractString; kwargs...) - # Check that all kwargs exist as assignments - code = read(elixir, String) - expr = Meta.parse("begin \n$code \nend") - expr = insert_maxiters(expr) - - for (key, val) in kwargs - # This will throw an error when `key` is not found - find_assignment(expr, key) - end - - # Print information on potential wait time only in non-parallel case - if !mpi_isparallel() - @info "You just called `trixi_include`. Julia may now compile the code, please be patient." - end - Base.include(ex -> replace_assignments(insert_maxiters(ex); kwargs...), mod, elixir) -end - -function trixi_include(elixir::AbstractString; kwargs...) - trixi_include(Main, elixir; kwargs...) -end - """ convergence_test([mod::Module=Main,] elixir::AbstractString, iterations; kwargs...) @@ -177,112 +125,15 @@ end # Helper methods used in the functions defined above -# Apply the function `f` to `expr` and all sub-expressions recursively. -walkexpr(f, expr::Expr) = f(Expr(expr.head, (walkexpr(f, arg) for arg in expr.args)...)) -walkexpr(f, x) = f(x) - -# Insert the keyword argument `maxiters` into calls to `solve` and `Trixi.solve` -# with default value `10^5` if it is not already present. -function insert_maxiters(expr) - maxiters_default = 10^5 - - expr = walkexpr(expr) do x - if x isa Expr - is_plain_solve = x.head === Symbol("call") && x.args[1] === Symbol("solve") - is_trixi_solve = (x.head === Symbol("call") && x.args[1] isa Expr && - x.args[1].head === Symbol(".") && - x.args[1].args[1] === Symbol("Trixi") && - x.args[1].args[2] isa QuoteNode && - x.args[1].args[2].value === Symbol("solve")) - - if is_plain_solve || is_trixi_solve - # Do nothing if `maxiters` is already set as keyword argument... - for arg in x.args - # This detects the case where `maxiters` is set as keyword argument - # without or before a semicolon - if (arg isa Expr && arg.head === Symbol("kw") && - arg.args[1] === Symbol("maxiters")) - return x - end - - # This detects the case where maxiters is set as keyword argument - # after a semicolon - if (arg isa Expr && arg.head === Symbol("parameters")) - # We need to check each keyword argument listed here - for nested_arg in arg.args - if (nested_arg isa Expr && - nested_arg.head === Symbol("kw") && - nested_arg.args[1] === Symbol("maxiters")) - return x - end - end - end - end - - # ...and insert it otherwise. - push!(x.args, Expr(Symbol("kw"), Symbol("maxiters"), maxiters_default)) - end - end - return x - end - - return expr -end - -# Replace assignments to `key` in `expr` by `key = val` for all `(key,val)` in `kwargs`. -function replace_assignments(expr; kwargs...) - # replace explicit and keyword assignments - expr = walkexpr(expr) do x - if x isa Expr - for (key, val) in kwargs - if (x.head === Symbol("=") || x.head === :kw) && - x.args[1] === Symbol(key) - x.args[2] = :($val) - # dump(x) - end - end - end - return x - end - - return expr -end - -# find a (keyword or common) assignment to `destination` in `expr` -# and return the assigned value -function find_assignment(expr, destination) - # declare result to be able to assign to it in the closure - local result - found = false - - # find explicit and keyword assignments - walkexpr(expr) do x - if x isa Expr - if (x.head === Symbol("=") || x.head === :kw) && - x.args[1] === Symbol(destination) - result = x.args[2] - found = true - # dump(x) - end - end - return x - end - - if !found - throw(ArgumentError("assignment `$destination` not found in expression")) - end - - result -end - -# searches the parameter that specifies the mesh reslution in the elixir +# Searches for the assignment that specifies the mesh resolution in the elixir function extract_initial_resolution(elixir, kwargs) code = read(elixir, String) expr = Meta.parse("begin \n$code \nend") try # get the initial_refinement_level from the elixir - initial_refinement_level = find_assignment(expr, :initial_refinement_level) + initial_refinement_level = TrixiBase.find_assignment(expr, + :initial_refinement_level) if haskey(kwargs, :initial_refinement_level) return kwargs[:initial_refinement_level] @@ -294,7 +145,8 @@ function extract_initial_resolution(elixir, kwargs) if isa(e, ArgumentError) try # get cells_per_dimension from the elixir - cells_per_dimension = eval(find_assignment(expr, :cells_per_dimension)) + cells_per_dimension = eval(TrixiBase.find_assignment(expr, + :cells_per_dimension)) if haskey(kwargs, :cells_per_dimension) return kwargs[:cells_per_dimension] diff --git a/src/callbacks_step/trivial.jl b/src/callbacks_step/trivial.jl index a55b7d85b13..fb93cf96c0c 100644 --- a/src/callbacks_step/trivial.jl +++ b/src/callbacks_step/trivial.jl @@ -8,8 +8,8 @@ """ TrivialCallback() -A callback that does nothing. This can be useful to disable some callbacks -easily via [`trixi_include`](@ref). +A callback that does nothing. This can be useful to disable some callbacks easily via +[`trixi_include`](@ref). """ function TrivialCallback() DiscreteCallback(trivial_callback, trivial_callback, diff --git a/test/test_unit.jl b/test/test_unit.jl index 7943d952f71..3b8dc3c4331 100644 --- a/test/test_unit.jl +++ b/test/test_unit.jl @@ -1529,103 +1529,6 @@ end @test mesh.boundary_faces[:entire_boundary] == [1, 2] end - -@testset "trixi_include" begin - @trixi_testset "Basic" begin - example = """ - x = 4 - """ - - filename = tempname() - try - open(filename, "w") do file - write(file, example) - end - - # Use `@trixi_testset`, which wraps code in a temporary module, and call - # `trixi_include` with `@__MODULE__` in order to isolate this test. - @test_warn "You just called" trixi_include(@__MODULE__, filename) - @test @isdefined x - @test x == 4 - - @test_warn "You just called" trixi_include(@__MODULE__, filename, x = 7) - @test x == 7 - - @test_throws "assignment `y` not found in expression" trixi_include(@__MODULE__, - filename, - y = 3) - finally - rm(filename, force = true) - end - end - - @trixi_testset "With `solve` Without `maxiters`" begin - # `trixi_include` assumes this to be the `solve` function of OrdinaryDiffEq, - # and therefore tries to insert the kwarg `maxiters`, which will fail here. - example = """ - solve() = 0 - x = solve() - """ - - filename = tempname() - try - open(filename, "w") do file - write(file, example) - end - - # Use `@trixi_testset`, which wraps code in a temporary module, and call - # `trixi_include` with `@__MODULE__` in order to isolate this test. - @test_throws "no method matching solve(; maxiters::Int64)" trixi_include(@__MODULE__, - filename) - - @test_throws "no method matching solve(; maxiters::Int64)" trixi_include(@__MODULE__, - filename, - maxiters = 3) - finally - rm(filename, force = true) - end - end - - @trixi_testset "With `solve` with `maxiters`" begin - # We need another example file that we include with `Base.include` first, in order to - # define the `solve` method without `trixi_include` trying to insert `maxiters` kwargs. - # Then, we can test that `trixi_include` inserts the kwarg in the `solve()` call. - example1 = """ - solve(; maxiters=0) = maxiters - """ - - example2 = """ - x = solve() - """ - - filename1 = tempname() - filename2 = tempname() - try - open(filename1, "w") do file - write(file, example1) - end - open(filename2, "w") do file - write(file, example2) - end - - # Use `@trixi_testset`, which wraps code in a temporary module, and call - # `Base.include` and `trixi_include` with `@__MODULE__` in order to isolate this test. - Base.include(@__MODULE__, filename1) - @test_warn "You just called" trixi_include(@__MODULE__, filename2) - @test @isdefined x - # This is the default `maxiters` inserted by `trixi_include` - @test x == 10^5 - - @test_warn "You just called" trixi_include(@__MODULE__, filename2, - maxiters = 7) - # Test that `maxiters` got overwritten - @test x == 7 - finally - rm(filename1, force = true) - rm(filename2, force = true) - end - end -end end end #module From 08c6034139451ba03be2abb6748bcd402f151b5d Mon Sep 17 00:00:00 2001 From: Erik Faulhaber <44124897+efaulhaber@users.noreply.github.com> Date: Thu, 15 Feb 2024 21:37:50 +0100 Subject: [PATCH 28/63] Don't export `TrixiBase` (#1846) --- src/Trixi.jl | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/src/Trixi.jl b/src/Trixi.jl index ea72fbc915f..8ab8085d4e8 100644 --- a/src/Trixi.jl +++ b/src/Trixi.jl @@ -70,7 +70,8 @@ using Triangulate: Triangulate, TriangulateIO, triangulate export TriangulateIO # for type parameter in DGMultiMesh using TriplotBase: TriplotBase using TriplotRecipes: DGTriPseudocolor -@reexport using TrixiBase: TrixiBase, trixi_include +@reexport using TrixiBase: trixi_include +using TrixiBase: TrixiBase @reexport using SimpleUnPack: @unpack using SimpleUnPack: @pack! using DataStructures: BinaryHeap, FasterForward, extract_all! From a872bc55e545baf36be91a949940434ae89f3426 Mon Sep 17 00:00:00 2001 From: Hendrik Ranocha Date: Fri, 16 Feb 2024 06:24:33 +0100 Subject: [PATCH 29/63] set version to v0.6.9 --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index b4a06a70688..10bf79cf9a5 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "Trixi" uuid = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb" authors = ["Michael Schlottke-Lakemper ", "Gregor Gassner ", "Hendrik Ranocha ", "Andrew R. Winters ", "Jesse Chan "] -version = "0.6.9-pre" +version = "0.6.9" [deps] CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2" From 29e173eb5f955771755cc28342e07c9903204327 Mon Sep 17 00:00:00 2001 From: Hendrik Ranocha Date: Fri, 16 Feb 2024 06:24:52 +0100 Subject: [PATCH 30/63] set development version to v0.6.10-pre --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 10bf79cf9a5..af3e6b4d078 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "Trixi" uuid = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb" authors = ["Michael Schlottke-Lakemper ", "Gregor Gassner ", "Hendrik Ranocha ", "Andrew R. Winters ", "Jesse Chan "] -version = "0.6.9" +version = "0.6.10-pre" [deps] CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2" From 3c9374bb6c336be32c56d5c13b213ae3900269a3 Mon Sep 17 00:00:00 2001 From: Daniel Doehring Date: Tue, 20 Feb 2024 16:15:48 +0100 Subject: [PATCH 31/63] Classic LWR traffic flow (#1840) * Add classic LWR traffic flow model to Trixi * fmt * shorten * Update examples/structured_1d_dgsem/elixir_traffic_flow_lwr_greenlight.jl * Update examples/structured_1d_dgsem/elixir_traffic_flow_lwr_greenlight.jl * rm IC const, fmt * add davis wave speed estimate for upcoming change * news and md * Use euler * fmt * Update examples/structured_1d_dgsem/elixir_traffic_flow_lwr_greenlight.jl * Update examples/tree_1d_dgsem/elixir_traffic_flow_lwr_trafficjam.jl * Update NEWS.md Co-authored-by: Andrew Winters * Andrew's suggestions * Apply suggestions from code review Co-authored-by: Hendrik Ranocha * add domain of u * back to carpenter kennedy * Update NEWS.md Co-authored-by: Andrew Winters --------- Co-authored-by: Andrew Winters Co-authored-by: Hendrik Ranocha --- NEWS.md | 1 + README.md | 2 +- .../elixir_traffic_flow_lwr_greenlight.jl | 80 ++++++++++++ .../elixir_traffic_flow_lwr_convergence.jl | 54 ++++++++ .../elixir_traffic_flow_lwr_trafficjam.jl | 82 +++++++++++++ src/Trixi.jl | 3 +- src/equations/equations.jl | 5 + src/equations/traffic_flow_lwr_1d.jl | 116 ++++++++++++++++++ test/test_structured_1d.jl | 15 +++ test/test_tree_1d.jl | 3 + test/test_tree_1d_traffic_flow_lwr.jl | 42 +++++++ 11 files changed, 401 insertions(+), 2 deletions(-) create mode 100644 examples/structured_1d_dgsem/elixir_traffic_flow_lwr_greenlight.jl create mode 100644 examples/tree_1d_dgsem/elixir_traffic_flow_lwr_convergence.jl create mode 100644 examples/tree_1d_dgsem/elixir_traffic_flow_lwr_trafficjam.jl create mode 100644 src/equations/traffic_flow_lwr_1d.jl create mode 100644 test/test_tree_1d_traffic_flow_lwr.jl diff --git a/NEWS.md b/NEWS.md index 02a723fca45..feccd1f9852 100644 --- a/NEWS.md +++ b/NEWS.md @@ -12,6 +12,7 @@ for human readability. - Different boundary conditions for quad/hex meshes in Abaqus format, even if not generated by HOHQMesh, can now be digested by Trixi in 2D and 3D. - Subcell (positivity) limiting support for nonlinear variables in 2D for `TreeMesh` +- Added Lighthill-Whitham-Richards (LWR) traffic model ## Changes when updating to v0.6 from v0.5.x diff --git a/README.md b/README.md index c531ab4d1a4..71370d3478e 100644 --- a/README.md +++ b/README.md @@ -53,7 +53,7 @@ installation and postprocessing procedures. Its features include: * Hyperbolic diffusion equations for elliptic problems * Lattice-Boltzmann equations (D2Q9 and D3Q27 schemes) * Shallow water equations - * Several scalar conservation laws (e.g., linear advection, Burgers' equation) + * Several scalar conservation laws (e.g., linear advection, Burgers' equation, LWR traffic flow) * Multi-physics simulations * [Self-gravitating gas dynamics](https://github.com/trixi-framework/paper-self-gravitating-gas-dynamics) * Shared-memory parallelization via multithreading diff --git a/examples/structured_1d_dgsem/elixir_traffic_flow_lwr_greenlight.jl b/examples/structured_1d_dgsem/elixir_traffic_flow_lwr_greenlight.jl new file mode 100644 index 00000000000..e5badf14451 --- /dev/null +++ b/examples/structured_1d_dgsem/elixir_traffic_flow_lwr_greenlight.jl @@ -0,0 +1,80 @@ + +using OrdinaryDiffEq +using Trixi + +############################################################################### + +equations = TrafficFlowLWREquations1D() + +solver = DGSEM(polydeg = 3, surface_flux = FluxHLL(min_max_speed_davis)) + +coordinates_min = (-1.0,) # minimum coordinate +coordinates_max = (1.0,) # maximum coordinate +cells_per_dimension = (64,) + +mesh = StructuredMesh(cells_per_dimension, coordinates_min, coordinates_max, + periodicity = false) + +# Example inspired from http://www.clawpack.org/riemann_book/html/Traffic_flow.html#Example:-green-light +# Green light that at x = 0 which switches at t = 0 from red to green. +# To the left there are cars bumper to bumper, to the right there are no cars. +function initial_condition_greenlight(x, t, equation::TrafficFlowLWREquations1D) + scalar = x[1] < 0.0 ? 1.0 : 0.0 + + return SVector(scalar) +end + +############################################################################### +# Specify non-periodic boundary conditions + +# Assume that there are always cars waiting at the left +function inflow(x, t, equations::TrafficFlowLWREquations1D) + return initial_condition_greenlight(coordinates_min, t, equations) +end +boundary_condition_inflow = BoundaryConditionDirichlet(inflow) + +# Cars may leave the modeled domain +function boundary_condition_outflow(u_inner, orientation, normal_direction, x, t, + surface_flux_function, + equations::TrafficFlowLWREquations1D) + # Calculate the boundary flux entirely from the internal solution state + flux = Trixi.flux(u_inner, orientation, equations) + + return flux +end + +boundary_conditions = (x_neg = boundary_condition_inflow, + x_pos = boundary_condition_outflow) + +initial_condition = initial_condition_greenlight + +semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver, + boundary_conditions = boundary_conditions) + +############################################################################### +# ODE solvers, callbacks etc. + +tspan = (0.0, 0.5) +ode = semidiscretize(semi, tspan) + +summary_callback = SummaryCallback() + +analysis_interval = 100 +analysis_callback = AnalysisCallback(semi, interval = analysis_interval) + +alive_callback = AliveCallback(analysis_interval = analysis_interval) + +stepsize_callback = StepsizeCallback(cfl = 1.2) + +callbacks = CallbackSet(summary_callback, + analysis_callback, alive_callback, + stepsize_callback) + +############################################################################### +# run the simulation + +sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false), + dt = 42, # solve needs some value here but it will be overwritten by the stepsize_callback + save_everystep = false, callback = callbacks); + +summary_callback() # print the timer summary diff --git a/examples/tree_1d_dgsem/elixir_traffic_flow_lwr_convergence.jl b/examples/tree_1d_dgsem/elixir_traffic_flow_lwr_convergence.jl new file mode 100644 index 00000000000..59258018f8c --- /dev/null +++ b/examples/tree_1d_dgsem/elixir_traffic_flow_lwr_convergence.jl @@ -0,0 +1,54 @@ + +using OrdinaryDiffEq +using Trixi + +############################################################################### + +equations = TrafficFlowLWREquations1D() + +# Use first order finite volume to prevent oscillations at the shock +solver = DGSEM(polydeg = 3, surface_flux = flux_hll) + +coordinates_min = 0.0 # minimum coordinate +coordinates_max = 2.0 # maximum coordinate + +# Create a uniformly refined mesh with periodic boundaries +mesh = TreeMesh(coordinates_min, coordinates_max, + initial_refinement_level = 4, + n_cells_max = 30_000) + +############################################################################### +# Specify non-periodic boundary conditions + +initial_condition = initial_condition_convergence_test +semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver, + source_terms = source_terms_convergence_test) + +############################################################################### +# ODE solvers, callbacks etc. + +tspan = (0.0, 2.0) +ode = semidiscretize(semi, tspan) + +summary_callback = SummaryCallback() + +analysis_interval = 100 +analysis_callback = AnalysisCallback(semi, interval = analysis_interval) + +alive_callback = AliveCallback(analysis_interval = analysis_interval) + +stepsize_callback = StepsizeCallback(cfl = 1.6) + +callbacks = CallbackSet(summary_callback, + analysis_callback, + alive_callback, + stepsize_callback) + +############################################################################### +# run the simulation + +sol = solve(ode, CarpenterKennedy2N54(), + dt = 42, # solve needs some value here but it will be overwritten by the stepsize_callback + save_everystep = false, callback = callbacks); + +summary_callback() # print the timer summary diff --git a/examples/tree_1d_dgsem/elixir_traffic_flow_lwr_trafficjam.jl b/examples/tree_1d_dgsem/elixir_traffic_flow_lwr_trafficjam.jl new file mode 100644 index 00000000000..d3a17b513fc --- /dev/null +++ b/examples/tree_1d_dgsem/elixir_traffic_flow_lwr_trafficjam.jl @@ -0,0 +1,82 @@ + +using OrdinaryDiffEq +using Trixi + +############################################################################### + +equations = TrafficFlowLWREquations1D() + +# Use first order finite volume to prevent oscillations at the shock +solver = DGSEM(polydeg = 0, surface_flux = flux_lax_friedrichs) + +coordinates_min = -1.0 # minimum coordinate +coordinates_max = 1.0 # maximum coordinate + +mesh = TreeMesh(coordinates_min, coordinates_max, + initial_refinement_level = 9, + n_cells_max = 30_000, + periodicity = false) + +# Example taken from http://www.clawpack.org/riemann_book/html/Traffic_flow.html#Example:-Traffic-jam +# Discontinuous initial condition (Riemann Problem) leading to a shock that moves to the left. +# The shock corresponds to the traffic congestion. +function initial_condition_traffic_jam(x, t, equation::TrafficFlowLWREquations1D) + scalar = x[1] < 0.0 ? 0.5 : 1.0 + + return SVector(scalar) +end + +############################################################################### +# Specify non-periodic boundary conditions + +function outflow(x, t, equations::TrafficFlowLWREquations1D) + return initial_condition_traffic_jam(coordinates_min, t, equations) +end +boundary_condition_outflow = BoundaryConditionDirichlet(outflow) + +function boundary_condition_inflow(u_inner, orientation, normal_direction, x, t, + surface_flux_function, + equations::TrafficFlowLWREquations1D) + # Calculate the boundary flux entirely from the internal solution state + flux = Trixi.flux(u_inner, orientation, equations) + + return flux +end + +boundary_conditions = (x_neg = boundary_condition_outflow, + x_pos = boundary_condition_inflow) + +initial_condition = initial_condition_traffic_jam + +semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver, + boundary_conditions = boundary_conditions) + +############################################################################### +# ODE solvers, callbacks etc. + +tspan = (0.0, 0.5) +ode = semidiscretize(semi, tspan) + +summary_callback = SummaryCallback() + +analysis_interval = 100 +analysis_callback = AnalysisCallback(semi, interval = analysis_interval) + +alive_callback = AliveCallback(analysis_interval = analysis_interval) + +stepsize_callback = StepsizeCallback(cfl = 1.0) + +callbacks = CallbackSet(summary_callback, + analysis_callback, alive_callback, + stepsize_callback) + +############################################################################### +# run the simulation + +# Note: Be careful when increasing the polynomial degree and switching from first order finite volume +# to some actual DG method - in that case, you should also exchange the ODE solver. +sol = solve(ode, Euler(), + dt = 42, # solve needs some value here but it will be overwritten by the stepsize_callback + save_everystep = false, callback = callbacks); + +summary_callback() # print the timer summary diff --git a/src/Trixi.jl b/src/Trixi.jl index 8ab8085d4e8..bf0986084af 100644 --- a/src/Trixi.jl +++ b/src/Trixi.jl @@ -157,7 +157,8 @@ export AcousticPerturbationEquations2D, ShallowWaterTwoLayerEquations1D, ShallowWaterTwoLayerEquations2D, ShallowWaterEquationsQuasi1D, LinearizedEulerEquations2D, - PolytropicEulerEquations2D + PolytropicEulerEquations2D, + TrafficFlowLWREquations1D export LaplaceDiffusion1D, LaplaceDiffusion2D, LaplaceDiffusion3D, CompressibleNavierStokesDiffusion1D, CompressibleNavierStokesDiffusion2D, diff --git a/src/equations/equations.jl b/src/equations/equations.jl index c041bf117ba..65875a2a7e5 100644 --- a/src/equations/equations.jl +++ b/src/equations/equations.jl @@ -507,4 +507,9 @@ include("linearized_euler_2d.jl") abstract type AbstractEquationsParabolic{NDIMS, NVARS, GradientVariables} <: AbstractEquations{NDIMS, NVARS} end + +# Lighthill-Witham-Richards (LWR) traffic flow model +abstract type AbstractTrafficFlowLWREquations{NDIMS, NVARS} <: + AbstractEquations{NDIMS, NVARS} end +include("traffic_flow_lwr_1d.jl") end # @muladd diff --git a/src/equations/traffic_flow_lwr_1d.jl b/src/equations/traffic_flow_lwr_1d.jl new file mode 100644 index 00000000000..a4d2613a5c8 --- /dev/null +++ b/src/equations/traffic_flow_lwr_1d.jl @@ -0,0 +1,116 @@ +# By default, Julia/LLVM does not use fused multiply-add operations (FMAs). +# Since these FMAs can increase the performance of many numerical algorithms, +# we need to opt-in explicitly. +# See https://ranocha.de/blog/Optimizing_EC_Trixi for further details. +@muladd begin +#! format: noindent + +@doc raw""" + TrafficFlowLWREquations1D + +The classic Lighthill-Witham Richards (LWR) model for 1D traffic flow. +The car density is denoted by $u \in [0, 1]$ and +the maximum possible speed (e.g. due to speed limits) is $v_{\text{max}}$. +```math +\partial_t u + v_{\text{max}} \partial_1 [u (1 - u)] = 0 +``` +For more details see e.g. Section 11.1 of +- Randall LeVeque (2002) +Finite Volume Methods for Hyperbolic Problems +[DOI: 10.1017/CBO9780511791253]https://doi.org/10.1017/CBO9780511791253 +""" +struct TrafficFlowLWREquations1D{RealT <: Real} <: AbstractTrafficFlowLWREquations{1, 1} + v_max::RealT + + function TrafficFlowLWREquations1D(v_max = 1.0) + new{typeof(v_max)}(v_max) + end +end + +varnames(::typeof(cons2cons), ::TrafficFlowLWREquations1D) = ("car-density",) +varnames(::typeof(cons2prim), ::TrafficFlowLWREquations1D) = ("car-density",) + +""" + initial_condition_convergence_test(x, t, equations::TrafficFlowLWREquations1D) + +A smooth initial condition used for convergence tests. +""" +function initial_condition_convergence_test(x, t, equations::TrafficFlowLWREquations1D) + c = 2.0 + A = 1.0 + L = 1 + f = 1 / L + omega = 2 * pi * f + scalar = c + A * sin(omega * (x[1] - t)) + + return SVector(scalar) +end + +""" + source_terms_convergence_test(u, x, t, equations::TrafficFlowLWREquations1D) + +Source terms used for convergence tests in combination with +[`initial_condition_convergence_test`](@ref). +""" +@inline function source_terms_convergence_test(u, x, t, + equations::TrafficFlowLWREquations1D) + # Same settings as in `initial_condition` + c = 2.0 + A = 1.0 + L = 1 + f = 1 / L + omega = 2 * pi * f + du = omega * cos(omega * (x[1] - t)) * + (-1 - equations.v_max * (2 * sin(omega * (x[1] - t)) + 3)) + + return SVector(du) +end + +# Calculate 1D flux in for a single point +@inline function flux(u, orientation::Integer, equations::TrafficFlowLWREquations1D) + return SVector(equations.v_max * u[1] * (1.0 - u[1])) +end + +# Calculate maximum wave speed for local Lax-Friedrichs-type dissipation +@inline function max_abs_speed_naive(u_ll, u_rr, orientation::Integer, + equations::TrafficFlowLWREquations1D) + λ_max = max(abs(equations.v_max * (1.0 - 2 * u_ll[1])), + abs(equations.v_max * (1.0 - 2 * u_rr[1]))) +end + +# Calculate minimum and maximum wave speeds for HLL-type fluxes +@inline function min_max_speed_naive(u_ll, u_rr, orientation::Integer, + equations::TrafficFlowLWREquations1D) + jac_L = equations.v_max * (1.0 - 2 * u_ll[1]) + jac_R = equations.v_max * (1.0 - 2 * u_rr[1]) + + λ_min = min(jac_L, jac_R) + λ_max = max(jac_L, jac_R) + + return λ_min, λ_max +end + +@inline function min_max_speed_davis(u_ll, u_rr, orientation::Integer, + equations::TrafficFlowLWREquations1D) + min_max_speed_naive(u_ll, u_rr, orientation, equations) +end + +@inline function max_abs_speeds(u, equations::TrafficFlowLWREquations1D) + return (abs(equations.v_max * (1.0 - 2 * u[1])),) +end + +# Convert conservative variables to primitive +@inline cons2prim(u, equations::TrafficFlowLWREquations1D) = u + +# Convert conservative variables to entropy variables +@inline cons2entropy(u, equations::TrafficFlowLWREquations1D) = u + +# Calculate entropy for a conservative state `cons` +@inline entropy(u::Real, ::TrafficFlowLWREquations1D) = 0.5 * u^2 +@inline entropy(u, equations::TrafficFlowLWREquations1D) = entropy(u[1], equations) + +# Calculate total energy for a conservative state `cons` +@inline energy_total(u::Real, ::TrafficFlowLWREquations1D) = 0.5 * u^2 +@inline energy_total(u, equations::TrafficFlowLWREquations1D) = energy_total(u[1], + equations) +end # @muladd diff --git a/test/test_structured_1d.jl b/test/test_structured_1d.jl index f0eecfa9acd..fea06554c57 100644 --- a/test/test_structured_1d.jl +++ b/test/test_structured_1d.jl @@ -138,6 +138,21 @@ end @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 end end + +@trixi_testset "elixir_traffic_flow_lwr_greenlight.jl" begin + @test_trixi_include(joinpath(EXAMPLES_DIR, + "elixir_traffic_flow_lwr_greenlight.jl"), + l2=[0.2005523261652845], + linf=[0.5052827913468407]) + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end +end end # Clean up afterwards: delete Trixi.jl output directory diff --git a/test/test_tree_1d.jl b/test/test_tree_1d.jl index 4654f6313f7..8b470278ffd 100644 --- a/test/test_tree_1d.jl +++ b/test/test_tree_1d.jl @@ -47,6 +47,9 @@ isdir(outdir) && rm(outdir, recursive = true) # FDSBP methods on the TreeMesh include("test_tree_1d_fdsbp.jl") + + # Traffic flow LWR + include("test_tree_1d_traffic_flow_lwr.jl") end # Coverage test for all initial conditions diff --git a/test/test_tree_1d_traffic_flow_lwr.jl b/test/test_tree_1d_traffic_flow_lwr.jl new file mode 100644 index 00000000000..54412e314b3 --- /dev/null +++ b/test/test_tree_1d_traffic_flow_lwr.jl @@ -0,0 +1,42 @@ +module TestExamples1DTrafficFlowLWR + +using Test +using Trixi + +include("test_trixi.jl") + +EXAMPLES_DIR = pkgdir(Trixi, "examples", "tree_1d_dgsem") + +@testset "Traffic-flow LWR" begin +#! format: noindent + +@trixi_testset "elixir_traffic_flow_lwr_convergence.jl" begin + @test_trixi_include(joinpath(EXAMPLES_DIR, + "elixir_traffic_flow_lwr_convergence.jl"), + l2=[0.0008455067389588569], + linf=[0.004591951086623913]) + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end +end + +@trixi_testset "elixir_traffic_flow_lwr_trafficjam.jl" begin + @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_traffic_flow_lwr_trafficjam.jl"), + l2=[0.1761758135539748], linf=[0.5]) + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end +end +end + +end # module From c5e743aa1b229562132e3bbfbd936e995404739f Mon Sep 17 00:00:00 2001 From: Simon Candelaresi <10759273+SimonCan@users.noreply.github.com> Date: Tue, 20 Feb 2024 18:38:26 +0000 Subject: [PATCH 32/63] WIP: Sc/polytropic 2d wave speed (#1816) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Added coupling converters. * Added generic converter_function for structured 2d meshes. * Added example elixir for coupling converters. * Cleaned up converter coupling elixir. * Added equations in coupling converters. * Added converter functions. * Added identity converter function. * Autoformat for converter coupling implementation. * Added coupled converter elixir. * Corrected file name of coupled converters test. * Removed redundant doc string. * Added function signature in doc string. * Removed coverage_override in coupled tests. * Removed old commented code. * Update make.jl Added interface coupling docs to the main menu. * Update make.jl Moved converter coupling section. * Create coupling.md * Update coupling.md Added some documentation on coupling converters. * Removed troublesome AnalysisCallbackCoupled from test. * Chenged coupling converter function. * Changed coupling converter function and updated tests. * Sepcialized coupling function call. * Removed volume coupling from documentation to avoit confusion. * Update src/coupling_converters/coupling_converters.jl Co-authored-by: Hendrik Ranocha * Removed redundant converter function for coupling. * Removed redundant coupling converter file mentioned in some files. * Autoreformatted. * Removed old coupled elixir and replaced it with one using converter functions. * Updated errors for coupled tests. * Corrected test results for coupled equations. * Corrected comment. * Removed coupled test from special tests. * Removed coupled test from specials. * Chaned the coupling function to the identity. * Updated coupling tests. * Updated errors for coupled test. * Added advice about binary compatability for coupled equations in the documentation. * Typo. * Added numerical fluxes. * Corrected rs copy routine. Now loop over this semi's components. * Reformatted equations source file. * Removed problemating include of time_integration.jl. * Removed export of deleted methods. * Reverted to old version of compressible Euler multicomponent with no support for structured grid. * Renamed documentation file for multi-physics coupling. * Renamed doc reference. * Update src/semidiscretization/semidiscretization_coupled.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/src/multi-physics_coupling.md Co-authored-by: Michael Schlottke-Lakemper * Update docs/src/multi-physics_coupling.md Co-authored-by: Michael Schlottke-Lakemper * Update docs/src/multi-physics_coupling.md Co-authored-by: Michael Schlottke-Lakemper * Reinstated structured_2d_dgsem coupled in special tests. * Update examples/structured_2d_dgsem/elixir_advection_coupled.jl Co-authored-by: Michael Schlottke-Lakemper * Renamed CouplingFunction to CouplingConverter. * Update src/semidiscretization/semidiscretization_coupled.jl Co-authored-by: Michael Schlottke-Lakemper * Cleaned the copy of coupled boundary values. * Reduced time span for example coupling elixir. * Removed redundant loop. * Applied formatter. * Removed default coupling covnerter function. * Moved coupling converter function into elixir. * Apply suggestions from code review Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com> * Update docs/make.jl Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com> * Removed coupling_converters.jl from the include. * Corrected introduced issue with coupling boundary copy. The latest change to clean up the boundary copying introduced a bug related to the determination of the wrong node indices. This is now corrected. * Corrected comment on final simulation time. * Updated errors for coupled test to reflect changed final simulation time. * Added miladd. * Corrected coordinate finding in semidiscretization_coupled. * Fixed issued related to memory allocation. * Corrected loop over semidiscretization. * Removed commented out code. * Fixed type instability with loops over semidiscretizations using lispy tuple programming. * Removed obsolete code. * Fixed another typa instability in coupled semidiscretization. * Cleaning up of the coupled semidiscretization. * Autoformatted coupled semidiscretization. * Fixed last type instability in coupling. * Autoformatter on semidiscretization. * Fixed bug in boundary values copy that arose when coupling multiple systems. * aplpied autoformatter on coupled semidiscretization. * Extended the structured 2d example elixir for the coupled advection to 4 semidiscretizations. This hase two purpuses: 1. Users are given an example fro 2d coupling avoiding common pitfalls. 2. This increases the code coverege for the test. * Updated test results for coupled advection in 2d to reflect the 4 semidiscretizations that are now used. * Added correct errors for tests for the coupled adveciton equations in structured 2d. * Update examples/structured_2d_dgsem/elixir_advection_coupled.jl Co-authored-by: Erik Faulhaber <44124897+efaulhaber@users.noreply.github.com> * Update examples/structured_2d_dgsem/elixir_advection_coupled.jl Co-authored-by: Erik Faulhaber <44124897+efaulhaber@users.noreply.github.com> * Update src/semidiscretization/semidiscretization_coupled.jl Co-authored-by: Erik Faulhaber <44124897+efaulhaber@users.noreply.github.com> * Update src/semidiscretization/semidiscretization_coupled.jl Co-authored-by: Erik Faulhaber <44124897+efaulhaber@users.noreply.github.com> * Update src/semidiscretization/semidiscretization_coupled.jl Co-authored-by: Erik Faulhaber <44124897+efaulhaber@users.noreply.github.com> * Update src/semidiscretization/semidiscretization_coupled.jl Co-authored-by: Erik Faulhaber <44124897+efaulhaber@users.noreply.github.com> * Update src/semidiscretization/semidiscretization_coupled.jl Co-authored-by: Erik Faulhaber <44124897+efaulhaber@users.noreply.github.com> * Update src/semidiscretization/semidiscretization_coupled.jl Co-authored-by: Erik Faulhaber <44124897+efaulhaber@users.noreply.github.com> * Update src/semidiscretization/semidiscretization_coupled.jl Co-authored-by: Erik Faulhaber <44124897+efaulhaber@users.noreply.github.com> * Corrected foreach_enumerate implementation. * Fix closing parens * Remove unused recursive rhs! * Pass equations to converter function * Apply formatting * Reverted copy_to_coupled_boundary to previou version to avoid type instability. * Corrected computation of coupled semidiscretizations and fixed memory issue. * Removed redundant nelements function, as it is no longer used. * Applied autoformatter. * Added max_abs_speed_naive( and max_abs_speed_naive for PolytropicEulerEquations2D. * Reverted coupling elixir to main branch version. The modified version should be part of a different PR. * Removed some modified coupling code as this should be part of a different PR. * Reverted changes on ooupling semidiscretization as this should be part of a different PR. * Reverted changes partaining the coupling PR. * Removed changes partaining coupling PR. * REverted to version including elixir_euler_warm_bubble.jl tests. * Update src/equations/polytropic_euler_2d.jl Co-authored-by: Andrew Winters * Update src/equations/polytropic_euler_2d.jl Co-authored-by: Andrew Winters * Update src/equations/polytropic_euler_2d.jl Co-authored-by: Andrew Winters * Update src/equations/polytropic_euler_2d.jl Co-authored-by: Andrés Rueda-Ramírez * Update src/equations/polytropic_euler_2d.jl Co-authored-by: Andrés Rueda-Ramírez * Update src/equations/polytropic_euler_2d.jl Co-authored-by: Daniel Doehring * Added consistency and rotation test for LAx-friedrich fluxes for polytropic equations in 2d. * Applied auto-formatter on polytropic 2d equation. * Update src/equations/polytropic_euler_2d.jl Co-authored-by: Andrew Winters --------- Co-authored-by: Michael Schlottke-Lakemper Co-authored-by: Hendrik Ranocha Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com> Co-authored-by: Erik Faulhaber <44124897+efaulhaber@users.noreply.github.com> Co-authored-by: Andrew Winters Co-authored-by: Andrés Rueda-Ramírez Co-authored-by: Daniel Doehring Co-authored-by: iomsn --- src/equations/polytropic_euler_2d.jl | 40 ++++++++++++++++++++++++++++ test/test_unit.jl | 24 +++++++++++++++++ 2 files changed, 64 insertions(+) diff --git a/src/equations/polytropic_euler_2d.jl b/src/equations/polytropic_euler_2d.jl index f5d2f7b0bad..e900fd64073 100644 --- a/src/equations/polytropic_euler_2d.jl +++ b/src/equations/polytropic_euler_2d.jl @@ -301,6 +301,46 @@ end return abs(v1) + c, abs(v2) + c end +# Calculate maximum wave speed for local Lax-Friedrichs-type dissipation as the +# maximum velocity magnitude plus the maximum speed of sound +@inline function max_abs_speed_naive(u_ll, u_rr, orientation::Integer, + equations::PolytropicEulerEquations2D) + rho_ll, v1_ll, v2_ll = cons2prim(u_ll, equations) + rho_rr, v1_rr, v2_rr = cons2prim(u_rr, equations) + + # Get the velocity value in the appropriate direction + if orientation == 1 + v_ll = v1_ll + v_rr = v1_rr + else # orientation == 2 + v_ll = v2_ll + v_rr = v2_rr + end + # Calculate sound speeds (we have p = kappa * rho^gamma) + c_ll = sqrt(equations.gamma * equations.kappa * rho_ll^(equations.gamma - 1)) + c_rr = sqrt(equations.gamma * equations.kappa * rho_rr^(equations.gamma - 1)) + + λ_max = max(abs(v_ll), abs(v_rr)) + max(c_ll, c_rr) +end + +@inline function max_abs_speed_naive(u_ll, u_rr, normal_direction::AbstractVector, + equations::PolytropicEulerEquations2D) + rho_ll, v1_ll, v2_ll = cons2prim(u_ll, equations) + rho_rr, v1_rr, v2_rr = cons2prim(u_rr, equations) + + # Calculate normal velocities and sound speed (we have p = kappa * rho^gamma) + # left + v_ll = (v1_ll * normal_direction[1] + + v2_ll * normal_direction[2]) + c_ll = sqrt(equations.gamma * equations.kappa * rho_ll^(equations.gamma - 1)) + # right + v_rr = (v1_rr * normal_direction[1] + + v2_rr * normal_direction[2]) + c_rr = sqrt(equations.gamma * equations.kappa * rho_rr^(equations.gamma - 1)) + + return max(abs(v_ll), abs(v_rr)) + max(c_ll, c_rr) * norm(normal_direction) +end + # Convert conservative variables to primitive @inline function cons2prim(u, equations::PolytropicEulerEquations2D) rho, rho_v1, rho_v2 = u diff --git a/test/test_unit.jl b/test/test_unit.jl index 3b8dc3c4331..c1379587cc8 100644 --- a/test/test_unit.jl +++ b/test/test_unit.jl @@ -858,6 +858,30 @@ end end end +@timed_testset "Consistency check for Lax-Friedrich flux: Polytropic CEE" begin + for gamma in [1.4, 1.0, 5 / 3] + kappa = 0.5 # Scaling factor for the pressure. + equations = PolytropicEulerEquations2D(gamma, kappa) + u = SVector(1.1, -0.5, 2.34) + + orientations = [1, 2] + for orientation in orientations + @test flux_lax_friedrichs(u, u, orientation, equations) ≈ + flux(u, orientation, equations) + end + + normal_directions = [SVector(1.0, 0.0), + SVector(0.0, 1.0), + SVector(0.5, -0.5), + SVector(-1.2, 0.3)] + + for normal_direction in normal_directions + @test flux_lax_friedrichs(u, u, normal_direction, equations) ≈ + flux(u, normal_direction, equations) + end + end +end + @timed_testset "Consistency check for HLL flux with Davis wave speed estimates: LEE" begin flux_hll = FluxHLL(min_max_speed_davis) From e98a76b92fa1272b547b2abc997cfb1d885012f4 Mon Sep 17 00:00:00 2001 From: Hendrik Ranocha Date: Wed, 21 Feb 2024 11:02:15 +0100 Subject: [PATCH 33/63] improve benchmarks --- benchmark/benchmarks.jl | 12 ++++++++---- benchmark/run_benchmarks.jl | 4 ++++ 2 files changed, 12 insertions(+), 4 deletions(-) diff --git a/benchmark/benchmarks.jl b/benchmark/benchmarks.jl index 15d1d96c05f..0d6fabcd4a9 100644 --- a/benchmark/benchmarks.jl +++ b/benchmark/benchmarks.jl @@ -2,6 +2,9 @@ # readability #! format: off +using Pkg +Pkg.activate(@__DIR__) + using BenchmarkTools using Trixi @@ -47,13 +50,14 @@ end let SUITE["latency"] = BenchmarkGroup() SUITE["latency"]["default_example"] = @benchmarkable run( - `$(Base.julia_cmd()) -e 'using Trixi; trixi_include(default_example())'`) seconds=60 + `$(Base.julia_cmd()) --project=$(@__DIR__) -e 'using Trixi; trixi_include(default_example())'`) seconds=60 for polydeg in [3, 7] command = "using Trixi; trixi_include(joinpath(examples_dir(), \"tree_2d_dgsem\", \"elixir_advection_extended.jl\"), tspan=(0.0, 1.0e-10), polydeg=$(polydeg), save_restart=TrivialCallback(), save_solution=TrivialCallback())" - SUITE["latency"]["polydeg_$polydeg"] = @benchmarkable run($`$(Base.julia_cmd()) -e $command`) seconds=60 + SUITE["latency"]["polydeg_$polydeg"] = @benchmarkable run( + $`$(Base.julia_cmd()) --project=$(@__DIR__) -e $command`) seconds=60 end SUITE["latency"]["euler_2d"] = @benchmarkable run( - `$(Base.julia_cmd()) -e 'using Trixi; trixi_include(joinpath(examples_dir(), "tree_2d_dgsem", "elixir_euler_kelvin_helmholtz_instability.jl"), tspan=(0.0, 1.0e-10), save_restart=TrivialCallback(), save_solution=TrivialCallback())'`) seconds=60 + `$(Base.julia_cmd()) --project=$(@__DIR__) -e 'using Trixi; trixi_include(joinpath(examples_dir(), "tree_2d_dgsem", "elixir_euler_kelvin_helmholtz_instability.jl"), tspan=(0.0, 1.0e-10), save_solution=TrivialCallback())'`) seconds=60 SUITE["latency"]["mhd_2d"] = @benchmarkable run( - `$(Base.julia_cmd()) -e 'using Trixi; trixi_include(joinpath(examples_dir(), "tree_2d_dgsem", "elixir_mhd_blast_wave.jl"), tspan=(0.0, 1.0e-10), save_solution=TrivialCallback())'`) seconds=60 + `$(Base.julia_cmd()) --project=$(@__DIR__) -e 'using Trixi; trixi_include(joinpath(examples_dir(), "tree_2d_dgsem", "elixir_mhd_blast_wave.jl"), tspan=(0.0, 1.0e-10), save_solution=TrivialCallback())'`) seconds=60 end diff --git a/benchmark/run_benchmarks.jl b/benchmark/run_benchmarks.jl index 3a92a9ba700..e4e15223ea7 100644 --- a/benchmark/run_benchmarks.jl +++ b/benchmark/run_benchmarks.jl @@ -1,3 +1,7 @@ +using Pkg +Pkg.activate(@__DIR__) +Pkg.develop(PackageSpec(path=dirname(@__DIR__))) +Pkg.instantiate() using PkgBenchmark using Trixi From 40b73cfde2a707dfc8d76ea92712a2287fd2e9e2 Mon Sep 17 00:00:00 2001 From: Hendrik Ranocha Date: Wed, 21 Feb 2024 11:12:54 +0100 Subject: [PATCH 34/63] format benchmarks --- benchmark/run_benchmarks.jl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/benchmark/run_benchmarks.jl b/benchmark/run_benchmarks.jl index e4e15223ea7..7b8c25752f8 100644 --- a/benchmark/run_benchmarks.jl +++ b/benchmark/run_benchmarks.jl @@ -1,6 +1,6 @@ using Pkg Pkg.activate(@__DIR__) -Pkg.develop(PackageSpec(path=dirname(@__DIR__))) +Pkg.develop(PackageSpec(path = dirname(@__DIR__))) Pkg.instantiate() using PkgBenchmark From c3c0986a2eaf52a145cd59ab591ea3af75b40571 Mon Sep 17 00:00:00 2001 From: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com> Date: Wed, 21 Feb 2024 11:39:41 +0100 Subject: [PATCH 35/63] Create Downgrade.yml (second try) (#1848) * add downgrade.yml and bump compats * also downgrade test/Project.toml * bump lower compat for ForwardDiff in tests * allow older version of HDF5 * allow newest versions of Makie and CairoMakie * allow newest version of T8code * remove compat 0.11 from CairoMakie --- .github/workflows/Downgrade.yml | 86 +++++++++++++++++++++++++++++++++ Project.toml | 24 ++++----- test/Project.toml | 6 +-- 3 files changed, 101 insertions(+), 15 deletions(-) create mode 100644 .github/workflows/Downgrade.yml diff --git a/.github/workflows/Downgrade.yml b/.github/workflows/Downgrade.yml new file mode 100644 index 00000000000..c84b1026d1b --- /dev/null +++ b/.github/workflows/Downgrade.yml @@ -0,0 +1,86 @@ +name: Downgrade + +on: + pull_request: + paths-ignore: + - 'AUTHORS.md' + - 'CITATION.bib' + - 'CONTRIBUTING.md' + - 'LICENSE.md' + - 'NEWS.md' + - 'README.md' + - '.zenodo.json' + - '.github/workflows/benchmark.yml' + - '.github/workflows/CompatHelper.yml' + - '.github/workflows/TagBot.yml' + - 'benchmark/**' + - 'docs/**' + - 'utils/**' + workflow_dispatch: + +# Cancel redundant CI tests automatically +concurrency: + group: ${{ github.workflow }}-${{ github.ref }} + cancel-in-progress: true + +jobs: + downgrade_test: + if: "!contains(github.event.head_commit.message, 'skip ci')" + # We could also include the Julia version as in + # name: ${{ matrix.trixi_test }} - ${{ matrix.os }} - Julia ${{ matrix.version }} - ${{ matrix.arch }} - ${{ github.event_name }} + # to be more specific. However, that requires us updating the required CI tests whenever we update Julia. + name: Downgrade ${{ matrix.trixi_test }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }} + runs-on: ${{ matrix.os }} + strategy: + fail-fast: false + matrix: + version: + - '1.9' + # - '~1.9.0-0' # including development versions + # - 'nightly' + os: + - ubuntu-latest + arch: + - x64 + trixi_test: + # - tree_part1 + # - tree_part2 + # - tree_part3 + # - tree_part4 + # - tree_part5 + # - tree_part6 + # - structured + # - p4est_part1 + # - p4est_part2 + # - t8code_part1 + # - unstructured_dgmulti + # - parabolic + # - paper_self_gravitating_gas_dynamics + # - misc_part1 + # - misc_part2 + # - performance_specializations_part1 + # - performance_specializations_part2 + # - mpi + - threaded + steps: + - uses: actions/checkout@v4 + - uses: julia-actions/setup-julia@v1 + with: + version: ${{ matrix.version }} + arch: ${{ matrix.arch }} + - run: julia -e 'using InteractiveUtils; versioninfo(verbose=true)' + - uses: julia-actions/cache@v1 + - uses: julia-actions/julia-downgrade-compat@v1 + with: + skip: LinearAlgebra,Printf,SparseArrays,DiffEqBase + projects: ., test + - uses: julia-actions/julia-buildpkg@v1 + env: + PYTHON: "" + - name: Run tests without coverage + uses: julia-actions/julia-runtest@v1 + with: + coverage: false + env: + PYTHON: "" + TRIXI_TEST: ${{ matrix.trixi_test }} diff --git a/Project.toml b/Project.toml index af3e6b4d078..9bed045637a 100644 --- a/Project.toml +++ b/Project.toml @@ -62,17 +62,17 @@ DiffEqCallbacks = "2.25" Downloads = "1.6" EllipsisNotation = "1.0" FillArrays = "0.13.2, 1" -ForwardDiff = "0.10.18" -HDF5 = "0.14, 0.15, 0.16, 0.17" +ForwardDiff = "0.10.24" +HDF5 = "0.16.10, 0.17" IfElse = "0.1" LinearAlgebra = "1" LinearMaps = "2.7, 3.0" -LoopVectorization = "0.12.118" +LoopVectorization = "0.12.151" MPI = "0.20" Makie = "0.19, 0.20" MuladdMacro = "0.2.2" -Octavian = "0.3.5" -OffsetArrays = "1.3" +Octavian = "0.3.21" +OffsetArrays = "1.12" P4est = "0.4.9" Polyester = "0.7.5" PrecompileTools = "1.1" @@ -81,19 +81,19 @@ RecipesBase = "1.1" Reexport = "1.0" Requires = "1.1" SciMLBase = "1.90, 2" -Setfield = "0.8, 1" +Setfield = "1" SimpleUnPack = "1.1" SparseArrays = "1" -StartUpDG = "0.17" -Static = "0.3, 0.4, 0.5, 0.6, 0.7, 0.8" +StartUpDG = "0.17.7" +Static = "0.8.7" StaticArrayInterface = "1.4" -StaticArrays = "1" -StrideArrays = "0.1.18" -StructArrays = "0.6" +StaticArrays = "1.5" +StrideArrays = "0.1.26" +StructArrays = "0.6.11" SummationByPartsOperators = "0.5.41" T8code = "0.4.3, 0.5" TimerOutputs = "0.5.7" -Triangulate = "2.0" +Triangulate = "2.2" TriplotBase = "0.1" TriplotRecipes = "0.1" TrixiBase = "0.1.1" diff --git a/test/Project.toml b/test/Project.toml index ecae0ac0900..a376c2805ea 100644 --- a/test/Project.toml +++ b/test/Project.toml @@ -13,13 +13,13 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" [compat] Aqua = "0.8" -CairoMakie = "0.6, 0.7, 0.8, 0.9, 0.10" +CairoMakie = "0.10" Downloads = "1" -ForwardDiff = "0.10" +ForwardDiff = "0.10.24" LinearAlgebra = "1" MPI = "0.20" OrdinaryDiffEq = "6.49.1" -Plots = "1.16" +Plots = "1.19" Printf = "1" Random = "1" Test = "1" From 1b2abd00e9b74d2cd185b0d06c5cf3182011e6c4 Mon Sep 17 00:00:00 2001 From: ArseniyKholod <119304909+ArseniyKholod@users.noreply.github.com> Date: Wed, 21 Feb 2024 12:48:03 +0200 Subject: [PATCH 36/63] Doc: Core aspects of the basic setup (#1699) * Doc: Core aspects of the basic setup * update pictures * Update innards_of_the_basic_setup.jl * mention ODE-Solvers * Revert "Revert "Merge branch 'main' into semidiscretization-doc"" This reverts commit 85d6e8b50261885ad198ae4036e8599189912e56. * Revert "Merge branch 'main' into semidiscretization-doc" This reverts commit b8f8b0bc167a476b3dead39f6aadf4fe43601e7d, reversing changes made to bb518f50053cef054220fd35542f52a47214a997. * Update docs/literate/src/files/innards_of_the_basic_setup.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/innards_of_the_basic_setup.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/innards_of_the_basic_setup.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/innards_of_the_basic_setup.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/innards_of_the_basic_setup.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/innards_of_the_basic_setup.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/innards_of_the_basic_setup.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/innards_of_the_basic_setup.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/innards_of_the_basic_setup.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/innards_of_the_basic_setup.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/innards_of_the_basic_setup.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/innards_of_the_basic_setup.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/innards_of_the_basic_setup.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/innards_of_the_basic_setup.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/innards_of_the_basic_setup.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/innards_of_the_basic_setup.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/innards_of_the_basic_setup.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/innards_of_the_basic_setup.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/innards_of_the_basic_setup.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/innards_of_the_basic_setup.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/innards_of_the_basic_setup.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/make.jl Co-authored-by: Michael Schlottke-Lakemper * Rename innards_of_the_basic_setup.jl to behind_the_scenes_simulation_setup.jl * add plot scripts * Format_and_last_review_changes * spell+output_directory_figures * spell * N->polydeg * add README for plots * line length <=100 * Update docs/literate/src/files/behind_the_scenes_simulation_setup_plots/README.md * add empty lines * Update docs/literate/src/files/behind_the_scenes_simulation_setup.jl Co-authored-by: Andrew Winters * Update docs/literate/src/files/behind_the_scenes_simulation_setup.jl Co-authored-by: Andrew Winters * Update docs/literate/src/files/behind_the_scenes_simulation_setup.jl Co-authored-by: Andrew Winters * Update docs/literate/src/files/behind_the_scenes_simulation_setup.jl Co-authored-by: Andrew Winters * Update docs/literate/src/files/behind_the_scenes_simulation_setup.jl Co-authored-by: Andrew Winters * Update docs/literate/src/files/behind_the_scenes_simulation_setup.jl Co-authored-by: Andrew Winters * Update docs/literate/src/files/behind_the_scenes_simulation_setup.jl Co-authored-by: Andrew Winters * Update docs/literate/src/files/behind_the_scenes_simulation_setup.jl Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com> * mention method of lines * Update behind_the_scenes_simulation_setup.jl * Update behind_the_scenes_simulation_setup.jl * Update docs/literate/src/files/behind_the_scenes_simulation_setup.jl Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com> * Update docs/literate/src/files/behind_the_scenes_simulation_setup.jl Co-authored-by: Daniel Doehring * Update docs/literate/src/files/behind_the_scenes_simulation_setup.jl Co-authored-by: Daniel Doehring * Update docs/literate/src/files/behind_the_scenes_simulation_setup.jl Co-authored-by: Daniel Doehring * Update docs/literate/src/files/behind_the_scenes_simulation_setup.jl Co-authored-by: Daniel Doehring * Update docs/literate/src/files/behind_the_scenes_simulation_setup.jl Co-authored-by: Daniel Doehring * Update docs/literate/src/files/behind_the_scenes_simulation_setup.jl Co-authored-by: Daniel Doehring * Update docs/literate/src/files/behind_the_scenes_simulation_setup.jl Co-authored-by: Daniel Doehring * Update docs/literate/src/files/behind_the_scenes_simulation_setup.jl Co-authored-by: Daniel Doehring * simplify rhs description * format * add interpolation to mortars * Update behind_the_scenes_simulation_setup.jl * Update docs/literate/src/files/behind_the_scenes_simulation_setup.jl * Update docs/literate/src/files/behind_the_scenes_simulation_setup.jl Co-authored-by: Daniel Doehring * Update docs/literate/src/files/behind_the_scenes_simulation_setup.jl Co-authored-by: Daniel Doehring * Update docs/literate/src/files/behind_the_scenes_simulation_setup.jl Co-authored-by: Daniel Doehring * Update docs/literate/src/files/behind_the_scenes_simulation_setup.jl Co-authored-by: Daniel Doehring * add resizability explanation * Update docs/literate/src/files/behind_the_scenes_simulation_setup.jl Co-authored-by: Daniel Doehring * format * add introduction as 2nd tutorial * fix * Update docs/literate/src/files/behind_the_scenes_simulation_setup.jl Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com> * add unsafe_wrap explanation --------- Co-authored-by: Michael Schlottke-Lakemper Co-authored-by: Andrew Winters Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com> Co-authored-by: Daniel Doehring --- .../behind_the_scenes_simulation_setup.jl | 253 ++++++++++++++++++ .../Project.toml | 2 + .../README.md | 15 ++ ...scretizationHyperbolic_structure_figure.jl | 64 +++++ .../src/generate_boundary_figure.jl | 190 +++++++++++++ .../src/generate_elements_figure.jl | 117 ++++++++ .../src/generate_interfaces_figure.jl | 157 +++++++++++ .../src/generate_mortars_figure.jl | 166 ++++++++++++ .../src/generate_nodes_figure.jl | 6 + .../src/generate_treemesh_figure.jl | 26 ++ .../src/rhs_structure_figure.jl | 43 +++ .../src/semidiscretize_structure_figure.jl | 51 ++++ docs/literate/src/files/index.jl | 45 ++-- docs/make.jl | 3 +- 14 files changed, 1119 insertions(+), 19 deletions(-) create mode 100644 docs/literate/src/files/behind_the_scenes_simulation_setup.jl create mode 100644 docs/literate/src/files/behind_the_scenes_simulation_setup_plots/Project.toml create mode 100644 docs/literate/src/files/behind_the_scenes_simulation_setup_plots/README.md create mode 100644 docs/literate/src/files/behind_the_scenes_simulation_setup_plots/src/SemidiscretizationHyperbolic_structure_figure.jl create mode 100644 docs/literate/src/files/behind_the_scenes_simulation_setup_plots/src/generate_boundary_figure.jl create mode 100644 docs/literate/src/files/behind_the_scenes_simulation_setup_plots/src/generate_elements_figure.jl create mode 100644 docs/literate/src/files/behind_the_scenes_simulation_setup_plots/src/generate_interfaces_figure.jl create mode 100644 docs/literate/src/files/behind_the_scenes_simulation_setup_plots/src/generate_mortars_figure.jl create mode 100644 docs/literate/src/files/behind_the_scenes_simulation_setup_plots/src/generate_nodes_figure.jl create mode 100644 docs/literate/src/files/behind_the_scenes_simulation_setup_plots/src/generate_treemesh_figure.jl create mode 100644 docs/literate/src/files/behind_the_scenes_simulation_setup_plots/src/rhs_structure_figure.jl create mode 100644 docs/literate/src/files/behind_the_scenes_simulation_setup_plots/src/semidiscretize_structure_figure.jl diff --git a/docs/literate/src/files/behind_the_scenes_simulation_setup.jl b/docs/literate/src/files/behind_the_scenes_simulation_setup.jl new file mode 100644 index 00000000000..c93660e9bc1 --- /dev/null +++ b/docs/literate/src/files/behind_the_scenes_simulation_setup.jl @@ -0,0 +1,253 @@ +#src # Behind the scenes of a simulation setup + +# This tutorial will guide you through a simple Trixi.jl setup ("elixir"), giving an overview of +# what happens in the background during the initialization of a simulation. While the setup +# described herein does not cover all details, it involves relatively stable parts of Trixi.jl that +# are unlikely to undergo significant changes in the near future. The goal is to clarify some of +# the more fundamental, *technical* concepts that are applicable to a variety of +# (also more complex) configurations. + +# Trixi.jl follows the [method of lines](http://www.scholarpedia.org/article/Method_of_lines) concept for solving partial differential equations (PDEs). +# Firstly, the PDEs are reduced to a (potentially huge) system of +# ordinary differential equations (ODEs) by discretizing the spatial derivatives. Subsequently, +# these generated ODEs may be solved with methods available in OrdinaryDiffEq.jl or those specifically +# implemented in Trixi.jl. The following steps elucidate the process of transitioning from PDEs to +# ODEs within the framework of Trixi.jl. + +# ## Basic setup + +# Import essential libraries and specify an equation. + +using Trixi, OrdinaryDiffEq +equations = LinearScalarAdvectionEquation2D((-0.2, 0.7)) + +# Generate a spatial discretization using a [`TreeMesh`](@ref) with a pre-coarsened set of cells. + +coordinates_min = (-2.0, -2.0) +coordinates_max = (2.0, 2.0) + +coarsening_patches = ((type = "box", coordinates_min = [0.0, -2.0], + coordinates_max = [2.0, 0.0]),) + +mesh = TreeMesh(coordinates_min, coordinates_max, initial_refinement_level = 2, + n_cells_max = 30_000, + coarsening_patches = coarsening_patches) + +# The created `TreeMesh` looks like the following: + +# ![TreeMesh_example](https://github.com/trixi-framework/Trixi.jl/assets/119304909/d5ef76ee-8246-4730-a692-b472c06063a3) + +# Instantiate a [`DGSEM`](@ref) solver with a user-specified polynomial degree. The solver +# will define `polydeg + 1` [Gauss-Lobatto nodes](https://en.wikipedia.org/wiki/Gaussian_quadrature#Gauss%E2%80%93Lobatto_rules) and their associated weights within +# the reference interval ``[-1, 1]`` in each spatial direction. These nodes will be subsequently +# used to approximate solutions on each leaf cell of the `TreeMesh`. + +solver = DGSEM(polydeg = 3) + +# Gauss-Lobatto nodes with `polydeg = 3`: + +# ![Gauss-Lobatto_nodes_example](https://github.com/trixi-framework/Trixi.jl/assets/119304909/1d894611-801e-4f75-bff0-d77ca1c672e5) + +# ## Overview of the [`SemidiscretizationHyperbolic`](@ref) type + +# At this stage, all necessary components for configuring the spatial discretization are in place. +# The remaining task is to combine these components into a single structure that will be used +# throughout the entire simulation process. This is where [`SemidiscretizationHyperbolic`](@ref) +# comes into play. + +semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition_convergence_test, + solver) + +# The constructor for the `SemidiscretizationHyperbolic` object calls numerous sub-functions to +# perform the necessary initialization steps. A brief description of the key sub-functions is +# provided below. + + +# - `init_elements(leaf_cell_ids, mesh, equations, dg.basis, RealT, uEltype)` + +# The fundamental elements for approximating the solution are the leaf +# cells. The solution is constructed as a polynomial of the degree specified in the `DGSEM` +# solver in each spatial direction on each leaf cell. This polynomial approximation is evaluated +# at the Gauss-Lobatto nodes mentioned earlier. The `init_elements` function extracts +# these leaf cells from the `TreeMesh`, assigns them the label "elements", records their +# coordinates, and maps the Gauss-Lobatto nodes from the 1D interval ``[-1, 1]`` onto each coordinate axis +# of every element. + + +# ![elements_example](https://github.com/trixi-framework/Trixi.jl/assets/119304909/9f486670-b579-4e42-8697-439540c8bbb4) + +# The visualization of elements with nodes shown here includes spaces between elements, which do +# not exist in reality. This spacing is included only for illustrative purposes to underscore the +# separation of elements and the independent projection of nodes onto each element. + + +# - `init_interfaces(leaf_cell_ids, mesh, elements)` + +# At this point, the elements with nodes have been defined; however, they lack the necessary +# communication functionality. This is crucial because the local solution polynomials on the +# elements are not independent of each other. Furthermore, nodes on the boundary of adjacent +# elements share the same spatial location, which requires a method to combine this into a +# meaningful solution. +# Here [Riemann solvers](https://en.wikipedia.org/wiki/Riemann_solver#Approximate_solvers) +# come into play which can handle the principal ambiguity of a multi-valued solution at the +# same spatial location. + +# As demonstrated earlier, the elements can have varying sizes. Let us initially consider +# neighbors with equal size. For these elements, the `init_interfaces` function generates +# interfaces that store information about adjacent elements, their relative positions, and +# allocate containers for sharing solution data between neighbors during the solution process. + +# In our visualization, these interfaces would conceptually resemble tubes connecting the +# corresponding elements. + +# ![interfaces_example](https://github.com/trixi-framework/Trixi.jl/assets/119304909/bc3b6b02-afbc-4371-aaf7-c7bdc5a6c540) + + +# - `init_mortars(leaf_cell_ids, mesh, elements, dg.mortar)` + +# Returning to the consideration of different sizes among adjacent elements, within the +# `TreeMesh`, adjacent leaf cells can vary in side length by a maximum factor of two. This +# implies that a large element has one neighbor of +# equal size with a connection through an interface, or two neighbors at half the size, +# requiring a connection through so called "mortars". In 3D, a large element would have +# four small neighbor elements. + +# Mortars store information about the connected elements, their relative positions, and allocate +# containers for storing the solutions along the boundaries between these elements. + +# Due to the differing sizes of adjacent elements, it is not feasible to directly map boundary +# nodes of adjacent elements. Therefore, the concept of mortars employs a mass-conserving +# interpolation function to map boundary nodes from a larger element to a smaller one. + +# In our visualization, mortars are represented as branched tubes. + +# ![mortars_example](https://github.com/trixi-framework/Trixi.jl/assets/119304909/43a95a60-3a31-4b1f-8724-14049e7a0481) + + +# - `init_boundaries(leaf_cell_ids, mesh, elements)` + +# In order to apply boundary conditions, it is necessary to identify the locations of the +# boundaries. Therefore, we initialize a "boundaries" object, which records the elements that +# contain boundaries, specifies which side of an element is a boundary, stores the coordinates +# of boundary nodes, and allocates containers for managing solutions at these boundaries. + +# In our visualization, boundaries and their corresponding nodes are highlighted with green, +# semi-transparent lines. + +# ![boundaries_example](https://github.com/trixi-framework/Trixi.jl/assets/119304909/21996b20-4a22-4dfb-b16a-e2c22c2f29fe) + +# All the structures mentioned earlier are collected as a cache of type `NamedTuple`. Subsequently, +# an object of type `SemidiscretizationHyperbolic` is initialized using this cache, initial and +# boundary conditions, equations, mesh and solver. + +# In conclusion, the primary purpose of a `SemidiscretizationHyperbolic` is to collect equations, +# the geometric representation of the domain, and approximation instructions, creating specialized +# structures to interconnect these components in a manner that enables their utilization for +# the numerical solution of partial differential equations (PDEs). + +# As evident from the earlier description of `SemidiscretizationHyperbolic`, it comprises numerous +# functions called subsequently. Without delving into details, the structure of the primary calls +# are illustrated as follows: + +# ![SemidiscretizationHyperbolic_structure](https://github.com/trixi-framework/Trixi.jl/assets/119304909/8bf59422-0537-4d7a-9f13-d9b2253c19d7) + +# ## Overview of the [`semidiscretize`](@ref) function + +# At this stage, we have defined the equations and configured the domain's discretization. The +# final step before solving is to select a suitable time span and apply the corresponding initial +# conditions, which are already stored in the initialized `SemidiscretizationHyperbolic` object. + +# The purpose of the [`semidiscretize`](@ref) function is to wrap the semidiscretization as an +# `ODEProblem` within the specified time interval. During this procedure the approximate solution +# is created at the given initial time via the specified `initial_condition` function from the +# `SemidiscretizationHyperbolic` object. This `ODEProblem` can be subsequently passed to the +# `solve` function from the [OrdinaryDiffEq.jl](https://github.com/SciML/OrdinaryDiffEq.jl) package +# or to [`Trixi.solve`](@ref). + +ode = semidiscretize(semi, (0.0, 1.0)); + +# The `semidiscretize` function involves a deep tree of subsequent calls, with the primary ones +# explained below. + + +# - `allocate_coefficients(mesh, equations, solver, cache)` + +# To apply initial conditions, a data structure ("container") needs to be generated to store the +# initial values of the target variables for each node within each element. + +# Since only one-dimensional `Array`s are `resize!`able in Julia, we use `Vector`s as an internal +# storage for the target variables and `resize!` them whenever needed, e.g. to change the number +# of elements. Then, during the solving process the same memory is reused by `unsafe_wrap`ping +# multi-dimensional `Array`s around the internal storage. + +# - `wrap_array(u_ode, semi)` + +# As previously noted, `u_ode` is constructed as a 1D vector to ensure compatibility with +# OrdinaryDiffEq.jl. However, for internal use within Trixi.jl, identifying which part of the +# vector relates to specific variables, elements, or nodes can be challenging. + +# This is why the `u_ode` vector is wrapped by the `wrap_array` function using `unsafe_wrap` +# to form a multidimensional array `u`. In this array, the first dimension corresponds to +# variables, followed by N dimensions corresponding to nodes for each of N space dimensions. +# The last dimension corresponds to the elements. +# Consequently, navigation within this multidimensional array becomes noticeably easier. + +# "Wrapping" in this context involves the creation of a reference to the same storage location +# but with an alternative structural representation. This approach enables the use of both +# instances `u` and `u_ode` as needed, so that changes are simultaneously reflected in both. +# This is possible because, from a storage perspective, they share the same stored data, while +# access to this data is provided in different ways. + + +# - `compute_coefficients!(u, initial_conditions, t, mesh::DG, equations, solver, cache)` + +# Now the variable `u`, intended to store solutions, has been allocated and wrapped, it is time +# to apply the initial conditions. The `compute_coefficients!` function calculates the initial +# conditions for each variable at every node within each element and properly stores them in the +# `u` array. + +# At this stage, the `semidiscretize` function has all the necessary components to initialize and +# return an `ODEProblem` object, which will be used by the `solve` function to compute the +# solution. + +# In summary, the internal workings of `semidiscretize` with brief descriptions can be presented +# as follows. + +# ![semidiscretize_structure](https://github.com/trixi-framework/Trixi.jl/assets/119304909/491eddc4-aadb-4e29-8c76-a7c821d0674e) + +# ## Functions `solve` and `rhs!` + +# Once the `ODEProblem` object is initialized, the `solve` function and one of the ODE solvers from +# the OrdinaryDiffEq.jl package can be utilized to compute an approximated solution using the +# instructions contained in the `ODEProblem` object. + +sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false), dt = 0.01, + save_everystep = false); + +# Since the `solve` function and the ODE solver have no knowledge +# of a particular spatial discretization, it is necessary to define a +# "right-hand-side function", `rhs!`, within Trixi.jl. + +# Trixi.jl includes a set of `rhs!` functions designed to compute `du`, i.e., +# ``\frac{\partial u}{\partial t}`` according to the structure +# of the setup. These `rhs!` functions calculate interface, mortars, and boundary fluxes, in +# addition to surface and volume integrals, in order to construct the `du` vector. This `du` vector +# is then used by the time integration method to obtain the solution at the subsequent time step. +# The `rhs!` function is called by time integration methods in each iteration of the solve loop +# within OrdinaryDiffEq.jl, with arguments `du`, `u`, `semidiscretization`, and the current time. + +# Trixi.jl uses a two-levels approach for `rhs!` functions. The first level is limited to a +# single function for each `semidiscretization` type, and its role is to redirect data to the +# target `rhs!` for specific solver and mesh types. This target `rhs!` function is responsible +# for calculating `du`. + +# Path from the `solve` function call to the appropriate `rhs!` function call: + +# ![rhs_structure](https://github.com/trixi-framework/Trixi.jl/assets/119304909/dbea9a0e-25a4-4afa-855e-01f1ad619982) + +# Computed solution: + +using Plots +plot(sol) +pd = PlotData2D(sol) +plot!(getmesh(pd)) diff --git a/docs/literate/src/files/behind_the_scenes_simulation_setup_plots/Project.toml b/docs/literate/src/files/behind_the_scenes_simulation_setup_plots/Project.toml new file mode 100644 index 00000000000..43aec5b7f54 --- /dev/null +++ b/docs/literate/src/files/behind_the_scenes_simulation_setup_plots/Project.toml @@ -0,0 +1,2 @@ +[deps] +Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" diff --git a/docs/literate/src/files/behind_the_scenes_simulation_setup_plots/README.md b/docs/literate/src/files/behind_the_scenes_simulation_setup_plots/README.md new file mode 100644 index 00000000000..011b5c75860 --- /dev/null +++ b/docs/literate/src/files/behind_the_scenes_simulation_setup_plots/README.md @@ -0,0 +1,15 @@ +# Plots for the tutorial "Behind the scenes of a simulation setup" + +To create all the images for the tutorial, execute the following command from the directory of this `README.md`: +```julia +pkg> activate . +julia> include.(readdir("src"; join=true)) +``` +To create all images from a different directory, substitute `"src"` with the path to the `src` +folder. The resulting images will be generated in your current directory as PNG files. + +To generate a specific image, run the following command while replacing `"path/to/src"` and `"file_name"` with the appropriate values: +```julia +pkg> activate . +julia> include(joinpath("path/to/src", "file_name")) +``` \ No newline at end of file diff --git a/docs/literate/src/files/behind_the_scenes_simulation_setup_plots/src/SemidiscretizationHyperbolic_structure_figure.jl b/docs/literate/src/files/behind_the_scenes_simulation_setup_plots/src/SemidiscretizationHyperbolic_structure_figure.jl new file mode 100644 index 00000000000..cae7b19d470 --- /dev/null +++ b/docs/literate/src/files/behind_the_scenes_simulation_setup_plots/src/SemidiscretizationHyperbolic_structure_figure.jl @@ -0,0 +1,64 @@ +using Plots +plot(Shape([(-2.3,4.5), (2.35,4.5), (2.35,2.5), (-2.3,2.5)]), linecolor="black", fillcolor="white", label=false,linewidth=2, size=(800,600), showaxis=false, grid=false, xlim=(-2.4,2.8), ylim=(-25,5.5)) +annotate!(2.3, 3.5, ("SemidiscretizationHyperbolic(mesh, equations, initial_conditions, solver; source_terms, +boundary_conditions, RealT, uEltype, initial_cache) ", 10, :black, :right)) +annotate!(-2.3, 1.5, ("creates and returns SemidiscretizationHyperbolic object, initialized using a mesh, equations, +initial_conditions, boundary_conditions, source_terms, solver and cache", 9, :black, :left)) +plot!([-1.2,-1.2],[0.6,-2],arrow=true,color=:black,linewidth=2,label="") +plot!([-1.2,-1.4],[0.6,-2],arrow=true,color=:black,linewidth=2,label="") +plot!([-1.2,-1.],[0.6,-2],arrow=true,color=:black,linewidth=2,label="") +annotate!(-1, -0.7, ("specialized for mesh +and solver types", 9, :black, :left)) +plot!([1.25,1.25],[0.6,-2],arrow=true,color=:black,linewidth=2,label="") +plot!([1.25,1.05],[0.6,-2],arrow=true,color=:black,linewidth=2,label="") +plot!([1.25,1.45],[0.6,-2],arrow=true,color=:black,linewidth=2,label="") +annotate!(1.48, -0.7, ("specialized for mesh +and boundary_conditions +types", 9, :black, :left)) + +plot!(Shape([(-2.3,-2), (-0.1,-2), (-0.1,-4), (-2.3,-4)]), linecolor="black", fillcolor="white", label=false,linewidth=2) +annotate!(-1.2, -3, ("create_cache(mesh::TreeMesh, equations, + solver::Dg, RealT, uEltype)", 10, :black, :center)) +plot!([-2.22,-2.22],[-4,-22],arrow=false,color=:black,linewidth=2,label="") + +plot!(Shape([(-0.05,-2), (2.6,-2), (2.6,-4), (-0.05,-4)]), linecolor="black", fillcolor="white", label=false,linewidth=2) +annotate!(1.27, -3, ("digest_boundary_conditions(boundary_conditions, + mesh, solver, cache)", 10, :black, :center)) +annotate!(2.6, -5, ("if necessary, converts passed boundary_conditions + into a suitable form for processing by Trixi.jl", 9, :black, :right)) + +plot!(Shape([(-2,-6), (-0.55,-6), (-0.55,-7.1), (-2,-7.1)]), linecolor="black", fillcolor="white", label=false,linewidth=2) +annotate!(-1.95, -6.5, ("local_leaf_cells(mesh.tree)", 10, :black, :left)) +annotate!(-2, -7.5, ("returns cells for which an element needs to be created (i.e. all leaf cells)", 9, :black, :left)) +plot!([-2.22,-2],[-6.5,-6.5],arrow=true,color=:black,linewidth=2,label="") + +plot!(Shape([(-2,-9), (1.73,-9), (1.73,-10.1), (-2,-10.1)]), linecolor="black", fillcolor="white", label=false,linewidth=2) +annotate!(-1.95, -9.5, ("init_elements(leaf_cell_ids, mesh, equations, dg.basis, RealT, uEltype)", 10, :black, :left)) +annotate!(-2, -10.5, ("creates and initializes elements, projects Gauss-Lobatto basis onto each of them", 9, :black, :left)) +plot!([-2.22,-2],[-9.5,-9.5],arrow=true,color=:black,linewidth=2,label="") + +plot!(Shape([(-2,-12), (0.4,-12), (0.4,-13.1), (-2,-13.1)]), linecolor="black", fillcolor="white", label=false,linewidth=2) +annotate!(-1.95, -12.5, ("init_interfaces(leaf_cell_ids, mesh, elements)", 10, :black, :left)) +annotate!(-2, -13.5, ("creates and initializes interfaces between each pair of adjacent elements of the same size", 9, :black, :left)) +plot!([-2.22,-2],[-12.5,-12.5],arrow=true,color=:black,linewidth=2,label="") + +plot!(Shape([(-2,-15), (0.5,-15), (0.5,-16.1), (-2,-16.1)]), linecolor="black", fillcolor="white", label=false,linewidth=2) +annotate!(-1.95, -15.5, ("init_boundaries(leaf_cell_ids, mesh, elements)", 10, :black, :left)) +annotate!(-2, -17, ("creates and initializes boundaries, remembers each boundary element, as well as the coordinates of +each boundary node", 9, :black, :left)) +plot!([-2.22,-2],[-15.5,-15.5],arrow=true,color=:black,linewidth=2,label="") + +plot!(Shape([(-1.6,-18), (1.3,-18), (1.3,-19.1), (-1.6,-19.1)]), linecolor="black", fillcolor="white", label=false,linewidth=2) +annotate!(-1.55, -18.5, ("init_mortars(leaf_cell_ids, mesh, elements, dg.mortar)", 10, :black, :left)) +annotate!(-1.6, -20, ("creates and initializes mortars (type of interfaces) between each triple of adjacent coarsened +and corresponding small elements", 9, :black, :left)) +plot!([-2.22,-1.6],[-18.5,-18.5],arrow=true,color=:black,linewidth=2,label="") +annotate!(-2.15, -19, ("2D and 3D", 8, :black, :left)) + +plot!(Shape([(-2,-21), (1.5,-21), (1.5,-23.1), (-2,-23.1)]), linecolor="black", fillcolor="white", label=false,linewidth=2) +annotate!(-1.95, -22, ("create_cache(mesh, equations, dg.volume_integral, dg, uEltype) +for 2D and 3D create_cache(mesh, equations, dg.mortar, uEltype)", 10, :black, :left)) +annotate!(-2, -23.5, ("add specialized parts of the cache required to compute the volume integral, etc.", 9, :black, :left)) +plot!([-2.22,-2],[-22,-22],arrow=true,color=:black,linewidth=2,label="") + +savefig("./SemidiscretizationHyperbolic") \ No newline at end of file diff --git a/docs/literate/src/files/behind_the_scenes_simulation_setup_plots/src/generate_boundary_figure.jl b/docs/literate/src/files/behind_the_scenes_simulation_setup_plots/src/generate_boundary_figure.jl new file mode 100644 index 00000000000..14475d21339 --- /dev/null +++ b/docs/literate/src/files/behind_the_scenes_simulation_setup_plots/src/generate_boundary_figure.jl @@ -0,0 +1,190 @@ +using Plots + +function min(coordinates::Vector{Tuple{Float64, Float64}}, i) + min=coordinates[1][i] + for j in coordinates + if min>j[i] + min=j[i] + end + end + return min +end + +function max(coordinates::Vector{Tuple{Float64, Float64}}, i) + max=coordinates[1][i] + for j in coordinates + if maxj[i] + min=j[i] + end + end + return min +end + +function max(coordinates::Vector{Tuple{Float64, Float64}}, i) + max=coordinates[1][i] + for j in coordinates + if maxj[i] + min=j[i] + end + end + return min +end + +function max(coordinates::Vector{Tuple{Float64, Float64}}, i) + max=coordinates[1][i] + for j in coordinates + if maxj[i] + min=j[i] + end + end + return min +end + +function max(coordinates::Vector{Tuple{Float64, Float64}}, i) + max=coordinates[1][i] + for j in coordinates + if max ("first_steps", "create_first_setup.jl"), "Changing Trixi.jl itself" => ("first_steps", "changing_trixi.jl"), ], + "Behind the scenes of a simulation setup" => "behind_the_scenes_simulation_setup.jl", # Topic: DG semidiscretizations "Introduction to DG methods" => "scalar_linear_advection_1d.jl", "DGSEM with flux differencing" => "DGSEM_FluxDiff.jl", @@ -76,7 +77,7 @@ files = [ # Topic: other stuff "Explicit time stepping" => "time_stepping.jl", "Differentiable programming" => "differentiable_programming.jl", - "Custom semidiscretizations" => "custom_semidiscretization.jl" + "Custom semidiscretizations" => "custom_semidiscretization.jl", ] tutorials = create_tutorials(files) From 88e4a09b919548ad308e94dfe1b515947b581558 Mon Sep 17 00:00:00 2001 From: Hendrik Ranocha Date: Thu, 22 Feb 2024 13:49:15 +0100 Subject: [PATCH 37/63] Update benchmarking docs (#1849) * Update benchmarking docs * Update performance.md * Update docs/src/performance.md Co-authored-by: Daniel Doehring --------- Co-authored-by: Daniel Doehring --- docs/src/performance.md | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/docs/src/performance.md b/docs/src/performance.md index 82d7f501f63..40970e58c5c 100644 --- a/docs/src/performance.md +++ b/docs/src/performance.md @@ -106,7 +106,22 @@ resulting performance improvements of Trixi.jl are given in the following blog p We use [PkgBenchmark.jl](https://github.com/JuliaCI/PkgBenchmark.jl) to provide a standard set of benchmarks for Trixi.jl. The relevant benchmark script is [benchmark/benchmarks.jl](https://github.com/trixi-framework/Trixi.jl/blob/main/benchmark/benchmarks.jl). -You can run a standard set of benchmarks via +To benchmark the changes made in a PR, please proceed as follows: + +1. Check out the latest `main` branch of your Trixi.jl development repository. +2. Check out the latest development branch of your PR. +3. Change your working directory to the `benchmark` directory of Trixi.jl. +4. Execute `julia run_benchmarks.jl`. + +This will take some hours to complete and requires at least 8 GiB of RAM. When everything is finished, some +output files will be created in the `benchmark` directory of Trixi.jl. + +!!! warning + Please note that the benchmark scripts use `--check-bounds=no` at the moment. + Thus, they will not work in any useful way for Julia v1.10 (and newer?), see + [Julia issue #50985](https://github.com/JuliaLang/julia/issues/50985). + +You can also run a standard set of benchmarks manually via ```julia julia> using PkgBenchmark, Trixi From 9f7eadb3c056ee63af051c1397bfe50fa9ba9a47 Mon Sep 17 00:00:00 2001 From: Hendrik Ranocha Date: Thu, 22 Feb 2024 14:13:39 +0100 Subject: [PATCH 38/63] set version to v0.6.10 --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 9bed045637a..221e96643ae 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "Trixi" uuid = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb" authors = ["Michael Schlottke-Lakemper ", "Gregor Gassner ", "Hendrik Ranocha ", "Andrew R. Winters ", "Jesse Chan "] -version = "0.6.10-pre" +version = "0.6.10" [deps] CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2" From 5185abd96a0319599d01d57d196ecabdaa083477 Mon Sep 17 00:00:00 2001 From: Hendrik Ranocha Date: Thu, 22 Feb 2024 14:13:52 +0100 Subject: [PATCH 39/63] set development version to v0.6.11-pre --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 221e96643ae..551e069b934 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "Trixi" uuid = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb" authors = ["Michael Schlottke-Lakemper ", "Gregor Gassner ", "Hendrik Ranocha ", "Andrew R. Winters ", "Jesse Chan "] -version = "0.6.10" +version = "0.6.11-pre" [deps] CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2" From 029ddea44cedc076251a5e6c832af7f0bec4ed90 Mon Sep 17 00:00:00 2001 From: Daniel Doehring Date: Fri, 23 Feb 2024 05:25:00 +0100 Subject: [PATCH 40/63] Own `sqrt` and `log` returning `NaN` for "correct" multi-thread behaviour (#1781) * Introduce NaNMath for unsafe sqrt and log * performance measurements * implement log myself * Try out different log implementation * remove NaNMath, own implementation * remove unrelated * Update src/equations/compressible_euler_2d.jl * NaNSqrt for quasi 1d CEE * fmt * Update src/auxiliary/math.jl * Update src/auxiliary/math.jl * Update src/auxiliary/math.jl * for comparison * Update src/auxiliary/math.jl Co-authored-by: Hendrik Ranocha * Update src/auxiliary/math.jl Co-authored-by: Hendrik Ranocha * llvm version log * Catch ints in sqrt_ * Use sqrt_ log_ everywhere * docu * fmt * replace in comment * try exporting nan funcs * enable SIMD again * Bring back SIMD * doc * Update src/auxiliary/math.jl Co-authored-by: Hendrik Ranocha * Update src/auxiliary/math.jl Co-authored-by: Hendrik Ranocha * docstring fmt * remove redundant docstrings * no own names * fmt * revert unintended * revert * remove unintended * revert * fmt * comments * update test vals * test vals * test vals * Preferences * Update Project.toml * Update src/Trixi.jl * fmt * docstrings * docstrings * docstrings * compat info * Apply suggestions from code review Co-authored-by: Hendrik Ranocha * escape " * fmt * fix benchmarks configuration * skip UUIDs in downgrade CI job * Update src/auxiliary/math.jl Co-authored-by: Hendrik Ranocha * Update Project.toml Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com> --------- Co-authored-by: Hendrik Ranocha Co-authored-by: Hendrik Ranocha Co-authored-by: Joshua Lampert <51029046+JoshuaLampert@users.noreply.github.com> --- .github/workflows/Downgrade.yml | 2 +- Project.toml | 4 ++ src/Trixi.jl | 6 ++ src/auxiliary/math.jl | 97 +++++++++++++++++++++++++++++++++ test/test_parabolic_1d.jl | 12 ++-- test/test_unstructured_2d.jl | 6 +- 6 files changed, 117 insertions(+), 10 deletions(-) diff --git a/.github/workflows/Downgrade.yml b/.github/workflows/Downgrade.yml index c84b1026d1b..dd5d8ee7e32 100644 --- a/.github/workflows/Downgrade.yml +++ b/.github/workflows/Downgrade.yml @@ -72,7 +72,7 @@ jobs: - uses: julia-actions/cache@v1 - uses: julia-actions/julia-downgrade-compat@v1 with: - skip: LinearAlgebra,Printf,SparseArrays,DiffEqBase + skip: LinearAlgebra,Printf,SparseArrays,UUIDs,DiffEqBase projects: ., test - uses: julia-actions/julia-buildpkg@v1 env: diff --git a/Project.toml b/Project.toml index 551e069b934..6b27e6e9999 100644 --- a/Project.toml +++ b/Project.toml @@ -25,6 +25,7 @@ OffsetArrays = "6fe1bfb0-de20-5000-8ca7-80f57d26f881" P4est = "7d669430-f675-4ae7-b43e-fab78ec5a902" Polyester = "f517fe37-dbe3-4b94-8317-1923a5111588" PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a" +Preferences = "21216c6a-2e73-6563-6e65-726566657250" Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7" RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01" Reexport = "189a3867-3050-52da-a836-e630ba90ab69" @@ -46,6 +47,7 @@ Triangulate = "f7e6ffb2-c36d-4f8f-a77e-16e897189344" TriplotBase = "981d1d27-644d-49a2-9326-4793e63143c3" TriplotRecipes = "808ab39a-a642-4abf-81ff-4cb34ebbffa3" TrixiBase = "9a0f1c46-06d5-4909-a5a3-ce25d3fa3284" +UUIDs = "cf7118a7-6976-5b1a-9a39-7adc72f591a4" [weakdeps] Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a" @@ -76,6 +78,7 @@ OffsetArrays = "1.12" P4est = "0.4.9" Polyester = "0.7.5" PrecompileTools = "1.1" +Preferences = "1.3" Printf = "1" RecipesBase = "1.1" Reexport = "1.0" @@ -97,6 +100,7 @@ Triangulate = "2.2" TriplotBase = "0.1" TriplotRecipes = "0.1" TrixiBase = "0.1.1" +UUIDs = "1.6" julia = "1.8" [extras] diff --git a/src/Trixi.jl b/src/Trixi.jl index bf0986084af..b7f7767a9d8 100644 --- a/src/Trixi.jl +++ b/src/Trixi.jl @@ -76,6 +76,12 @@ using TrixiBase: TrixiBase using SimpleUnPack: @pack! using DataStructures: BinaryHeap, FasterForward, extract_all! +using UUIDs: UUID +using Preferences: @load_preference, set_preferences! + +const _PREFERENCE_SQRT = @load_preference("sqrt", "sqrt_Trixi_NaN") +const _PREFERENCE_LOG = @load_preference("log", "log_Trixi_NaN") + # finite difference SBP operators using SummationByPartsOperators: AbstractDerivativeOperator, AbstractNonperiodicDerivativeOperator, DerivativeOperator, diff --git a/src/auxiliary/math.jl b/src/auxiliary/math.jl index 38ea0bda8c8..9e3aaa181bf 100644 --- a/src/auxiliary/math.jl +++ b/src/auxiliary/math.jl @@ -5,6 +5,103 @@ @muladd begin #! format: noindent +const TRIXI_UUID = UUID("a7f1ee26-1774-49b1-8366-f1abc58fbfcb") + +""" + Trixi.set_sqrt_type(type; force = true) + +Set the `type` of the square root function to be used in Trixi.jl. +The default is `"sqrt_Trixi_NaN"` which returns `NaN` for negative arguments +instead of throwing an error. +Alternatively, you can set `type` to `"sqrt_Base"` to use the Julia built-in `sqrt` function +which provides a stack-trace of the error which might come in handy when debugging code. +""" +function set_sqrt_type(type; force = true) + @assert type == "sqrt_Trixi_NaN"||type == "sqrt_Base" "Only allowed `sqrt` function types are `\"sqrt_Trixi_NaN\"` and `\"sqrt_Base\"`" + set_preferences!(TRIXI_UUID, "sqrt" => type, force = force) + @info "Please restart Julia and reload Trixi.jl for the `sqrt` computation change to take effect" +end + +@static if _PREFERENCE_SQRT == "sqrt_Trixi_NaN" + """ + Trixi.sqrt(x::Real) + + Custom square root function which returns `NaN` for negative arguments instead of throwing an error. + This is required to ensure [correct results for multithreaded computations](https://github.com/trixi-framework/Trixi.jl/issues/1766) + when using the [`Polyester` package](https://github.com/JuliaSIMD/Polyester.jl), + i.e., using the `@batch` macro instead of the Julia built-in `@threads` macro, see [`@threaded`](@ref). + + We dispatch this function for `Float64, Float32, Float16` to the LLVM intrinsics + `llvm.sqrt.f64`, `llvm.sqrt.f32`, `llvm.sqrt.f16` as for these the LLVM functions can be used out-of the box, + i.e., they return `NaN` for negative arguments. + In principle, one could also use the `sqrt_llvm` call, but for transparency and consistency with [`log`](@ref) we + spell out the datatype-dependent functions here. + For other types, such as integers or dual numbers required for algorithmic differentiation, we + fall back to the Julia built-in `sqrt` function after a check for negative arguments. + Since these cases are not performance critical, the check for negativity does not hurt here + and can (as of now) even be optimized away by the compiler due to the implementation of `sqrt` in Julia. + + When debugging code, it might be useful to change the implementation of this function to redirect to + the Julia built-in `sqrt` function, as this reports the exact place in code where the domain is violated + in the stacktrace. + + See also [`Trixi.set_sqrt_type`](@ref). + """ + @inline sqrt(x::Real) = x < zero(x) ? oftype(x, NaN) : Base.sqrt(x) + + # For `sqrt` we could use the `sqrt_llvm` call, ... + #@inline sqrt(x::Union{Float64, Float32, Float16}) = Base.sqrt_llvm(x) + + # ... but for transparency and consistency we use the direct LLVM calls here. + @inline sqrt(x::Float64) = ccall("llvm.sqrt.f64", llvmcall, Float64, (Float64,), x) + @inline sqrt(x::Float32) = ccall("llvm.sqrt.f32", llvmcall, Float32, (Float32,), x) + @inline sqrt(x::Float16) = ccall("llvm.sqrt.f16", llvmcall, Float16, (Float16,), x) +end + +""" + Trixi.set_log_type(type; force = true) + +Set the `type` of the (natural) `log` function to be used in Trixi.jl. +The default is `"sqrt_Trixi_NaN"` which returns `NaN` for negative arguments +instead of throwing an error. +Alternatively, you can set `type` to `"sqrt_Base"` to use the Julia built-in `sqrt` function +which provides a stack-trace of the error which might come in handy when debugging code. +""" +function set_log_type(type; force = true) + @assert type == "log_Trixi_NaN"||type == "log_Base" "Only allowed log function types are `\"log_Trixi_NaN\"` and `\"log_Base\"`." + set_preferences!(TRIXI_UUID, "log" => type, force = force) + @info "Please restart Julia and reload Trixi.jl for the `log` computation change to take effect" +end + +@static if _PREFERENCE_LOG == "log_Trixi_NaN" + """ + Trixi.log(x::Real) + + Custom natural logarithm function which returns `NaN` for negative arguments instead of throwing an error. + This is required to ensure [correct results for multithreaded computations](https://github.com/trixi-framework/Trixi.jl/issues/1766) + when using the [`Polyester` package](https://github.com/JuliaSIMD/Polyester.jl), + i.e., using the `@batch` macro instead of the Julia built-in `@threads` macro, see [`@threaded`](@ref). + + We dispatch this function for `Float64, Float32, Float16` to the respective LLVM intrinsics + `llvm.log.f64`, `llvm.log.f32`, `llvm.log.f16` as for this the LLVM functions can be used out-of the box, i.e., + they return `NaN` for negative arguments. + For other types, such as integers or dual numbers required for algorithmic differentiation, we + fall back to the Julia built-in `log` function after a check for negative arguments. + Since these cases are not performance critical, the check for negativity does not hurt here. + + When debugging code, it might be useful to change the implementation of this function to redirect to + the Julia built-in `log` function, as this reports the exact place in code where the domain is violated + in the stacktrace. + + See also [`Trixi.set_log_type`](@ref). + """ + @inline log(x::Real) = x < zero(x) ? oftype(x, NaN) : Base.log(x) + + @inline log(x::Float64) = ccall("llvm.log.f64", llvmcall, Float64, (Float64,), x) + @inline log(x::Float32) = ccall("llvm.log.f32", llvmcall, Float32, (Float32,), x) + @inline log(x::Float16) = ccall("llvm.log.f16", llvmcall, Float16, (Float16,), x) +end + """ ln_mean(x, y) diff --git a/test/test_parabolic_1d.jl b/test/test_parabolic_1d.jl index c1cfec052fe..41d375e2e31 100644 --- a/test/test_parabolic_1d.jl +++ b/test/test_parabolic_1d.jl @@ -195,14 +195,14 @@ end Prandtl = prandtl_number(), gradient_variables = GradientVariablesEntropy()), l2=[ - 2.459359632523962e-5, - 2.3928390718460263e-5, - 0.00011252414117082376, + 2.4593501090944024e-5, + 2.3928163240907908e-5, + 0.00011252309905552921, ], linf=[ - 0.0001185052018830568, - 0.00018987717854305393, - 0.0009597503607920999, + 0.0001185048754512863, + 0.0001898766501935486, + 0.0009597450028770993, ]) # Ensure that we do not have excessive memory allocations # (e.g., from type instabilities) diff --git a/test/test_unstructured_2d.jl b/test/test_unstructured_2d.jl index 139b423ead1..83b8318c926 100644 --- a/test/test_unstructured_2d.jl +++ b/test/test_unstructured_2d.jl @@ -710,9 +710,9 @@ end 1.0066867437607972e-13, 6.889210012578449e-14, 1.568290814572709e-13], - linf=[5.963762816918461e-10, - 5.08869890669672e-11, - 1.1581377523661729e-10, + linf=[2.353373051988683e-10, + 2.801543719233024e-11, + 3.930469838486772e-11, 4.61017890529547e-11], tspan=(0.0, 0.1), atol=1.0e-11) From 62610bb6a858eedfaf8fe61f074aa757441a08d1 Mon Sep 17 00:00:00 2001 From: Patrick Ersing <114223904+patrickersing@users.noreply.github.com> Date: Fri, 23 Feb 2024 05:30:08 +0100 Subject: [PATCH 41/63] Separation of TrixiShallowWater.jl (#1809) * remove wet_dry functionality for SWE-1D * remove wet_dry functionality for SWE-2D * remove twolayer equations * remove limiters from swe_quasi_1d * remove export of min_max_speed_chen_noelle * remove elixirs * update news.md * add unit tests to increase coverage * Change news.md according to code review Co-authored-by: Hendrik Ranocha --------- Co-authored-by: Andrew Winters Co-authored-by: Hendrik Ranocha --- NEWS.md | 13 + .../elixir_shallowwater_conical_island.jl | 114 --- .../elixir_shallowwater_parabolic_bowl.jl | 119 --- ...ixir_shallowwater_well_balanced_wet_dry.jl | 207 ----- .../elixir_shallowwater_beach.jl | 123 --- .../elixir_shallowwater_parabolic_bowl.jl | 119 --- ...lixir_shallowwater_twolayer_convergence.jl | 60 -- .../elixir_shallowwater_twolayer_dam_break.jl | 94 -- ...xir_shallowwater_twolayer_well_balanced.jl | 86 -- ...ixir_shallowwater_well_balanced_wet_dry.jl | 172 ---- .../elixir_shallowwater_conical_island.jl | 117 --- .../elixir_shallowwater_parabolic_bowl.jl | 121 --- ...lixir_shallowwater_twolayer_convergence.jl | 60 -- ...xir_shallowwater_twolayer_well_balanced.jl | 81 -- ...ixir_shallowwater_well_balanced_wet_dry.jl | 206 ----- ...ixir_shallowwater_three_mound_dam_break.jl | 133 --- ...lixir_shallowwater_twolayer_convergence.jl | 63 -- .../elixir_shallowwater_twolayer_dam_break.jl | 147 ---- ...xir_shallowwater_twolayer_well_balanced.jl | 81 -- src/Trixi.jl | 12 +- src/callbacks_stage/callbacks_stage.jl | 2 - .../positivity_shallow_water.jl | 89 -- .../positivity_shallow_water_dg1d.jl | 89 -- .../positivity_shallow_water_dg2d.jl | 90 -- src/equations/equations.jl | 2 - src/equations/numerical_fluxes.jl | 23 - src/equations/shallow_water_1d.jl | 187 +--- src/equations/shallow_water_2d.jl | 266 +----- src/equations/shallow_water_quasi_1d.jl | 37 +- src/equations/shallow_water_two_layer_1d.jl | 511 ----------- src/equations/shallow_water_two_layer_2d.jl | 805 ------------------ src/solvers/dgsem_tree/indicators.jl | 76 -- src/solvers/dgsem_tree/indicators_1d.jl | 109 --- src/solvers/dgsem_tree/indicators_2d.jl | 110 --- test/test_structured_2d.jl | 78 -- test/test_tree_1d.jl | 2 - test/test_tree_1d_shallowwater.jl | 75 -- test/test_tree_1d_shallowwater_twolayer.jl | 74 -- test/test_tree_2d_part3.jl | 3 - test/test_tree_2d_shallowwater.jl | 79 -- test/test_tree_2d_shallowwater_twolayer.jl | 88 -- test/test_unit.jl | 34 +- test/test_unstructured_2d.jl | 101 --- 43 files changed, 56 insertions(+), 5002 deletions(-) delete mode 100644 examples/structured_2d_dgsem/elixir_shallowwater_conical_island.jl delete mode 100644 examples/structured_2d_dgsem/elixir_shallowwater_parabolic_bowl.jl delete mode 100644 examples/structured_2d_dgsem/elixir_shallowwater_well_balanced_wet_dry.jl delete mode 100644 examples/tree_1d_dgsem/elixir_shallowwater_beach.jl delete mode 100644 examples/tree_1d_dgsem/elixir_shallowwater_parabolic_bowl.jl delete mode 100644 examples/tree_1d_dgsem/elixir_shallowwater_twolayer_convergence.jl delete mode 100644 examples/tree_1d_dgsem/elixir_shallowwater_twolayer_dam_break.jl delete mode 100644 examples/tree_1d_dgsem/elixir_shallowwater_twolayer_well_balanced.jl delete mode 100644 examples/tree_1d_dgsem/elixir_shallowwater_well_balanced_wet_dry.jl delete mode 100644 examples/tree_2d_dgsem/elixir_shallowwater_conical_island.jl delete mode 100644 examples/tree_2d_dgsem/elixir_shallowwater_parabolic_bowl.jl delete mode 100644 examples/tree_2d_dgsem/elixir_shallowwater_twolayer_convergence.jl delete mode 100644 examples/tree_2d_dgsem/elixir_shallowwater_twolayer_well_balanced.jl delete mode 100644 examples/tree_2d_dgsem/elixir_shallowwater_well_balanced_wet_dry.jl delete mode 100644 examples/unstructured_2d_dgsem/elixir_shallowwater_three_mound_dam_break.jl delete mode 100644 examples/unstructured_2d_dgsem/elixir_shallowwater_twolayer_convergence.jl delete mode 100644 examples/unstructured_2d_dgsem/elixir_shallowwater_twolayer_dam_break.jl delete mode 100644 examples/unstructured_2d_dgsem/elixir_shallowwater_twolayer_well_balanced.jl delete mode 100644 src/callbacks_stage/positivity_shallow_water.jl delete mode 100644 src/callbacks_stage/positivity_shallow_water_dg1d.jl delete mode 100644 src/callbacks_stage/positivity_shallow_water_dg2d.jl delete mode 100644 src/equations/shallow_water_two_layer_1d.jl delete mode 100644 src/equations/shallow_water_two_layer_2d.jl delete mode 100644 test/test_tree_1d_shallowwater_twolayer.jl delete mode 100644 test/test_tree_2d_shallowwater_twolayer.jl diff --git a/NEWS.md b/NEWS.md index feccd1f9852..ecc91581e9a 100644 --- a/NEWS.md +++ b/NEWS.md @@ -4,6 +4,19 @@ Trixi.jl follows the interpretation of [semantic versioning (semver)](https://ju used in the Julia ecosystem. Notable changes will be documented in this file for human readability. +## Changes when updating to v0.7 from v0.6.x + +#### Added + +#### Changed + +#### Deprecated + +#### Removed +- Some specialized shallow water specific features are no longer available directly in + Trixi.jl, but are moved to a dedicated repository: [TrixiShallowWater.jl](https://github.com/trixi-framework/TrixiShallowWater.jl). This includes all features related to wetting and drying, as well as the `ShallowWaterTwoLayerEquations1D` and `ShallowWaterTwoLayerEquations2D`. + However, the basic shallow water equations are still part of Trixi.jl. We'll also be updating the TrixiShallowWater.jl documentation with instructions on how to use these relocated features in the future. + ## Changes in the v0.6 lifecycle #### Added diff --git a/examples/structured_2d_dgsem/elixir_shallowwater_conical_island.jl b/examples/structured_2d_dgsem/elixir_shallowwater_conical_island.jl deleted file mode 100644 index e65ed19221e..00000000000 --- a/examples/structured_2d_dgsem/elixir_shallowwater_conical_island.jl +++ /dev/null @@ -1,114 +0,0 @@ - -using OrdinaryDiffEq -using Trixi - -############################################################################### -# Semidiscretization of the shallow water equations -# -# TODO: TrixiShallowWater: wet/dry example elixir - -equations = ShallowWaterEquations2D(gravity_constant = 9.81, H0 = 1.4) - -""" - initial_condition_conical_island(x, t, equations::ShallowWaterEquations2D) - -Initial condition for the [`ShallowWaterEquations2D`](@ref) to test the [`hydrostatic_reconstruction_chen_noelle`](@ref) -and its handling of discontinuous water heights at the start in combination with wetting and -drying. The bottom topography is given by a conical island in the middle of the domain. Around that -island, there is a cylindrical water column at t=0 and the rest of the domain is dry. This -discontinuous water height is smoothed by a logistic function. This simulation uses periodic -boundary conditions. -""" -function initial_condition_conical_island(x, t, equations::ShallowWaterEquations2D) - # Set the background values - - v1 = 0.0 - v2 = 0.0 - - x1, x2 = x - b = max(0.1, 1.0 - 4.0 * sqrt(x1^2 + x2^2)) - - # use a logistic function to transfer water height value smoothly - L = equations.H0 # maximum of function - x0 = 0.3 # center point of function - k = -25.0 # sharpness of transfer - - H = max(b, L / (1.0 + exp(-k * (sqrt(x1^2 + x2^2) - x0)))) - - # It is mandatory to shift the water level at dry areas to make sure the water height h - # stays positive. The system would not be stable for h set to a hard 0 due to division by h in - # the computation of velocity, e.g., (h v1) / h. Therefore, a small dry state threshold - # with a default value of 500*eps() ≈ 1e-13 in double precision, is set in the constructor above - # for the ShallowWaterEquations and added to the initial condition if h = 0. - # This default value can be changed within the constructor call depending on the simulation setup. - H = max(H, b + equations.threshold_limiter) - return prim2cons(SVector(H, v1, v2, b), equations) -end - -initial_condition = initial_condition_conical_island - -############################################################################### -# Get the DG approximation space - -volume_flux = (flux_wintermeyer_etal, flux_nonconservative_wintermeyer_etal) -surface_flux = (FluxHydrostaticReconstruction(flux_hll_chen_noelle, - hydrostatic_reconstruction_chen_noelle), - flux_nonconservative_chen_noelle) - -basis = LobattoLegendreBasis(4) - -indicator_sc = IndicatorHennemannGassnerShallowWater(equations, basis, - alpha_max = 0.5, - alpha_min = 0.001, - alpha_smooth = true, - variable = waterheight_pressure) -volume_integral = VolumeIntegralShockCapturingHG(indicator_sc; - volume_flux_dg = volume_flux, - volume_flux_fv = surface_flux) - -solver = DGSEM(basis, surface_flux, volume_integral) - -############################################################################### -# Get the StructuredMesh and setup a periodic mesh - -coordinates_min = (-1.0, -1.0) -coordinates_max = (1.0, 1.0) - -cells_per_dimension = (16, 16) - -mesh = StructuredMesh(cells_per_dimension, coordinates_min, coordinates_max) - -# Create the semi discretization object -semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver) - -############################################################################### -# ODE solver - -tspan = (0.0, 10.0) -ode = semidiscretize(semi, tspan) - -############################################################################### -# Callbacks - -summary_callback = SummaryCallback() - -analysis_interval = 1000 -analysis_callback = AnalysisCallback(semi, interval = analysis_interval) - -alive_callback = AliveCallback(analysis_interval = analysis_interval) - -save_solution = SaveSolutionCallback(interval = 100, - save_initial_solution = true, - save_final_solution = true) - -callbacks = CallbackSet(summary_callback, analysis_callback, alive_callback, save_solution) - -############################################################################### -# run the simulation - -stage_limiter! = PositivityPreservingLimiterShallowWater(variables = (Trixi.waterheight,)) - -sol = solve(ode, SSPRK43(stage_limiter!); - ode_default_options()..., callback = callbacks); - -summary_callback() # print the timer summary diff --git a/examples/structured_2d_dgsem/elixir_shallowwater_parabolic_bowl.jl b/examples/structured_2d_dgsem/elixir_shallowwater_parabolic_bowl.jl deleted file mode 100644 index bc198f18835..00000000000 --- a/examples/structured_2d_dgsem/elixir_shallowwater_parabolic_bowl.jl +++ /dev/null @@ -1,119 +0,0 @@ - -using OrdinaryDiffEq -using Trixi - -############################################################################### -# Semidiscretization of the shallow water equations -# -# TODO: TrixiShallowWater: wet/dry example elixir - -equations = ShallowWaterEquations2D(gravity_constant = 9.81) - -""" - initial_condition_parabolic_bowl(x, t, equations:: ShallowWaterEquations2D) - -Well-known initial condition to test the [`hydrostatic_reconstruction_chen_noelle`](@ref) and its -wet-dry mechanics. This test has an analytical solution. The initial condition is defined by the -analytical solution at time t=0. The bottom topography defines a bowl and the water level is given -by an oscillating lake. - -The original test and its analytical solution were first presented in -- William C. Thacker (1981) - Some exact solutions to the nonlinear shallow-water wave equations - [DOI: 10.1017/S0022112081001882](https://doi.org/10.1017/S0022112081001882). - -The particular setup below is taken from Section 6.2 of -- Niklas Wintermeyer, Andrew R. Winters, Gregor J. Gassner and Timothy Warburton (2018) - An entropy stable discontinuous Galerkin method for the shallow water equations on - curvilinear meshes with wet/dry fronts accelerated by GPUs - [DOI: 10.1016/j.jcp.2018.08.038](https://doi.org/10.1016/j.jcp.2018.08.038). -""" -function initial_condition_parabolic_bowl(x, t, equations::ShallowWaterEquations2D) - a = 1.0 - h_0 = 0.1 - sigma = 0.5 - ω = sqrt(2 * equations.gravity * h_0) / a - - v1 = -sigma * ω * sin(ω * t) - v2 = sigma * ω * cos(ω * t) - - b = h_0 * ((x[1])^2 + (x[2])^2) / a^2 - - H = sigma * h_0 / a^2 * (2 * x[1] * cos(ω * t) + 2 * x[2] * sin(ω * t) - sigma) + h_0 - - # It is mandatory to shift the water level at dry areas to make sure the water height h - # stays positive. The system would not be stable for h set to a hard 0 due to division by h in - # the computation of velocity, e.g., (h v1) / h. Therefore, a small dry state threshold - # with a default value of 500*eps() ≈ 1e-13 in double precision, is set in the constructor above - # for the ShallowWaterEquations and added to the initial condition if h = 0. - # This default value can be changed within the constructor call depending on the simulation setup. - H = max(H, b + equations.threshold_limiter) - return prim2cons(SVector(H, v1, v2, b), equations) -end - -initial_condition = initial_condition_parabolic_bowl - -############################################################################### -# Get the DG approximation space - -volume_flux = (flux_wintermeyer_etal, flux_nonconservative_wintermeyer_etal) -surface_flux = (FluxHydrostaticReconstruction(flux_hll_chen_noelle, - hydrostatic_reconstruction_chen_noelle), - flux_nonconservative_chen_noelle) - -basis = LobattoLegendreBasis(4) - -indicator_sc = IndicatorHennemannGassnerShallowWater(equations, basis, - alpha_max = 0.6, - alpha_min = 0.001, - alpha_smooth = true, - variable = waterheight_pressure) -volume_integral = VolumeIntegralShockCapturingHG(indicator_sc; - volume_flux_dg = volume_flux, - volume_flux_fv = surface_flux) - -solver = DGSEM(basis, surface_flux, volume_integral) - -############################################################################### - -coordinates_min = (-2.0, -2.0) -coordinates_max = (2.0, 2.0) - -cells_per_dimension = (150, 150) - -mesh = StructuredMesh(cells_per_dimension, coordinates_min, coordinates_max) - -# create the semi discretization object -semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver) - -############################################################################### -# ODE solvers, callbacks etc. - -tspan = (0.0, 1.0) -ode = semidiscretize(semi, tspan) - -summary_callback = SummaryCallback() - -analysis_interval = 1000 -analysis_callback = AnalysisCallback(semi, interval = analysis_interval, - save_analysis = false, - extra_analysis_integrals = (energy_kinetic, - energy_internal)) - -alive_callback = AliveCallback(analysis_interval = analysis_interval) - -save_solution = SaveSolutionCallback(interval = 100, - save_initial_solution = true, - save_final_solution = true) - -callbacks = CallbackSet(summary_callback, analysis_callback, alive_callback, save_solution) - -stage_limiter! = PositivityPreservingLimiterShallowWater(variables = (Trixi.waterheight,)) - -############################################################################### -# run the simulation - -sol = solve(ode, SSPRK43(stage_limiter!); - ode_default_options()..., callback = callbacks); - -summary_callback() # print the timer summary diff --git a/examples/structured_2d_dgsem/elixir_shallowwater_well_balanced_wet_dry.jl b/examples/structured_2d_dgsem/elixir_shallowwater_well_balanced_wet_dry.jl deleted file mode 100644 index 8e492b1ba05..00000000000 --- a/examples/structured_2d_dgsem/elixir_shallowwater_well_balanced_wet_dry.jl +++ /dev/null @@ -1,207 +0,0 @@ - -using OrdinaryDiffEq -using Trixi -using Printf: @printf, @sprintf - -############################################################################### -# Semidiscretization of the shallow water equations -# -# TODO: TrixiShallowWater: wet/dry example elixir - -equations = ShallowWaterEquations2D(gravity_constant = 9.812) - -""" - initial_condition_well_balanced_chen_noelle(x, t, equations:: ShallowWaterEquations2D) - -Initial condition with a complex (discontinuous) bottom topography to test the well-balanced -property for the [`hydrostatic_reconstruction_chen_noelle`](@ref) including dry areas within the -domain. The errors from the analysis callback are not important but the error for this -lake-at-rest test case `∑|H0-(h+b)|` should be around machine roundoff. - -The initial condition is taken from Section 5.2 of the paper: -- Guoxian Chen and Sebastian Noelle (2017) - A new hydrostatic reconstruction scheme based on subcell reconstructions - [DOI:10.1137/15M1053074](https://dx.doi.org/10.1137/15M1053074) -""" -function initial_condition_complex_bottom_well_balanced(x, t, - equations::ShallowWaterEquations2D) - v1 = 0 - v2 = 0 - b = sin(4 * pi * x[1]) + 3 - - if x[1] >= 0.5 - b = sin(4 * pi * x[1]) + 1 - end - - H = max(b, 2.5) - - if x[1] >= 0.5 - H = max(b, 1.5) - end - - # It is mandatory to shift the water level at dry areas to make sure the water height h - # stays positive. The system would not be stable for h set to a hard 0 due to division by h in - # the computation of velocity, e.g., (h v1) / h. Therefore, a small dry state threshold - # with a default value of 500*eps() ≈ 1e-13 in double precision, is set in the constructor above - # for the ShallowWaterEquations and added to the initial condition if h = 0. - # This default value can be changed within the constructor call depending on the simulation setup. - H = max(H, b + equations.threshold_limiter) - return prim2cons(SVector(H, v1, v2, b), equations) -end - -initial_condition = initial_condition_complex_bottom_well_balanced - -############################################################################### -# Get the DG approximation space - -volume_flux = (flux_wintermeyer_etal, flux_nonconservative_wintermeyer_etal) - -surface_flux = (FluxHydrostaticReconstruction(flux_hll_chen_noelle, - hydrostatic_reconstruction_chen_noelle), - flux_nonconservative_chen_noelle) - -basis = LobattoLegendreBasis(3) - -indicator_sc = IndicatorHennemannGassnerShallowWater(equations, basis, - alpha_max = 0.5, - alpha_min = 0.001, - alpha_smooth = true, - variable = waterheight_pressure) -volume_integral = VolumeIntegralShockCapturingHG(indicator_sc; - volume_flux_dg = volume_flux, - volume_flux_fv = surface_flux) - -solver = DGSEM(basis, surface_flux, volume_integral) - -############################################################################### -# Create the StructuredMesh for the domain [0, 1]^2 - -coordinates_min = (0.0, 0.0) -coordinates_max = (1.0, 1.0) - -cells_per_dimension = (16, 16) - -mesh = StructuredMesh(cells_per_dimension, coordinates_min, coordinates_max) - -# create the semi discretization object -semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver) - -############################################################################### -# ODE solvers, callbacks etc. - -tspan = (0.0, 10.0) -ode = semidiscretize(semi, tspan) - -############################################################################### -# Workaround to set a discontinuous water and bottom topography for -# debugging and testing. Essentially, this is a slight augmentation of the -# `compute_coefficients` where the `x` node value passed here is slightly -# perturbed to the left / right in order to set a true discontinuity that avoids -# the doubled value of the LGL nodes at a particular element interface. -# -# Note! The errors from the analysis callback are not important but the error -# for this lake at rest test case `∑|H0-(h+b)|` should be near machine roundoff. - -# point to the data we want to augment -u = Trixi.wrap_array(ode.u0, semi) -# reset the initial condition -for element in eachelement(semi.solver, semi.cache) - for j in eachnode(semi.solver), i in eachnode(semi.solver) - x_node = Trixi.get_node_coords(semi.cache.elements.node_coordinates, equations, - semi.solver, i, j, element) - # We know that the discontinuity is a vertical line. Slightly augment the x value by a factor - # of unit roundoff to avoid the repeted value from the LGL nodes at at interface. - if i == 1 - x_node = SVector(nextfloat(x_node[1]), x_node[2]) - elseif i == nnodes(semi.solver) - x_node = SVector(prevfloat(x_node[1]), x_node[2]) - end - u_node = initial_condition_complex_bottom_well_balanced(x_node, first(tspan), - equations) - Trixi.set_node_vars!(u, u_node, equations, semi.solver, i, j, element) - end -end - -############################################################################### -# Callbacks - -summary_callback = SummaryCallback() - -analysis_interval = 1000 -analysis_callback = AnalysisCallback(semi, interval = analysis_interval, - save_analysis = false) - -alive_callback = AliveCallback(analysis_interval = analysis_interval) - -save_solution = SaveSolutionCallback(interval = 1000, - save_initial_solution = true, - save_final_solution = true) - -stepsize_callback = StepsizeCallback(cfl = 1.0) - -callbacks = CallbackSet(summary_callback, analysis_callback, alive_callback, save_solution, - stepsize_callback) - -stage_limiter! = PositivityPreservingLimiterShallowWater(variables = (Trixi.waterheight,)) - -############################################################################### -# run the simulation - -sol = solve(ode, SSPRK43(stage_limiter!); dt = 1.0, - ode_default_options()..., callback = callbacks, adaptive = false); - -summary_callback() # print the timer summary - -############################################################################### -# Workaround to compute the well-balancedness error for this particular problem -# that has two reference water heights. One for a lake to the left of the -# discontinuous bottom topography `H0_upper = 2.5` and another for a lake to the -# right of the discontinuous bottom topography `H0_lower = 1.5`. - -# Declare a special version of the function to compute the lake-at-rest error -# OBS! The reference water height values are hardcoded for convenience. -function lake_at_rest_error_two_level(u, x, equations::ShallowWaterEquations2D) - h, _, _, b = u - - # For well-balancedness testing with possible wet/dry regions the reference - # water height `H0` accounts for the possibility that the bottom topography - # can emerge out of the water as well as for the threshold offset to avoid - # division by a "hard" zero water heights as well. - if x[1] < 0.5 - H0_wet_dry = max(2.5, b + equations.threshold_limiter) - else - H0_wet_dry = max(1.5, b + equations.threshold_limiter) - end - - return abs(H0_wet_dry - (h + b)) -end - -# point to the data we want to analyze -u = Trixi.wrap_array(sol[end], semi) -# Perform the actual integration of the well-balancedness error over the domain -l1_well_balance_error = Trixi.integrate_via_indices(u, mesh, equations, semi.solver, - semi.cache; - normalize = true) do u, i, j, element, - equations, solver - x_node = Trixi.get_node_coords(semi.cache.elements.node_coordinates, equations, solver, - i, j, element) - # We know that the discontinuity is a vertical line. Slightly augment the x value by a factor - # of unit roundoff to avoid the repeted value from the LGL nodes at at interface. - if i == 1 - x_node = SVector(nextfloat(x_node[1]), x_node[2]) - elseif i == nnodes(semi.solver) - x_node = SVector(prevfloat(x_node[1]), x_node[2]) - end - u_local = Trixi.get_node_vars(u, equations, solver, i, j, element) - return lake_at_rest_error_two_level(u_local, x_node, equations) -end - -# report the well-balancedness lake-at-rest error to the screen -println("─"^100) -println(" Lake-at-rest error for '", Trixi.get_name(equations), "' with ", summary(solver), - " at final time " * @sprintf("%10.8e", tspan[end])) - -@printf(" %-12s:", Trixi.pretty_form_utf(lake_at_rest_error)) -@printf(" % 10.8e", l1_well_balance_error) -println() -println("─"^100) diff --git a/examples/tree_1d_dgsem/elixir_shallowwater_beach.jl b/examples/tree_1d_dgsem/elixir_shallowwater_beach.jl deleted file mode 100644 index 378079ca334..00000000000 --- a/examples/tree_1d_dgsem/elixir_shallowwater_beach.jl +++ /dev/null @@ -1,123 +0,0 @@ - -using OrdinaryDiffEq -using Trixi - -############################################################################### -# Semidiscretization of the shallow water equations -# -# TODO: TrixiShallowWater: wet/dry example elixir - -equations = ShallowWaterEquations1D(gravity_constant = 9.812) - -""" - initial_condition_beach(x, t, equations:: ShallowWaterEquations1D) -Initial condition to simulate a wave running towards a beach and crashing. Difficult test -including both wetting and drying in the domain using slip wall boundary conditions. -The bottom topography is altered to be differentiable on the domain [0,8] and -differs from the reference below. - -The water height and speed functions used here, are adapted from the initial condition -found in section 5.2 of the paper: - - Andreas Bollermann, Sebastian Noelle, Maria Lukáčová-Medvid’ová (2011) - Finite volume evolution Galerkin methods for the shallow water equations with dry beds\n - [DOI: 10.4208/cicp.220210.020710a](https://dx.doi.org/10.4208/cicp.220210.020710a) -""" -function initial_condition_beach(x, t, equations::ShallowWaterEquations1D) - D = 1 - delta = 0.02 - gamma = sqrt((3 * delta) / (4 * D)) - x_a = sqrt((4 * D) / (3 * delta)) * acosh(sqrt(20)) - - f = D + 40 * delta * sech(gamma * (8 * x[1] - x_a))^2 - - # steep curved beach - b = 0.01 + 99 / 409600 * 4^x[1] - - if x[1] >= 6 - H = b - v = 0.0 - else - H = f - v = sqrt(equations.gravity / D) * H - end - - # It is mandatory to shift the water level at dry areas to make sure the water height h - # stays positive. The system would not be stable for h set to a hard 0 due to division by h in - # the computation of velocity, e.g., (h v) / h. Therefore, a small dry state threshold - # with a default value of 500*eps() ≈ 1e-13 in double precision, is set in the constructor above - # for the ShallowWaterEquations and added to the initial condition if h = 0. - # This default value can be changed within the constructor call depending on the simulation setup. - H = max(H, b + equations.threshold_limiter) - return prim2cons(SVector(H, v, b), equations) -end - -initial_condition = initial_condition_beach -boundary_condition = boundary_condition_slip_wall - -############################################################################### -# Get the DG approximation space - -volume_flux = (flux_wintermeyer_etal, flux_nonconservative_wintermeyer_etal) -surface_flux = (FluxHydrostaticReconstruction(flux_hll_chen_noelle, - hydrostatic_reconstruction_chen_noelle), - flux_nonconservative_chen_noelle) - -basis = LobattoLegendreBasis(3) - -indicator_sc = IndicatorHennemannGassnerShallowWater(equations, basis, - alpha_max = 0.5, - alpha_min = 0.001, - alpha_smooth = true, - variable = waterheight_pressure) -volume_integral = VolumeIntegralShockCapturingHG(indicator_sc; - volume_flux_dg = volume_flux, - volume_flux_fv = surface_flux) - -solver = DGSEM(basis, surface_flux, volume_integral) - -############################################################################### -# Create the TreeMesh for the domain [0, 8] - -coordinates_min = 0.0 -coordinates_max = 8.0 - -mesh = TreeMesh(coordinates_min, coordinates_max, - initial_refinement_level = 7, - n_cells_max = 10_000, - periodicity = false) - -# create the semi discretization object -semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver, - boundary_conditions = boundary_condition) - -############################################################################### -# ODE solvers, callbacks etc. - -tspan = (0.0, 10.0) -ode = semidiscretize(semi, tspan) - -summary_callback = SummaryCallback() - -analysis_interval = 1000 -analysis_callback = AnalysisCallback(semi, interval = analysis_interval, - save_analysis = false, - extra_analysis_integrals = (energy_kinetic, - energy_internal)) - -alive_callback = AliveCallback(analysis_interval = analysis_interval) - -save_solution = SaveSolutionCallback(dt = 0.5, - save_initial_solution = true, - save_final_solution = true) - -callbacks = CallbackSet(summary_callback, analysis_callback, alive_callback, save_solution) - -stage_limiter! = PositivityPreservingLimiterShallowWater(variables = (Trixi.waterheight,)) - -############################################################################### -# run the simulation - -sol = solve(ode, SSPRK43(stage_limiter!); - ode_default_options()..., callback = callbacks); - -summary_callback() # print the timer summary diff --git a/examples/tree_1d_dgsem/elixir_shallowwater_parabolic_bowl.jl b/examples/tree_1d_dgsem/elixir_shallowwater_parabolic_bowl.jl deleted file mode 100644 index a586562af7e..00000000000 --- a/examples/tree_1d_dgsem/elixir_shallowwater_parabolic_bowl.jl +++ /dev/null @@ -1,119 +0,0 @@ - -using OrdinaryDiffEq -using Trixi - -############################################################################### -# Semidiscretization of the shallow water equations -# -# TODO: TrixiShallowWater: wet/dry example elixir - -equations = ShallowWaterEquations1D(gravity_constant = 9.81) - -""" - initial_condition_parabolic_bowl(x, t, equations:: ShallowWaterEquations1D) - -Well-known initial condition to test the [`hydrostatic_reconstruction_chen_noelle`](@ref) and its -wet-dry mechanics. This test has analytical solutions. The initial condition is defined by the -analytical solution at time t=0. The bottom topography defines a bowl and the water level is given -by an oscillating lake. - -The original test and its analytical solution in two dimensions were first presented in -- William C. Thacker (1981) - Some exact solutions to the nonlinear shallow-water wave equations - [DOI: 10.1017/S0022112081001882](https://doi.org/10.1017/S0022112081001882). - -The particular setup below is taken from Section 6.2 of -- Niklas Wintermeyer, Andrew R. Winters, Gregor J. Gassner and Timothy Warburton (2018) - An entropy stable discontinuous Galerkin method for the shallow water equations on - curvilinear meshes with wet/dry fronts accelerated by GPUs - [DOI: 10.1016/j.jcp.2018.08.038](https://doi.org/10.1016/j.jcp.2018.08.038). -""" -function initial_condition_parabolic_bowl(x, t, equations::ShallowWaterEquations1D) - a = 1 - h_0 = 0.1 - sigma = 0.5 - ω = sqrt(2 * equations.gravity * h_0) / a - - v = -sigma * ω * sin(ω * t) - - b = h_0 * x[1]^2 / a^2 - - H = sigma * h_0 / a^2 * (2 * x[1] * cos(ω * t) - sigma) + h_0 - - # It is mandatory to shift the water level at dry areas to make sure the water height h - # stays positive. The system would not be stable for h set to a hard 0 due to division by h in - # the computation of velocity, e.g., (h v) / h. Therefore, a small dry state threshold - # with a default value of 500*eps() ≈ 1e-13 in double precision, is set in the constructor above - # for the ShallowWaterEquations and added to the initial condition if h = 0. - # This default value can be changed within the constructor call depending on the simulation setup. - H = max(H, b + equations.threshold_limiter) - return prim2cons(SVector(H, v, b), equations) -end - -initial_condition = initial_condition_parabolic_bowl - -############################################################################### -# Get the DG approximation space - -volume_flux = (flux_wintermeyer_etal, flux_nonconservative_wintermeyer_etal) -surface_flux = (FluxHydrostaticReconstruction(flux_hll_chen_noelle, - hydrostatic_reconstruction_chen_noelle), - flux_nonconservative_chen_noelle) - -basis = LobattoLegendreBasis(5) - -indicator_sc = IndicatorHennemannGassnerShallowWater(equations, basis, - alpha_max = 0.5, - alpha_min = 0.001, - alpha_smooth = true, - variable = waterheight_pressure) -volume_integral = VolumeIntegralShockCapturingHG(indicator_sc; - volume_flux_dg = volume_flux, - volume_flux_fv = surface_flux) - -solver = DGSEM(basis, surface_flux, volume_integral) - -############################################################################### -# Create the TreeMesh for the domain [-2, 2] - -coordinates_min = -2.0 -coordinates_max = 2.0 - -mesh = TreeMesh(coordinates_min, coordinates_max, - initial_refinement_level = 6, - n_cells_max = 10_000) - -# create the semi discretization object -semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver) - -############################################################################### -# ODE solvers, callbacks etc. - -tspan = (0.0, 10.0) -ode = semidiscretize(semi, tspan) - -summary_callback = SummaryCallback() - -analysis_interval = 1000 -analysis_callback = AnalysisCallback(semi, interval = analysis_interval, - save_analysis = false, - extra_analysis_integrals = (energy_kinetic, - energy_internal)) - -alive_callback = AliveCallback(analysis_interval = analysis_interval) - -save_solution = SaveSolutionCallback(interval = 1000, - save_initial_solution = true, - save_final_solution = true) - -callbacks = CallbackSet(summary_callback, analysis_callback, alive_callback, save_solution) - -stage_limiter! = PositivityPreservingLimiterShallowWater(variables = (Trixi.waterheight,)) - -############################################################################### -# run the simulation - -sol = solve(ode, SSPRK43(stage_limiter!); - ode_default_options()..., callback = callbacks); - -summary_callback() # print the timer summary diff --git a/examples/tree_1d_dgsem/elixir_shallowwater_twolayer_convergence.jl b/examples/tree_1d_dgsem/elixir_shallowwater_twolayer_convergence.jl deleted file mode 100644 index e6a01849852..00000000000 --- a/examples/tree_1d_dgsem/elixir_shallowwater_twolayer_convergence.jl +++ /dev/null @@ -1,60 +0,0 @@ - -using OrdinaryDiffEq -using Trixi - -############################################################################### -# Semidiscretization of the two-layer shallow water equations - -equations = ShallowWaterTwoLayerEquations1D(gravity_constant = 10.0, rho_upper = 0.9, - rho_lower = 1.0) - -initial_condition = initial_condition_convergence_test - -############################################################################### -# Get the DG approximation space - -volume_flux = (flux_wintermeyer_etal, flux_nonconservative_ersing_etal) -solver = DGSEM(polydeg = 3, - surface_flux = (flux_wintermeyer_etal, flux_nonconservative_ersing_etal), - volume_integral = VolumeIntegralFluxDifferencing(volume_flux)) - -############################################################################### -# Get the TreeMesh and setup a periodic mesh - -coordinates_min = 0.0 -coordinates_max = sqrt(2.0) -mesh = TreeMesh(coordinates_min, coordinates_max, - initial_refinement_level = 3, - n_cells_max = 10_000, - periodicity = true) - -# create the semi discretization object -semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver, - source_terms = source_terms_convergence_test) - -############################################################################### -# ODE solvers, callbacks etc. - -tspan = (0.0, 1.0) -ode = semidiscretize(semi, tspan) - -summary_callback = SummaryCallback() - -analysis_interval = 500 -analysis_callback = AnalysisCallback(semi, interval = analysis_interval) - -alive_callback = AliveCallback(analysis_interval = analysis_interval) - -save_solution = SaveSolutionCallback(interval = 500, - save_initial_solution = true, - save_final_solution = true) - -callbacks = CallbackSet(summary_callback, analysis_callback, alive_callback, save_solution) - -############################################################################### -# run the simulation - -# use a Runge-Kutta method with automatic (error based) time step size control -sol = solve(ode, RDPK3SpFSAL49(), abstol = 1.0e-8, reltol = 1.0e-8, - save_everystep = false, callback = callbacks); -summary_callback() # print the timer summary diff --git a/examples/tree_1d_dgsem/elixir_shallowwater_twolayer_dam_break.jl b/examples/tree_1d_dgsem/elixir_shallowwater_twolayer_dam_break.jl deleted file mode 100644 index 03b93754d0f..00000000000 --- a/examples/tree_1d_dgsem/elixir_shallowwater_twolayer_dam_break.jl +++ /dev/null @@ -1,94 +0,0 @@ - -using OrdinaryDiffEq -using Trixi - -############################################################################### -# Semidiscretization of the two-layer shallow water equations for a dam break -# test with a discontinuous bottom topography function to test entropy conservation - -equations = ShallowWaterTwoLayerEquations1D(gravity_constant = 9.81, H0 = 2.0, - rho_upper = 0.9, rho_lower = 1.0) - -# Initial condition of a dam break with a discontinuous water heights and bottom topography. -# Works as intended for TreeMesh1D with `initial_refinement_level=5`. If the mesh -# refinement level is changed the initial condition below may need changed as well to -# ensure that the discontinuities lie on an element interface. -function initial_condition_dam_break(x, t, equations::ShallowWaterTwoLayerEquations1D) - v1_upper = 0.0 - v1_lower = 0.0 - - # Set the discontinuity - if x[1] <= 10.0 - H_lower = 2.0 - H_upper = 4.0 - b = 0.0 - else - H_lower = 1.5 - H_upper = 3.0 - b = 0.5 - end - - return prim2cons(SVector(H_upper, v1_upper, H_lower, v1_lower, b), equations) -end - -initial_condition = initial_condition_dam_break - -############################################################################### -# Get the DG approximation space - -volume_flux = (flux_wintermeyer_etal, flux_nonconservative_ersing_etal) -solver = DGSEM(polydeg = 3, - surface_flux = (flux_wintermeyer_etal, flux_nonconservative_ersing_etal), - volume_integral = VolumeIntegralFluxDifferencing(volume_flux)) - -############################################################################### -# Get the TreeMesh and setup a non-periodic mesh - -coordinates_min = 0.0 -coordinates_max = 20.0 -mesh = TreeMesh(coordinates_min, coordinates_max, - initial_refinement_level = 5, - n_cells_max = 10000, - periodicity = false) - -boundary_condition = boundary_condition_slip_wall - -# create the semidiscretization object -semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver, - boundary_conditions = boundary_condition) - -############################################################################### -# ODE solvers - -tspan = (0.0, 0.4) -ode = semidiscretize(semi, tspan) - -############################################################################### -# Callbacks - -summary_callback = SummaryCallback() - -analysis_interval = 500 -analysis_callback = AnalysisCallback(semi, interval = analysis_interval, - save_analysis = false, - extra_analysis_integrals = (energy_total, - energy_kinetic, - energy_internal)) - -stepsize_callback = StepsizeCallback(cfl = 1.0) - -alive_callback = AliveCallback(analysis_interval = analysis_interval) - -save_solution = SaveSolutionCallback(interval = 500, - save_initial_solution = true, - save_final_solution = true) - -callbacks = CallbackSet(summary_callback, analysis_callback, alive_callback, save_solution) - -############################################################################### -# run the simulation - -# use a Runge-Kutta method with automatic (error based) time step size control -sol = solve(ode, RDPK3SpFSAL49(), abstol = 1.0e-8, reltol = 1.0e-8, - save_everystep = false, callback = callbacks); -summary_callback() # print the timer summary diff --git a/examples/tree_1d_dgsem/elixir_shallowwater_twolayer_well_balanced.jl b/examples/tree_1d_dgsem/elixir_shallowwater_twolayer_well_balanced.jl deleted file mode 100644 index 098e3aaf601..00000000000 --- a/examples/tree_1d_dgsem/elixir_shallowwater_twolayer_well_balanced.jl +++ /dev/null @@ -1,86 +0,0 @@ - -using OrdinaryDiffEq -using Trixi - -############################################################################### -# Semidiscretization of the two-layer shallow water equations to test well-balancedness - -equations = ShallowWaterTwoLayerEquations1D(gravity_constant = 1.0, H0 = 0.6, - rho_upper = 0.9, rho_lower = 1.0) - -""" - initial_condition_fjordholm_well_balanced(x, t, equations::ShallowWaterTwoLayerEquations1D) - -Initial condition to test well balanced with a bottom topography from Fjordholm -- Ulrik Skre Fjordholm (2012) - Energy conservative and stable schemes for the two-layer shallow water equations. - [DOI: 10.1142/9789814417099_0039](https://doi.org/10.1142/9789814417099_0039) -""" -function initial_condition_fjordholm_well_balanced(x, t, - equations::ShallowWaterTwoLayerEquations1D) - inicenter = 0.5 - x_norm = x[1] - inicenter - r = abs(x_norm) - - H_lower = 0.5 - H_upper = 0.6 - v1_upper = 0.0 - v1_lower = 0.0 - b = r <= 0.1 ? 0.2 * (cos(10 * pi * (x[1] - 0.5)) + 1) : 0.0 - return prim2cons(SVector(H_upper, v1_upper, H_lower, v1_lower, b), equations) -end - -initial_condition = initial_condition_fjordholm_well_balanced - -############################################################################### -# Get the DG approximation space - -volume_flux = (flux_wintermeyer_etal, flux_nonconservative_ersing_etal) -solver = DGSEM(polydeg = 3, - surface_flux = (flux_es_ersing_etal, flux_nonconservative_ersing_etal), - volume_integral = VolumeIntegralFluxDifferencing(volume_flux)) - -############################################################################### -# Get the TreeMesh and setup a periodic mesh - -coordinates_min = 0.0 -coordinates_max = 1.0 -mesh = TreeMesh(coordinates_min, coordinates_max, - initial_refinement_level = 4, - n_cells_max = 10_000, - periodicity = true) - -# create the semi discretization object -semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver) - -############################################################################### -# ODE solvers, callbacks etc. - -tspan = (0.0, 10.0) -ode = semidiscretize(semi, tspan) - -summary_callback = SummaryCallback() - -analysis_interval = 1000 -analysis_callback = AnalysisCallback(semi, interval = analysis_interval, - save_analysis = false, - extra_analysis_integrals = (lake_at_rest_error,)) - -stepsize_callback = StepsizeCallback(cfl = 1.0) - -alive_callback = AliveCallback(analysis_interval = analysis_interval) - -save_solution = SaveSolutionCallback(interval = 1000, - save_initial_solution = true, - save_final_solution = true) - -callbacks = CallbackSet(summary_callback, analysis_callback, alive_callback, save_solution, - stepsize_callback) - -############################################################################### -# run the simulation - -sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false), - dt = 1.0, # solve needs some value here but it will be overwritten by the stepsize_callback - save_everystep = false, callback = callbacks); -summary_callback() # print the timer summary diff --git a/examples/tree_1d_dgsem/elixir_shallowwater_well_balanced_wet_dry.jl b/examples/tree_1d_dgsem/elixir_shallowwater_well_balanced_wet_dry.jl deleted file mode 100644 index 26a8960ab46..00000000000 --- a/examples/tree_1d_dgsem/elixir_shallowwater_well_balanced_wet_dry.jl +++ /dev/null @@ -1,172 +0,0 @@ - -using OrdinaryDiffEq -using Trixi -using Printf: @printf, @sprintf - -############################################################################### -# Semidiscretization of the shallow water equations -# -# TODO: TrixiShallowWater: wet/dry example elixir - -equations = ShallowWaterEquations1D(gravity_constant = 9.812) - -""" - initial_condition_complex_bottom_well_balanced(x, t, equations:: ShallowWaterEquations1D) - -Initial condition with a complex (discontinuous) bottom topography to test the well-balanced -property for the [`hydrostatic_reconstruction_chen_noelle`](@ref) including dry areas within the -domain. The errors from the analysis callback are not important but the error for this -lake-at-rest test case `∑|H0-(h+b)|` should be around machine roundoff. - -The initial condition is taken from Section 5.2 of the paper: -- Guoxian Chen and Sebastian Noelle (2017) - A new hydrostatic reconstruction scheme based on subcell reconstructions - [DOI:10.1137/15M1053074](https://dx.doi.org/10.1137/15M1053074) -""" -function initial_condition_complex_bottom_well_balanced(x, t, - equations::ShallowWaterEquations1D) - v = 0.0 - b = sin(4 * pi * x[1]) + 3 - - if x[1] >= 0.5 - b = sin(4 * pi * x[1]) + 1 - end - - H = max(b, 2.5) - - if x[1] >= 0.5 - H = max(b, 1.5) - end - - # It is mandatory to shift the water level at dry areas to make sure the water height h - # stays positive. The system would not be stable for h set to a hard 0 due to division by h in - # the computation of velocity, e.g., (h v) / h. Therefore, a small dry state threshold - # with a default value of 500*eps() ≈ 1e-13 in double precision, is set in the constructor above - # for the ShallowWaterEquations and added to the initial condition if h = 0. - # This default value can be changed within the constructor call depending on the simulation setup. - H = max(H, b + equations.threshold_limiter) - return prim2cons(SVector(H, v, b), equations) -end - -initial_condition = initial_condition_complex_bottom_well_balanced - -############################################################################### -# Get the DG approximation space - -volume_flux = (flux_wintermeyer_etal, flux_nonconservative_wintermeyer_etal) -surface_flux = (FluxHydrostaticReconstruction(flux_hll_chen_noelle, - hydrostatic_reconstruction_chen_noelle), - flux_nonconservative_chen_noelle) - -basis = LobattoLegendreBasis(3) - -indicator_sc = IndicatorHennemannGassnerShallowWater(equations, basis, - alpha_max = 0.5, - alpha_min = 0.001, - alpha_smooth = true, - variable = waterheight_pressure) -volume_integral = VolumeIntegralShockCapturingHG(indicator_sc; - volume_flux_dg = volume_flux, - volume_flux_fv = surface_flux) - -solver = DGSEM(basis, surface_flux, volume_integral) - -############################################################################### -# Create the TreeMesh for the domain [0, 1] - -coordinates_min = 0.0 -coordinates_max = 1.0 - -mesh = TreeMesh(coordinates_min, coordinates_max, - initial_refinement_level = 6, - n_cells_max = 10_000) - -# create the semi discretization object -semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver) - -############################################################################### -# ODE solvers, callbacks etc. - -tspan = (0.0, 25.0) -ode = semidiscretize(semi, tspan) - -summary_callback = SummaryCallback() - -analysis_interval = 5000 -analysis_callback = AnalysisCallback(semi, interval = analysis_interval, - save_analysis = false) - -alive_callback = AliveCallback(analysis_interval = analysis_interval) - -save_solution = SaveSolutionCallback(interval = 5000, - save_initial_solution = true, - save_final_solution = true) - -stepsize_callback = StepsizeCallback(cfl = 1.5) - -callbacks = CallbackSet(summary_callback, analysis_callback, alive_callback, save_solution, - stepsize_callback) - -stage_limiter! = PositivityPreservingLimiterShallowWater(variables = (Trixi.waterheight,)) - -############################################################################### -# run the simulation - -sol = solve(ode, SSPRK43(stage_limiter!); dt = 1.0, - ode_default_options()..., callback = callbacks, adaptive = false); - -summary_callback() # print the timer summary - -############################################################################### -# Workaround to compute the well-balancedness error for this particular problem -# that has two reference water heights. One for a lake to the left of the -# discontinuous bottom topography `H0_upper = 2.5` and another for a lake to the -# right of the discontinuous bottom topography `H0_lower = 1.5`. - -# Declare a special version of the function to compute the lake-at-rest error -# OBS! The reference water height values are hardcoded for convenience. -function lake_at_rest_error_two_level(u, x, equations::ShallowWaterEquations1D) - h, _, b = u - - # For well-balancedness testing with possible wet/dry regions the reference - # water height `H0` accounts for the possibility that the bottom topography - # can emerge out of the water as well as for the threshold offset to avoid - # division by a "hard" zero water heights as well. - if x[1] < 0.5 - H0_wet_dry = max(2.5, b + equations.threshold_limiter) - else - H0_wet_dry = max(1.5, b + equations.threshold_limiter) - end - - return abs(H0_wet_dry - (h + b)) -end - -# point to the data we want to analyze -u = Trixi.wrap_array(sol[end], semi) -# Perform the actual integration of the well-balancedness error over the domain -l1_well_balance_error = Trixi.integrate_via_indices(u, mesh, equations, semi.solver, - semi.cache; - normalize = true) do u, i, element, - equations, solver - x_node = Trixi.get_node_coords(semi.cache.elements.node_coordinates, equations, solver, - i, element) - # We know that the discontinuity is a vertical line. Slightly augment the x value by a factor - # of unit roundoff to avoid the repeted value from the LGL nodes at at interface. - if i == 1 - x_node = SVector(nextfloat(x_node[1])) - elseif i == nnodes(semi.solver) - x_node = SVector(prevfloat(x_node[1])) - end - u_local = Trixi.get_node_vars(u, equations, solver, i, element) - return lake_at_rest_error_two_level(u_local, x_node, equations) -end - -# report the well-balancedness lake-at-rest error to the screen -println("─"^100) -println(" Lake-at-rest error for '", Trixi.get_name(equations), "' with ", summary(solver), - " at final time " * @sprintf("%10.8e", tspan[end])) - -@printf(" %-12s:", Trixi.pretty_form_utf(lake_at_rest_error)) -@printf(" % 10.8e", l1_well_balance_error) -println() -println("─"^100) diff --git a/examples/tree_2d_dgsem/elixir_shallowwater_conical_island.jl b/examples/tree_2d_dgsem/elixir_shallowwater_conical_island.jl deleted file mode 100644 index 349b3741869..00000000000 --- a/examples/tree_2d_dgsem/elixir_shallowwater_conical_island.jl +++ /dev/null @@ -1,117 +0,0 @@ - -using OrdinaryDiffEq -using Trixi - -############################################################################### -# semidiscretization of the shallow water equations -# -# TODO: TrixiShallowWater: wet/dry example elixir - -equations = ShallowWaterEquations2D(gravity_constant = 9.81, H0 = 1.4) - -""" - initial_condition_conical_island(x, t, equations::ShallowWaterEquations2D) - -Initial condition for the [`ShallowWaterEquations2D`](@ref) to test the [`hydrostatic_reconstruction_chen_noelle`](@ref) -and its handling of discontinuous water heights at the start in combination with wetting and -drying. The bottom topography is given by a conical island in the middle of the domain. Around that -island, there is a cylindrical water column at t=0 and the rest of the domain is dry. This -discontinuous water height is smoothed by a logistic function. This simulation uses a Dirichlet -boundary condition with the initial values. Due to the dry cells at the boundary, this has the -effect of an outflow which can be seen in the simulation. -""" -function initial_condition_conical_island(x, t, equations::ShallowWaterEquations2D) - # Set the background values - - v1 = 0.0 - v2 = 0.0 - - x1, x2 = x - b = max(0.1, 1.0 - 4.0 * sqrt(x1^2 + x2^2)) - - # use a logistic function to transfer water height value smoothly - L = equations.H0 # maximum of function - x0 = 0.3 # center point of function - k = -25.0 # sharpness of transfer - - H = max(b, L / (1.0 + exp(-k * (sqrt(x1^2 + x2^2) - x0)))) - - # It is mandatory to shift the water level at dry areas to make sure the water height h - # stays positive. The system would not be stable for h set to a hard 0 due to division by h in - # the computation of velocity, e.g., (h v1) / h. Therefore, a small dry state threshold - # with a default value of 500*eps() ≈ 1e-13 in double precision, is set in the constructor above - # for the ShallowWaterEquations and added to the initial condition if h = 0. - # This default value can be changed within the constructor call depending on the simulation setup. - H = max(H, b + equations.threshold_limiter) - return prim2cons(SVector(H, v1, v2, b), equations) -end - -initial_condition = initial_condition_conical_island -boundary_conditions = BoundaryConditionDirichlet(initial_condition) - -############################################################################### -# Get the DG approximation space - -volume_flux = (flux_wintermeyer_etal, flux_nonconservative_wintermeyer_etal) -surface_flux = (FluxHydrostaticReconstruction(flux_hll_chen_noelle, - hydrostatic_reconstruction_chen_noelle), - flux_nonconservative_chen_noelle) - -basis = LobattoLegendreBasis(4) - -indicator_sc = IndicatorHennemannGassnerShallowWater(equations, basis, - alpha_max = 0.5, - alpha_min = 0.001, - alpha_smooth = true, - variable = waterheight_pressure) -volume_integral = VolumeIntegralShockCapturingHG(indicator_sc; - volume_flux_dg = volume_flux, - volume_flux_fv = surface_flux) - -solver = DGSEM(basis, surface_flux, volume_integral) - -############################################################################### -# Get the TreeMesh and setup a mesh - -coordinates_min = (-1.0, -1.0) -coordinates_max = (1.0, 1.0) -mesh = TreeMesh(coordinates_min, coordinates_max, - initial_refinement_level = 4, - n_cells_max = 10_000, - periodicity = false) - -# Create the semi discretization object -semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver, - boundary_conditions = boundary_conditions) - -############################################################################### -# ODE solver - -tspan = (0.0, 10.0) -ode = semidiscretize(semi, tspan) - -############################################################################### -# Callbacks - -summary_callback = SummaryCallback() - -analysis_interval = 1000 -analysis_callback = AnalysisCallback(semi, interval = analysis_interval) - -alive_callback = AliveCallback(analysis_interval = analysis_interval) - -save_solution = SaveSolutionCallback(interval = 100, - save_initial_solution = true, - save_final_solution = true) - -callbacks = CallbackSet(summary_callback, analysis_callback, alive_callback, save_solution) - -############################################################################### -# run the simulation - -stage_limiter! = PositivityPreservingLimiterShallowWater(variables = (Trixi.waterheight,)) - -sol = solve(ode, SSPRK43(stage_limiter!); - ode_default_options()..., callback = callbacks); - -summary_callback() # print the timer summary diff --git a/examples/tree_2d_dgsem/elixir_shallowwater_parabolic_bowl.jl b/examples/tree_2d_dgsem/elixir_shallowwater_parabolic_bowl.jl deleted file mode 100644 index 2008019cc31..00000000000 --- a/examples/tree_2d_dgsem/elixir_shallowwater_parabolic_bowl.jl +++ /dev/null @@ -1,121 +0,0 @@ - -using OrdinaryDiffEq -using Trixi - -############################################################################### -# Semidiscretization of the shallow water equations -# -# TODO: TrixiShallowWater: wet/dry example elixir - -equations = ShallowWaterEquations2D(gravity_constant = 9.81) - -""" - initial_condition_parabolic_bowl(x, t, equations:: ShallowWaterEquations2D) - -Well-known initial condition to test the [`hydrostatic_reconstruction_chen_noelle`](@ref) and its -wet-dry mechanics. This test has an analytical solution. The initial condition is defined by the -analytical solution at time t=0. The bottom topography defines a bowl and the water level is given -by an oscillating lake. - -The original test and its analytical solution were first presented in -- William C. Thacker (1981) - Some exact solutions to the nonlinear shallow-water wave equations - [DOI: 10.1017/S0022112081001882](https://doi.org/10.1017/S0022112081001882). - -The particular setup below is taken from Section 6.2 of -- Niklas Wintermeyer, Andrew R. Winters, Gregor J. Gassner and Timothy Warburton (2018) - An entropy stable discontinuous Galerkin method for the shallow water equations on - curvilinear meshes with wet/dry fronts accelerated by GPUs - [DOI: 10.1016/j.jcp.2018.08.038](https://doi.org/10.1016/j.jcp.2018.08.038). -""" -function initial_condition_parabolic_bowl(x, t, equations::ShallowWaterEquations2D) - a = 1.0 - h_0 = 0.1 - sigma = 0.5 - ω = sqrt(2 * equations.gravity * h_0) / a - - v1 = -sigma * ω * sin(ω * t) - v2 = sigma * ω * cos(ω * t) - - b = h_0 * ((x[1])^2 + (x[2])^2) / a^2 - - H = sigma * h_0 / a^2 * (2 * x[1] * cos(ω * t) + 2 * x[2] * sin(ω * t) - sigma) + h_0 - - # It is mandatory to shift the water level at dry areas to make sure the water height h - # stays positive. The system would not be stable for h set to a hard 0 due to division by h in - # the computation of velocity, e.g., (h v1) / h. Therefore, a small dry state threshold - # with a default value of 500*eps() ≈ 1e-13 in double precision, is set in the constructor above - # for the ShallowWaterEquations and added to the initial condition if h = 0. - # This default value can be changed within the constructor call depending on the simulation setup. - H = max(H, b + equations.threshold_limiter) - return prim2cons(SVector(H, v1, v2, b), equations) -end - -initial_condition = initial_condition_parabolic_bowl -############################################################################### -# Get the DG approximation space - -volume_flux = (flux_wintermeyer_etal, flux_nonconservative_wintermeyer_etal) -surface_flux = (FluxHydrostaticReconstruction(flux_hll_chen_noelle, - hydrostatic_reconstruction_chen_noelle), - flux_nonconservative_chen_noelle) - -basis = LobattoLegendreBasis(7) - -indicator_sc = IndicatorHennemannGassnerShallowWater(equations, basis, - alpha_max = 0.6, - alpha_min = 0.001, - alpha_smooth = true, - variable = waterheight_pressure) -volume_integral = VolumeIntegralShockCapturingHG(indicator_sc; - volume_flux_dg = volume_flux, - volume_flux_fv = surface_flux) - -solver = DGSEM(basis, surface_flux, volume_integral) - -############################################################################### -# Create the TreeMesh for the domain [-2, 2]^2 - -coordinates_min = (-2.0, -2.0) -coordinates_max = (2.0, 2.0) - -mesh = TreeMesh(coordinates_min, coordinates_max, - initial_refinement_level = 5, - n_cells_max = 10_000) - -# create the semi discretization object -semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver) - -############################################################################### -# ODE solvers, callbacks etc. - -tspan = (0.0, 1.0) -ode = semidiscretize(semi, tspan) - -summary_callback = SummaryCallback() - -analysis_interval = 1000 -analysis_callback = AnalysisCallback(semi, interval = analysis_interval, - save_analysis = false, - extra_analysis_integrals = (energy_kinetic, - energy_internal)) - -alive_callback = AliveCallback(analysis_interval = analysis_interval) - -save_solution = SaveSolutionCallback(interval = 100, - save_initial_solution = true, - save_final_solution = true) - -callbacks = CallbackSet(summary_callback, analysis_callback, alive_callback, save_solution) - -stage_limiter! = PositivityPreservingLimiterShallowWater(variables = (Trixi.waterheight,)) - -############################################################################### -# run the simulation - -callbacks = CallbackSet(summary_callback, analysis_callback, alive_callback, save_solution) - -sol = solve(ode, SSPRK43(stage_limiter!); - ode_default_options()..., callback = callbacks); - -summary_callback() # print the timer summary diff --git a/examples/tree_2d_dgsem/elixir_shallowwater_twolayer_convergence.jl b/examples/tree_2d_dgsem/elixir_shallowwater_twolayer_convergence.jl deleted file mode 100644 index 790916e4467..00000000000 --- a/examples/tree_2d_dgsem/elixir_shallowwater_twolayer_convergence.jl +++ /dev/null @@ -1,60 +0,0 @@ - -using OrdinaryDiffEq -using Trixi - -############################################################################### -# Semidiscretization of the two-layer shallow water equations - -equations = ShallowWaterTwoLayerEquations2D(gravity_constant = 10.0, rho_upper = 0.9, - rho_lower = 1.0) - -initial_condition = initial_condition_convergence_test - -############################################################################### -# Get the DG approximation space - -volume_flux = (flux_wintermeyer_etal, flux_nonconservative_ersing_etal) -solver = DGSEM(polydeg = 3, - surface_flux = (flux_wintermeyer_etal, flux_nonconservative_ersing_etal), - volume_integral = VolumeIntegralFluxDifferencing(volume_flux)) - -############################################################################### -# Get the TreeMesh and setup a periodic mesh - -coordinates_min = (0.0, 0.0) -coordinates_max = (sqrt(2.0), sqrt(2.0)) -mesh = TreeMesh(coordinates_min, coordinates_max, - initial_refinement_level = 3, - n_cells_max = 20_000, - periodicity = true) - -# Create the semi discretization object -semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver, - source_terms = source_terms_convergence_test) - -############################################################################### -# ODE solvers, callbacks etc. - -tspan = (0.0, 1.0) -ode = semidiscretize(semi, tspan) - -summary_callback = SummaryCallback() - -analysis_interval = 500 -analysis_callback = AnalysisCallback(semi, interval = analysis_interval) - -alive_callback = AliveCallback(analysis_interval = analysis_interval) - -save_solution = SaveSolutionCallback(interval = 500, - save_initial_solution = true, - save_final_solution = true) - -callbacks = CallbackSet(summary_callback, analysis_callback, alive_callback, save_solution) - -############################################################################### -# run the simulation - -# use a Runge-Kutta method with automatic (error based) time step size control -sol = solve(ode, RDPK3SpFSAL49(), abstol = 1.0e-8, reltol = 1.0e-8, - save_everystep = false, callback = callbacks); -summary_callback() # print the timer summary diff --git a/examples/tree_2d_dgsem/elixir_shallowwater_twolayer_well_balanced.jl b/examples/tree_2d_dgsem/elixir_shallowwater_twolayer_well_balanced.jl deleted file mode 100644 index 264c26390fe..00000000000 --- a/examples/tree_2d_dgsem/elixir_shallowwater_twolayer_well_balanced.jl +++ /dev/null @@ -1,81 +0,0 @@ - -using OrdinaryDiffEq -using Trixi - -############################################################################### -# Semidiscretization of the two-layer shallow water equations with a bottom topography function -# to test well-balancedness - -equations = ShallowWaterTwoLayerEquations2D(gravity_constant = 9.81, H0 = 0.6, - rho_upper = 0.9, rho_lower = 1.0) - -# An initial condition with constant total water height, zero velocities and a bottom topography to -# test well-balancedness -function initial_condition_well_balanced(x, t, equations::ShallowWaterTwoLayerEquations2D) - H_lower = 0.5 - H_upper = 0.6 - v1_upper = 0.0 - v2_upper = 0.0 - v1_lower = 0.0 - v2_lower = 0.0 - b = (((x[1] - 0.5)^2 + (x[2] - 0.5)^2) < 0.04 ? - 0.2 * (cos(4 * pi * sqrt((x[1] - 0.5)^2 + (x[2] + - -0.5)^2)) + 1) : 0.0) - - return prim2cons(SVector(H_upper, v1_upper, v2_upper, H_lower, v1_lower, v2_lower, b), - equations) -end - -initial_condition = initial_condition_well_balanced - -############################################################################### -# Get the DG approximation space - -volume_flux = (flux_wintermeyer_etal, flux_nonconservative_ersing_etal) -surface_flux = (flux_es_ersing_etal, flux_nonconservative_ersing_etal) -solver = DGSEM(polydeg = 3, surface_flux = surface_flux, - volume_integral = VolumeIntegralFluxDifferencing(volume_flux)) - -############################################################################### -# Get the TreeMesh and setup a periodic mesh - -coordinates_min = (0.0, 0.0) -coordinates_max = (1.0, 1.0) -mesh = TreeMesh(coordinates_min, coordinates_max, - initial_refinement_level = 3, - n_cells_max = 10_000, - periodicity = true) - -# Create the semi discretization object -semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver) - -############################################################################### -# ODE solver - -tspan = (0.0, 10.0) -ode = semidiscretize(semi, tspan) - -summary_callback = SummaryCallback() - -analysis_interval = 1000 -analysis_callback = AnalysisCallback(semi, interval = analysis_interval, - extra_analysis_integrals = (lake_at_rest_error,)) - -stepsize_callback = StepsizeCallback(cfl = 1.0) - -alive_callback = AliveCallback(analysis_interval = analysis_interval) - -save_solution = SaveSolutionCallback(interval = 1000, - save_initial_solution = true, - save_final_solution = true) - -callbacks = CallbackSet(summary_callback, analysis_callback, alive_callback, save_solution, - stepsize_callback) - -############################################################################### -# run the simulation - -sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false), - dt = 1.0, # solve needs some value here but it will be overwritten by the stepsize_callback - save_everystep = false, callback = callbacks); -summary_callback() # print the timer summary diff --git a/examples/tree_2d_dgsem/elixir_shallowwater_well_balanced_wet_dry.jl b/examples/tree_2d_dgsem/elixir_shallowwater_well_balanced_wet_dry.jl deleted file mode 100644 index 034411c2b54..00000000000 --- a/examples/tree_2d_dgsem/elixir_shallowwater_well_balanced_wet_dry.jl +++ /dev/null @@ -1,206 +0,0 @@ - -using OrdinaryDiffEq -using Trixi -using Printf: @printf, @sprintf - -############################################################################### -# Semidiscretization of the shallow water equations -# -# TODO: TrixiShallowWater: wet/dry example elixir - -equations = ShallowWaterEquations2D(gravity_constant = 9.812) - -""" - initial_condition_well_balanced_chen_noelle(x, t, equations:: ShallowWaterEquations2D) - -Initial condition with a complex (discontinuous) bottom topography to test the well-balanced -property for the [`hydrostatic_reconstruction_chen_noelle`](@ref) including dry areas within the -domain. The errors from the analysis callback are not important but the error for this -lake-at-rest test case `∑|H0-(h+b)|` should be around machine roundoff. - -The initial condition is taken from Section 5.2 of the paper: -- Guoxian Chen and Sebastian Noelle (2017) - A new hydrostatic reconstruction scheme based on subcell reconstructions - [DOI:10.1137/15M1053074](https://dx.doi.org/10.1137/15M1053074) -""" -function initial_condition_complex_bottom_well_balanced(x, t, - equations::ShallowWaterEquations2D) - v1 = 0 - v2 = 0 - b = sin(4 * pi * x[1]) + 3 - - if x[1] >= 0.5 - b = sin(4 * pi * x[1]) + 1 - end - - H = max(b, 2.5) - if x[1] >= 0.5 - H = max(b, 1.5) - end - - # It is mandatory to shift the water level at dry areas to make sure the water height h - # stays positive. The system would not be stable for h set to a hard 0 due to division by h in - # the computation of velocity, e.g., (h v1) / h. Therefore, a small dry state threshold - # with a default value of 500*eps() ≈ 1e-13 in double precision, is set in the constructor above - # for the ShallowWaterEquations and added to the initial condition if h = 0. - # This default value can be changed within the constructor call depending on the simulation setup. - H = max(H, b + equations.threshold_limiter) - return prim2cons(SVector(H, v1, v2, b), equations) -end - -initial_condition = initial_condition_complex_bottom_well_balanced - -############################################################################### -# Get the DG approximation space - -volume_flux = (flux_wintermeyer_etal, flux_nonconservative_wintermeyer_etal) -surface_flux = (FluxHydrostaticReconstruction(flux_hll_chen_noelle, - hydrostatic_reconstruction_chen_noelle), - flux_nonconservative_chen_noelle) - -basis = LobattoLegendreBasis(3) - -indicator_sc = IndicatorHennemannGassnerShallowWater(equations, basis, - alpha_max = 0.5, - alpha_min = 0.001, - alpha_smooth = true, - variable = waterheight_pressure) -volume_integral = VolumeIntegralShockCapturingHG(indicator_sc; - volume_flux_dg = volume_flux, - volume_flux_fv = surface_flux) - -solver = DGSEM(basis, surface_flux, volume_integral) - -############################################################################### -# Create the TreeMesh for the domain [0, 1]^2 - -coordinates_min = (0.0, 0.0) -coordinates_max = (1.0, 1.0) - -mesh = TreeMesh(coordinates_min, coordinates_max, - initial_refinement_level = 3, - n_cells_max = 10_000) - -# create the semi discretization object -semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver) - -############################################################################### -# ODE solvers, callbacks etc. - -tspan = (0.0, 50.0) -ode = semidiscretize(semi, tspan) - -############################################################################### -# Workaround to set a discontinuous water and bottom topography for -# debugging and testing. Essentially, this is a slight augmentation of the -# `compute_coefficients` where the `x` node value passed here is slightly -# perturbed to the left / right in order to set a true discontinuity that avoids -# the doubled value of the LGL nodes at a particular element interface. -# -# Note! The errors from the analysis callback are not important but the error -# for this lake at rest test case `∑|H0-(h+b)|` should be near machine roundoff. - -# point to the data we want to augment -u = Trixi.wrap_array(ode.u0, semi) -# reset the initial condition -for element in eachelement(semi.solver, semi.cache) - for j in eachnode(semi.solver), i in eachnode(semi.solver) - x_node = Trixi.get_node_coords(semi.cache.elements.node_coordinates, equations, - semi.solver, i, j, element) - # We know that the discontinuity is a vertical line. Slightly augment the x value by a factor - # of unit roundoff to avoid the repeted value from the LGL nodes at at interface. - if i == 1 - x_node = SVector(nextfloat(x_node[1]), x_node[2]) - elseif i == nnodes(semi.solver) - x_node = SVector(prevfloat(x_node[1]), x_node[2]) - end - u_node = initial_condition_complex_bottom_well_balanced(x_node, first(tspan), - equations) - Trixi.set_node_vars!(u, u_node, equations, semi.solver, i, j, element) - end -end - -############################################################################### -# Callbacks - -summary_callback = SummaryCallback() - -analysis_interval = 1000 -analysis_callback = AnalysisCallback(semi, interval = analysis_interval, - save_analysis = false) - -alive_callback = AliveCallback(analysis_interval = analysis_interval) - -save_solution = SaveSolutionCallback(interval = 1000, - save_initial_solution = true, - save_final_solution = true) - -stepsize_callback = StepsizeCallback(cfl = 2.0) - -callbacks = CallbackSet(summary_callback, analysis_callback, alive_callback, save_solution, - stepsize_callback) - -stage_limiter! = PositivityPreservingLimiterShallowWater(variables = (Trixi.waterheight,)) - -############################################################################### -# run the simulation - -sol = solve(ode, SSPRK43(stage_limiter!); dt = 1.0, - ode_default_options()..., callback = callbacks, adaptive = false); - -summary_callback() # print the timer summary - -############################################################################### -# Workaround to compute the well-balancedness error for this particular problem -# that has two reference water heights. One for a lake to the left of the -# discontinuous bottom topography `H0_upper = 2.5` and another for a lake to the -# right of the discontinuous bottom topography `H0_lower = 1.5`. - -# Declare a special version of the function to compute the lake-at-rest error -# OBS! The reference water height values are hardcoded for convenience. -function lake_at_rest_error_two_level(u, x, equations::ShallowWaterEquations2D) - h, _, _, b = u - - # For well-balancedness testing with possible wet/dry regions the reference - # water height `H0` accounts for the possibility that the bottom topography - # can emerge out of the water as well as for the threshold offset to avoid - # division by a "hard" zero water heights as well. - - if x[1] < 0.5 - H0_wet_dry = max(2.5, b + equations.threshold_limiter) - else - H0_wet_dry = max(1.5, b + equations.threshold_limiter) - end - - return abs(H0_wet_dry - (h + b)) -end - -# point to the data we want to analyze -u = Trixi.wrap_array(sol[end], semi) -# Perform the actual integration of the well-balancedness error over the domain -l1_well_balance_error = Trixi.integrate_via_indices(u, mesh, equations, semi.solver, - semi.cache; - normalize = true) do u, i, j, element, - equations, solver - x_node = Trixi.get_node_coords(semi.cache.elements.node_coordinates, equations, solver, - i, j, element) - # We know that the discontinuity is a vertical line. Slightly augment the x value by a factor - # of unit roundoff to avoid the repeted value from the LGL nodes at at interface. - if i == 1 - x_node = SVector(nextfloat(x_node[1]), x_node[2]) - elseif i == nnodes(semi.solver) - x_node = SVector(prevfloat(x_node[1]), x_node[2]) - end - u_local = Trixi.get_node_vars(u, equations, solver, i, j, element) - return lake_at_rest_error_two_level(u_local, x_node, equations) -end - -# report the well-balancedness lake-at-rest error to the screen -println("─"^100) -println(" Lake-at-rest error for '", Trixi.get_name(equations), "' with ", summary(solver), - " at final time " * @sprintf("%10.8e", tspan[end])) - -@printf(" %-12s:", Trixi.pretty_form_utf(lake_at_rest_error)) -@printf(" % 10.8e", l1_well_balance_error) -println() -println("─"^100) diff --git a/examples/unstructured_2d_dgsem/elixir_shallowwater_three_mound_dam_break.jl b/examples/unstructured_2d_dgsem/elixir_shallowwater_three_mound_dam_break.jl deleted file mode 100644 index df321aad267..00000000000 --- a/examples/unstructured_2d_dgsem/elixir_shallowwater_three_mound_dam_break.jl +++ /dev/null @@ -1,133 +0,0 @@ - -using OrdinaryDiffEq -using Trixi - -############################################################################### -# semidiscretization of the shallow water equations -# -# TODO: TrixiShallowWater: wet/dry example elixir - -equations = ShallowWaterEquations2D(gravity_constant = 9.81, H0 = 1.875, - threshold_limiter = 1e-12, threshold_wet = 1e-14) - -""" - initial_condition_three_mounds(x, t, equations::ShallowWaterEquations2D) - -Initial condition simulating a dam break. The bottom topography is given by one large and two smaller -mounds. The mounds are flooded by the water for t > 0. To smooth the discontinuity, a logistic function -is applied. - -The initial conditions is taken from Section 6.3 of the paper: -- Niklas Wintermeyer, Andrew R. Winters, Gregor J. Gassner and Timothy Warburton (2018) - An entropy stable discontinuous Galerkin method for the shallow water equations on - curvilinear meshes with wet/dry fronts accelerated by GPUs\n - [DOI: 10.1016/j.jcp.2018.08.038](https://doi.org/10.1016/j.jcp.2018.08.038) -""" -function initial_condition_three_mounds(x, t, equations::ShallowWaterEquations2D) - - # Set the background values - v1 = 0.0 - v2 = 0.0 - - x1, x2 = x - M_1 = 1 - 0.1 * sqrt((x1 - 30.0)^2 + (x2 - 22.5)^2) - M_2 = 1 - 0.1 * sqrt((x1 - 30.0)^2 + (x2 - 7.5)^2) - M_3 = 2.8 - 0.28 * sqrt((x1 - 47.5)^2 + (x2 - 15.0)^2) - - b = max(0.0, M_1, M_2, M_3) - - # use a logistic function to transfer water height value smoothly - L = equations.H0 # maximum of function - x0 = 8 # center point of function - k = -75.0 # sharpness of transfer - - H = max(b, L / (1.0 + exp(-k * (x1 - x0)))) - - # Avoid division by zero by adjusting the initial condition with a small dry state threshold - # that defaults to 500*eps() ≈ 1e-13 in double precision and is set in the constructor above - # for the ShallowWaterEquations struct. - H = max(H, b + equations.threshold_limiter) - return prim2cons(SVector(H, v1, v2, b), equations) -end - -initial_condition = initial_condition_three_mounds - -function boundary_condition_outflow(u_inner, normal_direction::AbstractVector, x, t, - surface_flux_function, - equations::ShallowWaterEquations2D) - # Impulse and bottom from inside, height from external state - u_outer = SVector(equations.threshold_wet, u_inner[2], u_inner[3], u_inner[4]) - - # calculate the boundary flux - flux = surface_flux_function(u_inner, u_outer, normal_direction, equations) - - return flux -end - -boundary_conditions = Dict(:Bottom => boundary_condition_slip_wall, - :Top => boundary_condition_slip_wall, - :Right => boundary_condition_outflow, - :Left => boundary_condition_slip_wall) - -############################################################################### -# Get the DG approximation space - -volume_flux = (flux_wintermeyer_etal, flux_nonconservative_wintermeyer_etal) -surface_flux = (FluxHydrostaticReconstruction(flux_hll_chen_noelle, - hydrostatic_reconstruction_chen_noelle), - flux_nonconservative_chen_noelle) - -basis = LobattoLegendreBasis(4) - -indicator_sc = IndicatorHennemannGassnerShallowWater(equations, basis, - alpha_max = 0.5, - alpha_min = 0.001, - alpha_smooth = true, - variable = waterheight_pressure) -volume_integral = VolumeIntegralShockCapturingHG(indicator_sc; - volume_flux_dg = volume_flux, - volume_flux_fv = surface_flux) - -solver = DGSEM(basis, surface_flux, volume_integral) - -############################################################################### -# Get the unstructured quad mesh from a file (downloads the file if not available locally) -mesh_file = Trixi.download("https://gist.githubusercontent.com/svengoldberg/c3c87fecb3fc6e46be7f0d1c7cb35f83/raw/e817ecd9e6c4686581d63c46128f9b6468d396d3/mesh_three_mound.mesh", - joinpath(@__DIR__, "mesh_three_mound.mesh")) - -mesh = UnstructuredMesh2D(mesh_file) - -# Create the semi discretization object -semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver; - boundary_conditions = boundary_conditions) - -############################################################################### -# ODE solver - -tspan = (0.0, 20.0) -ode = semidiscretize(semi, tspan) - -############################################################################### -# Callbacks - -summary_callback = SummaryCallback() - -analysis_interval = 1000 -analysis_callback = AnalysisCallback(semi, interval = analysis_interval) - -alive_callback = AliveCallback(analysis_interval = analysis_interval) - -save_solution = SaveSolutionCallback(interval = 100, - save_initial_solution = true, - save_final_solution = true) - -callbacks = CallbackSet(summary_callback, analysis_callback, alive_callback, save_solution) - -############################################################################### -# run the simulation - -stage_limiter! = PositivityPreservingLimiterShallowWater(variables = (Trixi.waterheight,)) - -sol = solve(ode, SSPRK43(stage_limiter!); - ode_default_options()..., callback = callbacks); -summary_callback() # print the timer summary diff --git a/examples/unstructured_2d_dgsem/elixir_shallowwater_twolayer_convergence.jl b/examples/unstructured_2d_dgsem/elixir_shallowwater_twolayer_convergence.jl deleted file mode 100644 index fcc08b6f991..00000000000 --- a/examples/unstructured_2d_dgsem/elixir_shallowwater_twolayer_convergence.jl +++ /dev/null @@ -1,63 +0,0 @@ - -using OrdinaryDiffEq -using Trixi - -############################################################################### -# Semidiscretization of the two-layer shallow water equations with a periodic -# bottom topography function (set in the initial conditions) - -equations = ShallowWaterTwoLayerEquations2D(gravity_constant = 10.0, rho_upper = 0.9, - rho_lower = 1.0) - -initial_condition = initial_condition_convergence_test - -############################################################################### -# Get the DG approximation space - -volume_flux = (flux_wintermeyer_etal, flux_nonconservative_ersing_etal) -surface_flux = (flux_wintermeyer_etal, flux_nonconservative_ersing_etal) -solver = DGSEM(polydeg = 6, surface_flux = surface_flux, - volume_integral = VolumeIntegralFluxDifferencing(volume_flux)) - -############################################################################### -# This setup is for the curved, split form convergence test on a periodic domain - -# Get the unstructured quad mesh from a file (downloads the file if not available locally) -mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/8f8cd23df27fcd494553f2a89f3c1ba4/raw/85e3c8d976bbe57ca3d559d653087b0889535295/mesh_alfven_wave_with_twist_and_flip.mesh", - joinpath(@__DIR__, "mesh_alfven_wave_with_twist_and_flip.mesh")) - -mesh = UnstructuredMesh2D(mesh_file, periodicity = true) - -# Create the semidiscretization object -semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver, - source_terms = source_terms_convergence_test) - -############################################################################### -# ODE solvers, callbacks etc. - -tspan = (0.0, 1.0) -ode = semidiscretize(semi, tspan) - -summary_callback = SummaryCallback() - -analysis_interval = 500 -analysis_callback = AnalysisCallback(semi, interval = analysis_interval) - -alive_callback = AliveCallback(analysis_interval = analysis_interval) - -save_solution = SaveSolutionCallback(interval = 500, - save_initial_solution = true, - save_final_solution = true) - -stepsize_callback = StepsizeCallback(cfl = 1.0) - -callbacks = CallbackSet(summary_callback, analysis_callback, alive_callback, save_solution, - stepsize_callback) - -############################################################################### -# run the simulation - -sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false), - dt = 1.0, # solve needs some value here but it will be overwritten by the stepsize_callback - save_everystep = false, callback = callbacks); -summary_callback() # print the timer summary diff --git a/examples/unstructured_2d_dgsem/elixir_shallowwater_twolayer_dam_break.jl b/examples/unstructured_2d_dgsem/elixir_shallowwater_twolayer_dam_break.jl deleted file mode 100644 index 821f31c52ac..00000000000 --- a/examples/unstructured_2d_dgsem/elixir_shallowwater_twolayer_dam_break.jl +++ /dev/null @@ -1,147 +0,0 @@ - -using OrdinaryDiffEq -using Trixi - -############################################################################### -# Semidiscretization of the two-layer shallow water equations for a dam break test with a -# discontinuous bottom topography function to test energy conservation - -equations = ShallowWaterTwoLayerEquations2D(gravity_constant = 1.0, rho_upper = 0.9, - rho_lower = 1.0) - -# This test case uses a special work around to setup a truly discontinuous bottom topography -# function and initial condition for this academic testcase of entropy conservation. First, a -# dummy initial_condition_dam_break is introduced to create the semidiscretization. Then the initial -# condition is reset with the true discontinuous values from initial_condition_discontinuous_dam_break. - -function initial_condition_dam_break(x, t, equations::ShallowWaterTwoLayerEquations2D) - if x[1] < sqrt(2) / 2 - H_upper = 1.0 - H_lower = 0.6 - b = 0.1 - else - H_upper = 0.9 - H_lower = 0.5 - b = 0.0 - end - - v1_upper = 0.0 - v2_upper = 0.0 - v1_lower = 0.0 - v2_lower = 0.0 - return prim2cons(SVector(H_upper, v1_upper, v2_upper, H_lower, v1_lower, v2_lower, b), - equations) -end - -initial_condition = initial_condition_dam_break - -boundary_condition_constant = BoundaryConditionDirichlet(initial_condition_dam_break) - -############################################################################### -# Get the DG approximation space - -volume_flux = (flux_wintermeyer_etal, flux_nonconservative_ersing_etal) -surface_flux = (flux_wintermeyer_etal, flux_nonconservative_ersing_etal) -solver = DGSEM(polydeg = 6, surface_flux = surface_flux, - volume_integral = VolumeIntegralFluxDifferencing(volume_flux)) - -############################################################################### -# Get the unstructured quad mesh from a file (downloads the file if not available locally) -mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/8f8cd23df27fcd494553f2a89f3c1ba4/raw/85e3c8d976bbe57ca3d559d653087b0889535295/mesh_alfven_wave_with_twist_and_flip.mesh", - joinpath(@__DIR__, "mesh_alfven_wave_with_twist_and_flip.mesh")) - -mesh = UnstructuredMesh2D(mesh_file, periodicity = false) - -# Boundary conditions -boundary_condition = Dict(:Top => boundary_condition_slip_wall, - :Left => boundary_condition_slip_wall, - :Right => boundary_condition_slip_wall, - :Bottom => boundary_condition_slip_wall) - -# Create the semi discretization object -semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, - solver, boundary_conditions = boundary_condition) - -############################################################################### -# ODE solver - -tspan = (0.0, 0.5) -ode = semidiscretize(semi, tspan) - -############################################################################### -# Workaround to set a discontinuous bottom topography and initial condition for debugging and testing. - -# alternative version of the initial conditinon used to setup a truly discontinuous -# test case and initial condition. -# In contrast to the usual signature of initial conditions, this one get passed the -# `element_id` explicitly. In particular, this initial conditions works as intended -# only for the specific mesh loaded above! - -function initial_condition_discontinuous_dam_break(x, t, element_id, - equations::ShallowWaterTwoLayerEquations2D) - # Constant values - v1_upper = 0.0 - v2_upper = 0.0 - v1_lower = 0.0 - v2_lower = 0.0 - - # Left side of discontinuity - IDs = [1, 2, 5, 6, 9, 10, 13, 14] - if element_id in IDs - H_upper = 1.0 - H_lower = 0.6 - b = 0.0 - # Right side of discontinuity - else - H_upper = 0.9 - H_lower = 0.5 - b = 0.1 - end - - return prim2cons(SVector(H_upper, v1_upper, v2_upper, H_lower, v1_lower, v2_lower, b), - equations) -end - -# point to the data we want to augment -u = Trixi.wrap_array(ode.u0, semi) -# reset the initial condition -for element in eachelement(semi.solver, semi.cache) - for j in eachnode(semi.solver), i in eachnode(semi.solver) - x_node = Trixi.get_node_coords(semi.cache.elements.node_coordinates, equations, - semi.solver, i, j, element) - u_node = initial_condition_discontinuous_dam_break(x_node, first(tspan), element, - equations) - Trixi.set_node_vars!(u, u_node, equations, semi.solver, i, j, element) - end -end - -############################################################################### -# Callbacks - -summary_callback = SummaryCallback() - -analysis_interval = 500 -analysis_callback = AnalysisCallback(semi, interval = analysis_interval, - save_analysis = false, - extra_analysis_integrals = (energy_total, - energy_kinetic, - energy_internal)) - -alive_callback = AliveCallback(analysis_interval = analysis_interval) - -save_solution = SaveSolutionCallback(interval = 500, - save_initial_solution = true, - save_final_solution = true) - -stepsize_callback = StepsizeCallback(cfl = 1.0) - -callbacks = CallbackSet(summary_callback, analysis_callback, alive_callback, save_solution, - stepsize_callback) - -############################################################################### -# run the simulation - -sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false), - dt = 1.0, # solve needs some value here but it will be overwritten by the stepsize_callback - save_everystep = false, callback = callbacks); -summary_callback() # print the timer summary diff --git a/examples/unstructured_2d_dgsem/elixir_shallowwater_twolayer_well_balanced.jl b/examples/unstructured_2d_dgsem/elixir_shallowwater_twolayer_well_balanced.jl deleted file mode 100644 index ca1f54595bb..00000000000 --- a/examples/unstructured_2d_dgsem/elixir_shallowwater_twolayer_well_balanced.jl +++ /dev/null @@ -1,81 +0,0 @@ - -using OrdinaryDiffEq -using Trixi - -############################################################################### -# Semidiscretization of the two-layer shallow water equations with a discontinuous bottom -# topography to test well-balancedness - -equations = ShallowWaterTwoLayerEquations2D(gravity_constant = 1.0, H0 = 0.6, - rho_upper = 0.9, rho_lower = 1.0) - -# An initial condition with constant total water height, zero velocities and a bottom topography to -# test well-balancedness -function initial_condition_well_balanced(x, t, equations::ShallowWaterTwoLayerEquations2D) - H_lower = 0.5 - H_upper = 0.6 - v1_upper = 0.0 - v2_upper = 0.0 - v1_lower = 0.0 - v2_lower = 0.0 - - # Bottom Topography - b = (((x[1] - 0.5)^2 + (x[2] - 0.5)^2) < 0.04 ? - 0.2 * (cos(4 * pi * sqrt((x[1] - 0.5)^2 + (x[2] + - -0.5)^2)) + 1) : 0.0) - return prim2cons(SVector(H_upper, v1_upper, v2_upper, H_lower, v1_lower, v2_lower, b), - equations) -end - -initial_condition = initial_condition_well_balanced - -############################################################################### -# Get the DG approximation space - -volume_flux = (flux_wintermeyer_etal, flux_nonconservative_ersing_etal) -surface_flux = (flux_es_ersing_etal, flux_nonconservative_ersing_etal) -solver = DGSEM(polydeg = 6, surface_flux = surface_flux, - volume_integral = VolumeIntegralFluxDifferencing(volume_flux)) - -############################################################################### -# This setup is for the curved, split form well-balancedness testing - -# Get the unstructured quad mesh from a file (downloads the file if not available locally) -mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/8f8cd23df27fcd494553f2a89f3c1ba4/raw/85e3c8d976bbe57ca3d559d653087b0889535295/mesh_alfven_wave_with_twist_and_flip.mesh", - joinpath(@__DIR__, "mesh_alfven_wave_with_twist_and_flip.mesh")) - -mesh = UnstructuredMesh2D(mesh_file, periodicity = true) - -# Create the semi discretization object -semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver) - -############################################################################### -# ODE solver - -tspan = (0.0, 10.0) -ode = semidiscretize(semi, tspan) - -summary_callback = SummaryCallback() - -analysis_interval = 1000 -analysis_callback = AnalysisCallback(semi, interval = analysis_interval, - extra_analysis_integrals = (lake_at_rest_error,)) - -stepsize_callback = StepsizeCallback(cfl = 1.0) - -alive_callback = AliveCallback(analysis_interval = analysis_interval) - -save_solution = SaveSolutionCallback(interval = 1000, - save_initial_solution = true, - save_final_solution = true) - -callbacks = CallbackSet(summary_callback, analysis_callback, alive_callback, save_solution, - stepsize_callback) - -############################################################################### -# run the simulation - -sol = solve(ode, CarpenterKennedy2N54(williamson_condition = false), - dt = 1.0, # solve needs some value here but it will be overwritten by the stepsize_callback - save_everystep = false, callback = callbacks); -summary_callback() # print the timer summary diff --git a/src/Trixi.jl b/src/Trixi.jl index b7f7767a9d8..5f8cd9cae8e 100644 --- a/src/Trixi.jl +++ b/src/Trixi.jl @@ -160,7 +160,6 @@ export AcousticPerturbationEquations2D, InviscidBurgersEquation1D, LatticeBoltzmannEquations2D, LatticeBoltzmannEquations3D, ShallowWaterEquations1D, ShallowWaterEquations2D, - ShallowWaterTwoLayerEquations1D, ShallowWaterTwoLayerEquations2D, ShallowWaterEquationsQuasi1D, LinearizedEulerEquations2D, PolytropicEulerEquations2D, @@ -179,16 +178,12 @@ export flux, flux_central, flux_lax_friedrichs, flux_hll, flux_hllc, flux_hlle, flux_kennedy_gruber, flux_shima_etal, flux_ec, flux_fjordholm_etal, flux_nonconservative_fjordholm_etal, flux_wintermeyer_etal, flux_nonconservative_wintermeyer_etal, - flux_es_ersing_etal, flux_nonconservative_ersing_etal, + flux_nonconservative_ersing_etal, flux_chan_etal, flux_nonconservative_chan_etal, flux_winters_etal, hydrostatic_reconstruction_audusse_etal, flux_nonconservative_audusse_etal, -# TODO: TrixiShallowWater: move anything with "chen_noelle" to new file - hydrostatic_reconstruction_chen_noelle, flux_nonconservative_chen_noelle, - flux_hll_chen_noelle, FluxPlusDissipation, DissipationGlobalLaxFriedrichs, DissipationLocalLaxFriedrichs, FluxLaxFriedrichs, max_abs_speed_naive, FluxHLL, min_max_speed_naive, min_max_speed_davis, min_max_speed_einfeldt, - min_max_speed_chen_noelle, FluxLMARS, FluxRotated, flux_shima_etal_turbo, flux_ranocha_turbo, @@ -239,8 +234,6 @@ export DG, VolumeIntegralFluxDifferencing, VolumeIntegralPureLGLFiniteVolume, VolumeIntegralShockCapturingHG, IndicatorHennemannGassner, -# TODO: TrixiShallowWater: move new indicator - IndicatorHennemannGassnerShallowWater, VolumeIntegralUpwind, SurfaceIntegralWeakForm, SurfaceIntegralStrongForm, SurfaceIntegralUpwind, @@ -276,8 +269,7 @@ export load_mesh, load_time, load_timestep, load_timestep!, load_dt, export ControllerThreeLevel, ControllerThreeLevelCombined, IndicatorLöhner, IndicatorLoehner, IndicatorMax -# TODO: TrixiShallowWater: move new limiter -export PositivityPreservingLimiterZhangShu, PositivityPreservingLimiterShallowWater +export PositivityPreservingLimiterZhangShu export trixi_include, examples_dir, get_examples, default_example, default_example_unstructured, ode_default_options diff --git a/src/callbacks_stage/callbacks_stage.jl b/src/callbacks_stage/callbacks_stage.jl index 70d60de7914..d5abc1d227d 100644 --- a/src/callbacks_stage/callbacks_stage.jl +++ b/src/callbacks_stage/callbacks_stage.jl @@ -8,6 +8,4 @@ include("positivity_zhang_shu.jl") include("subcell_limiter_idp_correction.jl") include("subcell_bounds_check.jl") -# TODO: TrixiShallowWater: move specific limiter file -include("positivity_shallow_water.jl") end # @muladd diff --git a/src/callbacks_stage/positivity_shallow_water.jl b/src/callbacks_stage/positivity_shallow_water.jl deleted file mode 100644 index 36276026fe9..00000000000 --- a/src/callbacks_stage/positivity_shallow_water.jl +++ /dev/null @@ -1,89 +0,0 @@ -# By default, Julia/LLVM does not use fused multiply-add operations (FMAs). -# Since these FMAs can increase the performance of many numerical algorithms, -# we need to opt-in explicitly. -# See https://ranocha.de/blog/Optimizing_EC_Trixi for further details. -@muladd begin -#! format: noindent - -# TODO: TrixiShallowWater: generic wet/dry limiter - -""" - PositivityPreservingLimiterShallowWater(; variables) - -The limiter is specifically designed for the shallow water equations. -It is applied to all scalar `variables` in their given order -using the defined `threshold_limiter` from the [`ShallowWaterEquations1D`](@ref) struct -or the [`ShallowWaterEquations2D`](@ref) struct to determine the minimal acceptable values. -The order of the `variables` is important and might have a strong influence -on the robustness. - -As opposed to the standard version of the [`PositivityPreservingLimiterZhangShu`](@ref), -nodes with a water height below the `threshold_limiter` are treated in a special way. -To avoid numerical problems caused by velocities close to zero, -the velocity is cut off, such that the node can be identified as "dry". The special feature of the -`ShallowWaterEquations` used here is that the bottom topography is stored as an additional -quantity in the solution vector `u`. However, the value of the bottom topography -should not be changed. That is why, it is not limited. - -After the limiting process is applied to all degrees of freedom, for safety reasons, -the `threshold_limiter` is applied again on all the DG nodes in order to avoid water height below. -In the case where the cell mean value is below the threshold before applying the limiter, -there could still be dry nodes afterwards due to the logic of the limiter. - -This fully-discrete positivity-preserving limiter is based on the work of -- Zhang, Shu (2011) - Maximum-principle-satisfying and positivity-preserving high-order schemes - for conservation laws: survey and new developments - [doi: 10.1098/rspa.2011.0153](https://doi.org/10.1098/rspa.2011.0153) -""" -struct PositivityPreservingLimiterShallowWater{N, Variables <: NTuple{N, Any}} - variables::Variables -end - -function PositivityPreservingLimiterShallowWater(; variables) - PositivityPreservingLimiterShallowWater(variables) -end - -function (limiter!::PositivityPreservingLimiterShallowWater)(u_ode, integrator, - semi::AbstractSemidiscretization, - t) - u = wrap_array(u_ode, semi) - @trixi_timeit timer() "positivity-preserving limiter" limiter_shallow_water!(u, - limiter!.variables, - mesh_equations_solver_cache(semi)...) -end - -# Iterate over tuples in a type-stable way using "lispy tuple programming", -# similar to https://stackoverflow.com/a/55849398: -# Iterating over tuples of different functions isn't type-stable in general -# but accessing the first element of a tuple is type-stable. Hence, it's good -# to process one element at a time and replace iteration by recursion here. -# Note that you shouldn't use this with too many elements per tuple since the -# compile times can increase otherwise - but a handful of elements per tuple -# is definitely fine. -function limiter_shallow_water!(u, variables::NTuple{N, Any}, - mesh, - equations::Union{ShallowWaterEquations1D, - ShallowWaterEquations2D}, - solver, cache) where {N} - variable = first(variables) - remaining_variables = Base.tail(variables) - - limiter_shallow_water!(u, equations.threshold_limiter, variable, mesh, equations, - solver, cache) - limiter_shallow_water!(u, remaining_variables, mesh, equations, solver, cache) - return nothing -end - -# terminate the type-stable iteration over tuples -function limiter_shallow_water!(u, variables::Tuple{}, - mesh, - equations::Union{ShallowWaterEquations1D, - ShallowWaterEquations2D}, - solver, cache) - nothing -end - -include("positivity_shallow_water_dg1d.jl") -include("positivity_shallow_water_dg2d.jl") -end # @muladd diff --git a/src/callbacks_stage/positivity_shallow_water_dg1d.jl b/src/callbacks_stage/positivity_shallow_water_dg1d.jl deleted file mode 100644 index 13c6866e895..00000000000 --- a/src/callbacks_stage/positivity_shallow_water_dg1d.jl +++ /dev/null @@ -1,89 +0,0 @@ -# By default, Julia/LLVM does not use fused multiply-add operations (FMAs). -# Since these FMAs can increase the performance of many numerical algorithms, -# we need to opt-in explicitly. -# See https://ranocha.de/blog/Optimizing_EC_Trixi for further details. -@muladd begin -#! format: noindent - -# TODO: TrixiShallowWater: 1D wet/dry limiter should move - -function limiter_shallow_water!(u, threshold::Real, variable, - mesh::AbstractMesh{1}, - equations::ShallowWaterEquations1D, - dg::DGSEM, cache) - @unpack weights = dg.basis - - @threaded for element in eachelement(dg, cache) - # determine minimum value - value_min = typemax(eltype(u)) - for i in eachnode(dg) - u_node = get_node_vars(u, equations, dg, i, element) - value_min = min(value_min, variable(u_node, equations)) - end - - # detect if limiting is necessary - value_min < threshold || continue - - # compute mean value - u_mean = zero(get_node_vars(u, equations, dg, 1, element)) - for i in eachnode(dg) - u_node = get_node_vars(u, equations, dg, i, element) - u_mean += u_node * weights[i] - end - # note that the reference element is [-1,1]^ndims(dg), thus the weights sum to 2 - u_mean = u_mean / 2^ndims(mesh) - - # We compute the value directly with the mean values, as we assume that - # Jensen's inequality holds (e.g. pressure for compressible Euler equations). - value_mean = variable(u_mean, equations) - theta = (value_mean - threshold) / (value_mean - value_min) - for i in eachnode(dg) - u_node = get_node_vars(u, equations, dg, i, element) - - # Cut off velocity in case that the waterheight is smaller than the threshold - - h_node, h_v_node, b_node = u_node - h_mean, h_v_mean, _ = u_mean # b_mean is not used as b_node must not be overwritten - - # Set them both to zero to apply linear combination correctly - if h_node <= threshold - h_v_node = zero(eltype(u)) - h_v_mean = zero(eltype(u)) - end - - u_node = SVector(h_node, h_v_node, b_node) - u_mean = SVector(h_mean, h_v_mean, b_node) - - # When velocity is cut off, the only averaged value is the waterheight, - # because the velocity is set to zero and this value is passed. - # Otherwise, the velocity is averaged, as well. - # Note that the auxiliary bottom topography variable `b` is never limited. - set_node_vars!(u, theta * u_node + (1 - theta) * u_mean, - equations, dg, i, element) - end - end - - # "Safety" application of the wet/dry thresholds over all the DG nodes - # on the current `element` after the limiting above in order to avoid dry nodes. - # If the value_mean < threshold before applying limiter, there - # could still be dry nodes afterwards due to logic of the limiting - @threaded for element in eachelement(dg, cache) - for i in eachnode(dg) - u_node = get_node_vars(u, equations, dg, i, element) - - h, hv, b = u_node - - if h <= threshold - h = threshold - hv = zero(eltype(u)) - end - - u_node = SVector(h, hv, b) - - set_node_vars!(u, u_node, equations, dg, i, element) - end - end - - return nothing -end -end # @muladd diff --git a/src/callbacks_stage/positivity_shallow_water_dg2d.jl b/src/callbacks_stage/positivity_shallow_water_dg2d.jl deleted file mode 100644 index da3a25fdcf4..00000000000 --- a/src/callbacks_stage/positivity_shallow_water_dg2d.jl +++ /dev/null @@ -1,90 +0,0 @@ -# By default, Julia/LLVM does not use fused multiply-add operations (FMAs). -# Since these FMAs can increase the performance of many numerical algorithms, -# we need to opt-in explicitly. -# See https://ranocha.de/blog/Optimizing_EC_Trixi for further details. -@muladd begin -#! format: noindent - -# TODO: TrixiShallowWater: 2D wet/dry limiter should move - -function limiter_shallow_water!(u, threshold::Real, variable, - mesh::AbstractMesh{2}, - equations::ShallowWaterEquations2D, dg::DGSEM, cache) - @unpack weights = dg.basis - - @threaded for element in eachelement(dg, cache) - # determine minimum value - value_min = typemax(eltype(u)) - for j in eachnode(dg), i in eachnode(dg) - u_node = get_node_vars(u, equations, dg, i, j, element) - value_min = min(value_min, variable(u_node, equations)) - end - - # detect if limiting is necessary - value_min < threshold || continue - - # compute mean value - u_mean = zero(get_node_vars(u, equations, dg, 1, 1, element)) - for j in eachnode(dg), i in eachnode(dg) - u_node = get_node_vars(u, equations, dg, i, j, element) - u_mean += u_node * weights[i] * weights[j] - end - # note that the reference element is [-1,1]^ndims(dg), thus the weights sum to 2 - u_mean = u_mean / 2^ndims(mesh) - - # We compute the value directly with the mean values, as we assume that - # Jensen's inequality holds (e.g. pressure for compressible Euler equations). - value_mean = variable(u_mean, equations) - theta = (value_mean - threshold) / (value_mean - value_min) - for j in eachnode(dg), i in eachnode(dg) - u_node = get_node_vars(u, equations, dg, i, j, element) - - # Cut off velocity in case that the water height is smaller than the threshold - - h_node, h_v1_node, h_v2_node, b_node = u_node - h_mean, h_v1_mean, h_v2_mean, _ = u_mean # b_mean is not used as it must not be overwritten - - if h_node <= threshold - h_v1_node = zero(eltype(u)) - h_v2_node = zero(eltype(u)) - h_v1_mean = zero(eltype(u)) - h_v2_mean = zero(eltype(u)) - end - - u_node = SVector(h_node, h_v1_node, h_v2_node, b_node) - u_mean = SVector(h_mean, h_v1_mean, h_v2_mean, b_node) - - # When velocities are cut off, the only averaged value is the water height, - # because the velocities are set to zero and this value is passed. - # Otherwise, the velocities are averaged, as well. - # Note that the auxiliary bottom topography variable `b` is never limited. - set_node_vars!(u, theta * u_node + (1 - theta) * u_mean, - equations, dg, i, j, element) - end - end - - # "Safety" application of the wet/dry thresholds over all the DG nodes - # on the current `element` after the limiting above in order to avoid dry nodes. - # If the value_mean < threshold before applying limiter, there - # could still be dry nodes afterwards due to logic of the limiting - @threaded for element in eachelement(dg, cache) - for j in eachnode(dg), i in eachnode(dg) - u_node = get_node_vars(u, equations, dg, i, j, element) - - h, h_v1, h_v2, b = u_node - - if h <= threshold - h = threshold - h_v1 = zero(eltype(u)) - h_v2 = zero(eltype(u)) - end - - u_node = SVector(h, h_v1, h_v2, b) - - set_node_vars!(u, u_node, equations, dg, i, j, element) - end - end - - return nothing -end -end # @muladd diff --git a/src/equations/equations.jl b/src/equations/equations.jl index 65875a2a7e5..8f476cf6f16 100644 --- a/src/equations/equations.jl +++ b/src/equations/equations.jl @@ -405,8 +405,6 @@ abstract type AbstractShallowWaterEquations{NDIMS, NVARS} <: AbstractEquations{NDIMS, NVARS} end include("shallow_water_1d.jl") include("shallow_water_2d.jl") -include("shallow_water_two_layer_1d.jl") -include("shallow_water_two_layer_2d.jl") include("shallow_water_quasi_1d.jl") # CompressibleEulerEquations diff --git a/src/equations/numerical_fluxes.jl b/src/equations/numerical_fluxes.jl index 44d523b6e89..87fcb412244 100644 --- a/src/equations/numerical_fluxes.jl +++ b/src/equations/numerical_fluxes.jl @@ -326,29 +326,6 @@ This is a [`FluxHLL`](@ref)-type two-wave solver with special estimates of the w """ const flux_hlle = FluxHLL(min_max_speed_einfeldt) -# TODO: TrixiShallowWater: move the chen_noelle flux structure to the new package - -# An empty version of the `min_max_speed_chen_noelle` function is declared here -# in order to create a dimension agnostic version of `flux_hll_chen_noelle`. -# The full description of this wave speed estimate can be found in the docstrings -# for `min_max_speed_chen_noelle` in `shallow_water_1d.jl` or `shallow_water_2d.jl`. -function min_max_speed_chen_noelle end - -""" - flux_hll_chen_noelle = FluxHLL(min_max_speed_chen_noelle) - -An instance of [`FluxHLL`](@ref) specific to the shallow water equations that -uses the wave speed estimates from [`min_max_speed_chen_noelle`](@ref). -This HLL flux is guaranteed to have zero numerical mass flux out of a "dry" element, -maintain positivity of the water height, and satisfy an entropy inequality. - -For complete details see Section 2.4 of the following reference -- Guoxian Chen and Sebastian Noelle (2017) - A new hydrostatic reconstruction scheme based on subcell reconstructions - [DOI: 10.1137/15M1053074](https://doi.org/10.1137/15M1053074) -""" -const flux_hll_chen_noelle = FluxHLL(min_max_speed_chen_noelle) - """ flux_shima_etal_turbo(u_ll, u_rr, orientation_or_normal_direction, equations) diff --git a/src/equations/shallow_water_1d.jl b/src/equations/shallow_water_1d.jl index 25ce0fa79fe..e348ef946b7 100644 --- a/src/equations/shallow_water_1d.jl +++ b/src/equations/shallow_water_1d.jl @@ -6,7 +6,7 @@ #! format: noindent @doc raw""" - ShallowWaterEquations1D(; gravity, H0 = 0, threshold_limiter = nothing threshold_wet = nothing) + ShallowWaterEquations1D(; gravity, H0 = 0) Shallow water equations (SWE) in one space dimension. The equations are given by ```math @@ -24,12 +24,6 @@ also defines the total water height as ``H = h + b``. The additional quantity ``H_0`` is also available to store a reference value for the total water height that is useful to set initial conditions or test the "lake-at-rest" well-balancedness. -Also, there are two thresholds which prevent numerical problems as well as instabilities. Both of them do not -have to be passed, as default values are defined within the struct. The first one, `threshold_limiter`, is -used in [`PositivityPreservingLimiterShallowWater`](@ref) on the water height, as a (small) shift on the initial -condition and cutoff before the next time step. The second one, `threshold_wet`, is applied on the water height to -define when the flow is "wet" before calculating the numerical flux. - The bottom topography function ``b(x)`` is set inside the initial condition routine for a particular problem setup. To test the conservative form of the SWE one can set the bottom topography variable `b` to zero. @@ -51,35 +45,16 @@ References for the SWE are many but a good introduction is available in Chapter [DOI: 10.1017/CBO9780511791253](https://doi.org/10.1017/CBO9780511791253) """ struct ShallowWaterEquations1D{RealT <: Real} <: AbstractShallowWaterEquations{1, 3} - # TODO: TrixiShallowWater: where should the `threshold_limiter` and `threshold_wet` live? - # how to "properly" export these constants across the two packages? gravity::RealT # gravitational constant H0::RealT # constant "lake-at-rest" total water height - # `threshold_limiter` used in `PositivityPreservingLimiterShallowWater` on water height, - # as a (small) shift on the initial condition and cutoff before the next time step. - # Default is 500*eps() which in double precision is ≈1e-13. - threshold_limiter::RealT - # `threshold_wet` applied on water height to define when the flow is "wet" - # before calculating the numerical flux. - # Default is 5*eps() which in double precision is ≈1e-15. - threshold_wet::RealT end # Allow for flexibility to set the gravitational constant within an elixir depending on the # application where `gravity_constant=1.0` or `gravity_constant=9.81` are common values. # The reference total water height H0 defaults to 0.0 but is used for the "lake-at-rest" # well-balancedness test cases. -# Strict default values for thresholds that performed well in many numerical experiments -function ShallowWaterEquations1D(; gravity_constant, H0 = zero(gravity_constant), - threshold_limiter = nothing, threshold_wet = nothing) - T = promote_type(typeof(gravity_constant), typeof(H0)) - if threshold_limiter === nothing - threshold_limiter = 500 * eps(T) - end - if threshold_wet === nothing - threshold_wet = 5 * eps(T) - end - ShallowWaterEquations1D(gravity_constant, H0, threshold_limiter, threshold_wet) +function ShallowWaterEquations1D(; gravity_constant, H0 = zero(gravity_constant)) + ShallowWaterEquations1D(gravity_constant, H0) end have_nonconservative_terms(::ShallowWaterEquations1D) = True() @@ -332,54 +307,6 @@ Further details on the hydrostatic reconstruction and its motivation can be foun z) end -# TODO: TrixiShallowWater: move wet/dry specific routine -""" - flux_nonconservative_chen_noelle(u_ll, u_rr, - orientation::Integer, - equations::ShallowWaterEquations1D) - -Non-symmetric two-point surface flux that discretizes the nonconservative (source) term. -The discretization uses the `hydrostatic_reconstruction_chen_noelle` on the conservative -variables. - -Should be used together with [`FluxHydrostaticReconstruction`](@ref) and -[`hydrostatic_reconstruction_chen_noelle`](@ref) in the surface flux to ensure consistency. - -Further details on the hydrostatic reconstruction and its motivation can be found in -- Guoxian Chen and Sebastian Noelle (2017) - A new hydrostatic reconstruction scheme based on subcell reconstructions - [DOI:10.1137/15M1053074](https://dx.doi.org/10.1137/15M1053074) -""" -@inline function flux_nonconservative_chen_noelle(u_ll, u_rr, - orientation::Integer, - equations::ShallowWaterEquations1D) - - # Pull the water height and bottom topography on the left - h_ll, _, b_ll = u_ll - h_rr, _, b_rr = u_rr - - H_ll = h_ll + b_ll - H_rr = h_rr + b_rr - - b_star = min(max(b_ll, b_rr), min(H_ll, H_rr)) - - # Create the hydrostatic reconstruction for the left solution state - u_ll_star, _ = hydrostatic_reconstruction_chen_noelle(u_ll, u_rr, equations) - - # Copy the reconstructed water height for easier to read code - h_ll_star = u_ll_star[1] - - z = zero(eltype(u_ll)) - # Includes two parts: - # (i) Diagonal (consistent) term from the volume flux that uses `b_ll` to avoid - # cross-averaging across a discontinuous bottom topography - # (ii) True surface part that uses `h_ll` and `h_ll_star` to handle discontinuous bathymetry - return SVector(z, - equations.gravity * h_ll * b_ll - - equations.gravity * (h_ll_star + h_ll) * (b_ll - b_star), - z) -end - """ flux_nonconservative_ersing_etal(u_ll, u_rr, orientation::Integer, equations::ShallowWaterEquations1D) @@ -521,67 +448,6 @@ Further details on this hydrostatic reconstruction and its motivation can be fou return u_ll_star, u_rr_star end -# TODO: TrixiShallowWater: move wet/dry specific routine -""" - hydrostatic_reconstruction_chen_noelle(u_ll, u_rr, orientation::Integer, - equations::ShallowWaterEquations1D) - -A particular type of hydrostatic reconstruction of the water height to guarantee well-balancedness -for a general bottom topography of the [`ShallowWaterEquations1D`](@ref). The reconstructed solution states -`u_ll_star` and `u_rr_star` variables are used to evaluate the surface numerical flux at the interface. -The key idea is a linear reconstruction of the bottom and water height at the interfaces using subcells. -Use in combination with the generic numerical flux routine [`FluxHydrostaticReconstruction`](@ref). - -Further details on this hydrostatic reconstruction and its motivation can be found in -- Guoxian Chen and Sebastian Noelle (2017) - A new hydrostatic reconstruction scheme based on subcell reconstructions - [DOI:10.1137/15M1053074](https://dx.doi.org/10.1137/15M1053074) -""" -@inline function hydrostatic_reconstruction_chen_noelle(u_ll, u_rr, - equations::ShallowWaterEquations1D) - # Unpack left and right water heights and bottom topographies - h_ll, _, b_ll = u_ll - h_rr, _, b_rr = u_rr - - # Get the velocities on either side - v_ll = velocity(u_ll, equations) - v_rr = velocity(u_rr, equations) - - H_ll = b_ll + h_ll - H_rr = b_rr + h_rr - - b_star = min(max(b_ll, b_rr), min(H_ll, H_rr)) - - # Compute the reconstructed water heights - h_ll_star = min(H_ll - b_star, h_ll) - h_rr_star = min(H_rr - b_star, h_rr) - - # Set the water height to be at least the value stored in the variable threshold after - # the hydrostatic reconstruction is applied and before the numerical flux is calculated - # to avoid numerical problem with arbitrary small values. Interfaces with a water height - # lower or equal to the threshold can be declared as dry. - # The default value for `threshold_wet` is ≈ 5*eps(), or 1e-15 in double precision, is set - # in the `ShallowWaterEquations1D` struct. This threshold value can be changed in the constructor - # call of this equation struct in an elixir. - threshold = equations.threshold_wet - - if (h_ll_star <= threshold) - h_ll_star = threshold - v_ll = zero(v_ll) - end - - if (h_rr_star <= threshold) - h_rr_star = threshold - v_rr = zero(v_rr) - end - - # Create the conservative variables using the reconstruted water heights - u_ll_star = SVector(h_ll_star, h_ll_star * v_ll, b_ll) - u_rr_star = SVector(h_rr_star, h_rr_star * v_rr, b_rr) - - return u_ll_star, u_rr_star -end - # Calculate maximum wave speed for local Lax-Friedrichs-type dissipation as the # maximum velocity magnitude plus the maximum speed of sound @inline function max_abs_speed_naive(u_ll, u_rr, orientation::Integer, @@ -646,39 +512,6 @@ end return λ_min, λ_max end -# TODO: TrixiShallowWater: move wet/dry specific routine -""" - min_max_speed_chen_noelle(u_ll, u_rr, orientation::Integer, - equations::ShallowWaterEquations1D) - -The approximated speeds for the HLL type numerical flux used by Chen and Noelle for their -hydrostatic reconstruction. As they state in the paper, these speeds are chosen for the numerical -flux to ensure positivity and to satisfy an entropy inequality. - -Further details on this hydrostatic reconstruction and its motivation can be found in -- Guoxian Chen and Sebastian Noelle (2017) - A new hydrostatic reconstruction scheme based on subcell reconstructions - [DOI:10.1137/15M1053074](https://dx.doi.org/10.1137/15M1053074) -""" -@inline function min_max_speed_chen_noelle(u_ll, u_rr, orientation::Integer, - equations::ShallowWaterEquations1D) - # Get the velocity quantities - v_ll = velocity(u_ll, equations) - v_rr = velocity(u_rr, equations) - - # Calculate the wave celerity on the left and right - h_ll = waterheight(u_ll, equations) - h_rr = waterheight(u_rr, equations) - - a_ll = sqrt(equations.gravity * h_ll) - a_rr = sqrt(equations.gravity * h_rr) - - λ_min = min(v_ll - a_ll, v_rr - a_rr, zero(eltype(u_ll))) - λ_max = max(v_ll + a_ll, v_rr + a_rr, zero(eltype(u_ll))) - - return λ_min, λ_max -end - # More refined estimates for minimum and maximum wave speeds for HLL-type fluxes @inline function min_max_speed_davis(u_ll, u_rr, orientation::Integer, equations::ShallowWaterEquations1D) @@ -841,20 +674,10 @@ end end # Calculate the error for the "lake-at-rest" test case where H = h+b should -# be a constant value over time. Note, assumes there is a single reference -# water height `H0` with which to compare. -# -# TODO: TrixiShallowWater: where should `threshold_limiter` live? May need -# to modify or have different versions of the `lake_at_rest_error` function +# be a constant value over time. @inline function lake_at_rest_error(u, equations::ShallowWaterEquations1D) h, _, b = u - # For well-balancedness testing with possible wet/dry regions the reference - # water height `H0` accounts for the possibility that the bottom topography - # can emerge out of the water as well as for the threshold offset to avoid - # division by a "hard" zero water heights as well. - H0_wet_dry = max(equations.H0, b + equations.threshold_limiter) - - return abs(H0_wet_dry - (h + b)) + return abs(equations.H0 - (h + b)) end end # @muladd diff --git a/src/equations/shallow_water_2d.jl b/src/equations/shallow_water_2d.jl index 6728d7d5553..74a299a51e6 100644 --- a/src/equations/shallow_water_2d.jl +++ b/src/equations/shallow_water_2d.jl @@ -6,7 +6,7 @@ #! format: noindent @doc raw""" - ShallowWaterEquations2D(; gravity, H0 = 0, threshold_limiter = nothing, threshold_wet = nothing) + ShallowWaterEquations2D(; gravity, H0 = 0) Shallow water equations (SWE) in two space dimensions. The equations are given by ```math @@ -27,12 +27,6 @@ also defines the total water height as ``H = h + b``. The additional quantity ``H_0`` is also available to store a reference value for the total water height that is useful to set initial conditions or test the "lake-at-rest" well-balancedness. -Also, there are two thresholds which prevent numerical problems as well as instabilities. Both of them do not -have to be passed, as default values are defined within the struct. The first one, `threshold_limiter`, is -used in [`PositivityPreservingLimiterShallowWater`](@ref) on the water height, as a (small) shift on the initial -condition and cutoff before the next time step. The second one, `threshold_wet`, is applied on the water height to -define when the flow is "wet" before calculating the numerical flux. - The bottom topography function ``b(x,y)`` is set inside the initial condition routine for a particular problem setup. To test the conservative form of the SWE one can set the bottom topography variable `b` to zero. @@ -54,18 +48,8 @@ References for the SWE are many but a good introduction is available in Chapter [DOI: 10.1017/CBO9780511791253](https://doi.org/10.1017/CBO9780511791253) """ struct ShallowWaterEquations2D{RealT <: Real} <: AbstractShallowWaterEquations{2, 4} - # TODO: TrixiShallowWater: where should the `threshold_limiter` and `threshold_wet` live? - # how to "properly" export these constants across the two packages? gravity::RealT # gravitational constant H0::RealT # constant "lake-at-rest" total water height - # `threshold_limiter` used in `PositivityPreservingLimiterShallowWater` on water height, - # as a (small) shift on the initial condition and cutoff before the next time step. - # Default is 500*eps() which in double precision is ≈1e-13. - threshold_limiter::RealT - # `threshold_wet` applied on water height to define when the flow is "wet" - # before calculating the numerical flux. - # Default is 5*eps() which in double precision is ≈1e-15. - threshold_wet::RealT end # Allow for flexibility to set the gravitational constant within an elixir depending on the @@ -73,16 +57,8 @@ end # The reference total water height H0 defaults to 0.0 but is used for the "lake-at-rest" # well-balancedness test cases. # Strict default values for thresholds that performed well in many numerical experiments -function ShallowWaterEquations2D(; gravity_constant, H0 = zero(gravity_constant), - threshold_limiter = nothing, threshold_wet = nothing) - T = promote_type(typeof(gravity_constant), typeof(H0)) - if threshold_limiter === nothing - threshold_limiter = 500 * eps(T) - end - if threshold_wet === nothing - threshold_wet = 5 * eps(T) - end - ShallowWaterEquations2D(gravity_constant, H0, threshold_limiter, threshold_wet) +function ShallowWaterEquations2D(; gravity_constant, H0 = zero(gravity_constant)) + ShallowWaterEquations2D(gravity_constant, H0) end have_nonconservative_terms(::ShallowWaterEquations2D) = True() @@ -460,69 +436,6 @@ Further details for the hydrostatic reconstruction and its motivation can be fou return u_ll_star, u_rr_star end -# TODO: TrixiShallowWater: move wet/dry specific routine -""" - hydrostatic_reconstruction_chen_noelle(u_ll, u_rr, orientation::Integer, - equations::ShallowWaterEquations2D) - -A particular type of hydrostatic reconstruction of the water height to guarantee well-balancedness -for a general bottom topography of the [`ShallowWaterEquations2D`](@ref). The reconstructed solution states -`u_ll_star` and `u_rr_star` variables are then used to evaluate the surface numerical flux at the interface. -The key idea is a linear reconstruction of the bottom and water height at the interfaces using subcells. -Use in combination with the generic numerical flux routine [`FluxHydrostaticReconstruction`](@ref). - -Further details on this hydrostatic reconstruction and its motivation can be found in -- Guoxian Chen and Sebastian Noelle (2017) - A new hydrostatic reconstruction scheme based on subcell reconstructions - [DOI:10.1137/15M1053074](https://dx.doi.org/10.1137/15M1053074) -""" -@inline function hydrostatic_reconstruction_chen_noelle(u_ll, u_rr, - equations::ShallowWaterEquations2D) - # Unpack left and right water heights and bottom topographies - h_ll, _, _, b_ll = u_ll - h_rr, _, _, b_rr = u_rr - - # Get the velocities on either side - v1_ll, v2_ll = velocity(u_ll, equations) - v1_rr, v2_rr = velocity(u_rr, equations) - - H_ll = b_ll + h_ll - H_rr = b_rr + h_rr - - b_star = min(max(b_ll, b_rr), min(H_ll, H_rr)) - - # Compute the reconstructed water heights - h_ll_star = min(H_ll - b_star, h_ll) - h_rr_star = min(H_rr - b_star, h_rr) - - # Set the water height to be at least the value stored in the variable threshold after - # the hydrostatic reconstruction is applied and before the numerical flux is calculated - # to avoid numerical problem with arbitrary small values. Interfaces with a water height - # lower or equal to the threshold can be declared as dry. - # The default value for `threshold_wet` is ≈5*eps(), or 1e-15 in double precision, is set - # in the `ShallowWaterEquations2D` struct. This threshold value can be changed in the constructor - # call of this equation struct in an elixir. - threshold = equations.threshold_wet - - if (h_ll_star <= threshold) - h_ll_star = threshold - v1_ll = zero(v1_ll) - v2_ll = zero(v2_ll) - end - - if (h_rr_star <= threshold) - h_rr_star = threshold - v1_rr = zero(v1_rr) - v2_rr = zero(v2_rr) - end - - # Create the conservative variables using the reconstruted water heights - u_ll_star = SVector(h_ll_star, h_ll_star * v1_ll, h_ll_star * v2_ll, b_ll) - u_rr_star = SVector(h_rr_star, h_rr_star * v1_rr, h_rr_star * v2_rr, b_rr) - - return u_ll_star, u_rr_star -end - """ flux_nonconservative_audusse_etal(u_ll, u_rr, orientation::Integer, equations::ShallowWaterEquations2D) @@ -608,104 +521,6 @@ end return SVector(f1, f2, f3, f4) end -# TODO: TrixiShallowWater: move wet/dry specific routine -""" - flux_nonconservative_chen_noelle(u_ll, u_rr, - orientation::Integer, - equations::ShallowWaterEquations2D) - flux_nonconservative_chen_noelle(u_ll, u_rr, - normal_direction_ll ::AbstractVector, - normal_direction_average ::AbstractVector, - equations::ShallowWaterEquations2D) - -Non-symmetric two-point surface flux that discretizes the nonconservative (source) term. -The discretization uses the [`hydrostatic_reconstruction_chen_noelle`](@ref) on the conservative -variables. - -Should be used together with [`FluxHydrostaticReconstruction`](@ref) and -[`hydrostatic_reconstruction_chen_noelle`](@ref) in the surface flux to ensure consistency. - -Further details on the hydrostatic reconstruction and its motivation can be found in -- Guoxian Chen and Sebastian Noelle (2017) - A new hydrostatic reconstruction scheme based on subcell reconstructions - [DOI:10.1137/15M1053074](https://dx.doi.org/10.1137/15M1053074) -""" -@inline function flux_nonconservative_chen_noelle(u_ll, u_rr, orientation::Integer, - equations::ShallowWaterEquations2D) - # Pull the water height and bottom topography on the left - h_ll, _, _, b_ll = u_ll - h_rr, _, _, b_rr = u_rr - - H_ll = h_ll + b_ll - H_rr = h_rr + b_rr - - b_star = min(max(b_ll, b_rr), min(H_ll, H_rr)) - - # Create the hydrostatic reconstruction for the left solution state - u_ll_star, _ = hydrostatic_reconstruction_chen_noelle(u_ll, u_rr, equations) - - # Copy the reconstructed water height for easier to read code - h_ll_star = u_ll_star[1] - - z = zero(eltype(u_ll)) - # Includes two parts: - # (i) Diagonal (consistent) term from the volume flux that uses `b_ll` to avoid - # cross-averaging across a discontinuous bottom topography - # (ii) True surface part that uses `h_ll` and `h_ll_star` to handle discontinuous bathymetry - g = equations.gravity - if orientation == 1 - f = SVector(z, - g * h_ll * b_ll - g * (h_ll_star + h_ll) * (b_ll - b_star), - z, z) - else # orientation == 2 - f = SVector(z, z, - g * h_ll * b_ll - g * (h_ll_star + h_ll) * (b_ll - b_star), - z) - end - - return f -end - -@inline function flux_nonconservative_chen_noelle(u_ll, u_rr, - normal_direction_ll::AbstractVector, - normal_direction_average::AbstractVector, - equations::ShallowWaterEquations2D) - # Pull the water height and bottom topography on the left - h_ll, _, _, b_ll = u_ll - h_rr, _, _, b_rr = u_rr - - H_ll = h_ll + b_ll - H_rr = h_rr + b_rr - - b_star = min(max(b_ll, b_rr), min(H_ll, H_rr)) - - # Create the hydrostatic reconstruction for the left solution state - u_ll_star, _ = hydrostatic_reconstruction_chen_noelle(u_ll, u_rr, equations) - - # Copy the reconstructed water height for easier to read code - h_ll_star = u_ll_star[1] - - # Comes in two parts: - # (i) Diagonal (consistent) term from the volume flux that uses `normal_direction_average` - # but we use `b_ll` to avoid cross-averaging across a discontinuous bottom topography - - f2 = normal_direction_average[1] * equations.gravity * h_ll * b_ll - f3 = normal_direction_average[2] * equations.gravity * h_ll * b_ll - - # (ii) True surface part that uses `normal_direction_ll`, `h_ll` and `h_ll_star` - # to handle discontinuous bathymetry - - f2 -= normal_direction_ll[1] * equations.gravity * (h_ll_star + h_ll) * - (b_ll - b_star) - f3 -= normal_direction_ll[2] * equations.gravity * (h_ll_star + h_ll) * - (b_ll - b_star) - - # First and last equations do not have a nonconservative flux - f1 = f4 = zero(eltype(u_ll)) - - return SVector(f1, f2, f3, f4) -end - """ flux_nonconservative_ersing_etal(u_ll, u_rr, orientation::Integer, equations::ShallowWaterEquations2D) @@ -1020,67 +835,6 @@ end return λ_min, λ_max end -# TODO: TrixiShallowWater: move wet/dry specific routine -""" - min_max_speed_chen_noelle(u_ll, u_rr, orientation::Integer, - equations::ShallowWaterEquations2D) - min_max_speed_chen_noelle(u_ll, u_rr, normal_direction::AbstractVector, - equations::ShallowWaterEquations2D) - -Special estimate of the minimal and maximal wave speed of the shallow water equations for -the left and right states `u_ll, u_rr`. These approximate speeds are used for the HLL-type -numerical flux [`flux_hll_chen_noelle`](@ref). These wave speed estimates -together with a particular hydrostatic reconstruction technique guarantee -that the numerical flux is positive and satisfies an entropy inequality. - -Further details on this hydrostatic reconstruction and its motivation can be found in -the reference below. The definition of the wave speeds are given in Equation (2.20). -- Guoxian Chen and Sebastian Noelle (2017) - A new hydrostatic reconstruction scheme based on subcell reconstructions - [DOI:10.1137/15M1053074](https://dx.doi.org/10.1137/15M1053074) -""" -@inline function min_max_speed_chen_noelle(u_ll, u_rr, orientation::Integer, - equations::ShallowWaterEquations2D) - h_ll = waterheight(u_ll, equations) - v1_ll, v2_ll = velocity(u_ll, equations) - h_rr = waterheight(u_rr, equations) - v1_rr, v2_rr = velocity(u_rr, equations) - - a_ll = sqrt(equations.gravity * h_ll) - a_rr = sqrt(equations.gravity * h_rr) - - if orientation == 1 # x-direction - λ_min = min(v1_ll - a_ll, v1_rr - a_rr, zero(eltype(u_ll))) - λ_max = max(v1_ll + a_ll, v1_rr + a_rr, zero(eltype(u_ll))) - else # y-direction - λ_min = min(v2_ll - a_ll, v2_rr - a_rr, zero(eltype(u_ll))) - λ_max = max(v2_ll + a_ll, v2_rr + a_rr, zero(eltype(u_ll))) - end - - return λ_min, λ_max -end - -@inline function min_max_speed_chen_noelle(u_ll, u_rr, normal_direction::AbstractVector, - equations::ShallowWaterEquations2D) - h_ll = waterheight(u_ll, equations) - v1_ll, v2_ll = velocity(u_ll, equations) - h_rr = waterheight(u_rr, equations) - v1_rr, v2_rr = velocity(u_rr, equations) - - v_normal_ll = v1_ll * normal_direction[1] + v2_ll * normal_direction[2] - v_normal_rr = v1_rr * normal_direction[1] + v2_rr * normal_direction[2] - - norm_ = norm(normal_direction) - - a_ll = sqrt(equations.gravity * h_ll) * norm_ - a_rr = sqrt(equations.gravity * h_rr) * norm_ - - λ_min = min(v_normal_ll - a_ll, v_normal_rr - a_rr, zero(eltype(u_ll))) - λ_max = max(v_normal_ll + a_ll, v_normal_rr + a_rr, zero(eltype(u_ll))) - - return λ_min, λ_max -end - # More refined estimates for minimum and maximum wave speeds for HLL-type fluxes @inline function min_max_speed_davis(u_ll, u_rr, orientation::Integer, equations::ShallowWaterEquations2D) @@ -1327,20 +1081,10 @@ end end # Calculate the error for the "lake-at-rest" test case where H = h+b should -# be a constant value over time. Note, assumes there is a single reference -# water height `H0` with which to compare. -# -# TODO: TrixiShallowWater: where should `threshold_limiter` live? May need -# to modify or have different versions of the `lake_at_rest_error` function +# be a constant value over time. @inline function lake_at_rest_error(u, equations::ShallowWaterEquations2D) h, _, _, b = u - # For well-balancedness testing with possible wet/dry regions the reference - # water height `H0` accounts for the possibility that the bottom topography - # can emerge out of the water as well as for the threshold offset to avoid - # division by a "hard" zero water heights as well. - H0_wet_dry = max(equations.H0, b + equations.threshold_limiter) - - return abs(H0_wet_dry - (h + b)) + return abs(equations.H0 - (h + b)) end end # @muladd diff --git a/src/equations/shallow_water_quasi_1d.jl b/src/equations/shallow_water_quasi_1d.jl index d52fbab841d..51c360104a7 100644 --- a/src/equations/shallow_water_quasi_1d.jl +++ b/src/equations/shallow_water_quasi_1d.jl @@ -22,12 +22,6 @@ The gravitational constant is denoted by `g`, the (possibly) variable bottom top The additional quantity ``H_0`` is also available to store a reference value for the total water height that is useful to set initial conditions or test the "lake-at-rest" well-balancedness. -Also, there are two thresholds which prevent numerical problems as well as instabilities. Both of them do not -have to be passed, as default values are defined within the struct. The first one, `threshold_limiter`, is -used in [`PositivityPreservingLimiterShallowWater`](@ref) on the water height, as a (small) shift on the initial -condition and cutoff before the next time step. The second one, `threshold_wet`, is applied on the water height to -define when the flow is "wet" before calculating the numerical flux. - The bottom topography function ``b(x)`` and channel width ``a(x)`` are set inside the initial condition routine for a particular problem setup. To test the conservative form of the SWE one can set the bottom topography variable `b` to zero and ``a`` to one. @@ -47,14 +41,6 @@ struct ShallowWaterEquationsQuasi1D{RealT <: Real} <: AbstractShallowWaterEquations{1, 4} gravity::RealT # gravitational constant H0::RealT # constant "lake-at-rest" total water height - # `threshold_limiter` used in `PositivityPreservingLimiterShallowWater` on water height, - # as a (small) shift on the initial condition and cutoff before the next time step. - # Default is 500*eps() which in double precision is ≈1e-13. - threshold_limiter::RealT - # `threshold_wet` applied on water height to define when the flow is "wet" - # before calculating the numerical flux. - # Default is 5*eps() which in double precision is ≈1e-15. - threshold_wet::RealT end # Allow for flexibility to set the gravitational constant within an elixir depending on the @@ -62,17 +48,8 @@ end # The reference total water height H0 defaults to 0.0 but is used for the "lake-at-rest" # well-balancedness test cases. # Strict default values for thresholds that performed well in many numerical experiments -function ShallowWaterEquationsQuasi1D(; gravity_constant, H0 = zero(gravity_constant), - threshold_limiter = nothing, - threshold_wet = nothing) - T = promote_type(typeof(gravity_constant), typeof(H0)) - if threshold_limiter === nothing - threshold_limiter = 500 * eps(T) - end - if threshold_wet === nothing - threshold_wet = 5 * eps(T) - end - ShallowWaterEquationsQuasi1D(gravity_constant, H0, threshold_limiter, threshold_wet) +function ShallowWaterEquationsQuasi1D(; gravity_constant, H0 = zero(gravity_constant)) + ShallowWaterEquationsQuasi1D(gravity_constant, H0) end have_nonconservative_terms(::ShallowWaterEquationsQuasi1D) = True() @@ -338,18 +315,10 @@ end # be a constant value over time. Note, assumes there is a single reference # water height `H0` with which to compare. # -# TODO: TrixiShallowWater: where should `threshold_limiter` live? May need -# to modify or have different versions of the `lake_at_rest_error` function @inline function lake_at_rest_error(u, equations::ShallowWaterEquationsQuasi1D) _, _, b, _ = u h = waterheight(u, equations) - # For well-balancedness testing with possible wet/dry regions the reference - # water height `H0` accounts for the possibility that the bottom topography - # can emerge out of the water as well as for the threshold offset to avoid - # division by a "hard" zero water heights as well. - H0_wet_dry = max(equations.H0, b + equations.threshold_limiter) - - return abs(H0_wet_dry - (h + b)) + return abs(equations.H0 - (h + b)) end end # @muladd diff --git a/src/equations/shallow_water_two_layer_1d.jl b/src/equations/shallow_water_two_layer_1d.jl deleted file mode 100644 index 42ff393593e..00000000000 --- a/src/equations/shallow_water_two_layer_1d.jl +++ /dev/null @@ -1,511 +0,0 @@ -# By default, Julia/LLVM does not use fused multiply-add operations (FMAs). -# Since these FMAs can increase the performance of many numerical algorithms, -# we need to opt-in explicitly. -# See https://ranocha.de/blog/Optimizing_EC_Trixi for further details. -@muladd begin -#! format: noindent - -# TODO: TrixiShallowWater: 1D two layer equations should move to new package - -@doc raw""" - ShallowWaterTwoLayerEquations1D(gravity, H0, rho_upper, rho_lower) - -Two-Layer Shallow Water equations (2LSWE) in one space dimension. The equations are given by -```math -\begin{alignat*}{4} -&\frac{\partial}{\partial t}h_{upper} -&&+ \frac{\partial}{\partial x}\left(h_{upper} v_{1,upper}\right) -&&= 0 \\ -&\frac{\partial}{\partial t}\left(h_{upper}v_{1,upper}\right) -&&+ \frac{\partial}{\partial x}\left(h_{upper}v_{1,upper}^2 + \dfrac{gh_{upper}^2}{2}\right) -&&= -gh_{upper}\frac{\partial}{\partial x}\left(b+h_{lower}\right)\\ -&\frac{\partial}{\partial t}h_{lower} -&&+ \frac{\partial}{\partial x}\left(h_{lower}v_{1,lower}\right) -&&= 0 \\ -&\frac{\partial}{\partial t}\left(h_{lower}v_{1,lower}\right) -&&+ \frac{\partial}{\partial x}\left(h_{lower}v_{1,lower}^2 + \dfrac{gh_{lower}^2}{2}\right) -&&= -gh_{lower}\frac{\partial}{\partial x}\left(b+\dfrac{\rho_{upper}}{\rho_{lower}}h_{upper}\right). -\end{alignat*} -``` -The unknown quantities of the 2LSWE are the water heights of the {lower} layer ``h_{lower}`` and the -{upper} layer ``h_{upper}`` with respective velocities ``v_{1,upper}`` and ``v_{1,lower}``. The gravitational constant is -denoted by `g`, the layer densitites by ``\rho_{upper}``and ``\rho_{lower}`` and the (possibly) variable -bottom topography function ``b(x)``. The conservative variable water height ``h_{lower}`` is measured -from the bottom topography ``b`` and ``h_{upper}`` relative to ``h_{lower}``, therefore one also defines the -total water heights as ``H_{upper} = h_{upper} + h_{upper} + b`` and ``H_{lower} = h_{lower} + b``. - -The densities must be chosen such that ``\rho_{upper} < \rho_{lower}``, to make sure that the heavier fluid -``\rho_{lower}`` is in the bottom layer and the lighter fluid ``\rho_{upper}`` in the {upper} layer. - -The additional quantity ``H_0`` is also available to store a reference value for the total water -height that is useful to set initial conditions or test the "lake-at-rest" well-balancedness. - -The bottom topography function ``b(x)`` is set inside the initial condition routine -for a particular problem setup. - -In addition to the unknowns, Trixi currently stores the bottom topography values at the -approximation points despite being fixed in time. This is done for convenience of computing the -bottom topography gradients on the fly during the approximation as well as computing auxiliary -quantities like the total water height ``H`` or the entropy variables. -This affects the implementation and use of these equations in various ways: -* The flux values corresponding to the bottom topography must be zero. -* The bottom topography values must be included when defining initial conditions, boundary - conditions or source terms. -* [`AnalysisCallback`](@ref) analyzes this variable. -* Trixi's visualization tools will visualize the bottom topography by default. - -A good introduction for the 2LSWE is available in Chapter 12 of the book: -- Benoit Cushman-Roisin (2011)\ - Introduction to geophyiscal fluid dynamics: physical and numerical aspects\ - \ - ISBN: 978-0-12-088759-0 -""" -struct ShallowWaterTwoLayerEquations1D{RealT <: Real} <: - AbstractShallowWaterEquations{1, 5} - gravity::RealT # gravitational constant - H0::RealT # constant "lake-at-rest" total water height - rho_upper::RealT # lower layer density - rho_lower::RealT # upper layer density - r::RealT # ratio of rho_upper / rho_lower -end - -# Allow for flexibility to set the gravitational constant within an elixir depending on the -# application where `gravity_constant=1.0` or `gravity_constant=9.81` are common values. -# The reference total water height H0 defaults to 0.0 but is used for the "lake-at-rest" -# well-balancedness test cases. Densities must be specified such that rho_upper <= rho_lower. -function ShallowWaterTwoLayerEquations1D(; gravity_constant, - H0 = zero(gravity_constant), rho_upper, - rho_lower) - # Assign density ratio if rho_upper <= rho_lower - if rho_upper > rho_lower - error("Invalid input: Densities must be chosen such that rho_upper <= rho_lower") - else - r = rho_upper / rho_lower - end - ShallowWaterTwoLayerEquations1D(gravity_constant, H0, rho_upper, rho_lower, r) -end - -have_nonconservative_terms(::ShallowWaterTwoLayerEquations1D) = True() -function varnames(::typeof(cons2cons), ::ShallowWaterTwoLayerEquations1D) - ("h_upper", "h_v_upper", - "h_lower", "h_v_lower", "b") -end -# Note, we use the total water height, H_lower = h_upper + h_lower + b, and first layer total height -# H_upper = h_upper + b as the first primitive variable for easier visualization and setting initial -# conditions -function varnames(::typeof(cons2prim), ::ShallowWaterTwoLayerEquations1D) - ("H_upper", "v_upper", - "H_lower", "v_lower", "b") -end - -# Set initial conditions at physical location `x` for time `t` -""" - initial_condition_convergence_test(x, t, equations::ShallowWaterTwoLayerEquations1D) - -A smooth initial condition used for convergence tests in combination with -[`source_terms_convergence_test`](@ref) (and -[`BoundaryConditionDirichlet(initial_condition_convergence_test)`](@ref) in non-periodic domains). -""" -function initial_condition_convergence_test(x, t, - equations::ShallowWaterTwoLayerEquations1D) - # some constants are chosen such that the function is periodic on the domain [0,sqrt(2)] - ω = 2.0 * pi * sqrt(2.0) - - H_lower = 2.0 + 0.1 * sin(ω * x[1] + t) - H_upper = 4.0 + 0.1 * cos(ω * x[1] + t) - v_lower = 1.0 - v_upper = 0.9 - b = 1.0 + 0.1 * cos(2.0 * ω * x[1]) - - return prim2cons(SVector(H_upper, v_upper, H_lower, v_lower, b), equations) -end - -""" - source_terms_convergence_test(u, x, t, equations::ShallowWaterTwoLayerEquations1D) - -Source terms used for convergence tests in combination with -[`initial_condition_convergence_test`](@ref) -(and [`BoundaryConditionDirichlet(initial_condition_convergence_test)`](@ref) -in non-periodic domains). -""" -@inline function source_terms_convergence_test(u, x, t, - equations::ShallowWaterTwoLayerEquations1D) - # Same settings as in `initial_condition_convergence_test`. Some derivative simplify because - # this manufactured solution velocity is taken to be constant - ω = 2 * pi * sqrt(2.0) - - du1 = (-0.1 * cos(t + ω * x[1]) - 0.1 * sin(t + ω * x[1]) - - 0.09 * ω * cos(t + ω * x[1]) + - -0.09 * ω * sin(t + ω * x[1])) - du2 = (5.0 * (-0.1 * ω * cos(t + ω * x[1]) - 0.1 * ω * sin(t + ω * x[1])) * - (4.0 + 0.2 * cos(t + ω * x[1]) + - -0.2 * sin(t + ω * x[1])) + - 0.1 * ω * (20.0 + cos(t + ω * x[1]) - sin(t + ω * x[1])) * - cos(t + - ω * x[1]) - 0.09 * cos(t + ω * x[1]) - 0.09 * sin(t + ω * x[1]) - - 0.081 * ω * cos(t + ω * x[1]) + - -0.081 * ω * sin(t + ω * x[1])) - du3 = 0.1 * cos(t + ω * x[1]) + 0.1 * ω * cos(t + ω * x[1]) + - 0.2 * ω * sin(2.0 * ω * x[1]) - du4 = ((10.0 + sin(t + ω * x[1]) - cos(2ω * x[1])) * - (-0.09 * ω * cos(t + ω * x[1]) - 0.09 * ω * sin(t + - ω * x[1]) - - 0.2 * ω * sin(2 * ω * x[1])) + 0.1 * cos(t + ω * x[1]) + - 0.1 * ω * cos(t + ω * x[1]) + - 5.0 * (0.1 * ω * cos(t + ω * x[1]) + 0.2 * ω * sin(2.0 * ω * x[1])) * - (2.0 + 0.2 * sin(t + ω * x[1]) + - -0.2 * cos(2.0 * ω * x[1])) + 0.2 * ω * sin(2.0 * ω * x[1])) - - return SVector(du1, du2, du3, du4, zero(eltype(u))) -end - -""" - boundary_condition_slip_wall(u_inner, orientation_or_normal, x, t, surface_flux_function, - equations::ShallowWaterTwoLayerEquations1D) - -Create a boundary state by reflecting the normal velocity component and keep -the tangential velocity component unchanged. The boundary water height is taken from -the internal value. - -For details see Section 9.2.5 of the book: -- Eleuterio F. Toro (2001) - Shock-Capturing Methods for Free-Surface Shallow Flows - 1st edition - ISBN 0471987662 -""" -@inline function boundary_condition_slip_wall(u_inner, orientation_or_normal, direction, - x, t, surface_flux_function, - equations::ShallowWaterTwoLayerEquations1D) - # create the "external" boundary solution state - u_boundary = SVector(u_inner[1], - -u_inner[2], - u_inner[3], - -u_inner[4], - u_inner[5]) - - # calculate the boundary flux - if iseven(direction) # u_inner is "left" of boundary, u_boundary is "right" of boundary - f = surface_flux_function(u_inner, u_boundary, orientation_or_normal, equations) - else # u_boundary is "left" of boundary, u_inner is "right" of boundary - f = surface_flux_function(u_boundary, u_inner, orientation_or_normal, equations) - end - return f -end - -# Calculate 1D flux for a single point -# Note, the bottom topography has no flux -@inline function flux(u, orientation::Integer, - equations::ShallowWaterTwoLayerEquations1D) - h_upper, h_v_upper, h_lower, h_v_lower, _ = u - - # Calculate velocities - v_upper, v_lower = velocity(u, equations) - # Calculate pressure - p_upper = 0.5 * equations.gravity * h_upper^2 - p_lower = 0.5 * equations.gravity * h_lower^2 - - f1 = h_v_upper - f2 = h_v_upper * v_upper + p_upper - f3 = h_v_lower - f4 = h_v_lower * v_lower + p_lower - - return SVector(f1, f2, f3, f4, zero(eltype(u))) -end - -""" - flux_nonconservative_ersing_etal(u_ll, u_rr, orientation::Integer, - equations::ShallowWaterTwoLayerEquations1D) - -!!! warning "Experimental code" - This numerical flux is experimental and may change in any future release. - -Non-symmetric path-conservative two-point volume flux discretizing the nonconservative (source) term -that contains the gradient of the bottom topography [`ShallowWaterTwoLayerEquations1D`](@ref) and an -additional term that couples the momentum of both layers. - -This is a modified version of [`flux_nonconservative_wintermeyer_etal`](@ref) that gives entropy -conservation and well-balancedness in both the volume and surface when combined with -[`flux_wintermeyer_etal`](@ref). - -For further details see: -- Patrick Ersing, Andrew R. Winters (2023) - An entropy stable discontinuous Galerkin method for the two-layer shallow water equations on - curvilinear meshes - [DOI: 10.48550/arXiv.2306.12699](https://doi.org/10.48550/arXiv.2306.12699) -""" -@inline function flux_nonconservative_ersing_etal(u_ll, u_rr, - orientation::Integer, - equations::ShallowWaterTwoLayerEquations1D) - # Pull the necessary left and right state information - h_upper_ll, h_lower_ll = waterheight(u_ll, equations) - h_upper_rr, h_lower_rr = waterheight(u_rr, equations) - b_rr = u_rr[5] - b_ll = u_ll[5] - - # Calculate jumps - h_upper_jump = (h_upper_rr - h_upper_ll) - h_lower_jump = (h_lower_rr - h_lower_ll) - b_jump = (b_rr - b_ll) - - z = zero(eltype(u_ll)) - - # Bottom gradient nonconservative term: (0, g*h_upper*(b+h_lower)_x, - # 0, g*h_lower*(b+r*h_upper)_x, 0) - f = SVector(z, - equations.gravity * h_upper_ll * (b_jump + h_lower_jump), - z, - equations.gravity * h_lower_ll * (b_jump + equations.r * h_upper_jump), - z) - return f -end - -""" - flux_wintermeyer_etal(u_ll, u_rr, orientation, - equations::ShallowWaterTwoLayerEquations1D) - -Total energy conservative (mathematical entropy for two-layer shallow water equations) split form. -When the bottom topography is nonzero this scheme will be well-balanced when used with the -nonconservative [`flux_nonconservative_ersing_etal`](@ref). To obtain the flux for the -two-layer shallow water equations the flux that is described in the paper for the normal shallow -water equations is used within each layer. - -Further details are available in Theorem 1 of the paper: -- Niklas Wintermeyer, Andrew R. Winters, Gregor J. Gassner and David A. Kopriva (2017) - An entropy stable nodal discontinuous Galerkin method for the two dimensional - shallow water equations on unstructured curvilinear meshes with discontinuous bathymetry - [DOI: 10.1016/j.jcp.2017.03.036](https://doi.org/10.1016/j.jcp.2017.03.036) -""" -@inline function flux_wintermeyer_etal(u_ll, u_rr, - orientation::Integer, - equations::ShallowWaterTwoLayerEquations1D) - # Unpack left and right state - h_upper_ll, h_v_upper_ll, h_lower_ll, h_v_lower_ll, _ = u_ll - h_upper_rr, h_v_upper_rr, h_lower_rr, h_v_lower_rr, _ = u_rr - - # Get the velocities on either side - v_upper_ll, v_lower_ll = velocity(u_ll, equations) - v_upper_rr, v_lower_rr = velocity(u_rr, equations) - - # Average each factor of products in flux - v_upper_avg = 0.5 * (v_upper_ll + v_upper_rr) - v_lower_avg = 0.5 * (v_lower_ll + v_lower_rr) - p_upper_avg = 0.5 * equations.gravity * h_upper_ll * h_upper_rr - p_lower_avg = 0.5 * equations.gravity * h_lower_ll * h_lower_rr - - # Calculate fluxes - f1 = 0.5 * (h_v_upper_ll + h_v_upper_rr) - f2 = f1 * v_upper_avg + p_upper_avg - f3 = 0.5 * (h_v_lower_ll + h_v_lower_rr) - f4 = f3 * v_lower_avg + p_lower_avg - - return SVector(f1, f2, f3, f4, zero(eltype(u_ll))) -end - -""" - flux_es_ersing_etal(u_ll, u_rr, orientation_or_normal_direction, - equations::ShallowWaterTwoLayerEquations1D) -Entropy stable surface flux for the two-layer shallow water equations. Uses the entropy conservative -[`flux_wintermeyer_etal`](@ref) and adds a Lax-Friedrichs type dissipation dependent on the jump of -entropy variables. - -For further details see: -- Patrick Ersing, Andrew R. Winters (2023) - An entropy stable discontinuous Galerkin method for the two-layer shallow water equations on - curvilinear meshes - [DOI: 10.48550/arXiv.2306.12699](https://doi.org/10.48550/arXiv.2306.12699) -""" -@inline function flux_es_ersing_etal(u_ll, u_rr, - orientation::Integer, - equations::ShallowWaterTwoLayerEquations1D) - # Compute entropy conservative flux but without the bottom topography - f_ec = flux_wintermeyer_etal(u_ll, u_rr, - orientation, - equations) - - # Get maximum signal velocity - λ = max_abs_speed_naive(u_ll, u_rr, orientation, equations) - # Get entropy variables but without the bottom topography - q_rr = cons2entropy(u_rr, equations) - q_ll = cons2entropy(u_ll, equations) - - # Average values from left and right - u_avg = (u_ll + u_rr) / 2 - - # Introduce variables for better readability - rho_upper = equations.rho_upper - rho_lower = equations.rho_lower - g = equations.gravity - drho = rho_upper - rho_lower - - # Compute entropy Jacobian coefficients - h11 = -rho_lower / (g * rho_upper * drho) - h12 = -rho_lower * u_avg[2] / (g * rho_upper * u_avg[1] * drho) - h13 = 1.0 / (g * drho) - h14 = u_avg[4] / (g * u_avg[3] * drho) - h21 = -rho_lower * u_avg[2] / (g * rho_upper * u_avg[1] * drho) - h22 = ((g * rho_upper * u_avg[1]^3 - g * rho_lower * u_avg[1]^3 + - -rho_lower * u_avg[2]^2) / (g * rho_upper * u_avg[1]^2 * drho)) - h23 = u_avg[2] / (g * u_avg[1] * drho) - h24 = u_avg[2] * u_avg[4] / (g * u_avg[1] * u_avg[3] * drho) - h31 = 1.0 / (g * drho) - h32 = u_avg[2] / (g * u_avg[1] * drho) - h33 = -1.0 / (g * drho) - h34 = -u_avg[4] / (g * u_avg[3] * drho) - h41 = u_avg[4] / (g * u_avg[3] * drho) - h42 = u_avg[2] * u_avg[4] / (g * u_avg[1] * u_avg[3] * drho) - h43 = -u_avg[4] / (g * u_avg[3] * drho) - h44 = ((g * rho_upper * u_avg[3]^3 - g * rho_lower * u_avg[3]^3 + - -rho_lower * u_avg[4]^2) / (g * rho_lower * u_avg[3]^2 * drho)) - - # Entropy Jacobian matrix - H = @SMatrix [[h11;; h12;; h13;; h14;; 0]; - [h21;; h22;; h23;; h24;; 0]; - [h31;; h32;; h33;; h34;; 0]; - [h41;; h42;; h43;; h44;; 0]; - [0;; 0;; 0;; 0;; 0]] - - # Add dissipation to entropy conservative flux to obtain entropy stable flux - f_es = f_ec - 0.5 * λ * H * (q_rr - q_ll) - - return SVector(f_es[1], f_es[2], f_es[3], f_es[4], zero(eltype(u_ll))) -end - -# Calculate approximation for maximum wave speed for local Lax-Friedrichs-type dissipation as the -# maximum velocity magnitude plus the maximum speed of sound. This function uses approximate -# eigenvalues using the speed of the barotropic mode as there is no simple way to calculate them -# analytically. -# -# A good overview of the derivation is given in: -# - Jonas Nycander, Andrew McC. Hogg, Leela M. Frankcombe (2008) -# Open boundary conditions for nonlinear channel Flows -# [DOI: 10.1016/j.ocemod.2008.06.003](https://doi.org/10.1016/j.ocemod.2008.06.003) -@inline function max_abs_speed_naive(u_ll, u_rr, - orientation::Integer, - equations::ShallowWaterTwoLayerEquations1D) - # Unpack left and right state - h_upper_ll, h_v_upper_ll, h_lower_ll, h_v_lower_ll, _ = u_ll - h_upper_rr, h_v_upper_rr, h_lower_rr, h_v_lower_rr, _ = u_rr - - # Get the averaged velocity - v_m_ll = (h_v_upper_ll + h_v_lower_ll) / (h_upper_ll + h_lower_ll) - v_m_rr = (h_v_upper_rr + h_v_lower_rr) / (h_upper_rr + h_lower_rr) - - # Calculate the wave celerity on the left and right - h_upper_ll, h_lower_ll = waterheight(u_ll, equations) - h_upper_rr, h_lower_rr = waterheight(u_rr, equations) - c_ll = sqrt(equations.gravity * (h_upper_ll + h_lower_ll)) - c_rr = sqrt(equations.gravity * (h_upper_rr + h_lower_rr)) - - return (max(abs(v_m_ll) + c_ll, abs(v_m_rr) + c_rr)) -end - -# Specialized `DissipationLocalLaxFriedrichs` to avoid spurious dissipation in the bottom -# topography -@inline function (dissipation::DissipationLocalLaxFriedrichs)(u_ll, u_rr, - orientation_or_normal_direction, - equations::ShallowWaterTwoLayerEquations1D) - λ = dissipation.max_abs_speed(u_ll, u_rr, orientation_or_normal_direction, - equations) - diss = -0.5 * λ * (u_rr - u_ll) - return SVector(diss[1], diss[2], diss[3], diss[4], zero(eltype(u_ll))) -end - -# Absolute speed of the barotropic mode -@inline function max_abs_speeds(u, equations::ShallowWaterTwoLayerEquations1D) - h_upper, h_v_upper, h_lower, h_v_lower, _ = u - - # Calculate averaged velocity of both layers - v_m = (h_v_upper + h_v_lower) / (h_upper + h_lower) - c = sqrt(equations.gravity * (h_upper + h_lower)) - - return (abs(v_m) + c) -end - -# Helper function to extract the velocity vector from the conservative variables -@inline function velocity(u, equations::ShallowWaterTwoLayerEquations1D) - h_upper, h_v_upper, h_lower, h_v_lower, _ = u - - v_upper = h_v_upper / h_upper - v_lower = h_v_lower / h_lower - return SVector(v_upper, v_lower) -end - -# Convert conservative variables to primitive -@inline function cons2prim(u, equations::ShallowWaterTwoLayerEquations1D) - h_upper, _, h_lower, _, b = u - - H_lower = h_lower + b - H_upper = h_lower + h_upper + b - v_upper, v_lower = velocity(u, equations) - return SVector(H_upper, v_upper, H_lower, v_lower, b) -end - -# Convert conservative variables to entropy variables -# Note, only the first four are the entropy variables, the fifth entry still just carries the -# bottom topography values for convenience -@inline function cons2entropy(u, equations::ShallowWaterTwoLayerEquations1D) - h_upper, _, h_lower, _, b = u - v_upper, v_lower = velocity(u, equations) - - w1 = (equations.rho_upper * - (equations.gravity * (h_upper + h_lower + b) - 0.5 * v_upper^2)) - w2 = equations.rho_upper * v_upper - w3 = (equations.rho_lower * - (equations.gravity * (equations.r * h_upper + h_lower + b) - 0.5 * v_lower^2)) - w4 = equations.rho_lower * v_lower - return SVector(w1, w2, w3, w4, b) -end - -# Convert primitive to conservative variables -@inline function prim2cons(prim, equations::ShallowWaterTwoLayerEquations1D) - H_upper, v_upper, H_lower, v_lower, b = prim - - h_lower = H_lower - b - h_upper = H_upper - h_lower - b - h_v_upper = h_upper * v_upper - h_v_lower = h_lower * v_lower - return SVector(h_upper, h_v_upper, h_lower, h_v_lower, b) -end - -@inline function waterheight(u, equations::ShallowWaterTwoLayerEquations1D) - return SVector(u[1], u[3]) -end - -# Entropy function for the shallow water equations is the total energy -@inline function entropy(cons, equations::ShallowWaterTwoLayerEquations1D) - energy_total(cons, equations) -end - -# Calculate total energy for a conservative state `cons` -@inline function energy_total(cons, equations::ShallowWaterTwoLayerEquations1D) - h_upper, h_v_upper, h_lower, h_v_lower, b = cons - # Set new variables for better readability - g = equations.gravity - rho_upper = equations.rho_upper - rho_lower = equations.rho_lower - - e = (0.5 * rho_upper * (h_v_upper^2 / h_upper + g * h_upper^2) + - 0.5 * rho_lower * (h_v_lower^2 / h_lower + g * h_lower^2) + - g * rho_lower * h_lower * b + g * rho_upper * h_upper * (h_lower + b)) - return e -end - -# Calculate kinetic energy for a conservative state `cons` -@inline function energy_kinetic(u, equations::ShallowWaterTwoLayerEquations1D) - h_upper, h_v_upper, h_lower, h_v_lower, _ = u - return (0.5 * equations.rho_upper * h_v_upper^2 / h_upper + - 0.5 * equations.rho_lower * h_v_lower^2 / h_lower) -end - -# Calculate potential energy for a conservative state `cons` -@inline function energy_internal(cons, equations::ShallowWaterTwoLayerEquations1D) - return energy_total(cons, equations) - energy_kinetic(cons, equations) -end - -# Calculate the error for the "lake-at-rest" test case where H = h_upper+h_lower+b should -# be a constant value over time -@inline function lake_at_rest_error(u, equations::ShallowWaterTwoLayerEquations1D) - h_upper, _, h_lower, _, b = u - return abs(equations.H0 - (h_upper + h_lower + b)) -end -end # @muladd diff --git a/src/equations/shallow_water_two_layer_2d.jl b/src/equations/shallow_water_two_layer_2d.jl deleted file mode 100644 index a31d881f2ef..00000000000 --- a/src/equations/shallow_water_two_layer_2d.jl +++ /dev/null @@ -1,805 +0,0 @@ -# By default, Julia/LLVM does not use fused multiply-add operations (FMAs). -# Since these FMAs can increase the performance of many numerical algorithms, -# we need to opt-in explicitly. -# See https://ranocha.de/blog/Optimizing_EC_Trixi for further details. -@muladd begin -#! format: noindent - -# TODO: TrixiShallowWater: 2D two layer equations should move to new package - -@doc raw""" - ShallowWaterTwoLayerEquations2D(gravity, H0, rho_upper, rho_lower) - -Two-Layer Shallow water equations (2LSWE) in two space dimension. The equations are given by -```math -\begin{alignat*}{8} -&\frac{\partial}{\partial t}h_{upper} -&&+ \frac{\partial}{\partial x}\left(h_{upper} v_{1,upper}\right) -&&+ \frac{\partial}{\partial y}\left(h_{upper} v_{2,upper}\right) \quad -&&= \quad 0 \\ -&\frac{\partial}{\partial t}\left(h_{upper} v_{1,upper}\right) -&&+ \frac{\partial}{\partial x}\left(h_{upper} v_{1,upper}^2 + \frac{gh_{upper}^2}{2}\right) -&&+ \frac{\partial}{\partial y}\left(h_{upper} v_{1,upper} v_{2,upper}\right) \quad -&&= -gh_{upper}\frac{\partial}{\partial x}\left(b+h_{lower}\right) \\ -&\frac{\partial}{\partial t}\left(h_{upper} v_{2,upper}\right) -&&+ \frac{\partial}{\partial x}\left(h_{upper} v_{1,upper} v_{2,upper}\right) -&&+ \frac{\partial}{\partial y}\left(h_{upper} v_{2,upper}^2 + \frac{gh_{upper}^2}{2}\right) -&&= -gh_{upper}\frac{\partial}{\partial y}\left(b+h_{lower}\right)\\ -&\frac{\partial}{\partial t}h_{lower} -&&+ \frac{\partial}{\partial x}\left(h_{lower} v_{1,lower}\right) -&&+ \frac{\partial}{\partial y}\left(h_{lower} v_{2,lower}\right) -&&= \quad 0 \\ -&\frac{\partial}{\partial t}\left(h_{lower} v_{1,lower}\right) -&&+ \frac{\partial}{\partial x}\left(h_{lower} v_{1,lower}^2 + \frac{gh_{lower}^2}{2}\right) -&&+ \frac{\partial}{\partial y}\left(h_{lower} v_{1,lower} v_{2,lower}\right) -&&= -gh_{lower}\frac{\partial}{\partial x}\left(b+\frac{\rho_{upper}}{\rho_{lower}} h_{upper}\right)\\ -&\frac{\partial}{\partial t}\left(h_{lower} v_{2,lower}\right) -&&+ \frac{\partial}{\partial x}\left(h_{lower} v_{1,lower} v_{2,lower}\right) -&&+ \frac{\partial}{\partial y}\left(h_{lower} v_{2,lower}^2 + \frac{gh_{lower}^2}{2}\right) -&&= -gh_{lower}\frac{\partial}{\partial y}\left(b+\frac{\rho_{upper}}{\rho_{lower}} h_{upper}\right) -\end{alignat*} -``` -The unknown quantities of the 2LSWE are the water heights of the lower layer ``h_{lower}`` and the -upper -layer ``h_{upper}`` and the respective velocities in x-direction ``v_{1,lower}`` and ``v_{1,upper}`` and in y-direction -``v_{2,lower}`` and ``v_{2,upper}``. The gravitational constant is denoted by `g`, the layer densitites by -``\rho_{upper}``and ``\rho_{lower}`` and the (possibly) variable bottom topography function by ``b(x)``. -Conservative variable water height ``h_{lower}`` is measured from the bottom topography ``b`` and ``h_{upper}`` -relative to ``h_{lower}``, therefore one also defines the total water heights as ``H_{lower} = h_{lower} + b`` and -``H_{upper} = h_{upper} + h_{lower} + b``. - -The densities must be chosen such that ``\rho_{upper} < \rho_{lower}``, to make sure that the heavier fluid -``\rho_{lower}`` is in the bottom layer and the lighter fluid ``\rho_{upper}`` in the upper layer. - -The additional quantity ``H_0`` is also available to store a reference value for the total water -height that is useful to set initial conditions or test the "lake-at-rest" well-balancedness. - -The bottom topography function ``b(x)`` is set inside the initial condition routine -for a particular problem setup. - -In addition to the unknowns, Trixi currently stores the bottom topography values at the -approximation points despite being fixed in time. This is done for convenience of computing the -bottom topography gradients on the fly during the approximation as well as computing auxiliary -quantities like the total water height ``H`` or the entropy variables. -This affects the implementation and use of these equations in various ways: -* The flux values corresponding to the bottom topography must be zero. -* The bottom topography values must be included when defining initial conditions, boundary - conditions or source terms. -* [`AnalysisCallback`](@ref) analyzes this variable. -* Trixi's visualization tools will visualize the bottom topography by default. - -A good introduction for the 2LSWE is available in Chapter 12 of the book: - - Benoit Cushman-Roisin (2011)\ - Introduction to geophyiscal fluid dynamics: physical and numerical aspects\ - \ - ISBN: 978-0-12-088759-0 -""" -struct ShallowWaterTwoLayerEquations2D{RealT <: Real} <: - AbstractShallowWaterEquations{2, 7} - gravity::RealT # gravitational constant - H0::RealT # constant "lake-at-rest" total water height - rho_upper::RealT # lower layer density - rho_lower::RealT # upper layer density - r::RealT # ratio of rho_upper / rho_lower -end - -# Allow for flexibility to set the gravitational constant within an elixir depending on the -# application where `gravity_constant=1.0` or `gravity_constant=9.81` are common values. -# The reference total water height H0 defaults to 0.0 but is used for the "lake-at-rest" -# well-balancedness test cases. Densities must be specified such that rho_upper < rho_lower. -function ShallowWaterTwoLayerEquations2D(; gravity_constant, - H0 = zero(gravity_constant), rho_upper, - rho_lower) - # Assign density ratio if rho_upper <= rho_lower - if rho_upper > rho_lower - error("Invalid input: Densities must be chosen such that rho_upper <= rho_lower") - else - r = rho_upper / rho_lower - end - ShallowWaterTwoLayerEquations2D(gravity_constant, H0, rho_upper, rho_lower, r) -end - -have_nonconservative_terms(::ShallowWaterTwoLayerEquations2D) = True() -function varnames(::typeof(cons2cons), ::ShallowWaterTwoLayerEquations2D) - ("h_upper", "h_v1_upper", "h_v2_upper", "h_lower", "h_v1_lower", "h_v2_lower", "b") -end -# Note, we use the total water height, H_upper = h_upper + h_lower + b, and first layer total height -# H_lower = h_lower + b as the first primitive variable for easier visualization and setting initial -# conditions -function varnames(::typeof(cons2prim), ::ShallowWaterTwoLayerEquations2D) - ("H_upper", "v1_upper", "v2_upper", "H_lower", "v1_lower", "v2_lower", "b") -end - -# Set initial conditions at physical location `x` for time `t` -""" - initial_condition_convergence_test(x, t, equations::ShallowWaterTwoLayerEquations2D) - -A smooth initial condition used for convergence tests in combination with -[`source_terms_convergence_test`](@ref). Constants must be set to ``rho_{upper} = 0.9``, -``rho_{lower} = 1.0``, ``g = 10.0``. -""" -function initial_condition_convergence_test(x, t, - equations::ShallowWaterTwoLayerEquations2D) - # some constants are chosen such that the function is periodic on the domain [0,sqrt(2)]^2] - ω = 2.0 * pi * sqrt(2.0) - - H_lower = 2.0 + 0.1 * sin(ω * x[1] + t) * cos(ω * x[2] + t) - H_upper = 4.0 + 0.1 * cos(ω * x[1] + t) * sin(ω * x[2] + t) - v1_lower = 1.0 - v1_upper = 0.9 - v2_lower = 0.9 - v2_upper = 1.0 - b = 1.0 + 0.1 * cos(0.5 * ω * x[1]) * sin(0.5 * ω * x[2]) - - return prim2cons(SVector(H_upper, v1_upper, v2_upper, H_lower, v1_lower, v2_lower, - b), equations) -end - -""" - source_terms_convergence_test(u, x, t, equations::ShallowWaterTwoLayerEquations2D) - -Source terms used for convergence tests in combination with -[`initial_condition_convergence_test`](@ref). -""" -@inline function source_terms_convergence_test(u, x, t, - equations::ShallowWaterTwoLayerEquations2D) - # Same settings as in `initial_condition_convergence_test`. - # some constants are chosen such that the function is periodic on the domain [0,sqrt(2)]^2] - ω = 2.0 * pi * sqrt(2.0) - - # Source terms obtained with SymPy - du1 = 0.01 * ω * cos(t + ω * x[1]) * cos(t + ω * x[2]) + - 0.01 * ω * sin(t + ω * x[1]) * sin(t + ω * x[2]) - du2 = (5.0 * - (-0.1 * ω * cos(t + ω * x[1]) * cos(t + ω * x[2]) - - 0.1 * ω * sin(t + ω * x[1]) * sin(t + - ω * x[2])) * - (4.0 + 0.2cos(t + ω * x[1]) * sin(t + ω * x[2]) - - 0.2 * sin(t + ω * x[1]) * cos(t + - ω * x[2])) + - 0.009 * ω * cos(t + ω * x[1]) * cos(t + ω * x[2]) + - 0.009 * ω * sin(t + ω * x[1]) * sin(t + - ω * x[2]) + - 0.1 * ω * - (20.0 + cos(t + ω * x[1]) * sin(t + ω * x[2]) - - sin(t + ω * x[1]) * cos(t + - ω * x[2])) * cos(t + ω * x[1]) * cos(t + ω * x[2])) - du3 = (5.0 * - (0.1 * ω * cos(t + ω * x[1]) * cos(t + ω * x[2]) + - 0.1 * ω * sin(t + ω * x[1]) * sin(t + - ω * x[2])) * - (4.0 + 0.2 * cos(t + ω * x[1]) * sin(t + ω * x[2]) - - 0.2 * sin(t + ω * x[1]) * cos(t + - ω * x[2])) + - 0.01ω * cos(t + ω * x[1]) * cos(t + ω * x[2]) + - 0.01 * ω * sin(t + ω * x[1]) * sin(t + ω * x[2]) + - -0.1 * ω * - (20.0 + cos(t + ω * x[1]) * sin(t + ω * x[2]) - - sin(t + ω * x[1]) * cos(t + ω * x[2])) * sin(t + - ω * x[1]) * sin(t + ω * x[2])) - du4 = (0.1 * cos(t + ω * x[1]) * cos(t + ω * x[2]) + - 0.1 * ω * cos(t + ω * x[1]) * cos(t + ω * x[2]) + - 0.05 * ω * sin(0.5 * ω * x[1]) * sin(0.5 * ω * x[2]) - - 0.1 * sin(t + ω * x[1]) * sin(t + ω * x[2]) + - -0.045 * ω * cos(0.5 * ω * x[1]) * cos(0.5 * ω * x[2]) - - 0.09 * ω * sin(t + ω * x[1]) * sin(t + ω * x[2])) - du5 = ((10.0 + sin(t + ω * x[1]) * cos(t + ω * x[2]) - - cos(0.5 * ω * x[1]) * sin(0.5 * ω * x[2])) * (-0.09 * ω * cos(t + - ω * x[1]) * cos(t + ω * x[2]) - - 0.09 * ω * sin(t + ω * x[1]) * sin(t + ω * x[2]) + - -0.05 * ω * sin(0.5 * ω * x[1]) * sin(0.5 * ω * x[2])) + - 5.0 * - (0.1 * ω * cos(t + ω * x[1]) * cos(t + ω * x[2]) + - 0.05 * ω * sin(0.5 * ω * x[1]) * sin(0.5 * ω * x[2])) * - (2.0 + 0.2 * sin(t + ω * x[1]) * cos(t + ω * x[2]) + - -0.2 * cos(0.5 * ω * x[1]) * sin(0.5 * ω * x[2])) + - 0.1 * cos(t + ω * x[1]) * cos(t + ω * x[2]) + - 0.1 * ω * cos(t + - ω * x[1]) * cos(t + ω * x[2]) + - 0.05 * ω * sin(0.5 * ω * x[1]) * sin(0.5 * ω * x[2]) - - 0.1 * sin(t + - ω * x[1]) * sin(t + ω * x[2]) - - 0.045 * ω * cos(0.5 * ω * x[1]) * cos(0.5 * ω * x[2]) - - 0.09 * ω * sin(t + - ω * x[1]) * sin(t + ω * x[2])) - du6 = ((10.0 + sin(t + ω * x[1]) * cos(t + ω * x[2]) + - -cos(0.5 * ω * x[1]) * sin(0.5 * ω * x[2])) * - (0.05 * ω * cos(0.5 * ω * x[1]) * cos(0.5 * ω * x[2]) + - 0.09 * ω * cos(t + ω * x[1]) * cos(t + ω * x[2]) + - 0.09 * ω * sin(t + ω * x[1]) * sin(t + ω * x[2])) + - 5.0 * - (-0.05 * ω * cos(0.5 * ω * x[1]) * cos(0.5 * ω * x[2]) - - 0.1 * ω * sin(t + ω * x[1]) * sin(t + - ω * x[2])) * - (2.0 + 0.2 * sin(t + ω * x[1]) * cos(t + ω * x[2]) + - -0.2 * cos(0.5 * ω * x[1]) * sin(0.5 * ω * x[2])) + - 0.09cos(t + ω * x[1]) * cos(t + ω * x[2]) + - 0.09 * ω * cos(t + ω * x[1]) * cos(t + ω * x[2]) + - 0.045 * ω * sin(0.5 * ω * x[1]) * sin(0.5 * ω * x[2]) + - -0.09 * sin(t + ω * x[1]) * sin(t + ω * x[2]) - - 0.0405 * ω * cos(0.5 * ω * x[1]) * cos(0.5 * ω * x[2]) + - -0.081 * ω * sin(t + ω * x[1]) * sin(t + ω * x[2])) - - return SVector(du1, du2, du3, du4, du5, du6, zero(eltype(u))) -end - -""" - boundary_condition_slip_wall(u_inner, normal_direction, x, t, surface_flux_function, - equations::ShallowWaterTwoLayerEquations2D) - -Create a boundary state by reflecting the normal velocity component and keep -the tangential velocity component unchanged. The boundary water height is taken from -the internal value. - -For details see Section 9.2.5 of the book: -- Eleuterio F. Toro (2001) - Shock-Capturing Methods for Free-Surface Shallow Flows - 1st edition - ISBN 0471987662 -""" -@inline function boundary_condition_slip_wall(u_inner, normal_direction::AbstractVector, - x, t, surface_flux_function, - equations::ShallowWaterTwoLayerEquations2D) - # normalize the outward pointing direction - normal = normal_direction / norm(normal_direction) - - # compute the normal velocity - v_normal_upper = normal[1] * u_inner[2] + normal[2] * u_inner[3] - v_normal_lower = normal[1] * u_inner[5] + normal[2] * u_inner[6] - - # create the "external" boundary solution state - u_boundary = SVector(u_inner[1], - u_inner[2] - 2.0 * v_normal_upper * normal[1], - u_inner[3] - 2.0 * v_normal_upper * normal[2], - u_inner[4], - u_inner[5] - 2.0 * v_normal_lower * normal[1], - u_inner[6] - 2.0 * v_normal_lower * normal[2], - u_inner[7]) - - # calculate the boundary flux - flux = surface_flux_function(u_inner, u_boundary, normal_direction, equations) - return flux -end - -# Calculate 1D flux for a single point -# Note, the bottom topography has no flux -@inline function flux(u, orientation::Integer, - equations::ShallowWaterTwoLayerEquations2D) - h_upper, h_v1_upper, h_v2_upper, h_lower, h_v1_lower, h_v2_lower, _ = u - - # Calculate velocities - v1_upper, v2_upper, v1_lower, v2_lower = velocity(u, equations) - - # Calculate pressure - p_upper = 0.5 * equations.gravity * h_upper^2 - p_lower = 0.5 * equations.gravity * h_lower^2 - - # Calculate fluxes depending on orientation - if orientation == 1 - f1 = h_v1_upper - f2 = h_v1_upper * v1_upper + p_upper - f3 = h_v1_upper * v2_upper - f4 = h_v1_lower - f5 = h_v1_lower * v1_lower + p_lower - f6 = h_v1_lower * v2_lower - else - f1 = h_v2_upper - f2 = h_v2_upper * v1_upper - f3 = h_v2_upper * v2_upper + p_upper - f4 = h_v2_lower - f5 = h_v2_lower * v1_lower - f6 = h_v2_lower * v2_lower + p_lower - end - return SVector(f1, f2, f3, f4, f5, f6, zero(eltype(u))) -end - -# Calculate 1D flux for a single point in the normal direction -# Note, this directional vector is not normalized and the bottom topography has no flux -@inline function flux(u, normal_direction::AbstractVector, - equations::ShallowWaterTwoLayerEquations2D) - h_upper, h_lower = waterheight(u, equations) - v1_upper, v2_upper, v1_lower, v2_lower = velocity(u, equations) - - v_normal_upper = v1_upper * normal_direction[1] + v2_upper * normal_direction[2] - v_normal_lower = v1_lower * normal_direction[1] + v2_lower * normal_direction[2] - h_v_upper_normal = h_upper * v_normal_upper - h_v_lower_normal = h_lower * v_normal_lower - - p_upper = 0.5 * equations.gravity * h_upper^2 - p_lower = 0.5 * equations.gravity * h_lower^2 - - f1 = h_v_upper_normal - f2 = h_v_upper_normal * v1_upper + p_upper * normal_direction[1] - f3 = h_v_upper_normal * v2_upper + p_upper * normal_direction[2] - f4 = h_v_lower_normal - f5 = h_v_lower_normal * v1_lower + p_lower * normal_direction[1] - f6 = h_v_lower_normal * v2_lower + p_lower * normal_direction[2] - - return SVector(f1, f2, f3, f4, f5, f6, zero(eltype(u))) -end - -""" - flux_nonconservative_ersing_etal(u_ll, u_rr, orientation::Integer, - equations::ShallowWaterTwoLayerEquations2D) - flux_nonconservative_ersing_etal(u_ll, u_rr, - normal_direction_ll::AbstractVector, - normal_direction_average::AbstractVector, - equations::ShallowWaterTwoLayerEquations2D) - -!!! warning "Experimental code" - This numerical flux is experimental and may change in any future release. - -Non-symmetric path-conservative two-point volume flux discretizing the nonconservative (source) term -that contains the gradient of the bottom topography [`ShallowWaterTwoLayerEquations2D`](@ref) and an -additional term that couples the momentum of both layers. - -This is a modified version of [`flux_nonconservative_wintermeyer_etal`](@ref) that gives entropy -conservation and well-balancedness in both the volume and surface when combined with -[`flux_wintermeyer_etal`](@ref). - -For further details see: -- Patrick Ersing, Andrew R. Winters (2023) - An entropy stable discontinuous Galerkin method for the two-layer shallow water equations on - curvilinear meshes - [DOI: 10.48550/arXiv.2306.12699](https://doi.org/10.48550/arXiv.2306.12699) -""" -@inline function flux_nonconservative_ersing_etal(u_ll, u_rr, - orientation::Integer, - equations::ShallowWaterTwoLayerEquations2D) - # Pull the necessary left and right state information - h_upper_ll, h_lower_ll = waterheight(u_ll, equations) - h_upper_rr, h_lower_rr = waterheight(u_rr, equations) - b_rr = u_rr[7] - b_ll = u_ll[7] - - # Calculate jumps - h_upper_jump = (h_upper_rr - h_upper_ll) - h_lower_jump = (h_lower_rr - h_lower_ll) - b_jump = (b_rr - b_ll) - - z = zero(eltype(u_ll)) - - # Bottom gradient nonconservative term: (0, g*h_upper*(b + h_lower)_x, g*h_upper*(b + h_lower)_y , - # 0, g*h_lower*(b + r*h_upper)_x, - # g*h_lower*(b + r*h_upper)_y, 0) - if orientation == 1 - f = SVector(z, - equations.gravity * h_upper_ll * (b_jump + h_lower_jump), - z, z, - equations.gravity * h_lower_ll * - (b_jump + equations.r * h_upper_jump), - z, z) - else # orientation == 2 - f = SVector(z, z, - equations.gravity * h_upper_ll * (b_jump + h_lower_jump), - z, z, - equations.gravity * h_lower_ll * - (b_jump + equations.r * h_upper_jump), - z) - end - - return f -end - -@inline function flux_nonconservative_ersing_etal(u_ll, u_rr, - normal_direction_ll::AbstractVector, - normal_direction_average::AbstractVector, - equations::ShallowWaterTwoLayerEquations2D) - # Pull the necessary left and right state information - h_upper_ll, h_lower_ll = waterheight(u_ll, equations) - h_upper_rr, h_lower_rr = waterheight(u_rr, equations) - b_rr = u_rr[7] - b_ll = u_ll[7] - - # Calculate jumps - h_upper_jump = (h_upper_rr - h_upper_ll) - h_lower_jump = (h_lower_rr - h_lower_ll) - b_jump = (b_rr - b_ll) - - # Note this routine only uses the `normal_direction_average` and the average of the - # bottom topography to get a quadratic split form DG gradient on curved elements - return SVector(zero(eltype(u_ll)), - normal_direction_average[1] * equations.gravity * h_upper_ll * - (b_jump + h_lower_jump), - normal_direction_average[2] * equations.gravity * h_upper_ll * - (b_jump + h_lower_jump), - zero(eltype(u_ll)), - normal_direction_average[1] * equations.gravity * h_lower_ll * - (b_jump + equations.r * h_upper_jump), - normal_direction_average[2] * equations.gravity * h_lower_ll * - (b_jump + equations.r * h_upper_jump), - zero(eltype(u_ll))) -end - -""" - flux_wintermeyer_etal(u_ll, u_rr, orientation, - equations::ShallowWaterTwoLayerEquations2D) - flux_wintermeyer_etal(u_ll, u_rr, - normal_direction::AbstractVector, - equations::ShallowWaterTwoLayerEquations2D) - -Total energy conservative (mathematical entropy for two-layer shallow water equations) split form. -When the bottom topography is nonzero this scheme will be well-balanced when used with the -nonconservative [`flux_nonconservative_ersing_etal`](@ref). To obtain the flux for the -two-layer shallow water equations the flux that is described in the paper for the normal shallow -water equations is used within each layer. - -Further details are available in Theorem 1 of the paper: -- Niklas Wintermeyer, Andrew R. Winters, Gregor J. Gassner and David A. Kopriva (2017) - An entropy stable nodal discontinuous Galerkin method for the two dimensional - shallow water equations on unstructured curvilinear meshes with discontinuous bathymetry - [DOI: 10.1016/j.jcp.2017.03.036](https://doi.org/10.1016/j.jcp.2017.03.036) -""" -@inline function flux_wintermeyer_etal(u_ll, u_rr, - orientation::Integer, - equations::ShallowWaterTwoLayerEquations2D) - # Unpack left and right state - h_upper_ll, h_v1_upper_ll, h_v2_upper_ll, h_lower_ll, h_v1_lower_ll, h_v2_lower_ll, _ = u_ll - h_upper_rr, h_v1_upper_rr, h_v2_upper_rr, h_lower_rr, h_v1_lower_rr, h_v2_lower_rr, _ = u_rr - - # Get the velocities on either side - v1_upper_ll, v2_upper_ll, v1_lower_ll, v2_lower_ll = velocity(u_ll, equations) - v1_upper_rr, v2_upper_rr, v1_lower_rr, v2_lower_rr = velocity(u_rr, equations) - - # Average each factor of products in flux - v1_upper_avg = 0.5 * (v1_upper_ll + v1_upper_rr) - v1_lower_avg = 0.5 * (v1_lower_ll + v1_lower_rr) - v2_upper_avg = 0.5 * (v2_upper_ll + v2_upper_rr) - v2_lower_avg = 0.5 * (v2_lower_ll + v2_lower_rr) - p_upper_avg = 0.5 * equations.gravity * h_upper_ll * h_upper_rr - p_lower_avg = 0.5 * equations.gravity * h_lower_ll * h_lower_rr - - # Calculate fluxes depending on orientation - if orientation == 1 - f1 = 0.5 * (h_v1_upper_ll + h_v1_upper_rr) - f2 = f1 * v1_upper_avg + p_upper_avg - f3 = f1 * v2_upper_avg - f4 = 0.5 * (h_v1_lower_ll + h_v1_lower_rr) - f5 = f4 * v1_lower_avg + p_lower_avg - f6 = f4 * v2_lower_avg - else - f1 = 0.5 * (h_v2_upper_ll + h_v2_upper_rr) - f2 = f1 * v1_upper_avg - f3 = f1 * v2_upper_avg + p_upper_avg - f4 = 0.5 * (h_v2_lower_ll + h_v2_lower_rr) - f5 = f4 * v1_lower_avg - f6 = f4 * v2_lower_avg + p_lower_avg - end - - return SVector(f1, f2, f3, f4, f5, f6, zero(eltype(u_ll))) -end - -@inline function flux_wintermeyer_etal(u_ll, u_rr, - normal_direction::AbstractVector, - equations::ShallowWaterTwoLayerEquations2D) - # Unpack left and right state - h_upper_ll, h_v1_upper_ll, h_v2_upper_ll, h_lower_ll, h_v1_lower_ll, h_v2_lower_ll, _ = u_ll - h_upper_rr, h_v1_upper_rr, h_v2_upper_rr, h_lower_rr, h_v1_lower_rr, h_v2_lower_rr, _ = u_rr - - # Get the velocities on either side - v1_upper_ll, v2_upper_ll, v1_lower_ll, v2_lower_ll = velocity(u_ll, equations) - v1_upper_rr, v2_upper_rr, v1_lower_rr, v2_lower_rr = velocity(u_rr, equations) - - # Average each factor of products in flux - v1_upper_avg = 0.5 * (v1_upper_ll + v1_upper_rr) - v1_lower_avg = 0.5 * (v1_lower_ll + v1_lower_rr) - v2_upper_avg = 0.5 * (v2_upper_ll + v2_upper_rr) - v2_lower_avg = 0.5 * (v2_lower_ll + v2_lower_rr) - p_upper_avg = 0.5 * equations.gravity * h_upper_ll * h_upper_rr - p_lower_avg = 0.5 * equations.gravity * h_lower_ll * h_lower_rr - h_v1_upper_avg = 0.5 * (h_v1_upper_ll + h_v1_upper_rr) - h_v2_upper_avg = 0.5 * (h_v2_upper_ll + h_v2_upper_rr) - h_v1_lower_avg = 0.5 * (h_v1_lower_ll + h_v1_lower_rr) - h_v2_lower_avg = 0.5 * (h_v2_lower_ll + h_v2_lower_rr) - - # Calculate fluxes depending on normal_direction - f1 = h_v1_upper_avg * normal_direction[1] + h_v2_upper_avg * normal_direction[2] - f2 = f1 * v1_upper_avg + p_upper_avg * normal_direction[1] - f3 = f1 * v2_upper_avg + p_upper_avg * normal_direction[2] - f4 = h_v1_lower_avg * normal_direction[1] + h_v2_lower_avg * normal_direction[2] - f5 = f4 * v1_lower_avg + p_lower_avg * normal_direction[1] - f6 = f4 * v2_lower_avg + p_lower_avg * normal_direction[2] - - return SVector(f1, f2, f3, f4, f5, f6, zero(eltype(u_ll))) -end - -""" - flux_es_ersing_etal(u_ll, u_rr, orientation_or_normal_direction, - equations::ShallowWaterTwoLayerEquations2D) - -Entropy stable surface flux for the two-layer shallow water equations. Uses the entropy conservative -[`flux_wintermeyer_etal`](@ref) and adds a Lax-Friedrichs type dissipation dependent on the jump of -entropy variables. - -For further details see: -- Patrick Ersing, Andrew R. Winters (2023) - An entropy stable discontinuous Galerkin method for the two-layer shallow water equations on - curvilinear meshes - [DOI: 10.48550/arXiv.2306.12699](https://doi.org/10.48550/arXiv.2306.12699) -""" -@inline function flux_es_ersing_etal(u_ll, u_rr, - orientation_or_normal_direction, - equations::ShallowWaterTwoLayerEquations2D) - # Compute entropy conservative flux but without the bottom topography - f_ec = flux_wintermeyer_etal(u_ll, u_rr, - orientation_or_normal_direction, - equations) - - # Get maximum signal velocity - λ = max_abs_speed_naive(u_ll, u_rr, orientation_or_normal_direction, equations) - - # Get entropy variables but without the bottom topography - q_rr = cons2entropy(u_rr, equations) - q_ll = cons2entropy(u_ll, equations) - - # Average values from left and right - u_avg = (u_ll + u_rr) / 2 - - # Introduce variables for better readability - rho_upper = equations.rho_upper - rho_lower = equations.rho_lower - g = equations.gravity - drho = rho_upper - rho_lower - - # Compute entropy Jacobian coefficients - h11 = -rho_lower / (g * rho_upper * drho) - h12 = -rho_lower * u_avg[2] / (g * rho_upper * u_avg[1] * drho) - h13 = -rho_lower * u_avg[3] / (g * rho_upper * u_avg[1] * drho) - h14 = 1.0 / (g * drho) - h15 = u_avg[5] / (g * u_avg[4] * drho) - h16 = u_avg[6] / (g * u_avg[4] * drho) - h21 = -rho_lower * u_avg[2] / (g * rho_upper * u_avg[1] * drho) - h22 = ((g * rho_upper * u_avg[1]^3 - g * rho_lower * u_avg[1]^3 + - -rho_lower * u_avg[2]^2) / (g * rho_upper * u_avg[1]^2 * drho)) - h23 = -rho_lower * u_avg[2] * u_avg[3] / (g * rho_upper * u_avg[1]^2 * drho) - h24 = u_avg[2] / (g * u_avg[1] * drho) - h25 = u_avg[2] * u_avg[5] / (g * u_avg[1] * u_avg[4] * drho) - h26 = u_avg[2] * u_avg[6] / (g * u_avg[1] * u_avg[4] * drho) - h31 = -rho_lower * u_avg[3] / (g * rho_upper * u_avg[1] * drho) - h32 = -rho_lower * u_avg[2] * u_avg[3] / (g * rho_upper * u_avg[1]^2 * drho) - h33 = ((g * rho_upper * u_avg[1]^3 - g * rho_lower * u_avg[1]^3 + - -rho_lower * u_avg[3]^2) / (g * rho_upper * u_avg[1]^2 * drho)) - h34 = u_avg[3] / (g * u_avg[1] * drho) - h35 = u_avg[3] * u_avg[5] / (g * u_avg[1] * u_avg[4] * drho) - h36 = u_avg[3] * u_avg[6] / (g * u_avg[1] * u_avg[4] * drho) - h41 = 1.0 / (g * drho) - h42 = u_avg[2] / (g * u_avg[1] * drho) - h43 = u_avg[3] / (g * u_avg[1] * drho) - h44 = -1.0 / (g * drho) - h45 = -u_avg[5] / (g * u_avg[4] * drho) - h46 = -u_avg[6] / (g * u_avg[4] * drho) - h51 = u_avg[5] / (g * u_avg[4] * drho) - h52 = u_avg[2] * u_avg[5] / (g * u_avg[1] * u_avg[4] * drho) - h53 = u_avg[3] * u_avg[5] / (g * u_avg[1] * u_avg[4] * drho) - h54 = -u_avg[5] / (g * u_avg[4] * drho) - h55 = ((g * rho_upper * u_avg[4]^3 - g * rho_lower * u_avg[4]^3 + - -rho_lower * u_avg[5]^2) / (g * rho_lower * u_avg[4]^2 * drho)) - h56 = -u_avg[5] * u_avg[6] / (g * u_avg[4]^2 * drho) - h61 = u_avg[6] / (g * u_avg[4] * drho) - h62 = u_avg[2] * u_avg[6] / (g * u_avg[1] * u_avg[4] * drho) - h63 = u_avg[3] * u_avg[6] / (g * u_avg[1] * u_avg[4] * drho) - h64 = -u_avg[6] / (g * u_avg[4] * drho) - h65 = -u_avg[5] * u_avg[6] / (g * u_avg[4]^2 * drho) - h66 = ((g * rho_upper * u_avg[4]^3 - g * rho_lower * u_avg[4]^3 + - -rho_lower * u_avg[6]^2) / (g * rho_lower * u_avg[4]^2 * drho)) - - # Entropy Jacobian matrix - H = @SMatrix [[h11;; h12;; h13;; h14;; h15;; h16;; 0]; - [h21;; h22;; h23;; h24;; h25;; h26;; 0]; - [h31;; h32;; h33;; h34;; h35;; h36;; 0]; - [h41;; h42;; h43;; h44;; h45;; h46;; 0]; - [h51;; h52;; h53;; h54;; h55;; h56;; 0]; - [h61;; h62;; h63;; h64;; h65;; h66;; 0]; - [0;; 0;; 0;; 0;; 0;; 0;; 0]] - - # Add dissipation to entropy conservative flux to obtain entropy stable flux - f_es = f_ec - 0.5 * λ * H * (q_rr - q_ll) - - return SVector(f_es[1], f_es[2], f_es[3], f_es[4], f_es[5], f_es[6], - zero(eltype(u_ll))) -end - -# Calculate approximation for maximum wave speed for local Lax-Friedrichs-type dissipation as the -# maximum velocity magnitude plus the maximum speed of sound. This function uses approximate -# eigenvalues using the speed of the barotropic mode as there is no simple way to calculate them -# analytically. -# -# A good overview of the derivation is given in: -# - Jonas Nycander, Andrew McC. Hogg, Leela M. Frankcombe (2008) -# Open boundary conditions for nonlinear channel Flows -# [DOI: 10.1016/j.ocemod.2008.06.003](https://doi.org/10.1016/j.ocemod.2008.06.003) -@inline function max_abs_speed_naive(u_ll, u_rr, - orientation::Integer, - equations::ShallowWaterTwoLayerEquations2D) - # Unpack left and right state - h_upper_ll, h_v1_upper_ll, h_v2_upper_ll, h_lower_ll, h_v1_lower_ll, h_v2_lower_ll, _ = u_ll - h_upper_rr, h_v1_upper_rr, h_v2_upper_rr, h_lower_rr, h_v1_lower_rr, h_v2_lower_rr, _ = u_rr - - # Calculate averaged velocity of both layers - if orientation == 1 - v_m_ll = (h_v1_upper_ll + h_v1_lower_ll) / (h_upper_ll + h_lower_ll) - v_m_rr = (h_v1_upper_rr + h_v1_lower_rr) / (h_upper_rr + h_lower_rr) - else - v_m_ll = (h_v2_upper_ll + h_v2_lower_ll) / (h_upper_ll + h_lower_ll) - v_m_rr = (h_v2_upper_rr + h_v2_lower_rr) / (h_upper_rr + h_lower_rr) - end - - # Calculate the wave celerity on the left and right - h_upper_ll, h_lower_ll = waterheight(u_ll, equations) - h_upper_rr, h_lower_rr = waterheight(u_rr, equations) - - c_ll = sqrt(equations.gravity * (h_upper_ll + h_lower_ll)) - c_rr = sqrt(equations.gravity * (h_upper_rr + h_lower_rr)) - - return (max(abs(v_m_ll), abs(v_m_rr)) + max(c_ll, c_rr)) -end - -@inline function max_abs_speed_naive(u_ll, u_rr, - normal_direction::AbstractVector, - equations::ShallowWaterTwoLayerEquations2D) - # Unpack left and right state - h_upper_ll, _, _, h_lower_ll, _, _, _ = u_ll - h_upper_rr, _, _, h_lower_rr, _, _, _ = u_rr - - # Extract and compute the velocities in the normal direction - v1_upper_ll, v2_upper_ll, v1_lower_ll, v2_lower_ll = velocity(u_ll, equations) - v1_upper_rr, v2_upper_rr, v1_lower_rr, v2_lower_rr = velocity(u_rr, equations) - - v_upper_dot_n_ll = v1_upper_ll * normal_direction[1] + - v2_upper_ll * normal_direction[2] - v_upper_dot_n_rr = v1_upper_rr * normal_direction[1] + - v2_upper_rr * normal_direction[2] - v_lower_dot_n_ll = v1_lower_ll * normal_direction[1] + - v2_lower_ll * normal_direction[2] - v_lower_dot_n_rr = v1_lower_rr * normal_direction[1] + - v2_lower_rr * normal_direction[2] - - # Calculate averaged velocity of both layers - v_m_ll = (v_upper_dot_n_ll * h_upper_ll + v_lower_dot_n_ll * h_lower_ll) / - (h_upper_ll + h_lower_ll) - v_m_rr = (v_upper_dot_n_rr * h_upper_rr + v_lower_dot_n_rr * h_lower_rr) / - (h_upper_rr + h_lower_rr) - - # Compute the wave celerity on the left and right - h_upper_ll, h_lower_ll = waterheight(u_ll, equations) - h_upper_rr, h_lower_rr = waterheight(u_rr, equations) - - c_ll = sqrt(equations.gravity * (h_upper_ll + h_lower_ll)) - c_rr = sqrt(equations.gravity * (h_upper_rr + h_lower_rr)) - - # The normal velocities are already scaled by the norm - return max(abs(v_m_ll), abs(v_m_rr)) + max(c_ll, c_rr) * norm(normal_direction) -end - -# Specialized `DissipationLocalLaxFriedrichs` to avoid spurious dissipation in the bottom topography -@inline function (dissipation::DissipationLocalLaxFriedrichs)(u_ll, u_rr, - orientation_or_normal_direction, - equations::ShallowWaterTwoLayerEquations2D) - λ = dissipation.max_abs_speed(u_ll, u_rr, orientation_or_normal_direction, - equations) - diss = -0.5 * λ * (u_rr - u_ll) - return SVector(diss[1], diss[2], diss[3], diss[4], diss[5], diss[6], - zero(eltype(u_ll))) -end - -# Absolute speed of the barotropic mode -@inline function max_abs_speeds(u, equations::ShallowWaterTwoLayerEquations2D) - h_upper, h_v1_upper, h_v2_upper, h_lower, h_v1_lower, h_v2_lower, _ = u - - # Calculate averaged velocity of both layers - v1_m = (h_v1_upper + h_v1_lower) / (h_upper + h_lower) - v2_m = (h_v2_upper + h_v2_lower) / (h_upper + h_lower) - - h_upper, h_lower = waterheight(u, equations) - v1_upper, v2_upper, v1_lower, v2_lower = velocity(u, equations) - - c = sqrt(equations.gravity * (h_upper + h_lower)) - return (max(abs(v1_m) + c, abs(v1_upper), abs(v1_lower)), - max(abs(v2_m) + c, abs(v2_upper), abs(v2_lower))) -end - -# Helper function to extract the velocity vector from the conservative variables -@inline function velocity(u, equations::ShallowWaterTwoLayerEquations2D) - h_upper, h_v1_upper, h_v2_upper, h_lower, h_v1_lower, h_v2_lower, _ = u - - v1_upper = h_v1_upper / h_upper - v2_upper = h_v2_upper / h_upper - v1_lower = h_v1_lower / h_lower - v2_lower = h_v2_lower / h_lower - - return SVector(v1_upper, v2_upper, v1_lower, v2_lower) -end - -# Convert conservative variables to primitive -@inline function cons2prim(u, equations::ShallowWaterTwoLayerEquations2D) - h_upper, _, _, h_lower, _, _, b = u - - H_lower = h_lower + b - H_upper = h_lower + h_upper + b - v1_upper, v2_upper, v1_lower, v2_lower = velocity(u, equations) - - return SVector(H_upper, v1_upper, v2_upper, H_lower, v1_lower, v2_lower, b) -end - -# Convert conservative variables to entropy variables -# Note, only the first four are the entropy variables, the fifth entry still just carries the bottom -# topography values for convenience. -# In contrast to general usage the entropy variables are denoted with q instead of w, because w is -# already used for velocity in y-Direction -@inline function cons2entropy(u, equations::ShallowWaterTwoLayerEquations2D) - h_upper, _, _, h_lower, _, _, b = u - # Assign new variables for better readability - rho_upper = equations.rho_upper - rho_lower = equations.rho_lower - v1_upper, v2_upper, v1_lower, v2_lower = velocity(u, equations) - - w1 = (rho_upper * (equations.gravity * (h_upper + h_lower + b) + - -0.5 * (v1_upper^2 + v2_upper^2))) - w2 = rho_upper * v1_upper - w3 = rho_upper * v2_upper - w4 = (rho_lower * (equations.gravity * (equations.r * h_upper + h_lower + b) + - -0.5 * (v1_lower^2 + v2_lower^2))) - w5 = rho_lower * v1_lower - w6 = rho_lower * v2_lower - return SVector(w1, w2, w3, w4, w5, w6, b) -end - -# Convert primitive to conservative variables -@inline function prim2cons(prim, equations::ShallowWaterTwoLayerEquations2D) - H_upper, v1_upper, v2_upper, H_lower, v1_lower, v2_lower, b = prim - - h_lower = H_lower - b - h_upper = H_upper - h_lower - b - h_v1_upper = h_upper * v1_upper - h_v2_upper = h_upper * v2_upper - h_v1_lower = h_lower * v1_lower - h_v2_lower = h_lower * v2_lower - return SVector(h_upper, h_v1_upper, h_v2_upper, h_lower, h_v1_lower, h_v2_lower, b) -end - -@inline function waterheight(u, equations::ShallowWaterTwoLayerEquations2D) - return SVector(u[1], u[4]) -end - -# Entropy function for the shallow water equations is the total energy -@inline function entropy(cons, equations::ShallowWaterTwoLayerEquations2D) - energy_total(cons, equations) -end - -# Calculate total energy for a conservative state `cons` -@inline function energy_total(cons, equations::ShallowWaterTwoLayerEquations2D) - h_upper, h_v1_upper, h_v2_upper, h_lower, h_v2_lower, h_v2_lower, b = cons - g = equations.gravity - rho_upper = equations.rho_upper - rho_lower = equations.rho_lower - - e = (0.5 * rho_upper * - (h_v1_upper^2 / h_upper + h_v2_upper^2 / h_upper + g * h_upper^2) + - 0.5 * rho_lower * - (h_v2_lower^2 / h_lower + h_v2_lower^2 / h_lower + g * h_lower^2) + - g * rho_lower * h_lower * b + g * rho_upper * h_upper * (h_lower + b)) - return e -end - -# Calculate kinetic energy for a conservative state `cons` -@inline function energy_kinetic(u, equations::ShallowWaterTwoLayerEquations2D) - h_upper, h_v1_upper, h_v2_upper, h_lower, h_v2_lower, h_v2_lower, _ = u - - return (0.5 * equations.rho_upper * h_v1_upper^2 / h_upper + - 0.5 * equations.rho_upper * h_v2_upper^2 / h_upper + - 0.5 * equations.rho_lower * h_v2_lower^2 / h_lower + - 0.5 * equations.rho_lower * h_v2_lower^2 / h_lower) -end - -# Calculate potential energy for a conservative state `cons` -@inline function energy_internal(cons, equations::ShallowWaterTwoLayerEquations2D) - return energy_total(cons, equations) - energy_kinetic(cons, equations) -end - -# Calculate the error for the "lake-at-rest" test case where H = h_upper+h_lower+b should -# be a constant value over time -@inline function lake_at_rest_error(u, equations::ShallowWaterTwoLayerEquations2D) - h_upper, _, _, h_lower, _, _, b = u - return abs(equations.H0 - (h_upper + h_lower + b)) -end -end # @muladd diff --git a/src/solvers/dgsem_tree/indicators.jl b/src/solvers/dgsem_tree/indicators.jl index bb9109f2762..9f25a6d2dbb 100644 --- a/src/solvers/dgsem_tree/indicators.jl +++ b/src/solvers/dgsem_tree/indicators.jl @@ -101,82 +101,6 @@ function Base.show(io::IO, ::MIME"text/plain", indicator::IndicatorHennemannGass summary_box(io, "IndicatorHennemannGassner", setup) end -# TODO: TrixiShallowWater: move the new indicator and all associated routines to the new package -""" - IndicatorHennemannGassnerShallowWater(equations::AbstractEquations, basis; - alpha_max=0.5, - alpha_min=0.001, - alpha_smooth=true, - variable) - -Modified version of the [`IndicatorHennemannGassner`](@ref) -indicator used for shock-capturing for shallow water equations. After -the element-wise values for the blending factors are computed an additional check -is made to see if the element is partially wet. In this case, partially wet elements -are set to use the pure finite volume scheme that is guaranteed to be well-balanced -for this wet/dry transition state of the flow regime. - -See also [`VolumeIntegralShockCapturingHG`](@ref). - -## References - -- Hennemann, Gassner (2020) - "A provably entropy stable subcell shock capturing approach for high order split form DG" - [arXiv: 2008.12044](https://arxiv.org/abs/2008.12044) -""" -struct IndicatorHennemannGassnerShallowWater{RealT <: Real, Variable, Cache} <: - AbstractIndicator - alpha_max::RealT - alpha_min::RealT - alpha_smooth::Bool - variable::Variable - cache::Cache -end - -# this method is used when the indicator is constructed as for shock-capturing volume integrals -# of the shallow water equations -# It modifies the shock-capturing indicator to use full FV method in dry cells -function IndicatorHennemannGassnerShallowWater(equations::AbstractShallowWaterEquations, - basis; - alpha_max = 0.5, - alpha_min = 0.001, - alpha_smooth = true, - variable) - alpha_max, alpha_min = promote(alpha_max, alpha_min) - cache = create_cache(IndicatorHennemannGassner, equations, basis) - IndicatorHennemannGassnerShallowWater{typeof(alpha_max), typeof(variable), - typeof(cache)}(alpha_max, alpha_min, - alpha_smooth, variable, cache) -end - -function Base.show(io::IO, indicator::IndicatorHennemannGassnerShallowWater) - @nospecialize indicator # reduce precompilation time - - print(io, "IndicatorHennemannGassnerShallowWater(") - print(io, indicator.variable) - print(io, ", alpha_max=", indicator.alpha_max) - print(io, ", alpha_min=", indicator.alpha_min) - print(io, ", alpha_smooth=", indicator.alpha_smooth) - print(io, ")") -end - -function Base.show(io::IO, ::MIME"text/plain", - indicator::IndicatorHennemannGassnerShallowWater) - @nospecialize indicator # reduce precompilation time - - if get(io, :compact, false) - show(io, indicator) - else - setup = [ - "indicator variable" => indicator.variable, - "max. α" => indicator.alpha_max, - "min. α" => indicator.alpha_min, - "smooth α" => (indicator.alpha_smooth ? "yes" : "no"), - ] - summary_box(io, "IndicatorHennemannGassnerShallowWater", setup) - end -end - function (indicator_hg::IndicatorHennemannGassner)(u, mesh, equations, dg::DGSEM, cache; kwargs...) @unpack alpha_smooth = indicator_hg diff --git a/src/solvers/dgsem_tree/indicators_1d.jl b/src/solvers/dgsem_tree/indicators_1d.jl index dff87bfe06c..4796ddcc602 100644 --- a/src/solvers/dgsem_tree/indicators_1d.jl +++ b/src/solvers/dgsem_tree/indicators_1d.jl @@ -24,115 +24,6 @@ function create_cache(typ::Type{IndicatorHennemannGassner}, mesh, create_cache(typ, equations, dg.basis) end -# Modified indicator for ShallowWaterEquations1D to apply full FV method on cells -# containing some "dry" LGL nodes. That is, if an element is partially "wet" then it becomes a -# full FV element. -# -# TODO: TrixiShallowWater: move new indicator type -function (indicator_hg::IndicatorHennemannGassnerShallowWater)(u::AbstractArray{<:Any, - 3}, - mesh, - equations::ShallowWaterEquations1D, - dg::DGSEM, cache; - kwargs...) - @unpack alpha_max, alpha_min, alpha_smooth, variable = indicator_hg - @unpack alpha, alpha_tmp, indicator_threaded, modal_threaded = indicator_hg.cache - # TODO: Taal refactor, when to `resize!` stuff changed possibly by AMR? - # Shall we implement `resize!(semi::AbstractSemidiscretization, new_size)` - # or just `resize!` whenever we call the relevant methods as we do now? - resize!(alpha, nelements(dg, cache)) - if alpha_smooth - resize!(alpha_tmp, nelements(dg, cache)) - end - - # magic parameters - threshold = 0.5 * 10^(-1.8 * (nnodes(dg))^0.25) - parameter_s = log((1 - 0.0001) / 0.0001) - - # If the water height `h` at one LGL node is lower than `threshold_partially_wet` - # the indicator sets the element-wise blending factor alpha[element] = 1 - # via the local variable `indicator_wet`. In turn, this ensures that a pure - # FV method is used in partially wet cells and guarantees the well-balanced property. - # - # Hard-coded cut-off value of `threshold_partially_wet = 1e-4` was determined through many numerical experiments. - # Overall idea is to increase robustness when computing the velocity on (nearly) dry cells which - # could be "dangerous" due to division of conservative variables, e.g., v = hv / h. - # Here, the impact of the threshold on the number of cells being updated with FV is not that - # significant. However, its impact on the robustness is very significant. - # The value can be seen as a trade-off between accuracy and stability. - # Well-balancedness of the scheme on partially wet cells with hydrostatic reconstruction - # can only be proven for the FV method (see Chen and Noelle). - # Therefore we set alpha to one regardless of its given maximum value. - threshold_partially_wet = 1e-4 - - @threaded for element in eachelement(dg, cache) - indicator = indicator_threaded[Threads.threadid()] - modal = modal_threaded[Threads.threadid()] - - # (Re-)set dummy variable for alpha_dry - indicator_wet = 1 - - # Calculate indicator variables at Gauss-Lobatto nodes - for i in eachnode(dg) - u_local = get_node_vars(u, equations, dg, i, element) - h, _, _ = u_local - - if h <= threshold_partially_wet - indicator_wet = 0 - end - - indicator[i] = indicator_hg.variable(u_local, equations) - end - - # Convert to modal representation - multiply_scalar_dimensionwise!(modal, dg.basis.inverse_vandermonde_legendre, - indicator) - - # Calculate total energies for all modes, without highest, without two highest - total_energy = zero(eltype(modal)) - for i in 1:nnodes(dg) - total_energy += modal[i]^2 - end - total_energy_clip1 = zero(eltype(modal)) - for i in 1:(nnodes(dg) - 1) - total_energy_clip1 += modal[i]^2 - end - total_energy_clip2 = zero(eltype(modal)) - for i in 1:(nnodes(dg) - 2) - total_energy_clip2 += modal[i]^2 - end - - # Calculate energy in higher modes - energy = max((total_energy - total_energy_clip1) / total_energy, - (total_energy_clip1 - total_energy_clip2) / total_energy_clip1) - - alpha_element = 1 / (1 + exp(-parameter_s / threshold * (energy - threshold))) - - # Take care of the case close to pure DG - if alpha_element < alpha_min - alpha_element = zero(alpha_element) - end - - # Take care of the case close to pure FV - if alpha_element > 1 - alpha_min - alpha_element = one(alpha_element) - end - - # Clip the maximum amount of FV allowed or set to one depending on indicator_wet - if indicator_wet == 0 - alpha[element] = 1 - else # Element is not defined as dry but wet - alpha[element] = min(alpha_max, alpha_element) - end - end - - if alpha_smooth - apply_smoothing!(mesh, alpha, alpha_tmp, dg, cache) - end - - return alpha -end - # Use this function barrier and unpack inside to avoid passing closures to Polyester.jl # with @batch (@threaded). # Otherwise, @threaded does not work here with Julia ARM on macOS. diff --git a/src/solvers/dgsem_tree/indicators_2d.jl b/src/solvers/dgsem_tree/indicators_2d.jl index fa8ed481eb9..665d2254e5d 100644 --- a/src/solvers/dgsem_tree/indicators_2d.jl +++ b/src/solvers/dgsem_tree/indicators_2d.jl @@ -28,116 +28,6 @@ function create_cache(typ::Type{IndicatorHennemannGassner}, mesh, create_cache(typ, equations, dg.basis) end -# Modified indicator for ShallowWaterEquations2D to apply full FV method on cells -# containing some "dry" LGL nodes. That is, if an element is partially "wet" then it becomes a -# full FV element. -# -# TODO: TrixiShallowWater: move new indicator type -function (indicator_hg::IndicatorHennemannGassnerShallowWater)(u::AbstractArray{<:Any, - 4}, - mesh, - equations::ShallowWaterEquations2D, - dg::DGSEM, cache; - kwargs...) - @unpack alpha_max, alpha_min, alpha_smooth, variable = indicator_hg - @unpack alpha, alpha_tmp, indicator_threaded, modal_threaded, modal_tmp1_threaded = indicator_hg.cache - # TODO: Taal refactor, when to `resize!` stuff changed possibly by AMR? - # Shall we implement `resize!(semi::AbstractSemidiscretization, new_size)` - # or just `resize!` whenever we call the relevant methods as we do now? - resize!(alpha, nelements(dg, cache)) - if alpha_smooth - resize!(alpha_tmp, nelements(dg, cache)) - end - - # magic parameters - threshold = 0.5 * 10^(-1.8 * (nnodes(dg))^0.25) - parameter_s = log((1 - 0.0001) / 0.0001) - - # If the water height `h` at one LGL node is lower than `threshold_partially_wet` - # the indicator sets the element-wise blending factor alpha[element] = 1 - # via the local variable `indicator_wet`. In turn, this ensures that a pure - # FV method is used in partially wet cells and guarantees the well-balanced property. - # - # Hard-coded cut-off value of `threshold_partially_wet = 1e-4` was determined through many numerical experiments. - # Overall idea is to increase robustness when computing the velocity on (nearly) dry cells which - # could be "dangerous" due to division of conservative variables, e.g., v1 = hv1 / h. - # Here, the impact of the threshold on the number of cells being updated with FV is not that - # significant. However, its impact on the robustness is very significant. - # The value can be seen as a trade-off between accuracy and stability. - # Well-balancedness of the scheme on partially wet cells with hydrostatic reconstruction - # can only be proven for the FV method (see Chen and Noelle). - # Therefore we set alpha to be one regardless of its given value from the modal indicator. - threshold_partially_wet = 1e-4 - - @threaded for element in eachelement(dg, cache) - indicator = indicator_threaded[Threads.threadid()] - modal = modal_threaded[Threads.threadid()] - modal_tmp1 = modal_tmp1_threaded[Threads.threadid()] - - # (Re-)set dummy variable for alpha_dry - indicator_wet = 1 - - # Calculate indicator variables at Gauss-Lobatto nodes - for j in eachnode(dg), i in eachnode(dg) - u_local = get_node_vars(u, equations, dg, i, j, element) - h, _, _, _ = u_local - - if h <= threshold_partially_wet - indicator_wet = 0 - end - - indicator[i, j] = indicator_hg.variable(u_local, equations) - end - - # Convert to modal representation - multiply_scalar_dimensionwise!(modal, dg.basis.inverse_vandermonde_legendre, - indicator, modal_tmp1) - - # Calculate total energies for all modes, without highest, without two highest - total_energy = zero(eltype(modal)) - for j in 1:nnodes(dg), i in 1:nnodes(dg) - total_energy += modal[i, j]^2 - end - total_energy_clip1 = zero(eltype(modal)) - for j in 1:(nnodes(dg) - 1), i in 1:(nnodes(dg) - 1) - total_energy_clip1 += modal[i, j]^2 - end - total_energy_clip2 = zero(eltype(modal)) - for j in 1:(nnodes(dg) - 2), i in 1:(nnodes(dg) - 2) - total_energy_clip2 += modal[i, j]^2 - end - - # Calculate energy in higher modes - energy = max((total_energy - total_energy_clip1) / total_energy, - (total_energy_clip1 - total_energy_clip2) / total_energy_clip1) - - alpha_element = 1 / (1 + exp(-parameter_s / threshold * (energy - threshold))) - - # Take care of the case close to pure DG - if alpha_element < alpha_min - alpha_element = zero(alpha_element) - end - - # Take care of the case close to pure FV - if alpha_element > 1 - alpha_min - alpha_element = one(alpha_element) - end - - # Clip the maximum amount of FV allowed or set to 1 depending on indicator_wet - if indicator_wet == 0 - alpha[element] = 1 - else # Element is not defined as dry but wet - alpha[element] = min(alpha_max, alpha_element) - end - end - - if alpha_smooth - apply_smoothing!(mesh, alpha, alpha_tmp, dg, cache) - end - - return alpha -end - # Use this function barrier and unpack inside to avoid passing closures to Polyester.jl # with @batch (@threaded). # Otherwise, @threaded does not work here with Julia ARM on macOS. diff --git a/test/test_structured_2d.jl b/test/test_structured_2d.jl index 522510a42e3..f5fb169033a 100644 --- a/test/test_structured_2d.jl +++ b/test/test_structured_2d.jl @@ -1,7 +1,5 @@ module TestExamplesStructuredMesh2D -# TODO: TrixiShallowWater: move any wet/dry tests to new package - using Test using Trixi @@ -907,82 +905,6 @@ end end end -@trixi_testset "elixir_shallowwater_well_balanced_wet_dry.jl" begin - @test_trixi_include(joinpath(EXAMPLES_DIR, - "elixir_shallowwater_well_balanced_wet_dry.jl"), - l2=[ - 0.019731646454942086, - 1.0694532773278277e-14, - 1.1969913383405568e-14, - 0.0771517260037954, - ], - linf=[ - 0.4999999999998892, - 6.067153702623552e-14, - 4.4849667259339357e-14, - 1.9999999999999993, - ], - tspan=(0.0, 0.25)) - # Ensure that we do not have excessive memory allocations - # (e.g., from type instabilities) - let - t = sol.t[end] - u_ode = sol.u[end] - du_ode = similar(u_ode) - @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 - end -end - -@trixi_testset "elixir_shallowwater_conical_island.jl" begin - @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_shallowwater_conical_island.jl"), - l2=[ - 0.04593154164306353, - 0.1644534881916908, - 0.16445348819169076, - 0.0011537702354532122, - ], - linf=[ - 0.21100717610846442, - 0.9501592344310412, - 0.950159234431041, - 0.021790250683516296, - ], - tspan=(0.0, 0.025)) - # Ensure that we do not have excessive memory allocations - # (e.g., from type instabilities) - let - t = sol.t[end] - u_ode = sol.u[end] - du_ode = similar(u_ode) - @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 - end -end - -@trixi_testset "elixir_shallowwater_parabolic_bowl.jl" begin - @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_shallowwater_parabolic_bowl.jl"), - l2=[ - 0.00015285369980313484, - 1.9536806395943226e-5, - 9.936906607758672e-5, - 5.0686313334616055e-15, - ], - linf=[ - 0.003316119030459211, - 0.0005075409427972817, - 0.001986721761060583, - 4.701794509287538e-14, - ], - tspan=(0.0, 0.025), cells_per_dimension=(40, 40)) - # Ensure that we do not have excessive memory allocations - # (e.g., from type instabilities) - let - t = sol.t[end] - u_ode = sol.u[end] - du_ode = similar(u_ode) - @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 - end -end - @trixi_testset "elixir_mhd_ec_shockcapturing.jl" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_mhd_ec_shockcapturing.jl"), l2=[0.0364192725149364, 0.0426667193422069, 0.04261673001449095, diff --git a/test/test_tree_1d.jl b/test/test_tree_1d.jl index 8b470278ffd..4a25a51a45e 100644 --- a/test/test_tree_1d.jl +++ b/test/test_tree_1d.jl @@ -42,8 +42,6 @@ isdir(outdir) && rm(outdir, recursive = true) # Shallow water include("test_tree_1d_shallowwater.jl") - # Two-layer Shallow Water - include("test_tree_1d_shallowwater_twolayer.jl") # FDSBP methods on the TreeMesh include("test_tree_1d_fdsbp.jl") diff --git a/test/test_tree_1d_shallowwater.jl b/test/test_tree_1d_shallowwater.jl index 2269e858928..f9be63b87fd 100644 --- a/test/test_tree_1d_shallowwater.jl +++ b/test/test_tree_1d_shallowwater.jl @@ -1,7 +1,5 @@ module TestExamples1DShallowWater -# TODO: TrixiShallowWater: move any wet/dry tests to new package - using Test using Trixi @@ -119,32 +117,6 @@ end end end -@trixi_testset "elixir_shallowwater_well_balanced_wet_dry.jl with FluxHydrostaticReconstruction" begin - @test_trixi_include(joinpath(EXAMPLES_DIR, - "elixir_shallowwater_well_balanced_wet_dry.jl"), - l2=[ - 0.00965787167169024, - 5.345454081916856e-14, - 0.03857583749209928, - ], - linf=[ - 0.4999999999998892, - 2.2447689894899726e-13, - 1.9999999999999714, - ], - tspan=(0.0, 0.25), - # Soften the tolerance as test results vary between different CPUs - atol=1000 * eps()) - # Ensure that we do not have excessive memory allocations - # (e.g., from type instabilities) - let - t = sol.t[end] - u_ode = sol.u[end] - du_ode = similar(u_ode) - @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 - end -end - @trixi_testset "elixir_shallowwater_source_terms.jl" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_shallowwater_source_terms.jl"), l2=[ @@ -339,53 +311,6 @@ end end end -@trixi_testset "elixir_shallowwater_beach.jl" begin - @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_shallowwater_beach.jl"), - l2=[ - 0.17979210479598923, - 1.2377495706611434, - 6.289818963361573e-8, - ], - linf=[ - 0.845938394800688, - 3.3740800777086575, - 4.4541473087633676e-7, - ], - tspan=(0.0, 0.05), - atol=3e-10) # see https://github.com/trixi-framework/Trixi.jl/issues/1617 - # Ensure that we do not have excessive memory allocations - # (e.g., from type instabilities) - let - t = sol.t[end] - u_ode = sol.u[end] - du_ode = similar(u_ode) - @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 - end -end - -@trixi_testset "elixir_shallowwater_parabolic_bowl.jl" begin - @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_shallowwater_parabolic_bowl.jl"), - l2=[ - 8.965981683033589e-5, - 1.8565707397810857e-5, - 4.1043039226164336e-17, - ], - linf=[ - 0.00041080213807871235, - 0.00014823261488938177, - 2.220446049250313e-16, - ], - tspan=(0.0, 0.05)) - # Ensure that we do not have excessive memory allocations - # (e.g., from type instabilities) - let - t = sol.t[end] - u_ode = sol.u[end] - du_ode = similar(u_ode) - @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 - end -end - @trixi_testset "elixir_shallow_water_quasi_1d_source_terms.jl" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_shallow_water_quasi_1d_source_terms.jl"), diff --git a/test/test_tree_1d_shallowwater_twolayer.jl b/test/test_tree_1d_shallowwater_twolayer.jl deleted file mode 100644 index 180fb3ec3b3..00000000000 --- a/test/test_tree_1d_shallowwater_twolayer.jl +++ /dev/null @@ -1,74 +0,0 @@ -module TestExamples1DShallowWaterTwoLayer - -# TODO: TrixiShallowWater: move two layer tests to new package - -using Test -using Trixi - -include("test_trixi.jl") - -EXAMPLES_DIR = pkgdir(Trixi, "examples", "tree_1d_dgsem") - -@testset "Shallow Water Two layer" begin - @trixi_testset "elixir_shallowwater_twolayer_convergence.jl" begin - @test_trixi_include(joinpath(EXAMPLES_DIR, - "elixir_shallowwater_twolayer_convergence.jl"), - l2=[0.005012009872109003, 0.002091035326731071, - 0.005049271397924551, - 0.0024633066562966574, 0.0004744186597732739], - linf=[0.0213772149343594, 0.005385752427290447, - 0.02175023787351349, - 0.008212004668840978, 0.0008992474511784199], - tspan=(0.0, 0.25)) - # Ensure that we do not have excessive memory allocations - # (e.g., from type instabilities) - let - t = sol.t[end] - u_ode = sol.u[end] - du_ode = similar(u_ode) - @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 - end - end - - @trixi_testset "elixir_shallowwater_twolayer_well_balanced.jl" begin - @test_trixi_include(joinpath(EXAMPLES_DIR, - "elixir_shallowwater_twolayer_well_balanced.jl"), - l2=[8.949288784402005e-16, 4.0636427176237915e-17, - 0.001002881985401548, - 2.133351105037203e-16, 0.0010028819854016578], - linf=[2.6229018956769323e-15, 1.878451903240623e-16, - 0.005119880996670156, - 8.003199803957679e-16, 0.005119880996670666], - tspan=(0.0, 0.25)) - # Ensure that we do not have excessive memory allocations - # (e.g., from type instabilities) - let - t = sol.t[end] - u_ode = sol.u[end] - du_ode = similar(u_ode) - @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 - end - end - - @trixi_testset "elixir_shallowwater_twolayer_dam_break.jl with flux_lax_friedrichs" begin - @test_trixi_include(joinpath(EXAMPLES_DIR, - "elixir_shallowwater_twolayer_dam_break.jl"), - l2=[0.1000774903431289, 0.5670692949571057, 0.08764242501014498, - 0.45412307886094555, 0.013638618139749523], - linf=[0.586718937495144, 2.1215606128311584, 0.5185911311186155, - 1.820382495072612, 0.5], - surface_flux=(flux_lax_friedrichs, - flux_nonconservative_ersing_etal), - tspan=(0.0, 0.25)) - # Ensure that we do not have excessive memory allocations - # (e.g., from type instabilities) - let - t = sol.t[end] - u_ode = sol.u[end] - du_ode = similar(u_ode) - @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 - end - end -end - -end # module diff --git a/test/test_tree_2d_part3.jl b/test/test_tree_2d_part3.jl index ce9b3bc04f8..0eff564132c 100644 --- a/test/test_tree_2d_part3.jl +++ b/test/test_tree_2d_part3.jl @@ -26,9 +26,6 @@ isdir(outdir) && rm(outdir, recursive = true) # Shallow water include("test_tree_2d_shallowwater.jl") - # Two-Layer Shallow Water - include("test_tree_2d_shallowwater_twolayer.jl") - # FDSBP methods on the TreeMesh include("test_tree_2d_fdsbp.jl") end diff --git a/test/test_tree_2d_shallowwater.jl b/test/test_tree_2d_shallowwater.jl index 1f3dfbf5267..93a8cb63667 100644 --- a/test/test_tree_2d_shallowwater.jl +++ b/test/test_tree_2d_shallowwater.jl @@ -1,7 +1,5 @@ module TestExamples2DShallowWater -# TODO: TrixiShallowWater: move any wet/dry tests to new package - using Test using Trixi @@ -145,32 +143,6 @@ end end end -@trixi_testset "elixir_shallowwater_well_balanced_wet_dry.jl with FluxHydrostaticReconstruction" begin - @test_trixi_include(joinpath(EXAMPLES_DIR, - "elixir_shallowwater_well_balanced_wet_dry.jl"), - l2=[ - 0.030186039395610056, - 2.513287752536758e-14, - 1.3631397744897607e-16, - 0.10911781485920438, - ], - linf=[ - 0.49999999999993505, - 5.5278950497971455e-14, - 7.462550826772548e-16, - 2.0, - ], - tspan=(0.0, 0.25)) - # Ensure that we do not have excessive memory allocations - # (e.g., from type instabilities) - let - t = sol.t[end] - u_ode = sol.u[end] - du_ode = similar(u_ode) - @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 - end -end - @trixi_testset "elixir_shallowwater_source_terms.jl" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_shallowwater_source_terms.jl"), l2=[ @@ -277,57 +249,6 @@ end end end -@trixi_testset "elixir_shallowwater_conical_island.jl" begin - @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_shallowwater_conical_island.jl"), - l2=[ - 0.0459315416430658, - 0.1644534881916991, - 0.16445348819169914, - 0.0011537702354532694, - ], - linf=[ - 0.21100717610846464, - 0.9501592344310412, - 0.9501592344310417, - 0.021790250683516282, - ], - tspan=(0.0, 0.025)) - # Ensure that we do not have excessive memory allocations - # (e.g., from type instabilities) - let - t = sol.t[end] - u_ode = sol.u[end] - du_ode = similar(u_ode) - @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 - end -end - -@trixi_testset "elixir_shallowwater_parabolic_bowl.jl" begin - @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_shallowwater_parabolic_bowl.jl"), - l2=[ - 0.00025345501281482687, - 4.4525120338817177e-5, - 0.00015991819160294247, - 7.750412064917294e-15, - ], - linf=[ - 0.004664246019836723, - 0.0004972780116736669, - 0.0028735707270457628, - 6.866729407306593e-14, - ], - tspan=(0.0, 0.025), - basis=LobattoLegendreBasis(3)) - # Ensure that we do not have excessive memory allocations - # (e.g., from type instabilities) - let - t = sol.t[end] - u_ode = sol.u[end] - du_ode = similar(u_ode) - @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 - end -end - @trixi_testset "elixir_shallowwater_wall.jl" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_shallowwater_wall.jl"), l2=[ diff --git a/test/test_tree_2d_shallowwater_twolayer.jl b/test/test_tree_2d_shallowwater_twolayer.jl deleted file mode 100644 index 802bf4e021c..00000000000 --- a/test/test_tree_2d_shallowwater_twolayer.jl +++ /dev/null @@ -1,88 +0,0 @@ -module TestExamples2DShallowWaterTwoLayer - -# TODO: TrixiShallowWater: move two layer tests to new package - -using Test -using Trixi - -include("test_trixi.jl") - -EXAMPLES_DIR = joinpath(examples_dir(), "tree_2d_dgsem") - -@testset "Two-Layer Shallow Water" begin - @trixi_testset "elixir_shallowwater_twolayer_convergence.jl" begin - @test_trixi_include(joinpath(EXAMPLES_DIR, - "elixir_shallowwater_twolayer_convergence.jl"), - l2=[0.0004016779699408397, 0.005466339651545468, - 0.006148841330156112, - 0.0002882339012602492, 0.0030120142442780313, - 0.002680752838455618, - 8.873630921431545e-6], - linf=[0.002788654460984752, 0.01484602033450666, - 0.017572229756493973, - 0.0016010835493927011, 0.009369847995372549, - 0.008407961775489636, - 3.361991620143279e-5], - tspan=(0.0, 0.25)) - # Ensure that we do not have excessive memory allocations - # (e.g., from type instabilities) - let - t = sol.t[end] - u_ode = sol.u[end] - du_ode = similar(u_ode) - @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 - end - end - - @trixi_testset "elixir_shallowwater_twolayer_well_balanced.jl" begin - @test_trixi_include(joinpath(EXAMPLES_DIR, - "elixir_shallowwater_twolayer_well_balanced.jl"), - l2=[3.2935164267930016e-16, 4.6800825611195103e-17, - 4.843057532147818e-17, - 0.0030769233188015013, 1.4809161150389857e-16, - 1.509071695038043e-16, - 0.0030769233188014935], - linf=[2.248201624865942e-15, 2.346382070278936e-16, - 2.208565017494899e-16, - 0.026474051138910493, 9.237568031609006e-16, - 7.520758026187046e-16, - 0.026474051138910267], - tspan=(0.0, 0.25)) - # Ensure that we do not have excessive memory allocations - # (e.g., from type instabilities) - let - t = sol.t[end] - u_ode = sol.u[end] - du_ode = similar(u_ode) - @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 - end - end - - @trixi_testset "elixir_shallowwater_twolayer_well_balanced with flux_lax_friedrichs.jl" begin - @test_trixi_include(joinpath(EXAMPLES_DIR, - "elixir_shallowwater_twolayer_well_balanced.jl"), - l2=[2.0525741072929735e-16, 6.000589392730905e-17, - 6.102759428478984e-17, - 0.0030769233188014905, 1.8421386173122792e-16, - 1.8473184927121752e-16, - 0.0030769233188014935], - linf=[7.355227538141662e-16, 2.960836949170518e-16, - 4.2726562436938764e-16, - 0.02647405113891016, 1.038795478061861e-15, - 1.0401789378532516e-15, - 0.026474051138910267], - surface_flux=(flux_lax_friedrichs, - flux_nonconservative_ersing_etal), - tspan=(0.0, 0.25)) - # Ensure that we do not have excessive memory allocations - # (e.g., from type instabilities) - let - t = sol.t[end] - u_ode = sol.u[end] - du_ode = similar(u_ode) - @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 - end - end -end - -end # module diff --git a/test/test_unit.jl b/test/test_unit.jl index c1379587cc8..1907a281718 100644 --- a/test/test_unit.jl +++ b/test/test_unit.jl @@ -420,11 +420,6 @@ end (1.0, 1.0), 1.0) @test_nowarn show(stdout, limiter_idp) - # TODO: TrixiShallowWater: move unit test - indicator_hg_swe = IndicatorHennemannGassnerShallowWater(1.0, 0.0, true, "variable", - "cache") - @test_nowarn show(stdout, indicator_hg_swe) - indicator_loehner = IndicatorLöhner(1.0, "variable", (; cache = nothing)) @test_nowarn show(stdout, indicator_loehner) @@ -543,7 +538,7 @@ end end @timed_testset "Shallow water conversion between conservative/entropy variables" begin - H, v1, v2, b = 3.5, 0.25, 0.1, 0.4 + H, v1, v2, b, a = 3.5, 0.25, 0.1, 0.4, 0.3 let equations = ShallowWaterEquations1D(gravity_constant = 9.8) cons_vars = prim2cons(SVector(H, v1, b), equations) @@ -572,6 +567,14 @@ end entropy_vars = cons2entropy(cons_vars, equations) @test cons_vars ≈ entropy2cons(entropy_vars, equations) end + + let equations = ShallowWaterEquationsQuasi1D(gravity_constant = 9.8) + cons_vars = prim2cons(SVector(H, v1, b, a), equations) + entropy_vars = cons2entropy(cons_vars, equations) + + total_energy = energy_total(cons_vars, equations) + @test entropy(cons_vars, equations) ≈ a * total_energy + end end @timed_testset "boundary_condition_do_nothing" begin @@ -697,6 +700,14 @@ end u = SVector(1, 0.5, 0.0) @test flux_hll(u, u, 1, equations) ≈ flux(u, 1, equations) + u_ll = SVector(0.1, 1.0, 0.0) + u_rr = SVector(0.1, 1.0, 0.0) + @test flux_hll(u_ll, u_rr, 1, equations) ≈ flux(u_ll, 1, equations) + + u_ll = SVector(0.1, -1.0, 0.0) + u_rr = SVector(0.1, -1.0, 0.0) + @test flux_hll(u_ll, u_rr, 1, equations) ≈ flux(u_rr, 1, equations) + equations = ShallowWaterEquations2D(gravity_constant = 9.81) normal_directions = [SVector(1.0, 0.0), SVector(0.0, 1.0), @@ -707,6 +718,17 @@ end @test flux_hll(u, u, normal_direction, equations) ≈ flux(u, normal_direction, equations) end + + normal_direction = SVector(1.0, 0.0, 0.0) + u_ll = SVector(0.1, 1.0, 1.0, 0.0) + u_rr = SVector(0.1, 1.0, 1.0, 0.0) + @test flux_hll(u_ll, u_rr, normal_direction, equations) ≈ + flux(u_ll, normal_direction, equations) + + u_ll = SVector(0.1, -1.0, -1.0, 0.0) + u_rr = SVector(0.1, -1.0, -1.0, 0.0) + @test flux_hll(u_ll, u_rr, normal_direction, equations) ≈ + flux(u_rr, normal_direction, equations) end @timed_testset "Consistency check for HLL flux (naive): MHD" begin diff --git a/test/test_unstructured_2d.jl b/test/test_unstructured_2d.jl index 83b8318c926..04eb9f679aa 100644 --- a/test/test_unstructured_2d.jl +++ b/test/test_unstructured_2d.jl @@ -1,7 +1,5 @@ module TestExamplesUnstructuredMesh2D -# TODO: TrixiShallowWater: move any wet/dry and two layer tests - using Test using Trixi @@ -566,105 +564,6 @@ end end end -@trixi_testset "elixir_shallowwater_three_mound_dam_break.jl" begin - @test_trixi_include(joinpath(EXAMPLES_DIR, - "elixir_shallowwater_three_mound_dam_break.jl"), - l2=[ - 0.0892957892027502, - 0.30648836484407915, - 2.28712547616214e-15, - 0.0008778654298684622, - ], - linf=[ - 0.850329472915091, - 2.330631694956507, - 5.783660020252348e-14, - 0.04326237921249021, - ], - basis=LobattoLegendreBasis(3), - tspan=(0.0, 0.25)) - # Ensure that we do not have excessive memory allocations - # (e.g., from type instabilities) - let - t = sol.t[end] - u_ode = sol.u[end] - du_ode = similar(u_ode) - @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 - end -end - -@trixi_testset "elixir_shallowwater_twolayer_convergence.jl" begin - @test_trixi_include(joinpath(EXAMPLES_DIR, - "elixir_shallowwater_twolayer_convergence.jl"), - l2=[0.0007935561625451243, 0.008825315509943844, - 0.002429969315645897, - 0.0007580145888686304, 0.004495741879625235, - 0.0015758146898767814, - 6.849532064729749e-6], - linf=[0.0059205195991136605, 0.08072126590166251, - 0.03463806075399023, - 0.005884818649227186, 0.042658506561995546, - 0.014125956138838602, 2.5829318284764646e-5], - tspan=(0.0, 0.25)) - # Ensure that we do not have excessive memory allocations - # (e.g., from type instabilities) - let - t = sol.t[end] - u_ode = sol.u[end] - du_ode = similar(u_ode) - @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 - end -end - -@trixi_testset "elixir_shallowwater_twolayer_well_balanced.jl" begin - @test_trixi_include(joinpath(EXAMPLES_DIR, - "elixir_shallowwater_twolayer_well_balanced.jl"), - l2=[4.706532184998499e-16, 1.1215950712872183e-15, - 6.7822712922421565e-16, - 0.002192812926266047, 5.506855295923691e-15, - 3.3105180099689275e-15, - 0.0021928129262660085], - linf=[4.468647674116255e-15, 1.3607872120431166e-14, - 9.557155049520056e-15, - 0.024280130945632084, 6.68910907640583e-14, - 4.7000983997100496e-14, - 0.024280130945632732], - tspan=(0.0, 0.25)) - # Ensure that we do not have excessive memory allocations - # (e.g., from type instabilities) - let - t = sol.t[end] - u_ode = sol.u[end] - du_ode = similar(u_ode) - @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 - end -end - -@trixi_testset "elixir_shallowwater_twolayer_dam_break.jl with flux_lax_friedrichs" begin - @test_trixi_include(joinpath(EXAMPLES_DIR, - "elixir_shallowwater_twolayer_dam_break.jl"), - l2=[0.012447632879122346, 0.012361250464676683, - 0.0009551519536340908, - 0.09119400061322577, 0.015276216721920347, - 0.0012126995108983853, 0.09991983966647647], - linf=[0.044305765721807444, 0.03279620980615845, - 0.010754320388190101, - 0.111309922939555, 0.03663360204931427, - 0.014332822306649284, - 0.10000000000000003], - surface_flux=(flux_lax_friedrichs, - flux_nonconservative_ersing_etal), - tspan=(0.0, 0.25)) - # Ensure that we do not have excessive memory allocations - # (e.g., from type instabilities) - let - t = sol.t[end] - u_ode = sol.u[end] - du_ode = similar(u_ode) - @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 - end -end - # TODO: FD; for now put the unstructured tests for the 2D FDSBP here. @trixi_testset "FDSBP (central): elixir_advection_basic.jl" begin @test_trixi_include(joinpath(pkgdir(Trixi, "examples", "unstructured_2d_fdsbp"), From 5418274987eec6bade5432ead7c91f1d4a842610 Mon Sep 17 00:00:00 2001 From: Daniel Doehring Date: Fri, 23 Feb 2024 05:31:01 +0100 Subject: [PATCH 42/63] Make `min_max_speed_davis` default wave speed estimate for `FluxHLL()` (#1743) * make min_max_speed_davis default wave speed * fmt * exchange hll * exchange some min_max_speed_naive for min_max_speed_davis for some examples * fmt * add news entry * news * debug * revert unintended elixir changes * news entry * correct test vals * Update test vals * Exchange some tests * update test vals for threaded * test vals for fdsbp unstructured * fmt * tests for coverage --------- Co-authored-by: Hendrik Ranocha --- NEWS.md | 5 ++ .../elixir_eulergravity_convergence.jl | 2 +- ..._euler_source_terms_nonconforming_earth.jl | 2 +- .../elixir_euler_convergence.jl | 2 +- .../elixir_eulergravity_convergence.jl | 2 +- .../elixir_eulergravity_jeans_instability.jl | 2 +- .../elixir_eulergravity_sedov_blast_wave.jl | 2 +- .../elixir_eulergravity_convergence.jl | 2 +- ..._shallowwater_well_balanced_nonperiodic.jl | 4 +- .../elixir_eulergravity_convergence.jl | 2 +- .../elixir_shallowwater_dirichlet.jl | 4 +- src/equations/numerical_fluxes.jl | 16 +++- test/test_dgmulti_1d.jl | 10 +-- test/test_dgmulti_2d.jl | 82 +++++++----------- test/test_dgmulti_3d.jl | 71 ++++++--------- test/test_parabolic_3d.jl | 1 + test/test_special_elixirs.jl | 3 +- test/test_structured_2d.jl | 57 ++++++------ test/test_threaded.jl | 24 +++--- test/test_tree_1d_euler.jl | 8 +- test/test_tree_1d_eulergravity.jl | 10 +-- test/test_tree_1d_shallowwater.jl | 19 ++-- test/test_tree_2d_mhd.jl | 2 +- test/test_tree_2d_shallowwater.jl | 30 ++++++- test/test_tree_3d_euler.jl | 17 ++-- test/test_tree_3d_mhd.jl | 4 +- test/test_unstructured_2d.jl | 86 ++++++++----------- 27 files changed, 230 insertions(+), 239 deletions(-) diff --git a/NEWS.md b/NEWS.md index ecc91581e9a..d70504d8c85 100644 --- a/NEWS.md +++ b/NEWS.md @@ -10,6 +10,9 @@ for human readability. #### Changed +- The default wave speed estimate used within `flux_hll` is now `min_max_speed_davis` + instead of `min_max_speed_naive`. + #### Deprecated #### Removed @@ -17,6 +20,7 @@ for human readability. Trixi.jl, but are moved to a dedicated repository: [TrixiShallowWater.jl](https://github.com/trixi-framework/TrixiShallowWater.jl). This includes all features related to wetting and drying, as well as the `ShallowWaterTwoLayerEquations1D` and `ShallowWaterTwoLayerEquations2D`. However, the basic shallow water equations are still part of Trixi.jl. We'll also be updating the TrixiShallowWater.jl documentation with instructions on how to use these relocated features in the future. + ## Changes in the v0.6 lifecycle #### Added @@ -27,6 +31,7 @@ for human readability. - Subcell (positivity) limiting support for nonlinear variables in 2D for `TreeMesh` - Added Lighthill-Whitham-Richards (LWR) traffic model + ## Changes when updating to v0.6 from v0.5.x #### Added diff --git a/examples/p4est_2d_dgsem/elixir_eulergravity_convergence.jl b/examples/p4est_2d_dgsem/elixir_eulergravity_convergence.jl index d55a59ca5ce..974466e3b3b 100644 --- a/examples/p4est_2d_dgsem/elixir_eulergravity_convergence.jl +++ b/examples/p4est_2d_dgsem/elixir_eulergravity_convergence.jl @@ -10,7 +10,7 @@ gamma = 2.0 equations_euler = CompressibleEulerEquations2D(gamma) polydeg = 3 -solver_euler = DGSEM(polydeg, flux_hll) +solver_euler = DGSEM(polydeg, FluxHLL(min_max_speed_naive)) coordinates_min = (0.0, 0.0) coordinates_max = (2.0, 2.0) diff --git a/examples/p4est_3d_dgsem/elixir_euler_source_terms_nonconforming_earth.jl b/examples/p4est_3d_dgsem/elixir_euler_source_terms_nonconforming_earth.jl index 28a300cd681..28cdec12da5 100644 --- a/examples/p4est_3d_dgsem/elixir_euler_source_terms_nonconforming_earth.jl +++ b/examples/p4est_3d_dgsem/elixir_euler_source_terms_nonconforming_earth.jl @@ -68,7 +68,7 @@ boundary_condition = BoundaryConditionDirichlet(initial_condition) boundary_conditions = Dict(:inside => boundary_condition, :outside => boundary_condition) -surface_flux = flux_hll +surface_flux = FluxHLL(min_max_speed_naive) # Note that a free stream is not preserved if N < 2 * N_geo, where N is the # polydeg of the solver and N_geo is the polydeg of the mesh. # However, the FSP error is negligible in this example. diff --git a/examples/paper_self_gravitating_gas_dynamics/elixir_euler_convergence.jl b/examples/paper_self_gravitating_gas_dynamics/elixir_euler_convergence.jl index aabfce0f66b..4f44d7b12ac 100644 --- a/examples/paper_self_gravitating_gas_dynamics/elixir_euler_convergence.jl +++ b/examples/paper_self_gravitating_gas_dynamics/elixir_euler_convergence.jl @@ -8,7 +8,7 @@ equations = CompressibleEulerEquations2D(2.0) initial_condition = initial_condition_eoc_test_coupled_euler_gravity -solver = DGSEM(polydeg = 3, surface_flux = flux_hll) +solver = DGSEM(polydeg = 3, surface_flux = FluxHLL(min_max_speed_naive)) coordinates_min = (0.0, 0.0) coordinates_max = (2.0, 2.0) diff --git a/examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_convergence.jl b/examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_convergence.jl index ce1d2cd05bd..49b98803577 100644 --- a/examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_convergence.jl +++ b/examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_convergence.jl @@ -10,7 +10,7 @@ gamma = 2.0 equations_euler = CompressibleEulerEquations2D(gamma) polydeg = 3 -solver_euler = DGSEM(polydeg, flux_hll) +solver_euler = DGSEM(polydeg, FluxHLL(min_max_speed_naive)) coordinates_min = (0.0, 0.0) coordinates_max = (2.0, 2.0) diff --git a/examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_jeans_instability.jl b/examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_jeans_instability.jl index f081f6bb91a..7461198fbb2 100644 --- a/examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_jeans_instability.jl +++ b/examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_jeans_instability.jl @@ -66,7 +66,7 @@ gamma = 5 / 3 equations_euler = CompressibleEulerEquations2D(gamma) polydeg = 3 -solver_euler = DGSEM(polydeg, flux_hll) +solver_euler = DGSEM(polydeg, FluxHLL(min_max_speed_naive)) coordinates_min = (0.0, 0.0) coordinates_max = (1.0, 1.0) diff --git a/examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_sedov_blast_wave.jl b/examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_sedov_blast_wave.jl index b7be2320228..bc7ceb97c8b 100644 --- a/examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_sedov_blast_wave.jl +++ b/examples/paper_self_gravitating_gas_dynamics/elixir_eulergravity_sedov_blast_wave.jl @@ -85,7 +85,7 @@ function boundary_condition_sedov_self_gravity(u_inner, orientation, direction, end boundary_conditions = boundary_condition_sedov_self_gravity -surface_flux = flux_hll +surface_flux = FluxHLL(min_max_speed_naive) volume_flux = flux_chandrashekar polydeg = 3 basis = LobattoLegendreBasis(polydeg) diff --git a/examples/t8code_2d_dgsem/elixir_eulergravity_convergence.jl b/examples/t8code_2d_dgsem/elixir_eulergravity_convergence.jl index 98a9a5521a9..cd10315945a 100644 --- a/examples/t8code_2d_dgsem/elixir_eulergravity_convergence.jl +++ b/examples/t8code_2d_dgsem/elixir_eulergravity_convergence.jl @@ -9,7 +9,7 @@ gamma = 2.0 equations_euler = CompressibleEulerEquations2D(gamma) polydeg = 3 -solver_euler = DGSEM(polydeg, flux_hll) +solver_euler = DGSEM(polydeg, FluxHLL(min_max_speed_naive)) coordinates_min = (0.0, 0.0) coordinates_max = (2.0, 2.0) diff --git a/examples/tree_1d_dgsem/elixir_shallowwater_well_balanced_nonperiodic.jl b/examples/tree_1d_dgsem/elixir_shallowwater_well_balanced_nonperiodic.jl index e55fffc101e..9ed02c0e378 100644 --- a/examples/tree_1d_dgsem/elixir_shallowwater_well_balanced_nonperiodic.jl +++ b/examples/tree_1d_dgsem/elixir_shallowwater_well_balanced_nonperiodic.jl @@ -26,7 +26,9 @@ boundary_condition = BoundaryConditionDirichlet(initial_condition) # Get the DG approximation space volume_flux = (flux_wintermeyer_etal, flux_nonconservative_wintermeyer_etal) -solver = DGSEM(polydeg = 4, surface_flux = (flux_hll, flux_nonconservative_fjordholm_etal), +solver = DGSEM(polydeg = 4, + surface_flux = (flux_hll, + flux_nonconservative_fjordholm_etal), volume_integral = VolumeIntegralFluxDifferencing(volume_flux)) ############################################################################### diff --git a/examples/tree_3d_dgsem/elixir_eulergravity_convergence.jl b/examples/tree_3d_dgsem/elixir_eulergravity_convergence.jl index 21ef661d0b6..0a8c427bf8d 100644 --- a/examples/tree_3d_dgsem/elixir_eulergravity_convergence.jl +++ b/examples/tree_3d_dgsem/elixir_eulergravity_convergence.jl @@ -10,7 +10,7 @@ equations_euler = CompressibleEulerEquations3D(gamma) initial_condition = initial_condition_eoc_test_coupled_euler_gravity polydeg = 3 -solver_euler = DGSEM(polydeg, flux_hll) +solver_euler = DGSEM(polydeg, FluxHLL(min_max_speed_naive)) coordinates_min = (0.0, 0.0, 0.0) coordinates_max = (2.0, 2.0, 2.0) diff --git a/examples/unstructured_2d_dgsem/elixir_shallowwater_dirichlet.jl b/examples/unstructured_2d_dgsem/elixir_shallowwater_dirichlet.jl index df1a69192ce..38e1279e220 100644 --- a/examples/unstructured_2d_dgsem/elixir_shallowwater_dirichlet.jl +++ b/examples/unstructured_2d_dgsem/elixir_shallowwater_dirichlet.jl @@ -30,7 +30,9 @@ boundary_condition = Dict(:OuterCircle => boundary_condition_constant) # Get the DG approximation space volume_flux = (flux_wintermeyer_etal, flux_nonconservative_wintermeyer_etal) -solver = DGSEM(polydeg = 4, surface_flux = (flux_hll, flux_nonconservative_fjordholm_etal), +solver = DGSEM(polydeg = 4, + surface_flux = (flux_hll, + flux_nonconservative_fjordholm_etal), volume_integral = VolumeIntegralFluxDifferencing(volume_flux)) ############################################################################### diff --git a/src/equations/numerical_fluxes.jl b/src/equations/numerical_fluxes.jl index 87fcb412244..6794c71a32b 100644 --- a/src/equations/numerical_fluxes.jl +++ b/src/equations/numerical_fluxes.jl @@ -222,12 +222,12 @@ See [`FluxLaxFriedrichs`](@ref). const flux_lax_friedrichs = FluxLaxFriedrichs() """ - FluxHLL(min_max_speed=min_max_speed_naive) + FluxHLL(min_max_speed=min_max_speed_davis) Create an HLL (Harten, Lax, van Leer) numerical flux where the minimum and maximum wave speeds are estimated as `λ_min, λ_max = min_max_speed(u_ll, u_rr, orientation_or_normal_direction, equations)`, -defaulting to [`min_max_speed_naive`](@ref). +defaulting to [`min_max_speed_davis`](@ref). Original paper: - Amiram Harten, Peter D. Lax, Bram van Leer (1983) On Upstream Differencing and Godunov-Type Schemes for Hyperbolic Conservation Laws @@ -237,7 +237,7 @@ struct FluxHLL{MinMaxSpeed} min_max_speed::MinMaxSpeed end -FluxHLL() = FluxHLL(min_max_speed_naive) +FluxHLL() = FluxHLL(min_max_speed_davis) """ min_max_speed_naive(u_ll, u_rr, orientation::Integer, equations) @@ -246,10 +246,16 @@ FluxHLL() = FluxHLL(min_max_speed_naive) Simple and fast estimate(!) of the minimal and maximal wave speed of the Riemann problem with left and right states `u_ll, u_rr`, usually based only on the local wave speeds associated to `u_ll` and `u_rr`. +Slightly more diffusive than [`min_max_speed_davis`](@ref). - Amiram Harten, Peter D. Lax, Bram van Leer (1983) On Upstream Differencing and Godunov-Type Schemes for Hyperbolic Conservation Laws [DOI: 10.1137/1025002](https://doi.org/10.1137/1025002) +See eq. (10.37) from +- Eleuterio F. Toro (2009) + Riemann Solvers and Numerical Methods for Fluid Dynamics: A Practical Introduction + [DOI: 10.1007/b79761](https://doi.org/10.1007/b79761) + See also [`FluxHLL`](@ref), [`min_max_speed_davis`](@ref), [`min_max_speed_einfeldt`](@ref). """ function min_max_speed_naive end @@ -266,6 +272,10 @@ left and right states `u_ll, u_rr`, usually based only on the local wave speeds Simplified Second-Order Godunov-Type Methods [DOI: 10.1137/0909030](https://doi.org/10.1137/0909030) +See eq. (10.38) from +- Eleuterio F. Toro (2009) + Riemann Solvers and Numerical Methods for Fluid Dynamics: A Practical Introduction + [DOI: 10.1007/b79761](https://doi.org/10.1007/b79761) See also [`FluxHLL`](@ref), [`min_max_speed_naive`](@ref), [`min_max_speed_einfeldt`](@ref). """ function min_max_speed_davis end diff --git a/test/test_dgmulti_1d.jl b/test/test_dgmulti_1d.jl index 0363086341f..e470de71efb 100644 --- a/test/test_dgmulti_1d.jl +++ b/test/test_dgmulti_1d.jl @@ -128,14 +128,12 @@ end @trixi_testset "elixir_euler_fdsbp_periodic.jl" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_fdsbp_periodic.jl"), l2=[ - 9.146929180585711e-7, - 1.8997616878017292e-6, - 3.991417702211889e-6, + 9.146929178341782e-7, 1.8997616876521201e-6, + 3.991417701005622e-6, ], linf=[ - 1.7321089884614338e-6, - 3.3252888855805907e-6, - 6.5252787737613005e-6, + 1.7321089882393892e-6, 3.3252888869128583e-6, + 6.525278767988141e-6, ]) show(stdout, semi.solver.basis) show(stdout, MIME"text/plain"(), semi.solver.basis) diff --git a/test/test_dgmulti_2d.jl b/test/test_dgmulti_2d.jl index 892c8ed37f0..ab6b505e208 100644 --- a/test/test_dgmulti_2d.jl +++ b/test/test_dgmulti_2d.jl @@ -17,6 +17,7 @@ isdir(outdir) && rm(outdir, recursive = true) @trixi_testset "elixir_euler_weakform.jl" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_weakform.jl"), cells_per_dimension=(4, 4), + surface_integral=SurfaceIntegralWeakForm(FluxHLL(min_max_speed_naive)), # division by 2.0 corresponds to normalization by the square root of the size of the domain l2=[ 0.0013536930300254945, @@ -44,6 +45,7 @@ end @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_weakform.jl"), cells_per_dimension=(4, 4), approximation_type=SBP(), + surface_integral=SurfaceIntegralWeakForm(FluxHLL(min_max_speed_naive)), # division by 2.0 corresponds to normalization by the square root of the size of the domain l2=[ 0.0074706882014934735, @@ -71,6 +73,7 @@ end @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_weakform.jl"), cells_per_dimension=(4, 4), element_type=Quad(), + surface_integral=SurfaceIntegralWeakForm(FluxHLL(min_max_speed_naive)), # division by 2.0 corresponds to normalization by the square root of the size of the domain l2=[ 0.00031892254415307093, @@ -184,16 +187,12 @@ end @trixi_testset "elixir_euler_bilinear.jl (Bilinear quadrilateral elements, SBP, flux differencing)" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_bilinear.jl"), l2=[ - 1.0259435706215337e-5, - 9.014090233720625e-6, - 9.014090233223014e-6, - 2.738953587401793e-5, + 1.0259432774540821e-5, 9.014087689495575e-6, + 9.01408768888544e-6, 2.738953324859446e-5, ], linf=[ - 7.362609083649829e-5, - 6.874188055272512e-5, - 6.874188052830021e-5, - 0.0001912435192696904, + 7.362605996297233e-5, 6.874189724781488e-5, + 6.874189703509614e-5, 0.00019124355334110277, ]) # Ensure that we do not have excessive memory allocations # (e.g., from type instabilities) @@ -208,16 +207,12 @@ end @trixi_testset "elixir_euler_curved.jl (Quadrilateral elements, SBP, flux differencing)" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_curved.jl"), l2=[ - 1.720476068165337e-5, - 1.592168205710526e-5, - 1.592168205812963e-5, - 4.894094865697305e-5, + 1.7204593127904542e-5, 1.5921547179522804e-5, + 1.5921547180107928e-5, 4.894071422525737e-5, ], linf=[ - 0.00010525416930584619, - 0.00010003778091061122, - 0.00010003778085621029, - 0.00036426282101720275, + 0.00010525416937667842, 0.00010003778102718464, + 0.00010003778071832059, 0.0003642628211952825, ]) # Ensure that we do not have excessive memory allocations # (e.g., from type instabilities) @@ -232,6 +227,7 @@ end @trixi_testset "elixir_euler_curved.jl (Quadrilateral elements, GaussSBP, flux differencing)" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_curved.jl"), approximation_type=GaussSBP(), + surface_integral=SurfaceIntegralWeakForm(FluxHLL(min_max_speed_naive)), l2=[ 3.4666312079259457e-6, 3.4392774480368986e-6, @@ -259,6 +255,7 @@ end @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_curved.jl"), element_type=Tri(), approximation_type=Polynomial(), volume_integral=VolumeIntegralWeakForm(), + surface_integral=SurfaceIntegralWeakForm(FluxHLL(min_max_speed_naive)), l2=[ 7.905498158659466e-6, 8.731690809663625e-6, @@ -330,16 +327,12 @@ end @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_weakform_periodic.jl"), # division by 2.0 corresponds to normalization by the square root of the size of the domain l2=[ - 0.0014986508075708323, - 0.001528523420746786, - 0.0015285234207473158, - 0.004846505183839211, - ] ./ 2.0, + 0.0007492755162295128, 0.0007641875305302599, + 0.0007641875305306243, 0.0024232389721009447, + ], linf=[ - 0.0015062108658376872, - 0.0019373508504645365, - 0.0019373508504538783, - 0.004742686826709086, + 0.0015060064614331736, 0.0019371156800773726, + 0.0019371156800769285, 0.004742431684202408, ]) # Ensure that we do not have excessive memory allocations # (e.g., from type instabilities) @@ -354,16 +347,12 @@ end @trixi_testset "elixir_euler_triangulate_pkg_mesh.jl" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_triangulate_pkg_mesh.jl"), l2=[ - 2.344080455438114e-6, - 1.8610038753097983e-6, - 2.4095165666095305e-6, - 6.373308158814308e-6, + 2.344076909832665e-6, 1.8610002398709756e-6, + 2.4095132179484066e-6, 6.37330249340445e-6, ], linf=[ - 2.5099852761334418e-5, - 2.2683684021362893e-5, - 2.6180448559287584e-5, - 5.5752932611508044e-5, + 2.509979394305084e-5, 2.2683711321080935e-5, + 2.6180377720841363e-5, 5.575278031910713e-5, ]) # Ensure that we do not have excessive memory allocations # (e.g., from type instabilities) @@ -435,16 +424,12 @@ end "elixir_euler_rayleigh_taylor_instability.jl"), cells_per_dimension=(8, 8), tspan=(0.0, 0.2), l2=[ - 0.0709665896982514, - 0.005182828752164663, - 0.013832655585206478, - 0.03247013800580221, + 0.07097806723891838, 0.005168550941966817, + 0.013820912272220933, 0.03243357220022434, ], linf=[ - 0.4783963902824797, - 0.022527207050681054, - 0.040307056293369226, - 0.0852365428206836, + 0.4783395896753895, 0.02244629340135818, + 0.04023357731088538, 0.08515807256615027, ]) # Ensure that we do not have excessive memory allocations # (e.g., from type instabilities) @@ -604,16 +589,12 @@ end @trixi_testset "elixir_euler_fdsbp_periodic.jl" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_fdsbp_periodic.jl"), l2=[ - 1.3333320340010056e-6, - 2.044834627970641e-6, - 2.044834627855601e-6, - 5.282189803559564e-6, + 1.333332033888785e-6, 2.044834627786368e-6, + 2.0448346278315884e-6, 5.282189803437435e-6, ], linf=[ - 2.7000151718858945e-6, - 3.988595028259212e-6, - 3.9885950273710336e-6, - 8.848583042286862e-6, + 2.7000151703315822e-6, 3.988595025372632e-6, + 3.9885950240403645e-6, 8.848583036513702e-6, ]) # Ensure that we do not have excessive memory allocations # (e.g., from type instabilities) @@ -628,6 +609,7 @@ end @trixi_testset "elixir_euler_fdsbp_periodic.jl (arbitrary reference domain)" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_fdsbp_periodic.jl"), xmin=-200.0, xmax=100.0, #= parameters for reference interval =# + surface_flux=FluxHLL(min_max_speed_naive), l2=[ 1.333332034149886e-6, 2.0448346280892024e-6, @@ -659,6 +641,7 @@ end @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_fdsbp_periodic.jl"), approximation_type=D, coordinates_min=(-3.0, -4.0), coordinates_max=(0.0, -1.0), + surface_flux=FluxHLL(min_max_speed_naive), l2=[ 0.07318831033918516, 0.10039910610067465, @@ -691,6 +674,7 @@ end global D = SummationByPartsOperators.couple_continuously(D_local, mesh_local) @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_fdsbp_periodic.jl"), approximation_type=D, + surface_flux=FluxHLL(min_max_speed_naive), l2=[ 1.5440402410017893e-5, 1.4913189903083485e-5, diff --git a/test/test_dgmulti_3d.jl b/test/test_dgmulti_3d.jl index 3a1db255484..fa70b11447c 100644 --- a/test/test_dgmulti_3d.jl +++ b/test/test_dgmulti_3d.jl @@ -17,20 +17,15 @@ isdir(outdir) && rm(outdir, recursive = true) # 3d tet/hex tests @trixi_testset "elixir_euler_weakform.jl" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_weakform.jl"), - # division by sqrt(8.0) corresponds to normalization by the square root of the size of the domain l2=[ - 0.0010029534292051608, - 0.0011682205957721673, - 0.001072975385793516, - 0.000997247778892257, - 0.0039364354651358294, - ] ./ sqrt(8), + 0.000354593110864001, 0.00041301573702385284, + 0.00037934556184883277, 0.0003525767114354012, + 0.0013917457634530887, + ], linf=[ - 0.003660737033303718, - 0.005625620600749226, - 0.0030566354814669516, - 0.0041580358824311325, - 0.019326660236036464, + 0.0036608123230692513, 0.005625540942772123, + 0.0030565781898950206, 0.004158099048202857, + 0.01932716837214299, ]) # Ensure that we do not have excessive memory allocations # (e.g., from type instabilities) @@ -74,6 +69,7 @@ end @trixi_testset "elixir_euler_weakform.jl (Hexahedral elements)" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_weakform.jl"), element_type=Hex(), + surface_integral=SurfaceIntegralWeakForm(FluxHLL(min_max_speed_naive)), # division by sqrt(8.0) corresponds to normalization by the square root of the size of the domain l2=[ 0.00030580190715769566, @@ -102,18 +98,13 @@ end @trixi_testset "elixir_euler_curved.jl (Hex elements, SBP, flux differencing)" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_curved.jl"), l2=[ - 0.018354883045936066, - 0.024412704052042846, - 0.024408520416087945, - 0.01816314570880129, - 0.039342805507972006, + 0.01835488304593566, 0.024412704052042534, + 0.02440852041608929, 0.018163145708800853, + 0.03934280550797125, ], linf=[ - 0.14862225990775757, - 0.28952368161864683, - 0.2912054484817035, - 0.1456603133854122, - 0.3315354586775472, + 0.14862225990793032, 0.2895236816183626, 0.291205448481636, + 0.14566031338563246, 0.33153545867790246, ]) # Ensure that we do not have excessive memory allocations # (e.g., from type instabilities) @@ -129,18 +120,14 @@ end @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_curved.jl"), approximation_type=GaussSBP(), l2=[ - 0.002631131519508634, - 0.0029144224044954105, - 0.002913889110662827, - 0.002615140832314194, - 0.006881528610614373, + 0.0026311315195097097, 0.002914422404496567, + 0.0029138891106640368, 0.002615140832315232, + 0.006881528610616624, ], linf=[ - 0.020996114874140215, - 0.021314522450134543, - 0.021288322783006297, - 0.020273381695435244, - 0.052598740390024545, + 0.02099611487415931, 0.021314522450152307, + 0.021288322783027613, 0.020273381695449455, + 0.05259874039006007, ]) # Ensure that we do not have excessive memory allocations # (e.g., from type instabilities) @@ -154,20 +141,15 @@ end @trixi_testset "elixir_euler_weakform_periodic.jl" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_weakform_periodic.jl"), - # division by sqrt(8.0) corresponds to normalization by the square root of the size of the domain l2=[ - 0.0010317074322517949, - 0.0012277090547035293, - 0.0011273991123913515, - 0.0010418496196130177, - 0.004058878478404962, - ] ./ sqrt(8), + 0.00036475807571383924, 0.00043404536371780537, + 0.0003985850214093045, 0.0003683451584072326, + 0.00143503620472638, + ], linf=[ - 0.003227752881827861, - 0.005620317864620361, - 0.0030514833972379307, - 0.003987027618439498, - 0.019282224709831652, + 0.0032278615418719347, 0.005620238272054934, + 0.0030514261010661237, 0.0039871165455998, + 0.019282771780667396, ]) # Ensure that we do not have excessive memory allocations # (e.g., from type instabilities) @@ -182,6 +164,7 @@ end @trixi_testset "elixir_euler_weakform_periodic.jl (Hexahedral elements)" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_weakform_periodic.jl"), element_type=Hex(), + surface_integral=SurfaceIntegralWeakForm(FluxHLL(min_max_speed_naive)), # division by sqrt(8.0) corresponds to normalization by the square root of the size of the domain l2=[ 0.00034230612468547436, diff --git a/test/test_parabolic_3d.jl b/test/test_parabolic_3d.jl index 1eaa9f51a56..863daeeaf35 100644 --- a/test/test_parabolic_3d.jl +++ b/test/test_parabolic_3d.jl @@ -400,6 +400,7 @@ end @test_trixi_include(joinpath(examples_dir(), "p4est_3d_dgsem", "elixir_navierstokes_taylor_green_vortex.jl"), initial_refinement_level=2, tspan=(0.0, 0.25), + surface_flux=FluxHLL(min_max_speed_naive), l2=[ 0.0001547509861140407, 0.015637861347119624, diff --git a/test/test_special_elixirs.jl b/test/test_special_elixirs.jl index ba670a6025e..277ade9bd5c 100644 --- a/test/test_special_elixirs.jl +++ b/test/test_special_elixirs.jl @@ -286,7 +286,8 @@ end equations = CompressibleEulerEquations1D(1.4) mesh = TreeMesh((-1.0,), (1.0,), initial_refinement_level = 3, n_cells_max = 10^4) - solver = DGSEM(3, flux_hll, VolumeIntegralFluxDifferencing(flux_ranocha)) + solver = DGSEM(3, FluxHLL(min_max_speed_naive), + VolumeIntegralFluxDifferencing(flux_ranocha)) initial_condition = (x, t, equations) -> begin rho = 2 + sinpi(k * sum(x)) v1 = 0.1 diff --git a/test/test_structured_2d.jl b/test/test_structured_2d.jl index f5fb169033a..64a1faf05b8 100644 --- a/test/test_structured_2d.jl +++ b/test/test_structured_2d.jl @@ -606,16 +606,12 @@ end @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_rayleigh_taylor_instability.jl"), l2=[ - 0.06365630381017849, - 0.007166887387738937, - 0.002878708825497772, - 0.010247678114070121, + 0.06365630515019809, 0.007166887172039836, + 0.0028787103533600804, 0.010247678008197966, ], linf=[ - 0.4799214336153155, - 0.024595483032220266, - 0.02059808120543466, - 0.03190756362943725, + 0.47992143569849377, 0.02459548251933757, + 0.02059810091623976, 0.0319077000843877, ], cells_per_dimension=(8, 8), tspan=(0.0, 0.3)) @@ -659,14 +655,12 @@ end @trixi_testset "elixir_eulerpolytropic_convergence.jl" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_eulerpolytropic_convergence.jl"), l2=[ - 0.0016688820596537988, - 0.0025921681885685425, - 0.003280950351435014, + 0.00166898321776379, 0.00259202637930991, + 0.0032810744946276406, ], linf=[ - 0.010994679664394269, - 0.01331197845637, - 0.020080117011346488, + 0.010994883201888683, 0.013309526619369905, + 0.020080326611175536, ]) # Ensure that we do not have excessive memory allocations # (e.g., from type instabilities) @@ -678,18 +672,19 @@ end end end -@trixi_testset "elixir_eulerpolytropic_convergence.jl: HLL(Davis)" begin - @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_eulerpolytropic_convergence.jl"), +@trixi_testset "elixir_eulerpolytropic_convergence.jl with FluxHLL(min_max_speed_naive)" begin + @test_trixi_include(joinpath(EXAMPLES_DIR, + "elixir_eulerpolytropic_convergence.jl"), solver=DGSEM(polydeg = 3, - surface_flux = FluxHLL(min_max_speed_davis), + surface_flux = FluxHLL(min_max_speed_naive), volume_integral = VolumeIntegralFluxDifferencing(volume_flux)), l2=[ - 0.0016689832177644243, 0.0025920263793104445, - 0.003281074494629298, + 0.001668882059653298, 0.002592168188567654, + 0.0032809503514328307, ], linf=[ - 0.01099488320190023, 0.013309526619350365, - 0.02008032661117909, + 0.01099467966437917, 0.013311978456333584, + 0.020080117011337606, ]) # Ensure that we do not have excessive memory allocations # (e.g., from type instabilities) @@ -727,14 +722,12 @@ end @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_eulerpolytropic_isothermal_wave.jl"), l2=[ - 0.004998778491726366, - 0.004998916000294425, - 9.259136963058664e-17, + 0.004998778512795407, 0.004998916021367992, + 8.991558055435833e-17, ], linf=[ - 0.010001103673834888, - 0.010051165098399503, - 7.623942913643681e-16, + 0.010001103632831354, 0.010051165055185603, + 7.60697457718599e-16, ]) # Ensure that we do not have excessive memory allocations # (e.g., from type instabilities) @@ -749,14 +742,12 @@ end @trixi_testset "elixir_eulerpolytropic_wave.jl" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_eulerpolytropic_wave.jl"), l2=[ - 0.23642682112204072, - 0.20904264390331334, - 8.174982691297391e-17, + 0.23642871172548174, 0.2090519382039672, + 8.778842676292274e-17, ], linf=[ - 0.4848250368349989, - 0.253350873815695, - 4.984552457753618e-16, + 0.4852276879687425, 0.25327870807625175, + 5.533921691832115e-16, ]) # Ensure that we do not have excessive memory allocations # (e.g., from type instabilities) diff --git a/test/test_threaded.jl b/test/test_threaded.jl index a8a1b1b425a..7365dcef21c 100644 --- a/test/test_threaded.jl +++ b/test/test_threaded.jl @@ -394,10 +394,10 @@ end "elixir_euler_curved.jl"), alg=RDPK3SpFSAL49(thread = OrdinaryDiffEq.True()), l2=[ - 1.720476068165337e-5, - 1.592168205710526e-5, - 1.592168205812963e-5, - 4.894094865697305e-5, + 1.7204593127904542e-5, + 1.5921547179522804e-5, + 1.5921547180107928e-5, + 4.894071422525737e-5, ], linf=[ 0.00010525416930584619, @@ -420,16 +420,16 @@ end @test_trixi_include(joinpath(examples_dir(), "dgmulti_2d", "elixir_euler_triangulate_pkg_mesh.jl"), l2=[ - 2.344080455438114e-6, - 1.8610038753097983e-6, - 2.4095165666095305e-6, - 6.373308158814308e-6, + 2.344076909832665e-6, + 1.8610002398709756e-6, + 2.4095132179484066e-6, + 6.37330249340445e-6, ], linf=[ - 2.5099852761334418e-5, - 2.2683684021362893e-5, - 2.6180448559287584e-5, - 5.5752932611508044e-5, + 2.509979394305084e-5, + 2.2683711321080935e-5, + 2.6180377720841363e-5, + 5.575278031910713e-5, ]) # Ensure that we do not have excessive memory allocations diff --git a/test/test_tree_1d_euler.jl b/test/test_tree_1d_euler.jl index 39a1f6e30ba..f26500b411c 100644 --- a/test/test_tree_1d_euler.jl +++ b/test/test_tree_1d_euler.jl @@ -221,11 +221,11 @@ end @trixi_testset "elixir_euler_ec.jl with flux_hll" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_ec.jl"), - l2=[0.07852272782240548, 0.10209790867523805, 0.293873048809011], + l2=[0.07855251823583848, 0.10213903748267686, 0.293985892532479], linf=[ - 0.19244768908604093, - 0.2515941686151897, - 0.7258000837553769, + 0.192621556068018, + 0.25184744005299536, + 0.7264977555504792, ], maxiters=10, surface_flux=flux_hll, diff --git a/test/test_tree_1d_eulergravity.jl b/test/test_tree_1d_eulergravity.jl index 9ab5b287d0b..17bc0c71a7a 100644 --- a/test/test_tree_1d_eulergravity.jl +++ b/test/test_tree_1d_eulergravity.jl @@ -13,14 +13,12 @@ EXAMPLES_DIR = pkgdir(Trixi, "examples", "tree_1d_dgsem") @trixi_testset "elixir_eulergravity_convergence.jl" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_eulergravity_convergence.jl"), l2=[ - 0.0002170799126638106, - 0.0002913792848717502, - 0.0006112320856262327, + 0.00021708496949694728, 0.0002913795242132917, + 0.0006112500956552259, ], linf=[ - 0.0004977401033188222, - 0.0013594223337776157, - 0.002041891084400227, + 0.0004977733237385706, 0.0013594226727522418, + 0.0020418739554664, ]) # Ensure that we do not have excessive memory allocations # (e.g., from type instabilities) diff --git a/test/test_tree_1d_shallowwater.jl b/test/test_tree_1d_shallowwater.jl index f9be63b87fd..41ad5c32bbd 100644 --- a/test/test_tree_1d_shallowwater.jl +++ b/test/test_tree_1d_shallowwater.jl @@ -143,17 +143,18 @@ end @trixi_testset "elixir_shallowwater_source_terms.jl with flux_hll" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_shallowwater_source_terms.jl"), l2=[ - 0.0022758146627220154, - 0.015864082886204556, + 0.002275023323848826, + 0.015861093821754046, 4.436491725585346e-5, ], linf=[ - 0.008457195427364006, - 0.057201667446161064, + 0.008461451098266792, + 0.05722331401673486, 9.098379777405796e-5, ], tspan=(0.0, 0.025), - surface_flux=(flux_hll, flux_nonconservative_fjordholm_etal)) + surface_flux=(flux_hll, + flux_nonconservative_fjordholm_etal)) # Ensure that we do not have excessive memory allocations # (e.g., from type instabilities) let @@ -228,7 +229,7 @@ end 0.05720939349382359, 9.098379777405796e-5, ], - surface_flux=(FluxHydrostaticReconstruction(flux_hll, + surface_flux=(FluxHydrostaticReconstruction(FluxHLL(min_max_speed_naive), hydrostatic_reconstruction_audusse_etal), flux_nonconservative_audusse_etal), tspan=(0.0, 0.025)) @@ -255,7 +256,9 @@ end 3.469453422316143e-15, 3.844551077492042e-8, ], - tspan=(0.0, 0.25)) + tspan=(0.0, 0.25), + surface_flux=(FluxHLL(min_max_speed_naive), + flux_nonconservative_fjordholm_etal),) # Ensure that we do not have excessive memory allocations # (e.g., from type instabilities) let @@ -280,6 +283,8 @@ end 3.844551077492042e-8, ], tspan=(0.0, 0.25), + surface_flux=(FluxHLL(min_max_speed_naive), + flux_nonconservative_fjordholm_etal), boundary_condition=boundary_condition_slip_wall) # Ensure that we do not have excessive memory allocations # (e.g., from type instabilities) diff --git a/test/test_tree_2d_mhd.jl b/test/test_tree_2d_mhd.jl index 1f8458075aa..66b47138a44 100644 --- a/test/test_tree_2d_mhd.jl +++ b/test/test_tree_2d_mhd.jl @@ -183,7 +183,7 @@ end end end -@trixi_testset "elixir_mhd_orszag_tang.jl with flux_hll" begin +@trixi_testset "elixir_mhd_orszag_tang.jl with flux_hlle" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_mhd_orszag_tang.jl"), l2=[ 0.10806619664693064, diff --git a/test/test_tree_2d_shallowwater.jl b/test/test_tree_2d_shallowwater.jl index 93a8cb63667..01742644736 100644 --- a/test/test_tree_2d_shallowwater.jl +++ b/test/test_tree_2d_shallowwater.jl @@ -195,6 +195,33 @@ end end @trixi_testset "elixir_shallowwater_source_terms.jl with flux_hll" begin + @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_shallowwater_source_terms.jl"), + l2=[ + 0.0018952610547425214, + 0.016943425162728183, + 0.017556784292859465, + 6.274146767717414e-5, + ], + linf=[ + 0.0151635341334182, + 0.07967467926956129, + 0.08400050790965174, + 0.0001819675955490041, + ], + tspan=(0.0, 0.025), + surface_flux=(flux_hll, + flux_nonconservative_fjordholm_etal)) + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end +end + +@trixi_testset "elixir_shallowwater_source_terms.jl with FluxHLL(min_max_speed_naive)" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_shallowwater_source_terms.jl"), l2=[ 0.0018957692481057034, @@ -209,7 +236,8 @@ end 0.0001819675955490041, ], tspan=(0.0, 0.025), - surface_flux=(flux_hll, flux_nonconservative_fjordholm_etal)) + surface_flux=(FluxHLL(min_max_speed_naive), + flux_nonconservative_fjordholm_etal)) # Ensure that we do not have excessive memory allocations # (e.g., from type instabilities) let diff --git a/test/test_tree_3d_euler.jl b/test/test_tree_3d_euler.jl index 02e657e001a..e9e2b82fec5 100644 --- a/test/test_tree_3d_euler.jl +++ b/test/test_tree_3d_euler.jl @@ -92,18 +92,14 @@ end @trixi_testset "elixir_euler_convergence.jl" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_convergence.jl"), l2=[ - 0.0003637241020254405, - 0.0003955570866382718, - 0.0003955570866383613, - 0.00039555708663834417, - 0.0007811613481640202, + 0.0003637241020254673, 0.00039555708663848046, + 0.00039555708663832644, 0.0003955570866385083, + 0.0007811613481643962, ], linf=[ - 0.0024000660244674066, - 0.0029635410025339315, - 0.0029635410025292686, - 0.002963541002525938, - 0.007191437359396424, + 0.0024000660244567484, 0.002963541002521053, + 0.0029635410025201647, 0.002963541002522385, + 0.007191437359379549, ]) # Ensure that we do not have excessive memory allocations # (e.g., from type instabilities) @@ -462,6 +458,7 @@ end 2.397746252817731, ], maxiters=5, max_level=6, + surface_flux=FluxHLL(min_max_speed_naive), coverage_override=(maxiters = 2, initial_refinement_level = 1, base_level = 1, max_level = 3)) # Ensure that we do not have excessive memory allocations diff --git a/test/test_tree_3d_mhd.jl b/test/test_tree_3d_mhd.jl index e75685f0b43..74107d462de 100644 --- a/test/test_tree_3d_mhd.jl +++ b/test/test_tree_3d_mhd.jl @@ -184,9 +184,9 @@ end end end -@trixi_testset "elixir_mhd_alfven_wave.jl with Orszag-Tang setup + flux_hll" begin +@trixi_testset "elixir_mhd_alfven_wave.jl with Orszag-Tang setup + flux_hlle" begin # OBS! This setup does not make much sense and is only used to exercise all components of the - # flux_hll implementation + # flux_hlle implementation @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_mhd_alfven_wave.jl"), l2=[ 0.004391143689111404, diff --git a/test/test_unstructured_2d.jl b/test/test_unstructured_2d.jl index 04eb9f679aa..87d677e1623 100644 --- a/test/test_unstructured_2d.jl +++ b/test/test_unstructured_2d.jl @@ -17,16 +17,12 @@ isdir(outdir) && rm(outdir, recursive = true) @trixi_testset "elixir_euler_periodic.jl" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_periodic.jl"), l2=[ - 0.00010978828464875207, - 0.00013010359527356914, - 0.00013010359527326057, - 0.0002987656724828824, + 0.0001099216141882387, 0.0001303795774982892, + 0.00013037957749794242, 0.0002993727892598759, ], linf=[ - 0.00638626102818618, - 0.009804042508242183, - 0.009804042508253286, - 0.02183139311614468, + 0.006407280810928562, 0.009836067015418948, + 0.009836067015398076, 0.021903519038095176, ]) # Ensure that we do not have excessive memory allocations # (e.g., from type instabilities) @@ -41,16 +37,12 @@ end @trixi_testset "elixir_euler_free_stream.jl" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_free_stream.jl"), l2=[ - 3.3937971107485363e-14, - 2.447586447887882e-13, - 1.4585205789296455e-13, - 4.716993468962946e-13, + 3.3937365073416665e-14, 2.44759188939065e-13, + 1.4585198700082895e-13, 4.716940764877479e-13, ], linf=[ - 8.804734719092266e-12, - 6.261270668606045e-11, - 2.93670088247211e-11, - 1.205400224080222e-10, + 8.804956763697191e-12, 6.261199891888225e-11, + 2.936639820205755e-11, 1.20543575121701e-10, ], tspan=(0.0, 0.1), atol=3.0e-13) @@ -78,7 +70,8 @@ end 0.29339040847600434, 0.5915610037764794, ], - tspan=(0.0, 0.25)) + tspan=(0.0, 0.25), + surface_flux=FluxHLL(min_max_speed_naive)) # Ensure that we do not have excessive memory allocations # (e.g., from type instabilities) let @@ -407,15 +400,15 @@ end @trixi_testset "elixir_shallowwater_source_terms.jl with FluxHydrostaticReconstruction" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_shallowwater_source_terms.jl"), l2=[ - 0.0011197139793938152, - 0.015430259691310781, - 0.017081031802719724, + 0.001119678684752799, + 0.015429108794630785, + 0.01708275441241111, 5.089218476758271e-6, ], linf=[ - 0.014300809338967824, - 0.12783372461225184, - 0.17625472321992852, + 0.014299564388827513, + 0.12785126473870534, + 0.17626788561725526, 2.6407324614341476e-5, ], surface_flux=(FluxHydrostaticReconstruction(flux_hll, @@ -464,18 +457,19 @@ end @trixi_testset "elixir_shallowwater_source_terms.jl with flux_hll" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_shallowwater_source_terms.jl"), l2=[ - 0.0011197139793938727, - 0.015430259691311309, - 0.017081031802719554, + 0.0011196786847528799, + 0.015429108794631075, + 0.017082754412411742, 5.089218476759981e-6, ], linf=[ - 0.014300809338967824, - 0.12783372461224918, - 0.17625472321993918, + 0.014299564388830177, + 0.12785126473870667, + 0.17626788561728546, 2.6407324614341476e-5, ], - surface_flux=(flux_hll, flux_nonconservative_fjordholm_etal), + surface_flux=(flux_hll, + flux_nonconservative_fjordholm_etal), tspan=(0.0, 0.025)) # Ensure that we do not have excessive memory allocations # (e.g., from type instabilities) @@ -490,16 +484,12 @@ end @trixi_testset "elixir_shallowwater_dirichlet.jl" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_shallowwater_dirichlet.jl"), l2=[ - 1.1577518608940115e-5, - 4.867189932537344e-13, - 4.647273240470541e-13, - 1.1577518608933468e-5, + 1.1577518608938916e-5, 4.859252379740366e-13, + 4.639600837197925e-13, 1.1577518608952174e-5, ], linf=[ - 8.394063878602864e-5, - 1.1469760027632646e-10, - 1.1146619484429974e-10, - 8.394063879602065e-5, + 8.3940638787805e-5, 1.1446362498574484e-10, + 1.1124515748367981e-10, 8.39406387962427e-5, ], tspan=(0.0, 2.0)) # Ensure that we do not have excessive memory allocations @@ -516,16 +506,12 @@ end @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_shallowwater_wall_bc_shockcapturing.jl"), l2=[ - 0.04444388691670699, - 0.1527771788033111, - 0.1593763537203512, - 6.225080476986749e-8, + 0.0442113635677511, 0.1537465759364839, 0.16003586586203947, + 6.225080477067782e-8, ], linf=[ - 0.6526506870169639, - 1.980765893182952, - 2.4807635459119757, - 3.982097158683473e-7, + 0.6347820607387928, 2.0078125433846736, 2.530726684667019, + 3.982097165344811e-7, ], tspan=(0.0, 0.05)) # Ensure that we do not have excessive memory allocations @@ -609,12 +595,12 @@ end 1.0066867437607972e-13, 6.889210012578449e-14, 1.568290814572709e-13], - linf=[2.353373051988683e-10, - 2.801543719233024e-11, - 3.930469838486772e-11, + linf=[5.6139981552405516e-11, + 2.842849566864203e-11, + 1.8290174930157832e-11, 4.61017890529547e-11], tspan=(0.0, 0.1), - atol=1.0e-11) + atol=1.0e-10) # Ensure that we do not have excessive memory allocations # (e.g., from type instabilities) let From c7693aaf06587de194147c9c70888c124ed2daf3 Mon Sep 17 00:00:00 2001 From: Hendrik Ranocha Date: Fri, 23 Feb 2024 13:47:12 +0100 Subject: [PATCH 43/63] set version to v0.7.0; closes #1726 --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 6b27e6e9999..2fb8e196829 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "Trixi" uuid = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb" authors = ["Michael Schlottke-Lakemper ", "Gregor Gassner ", "Hendrik Ranocha ", "Andrew R. Winters ", "Jesse Chan "] -version = "0.6.11-pre" +version = "0.7.0" [deps] CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2" From 27d91b3ceeb15e1079b815268738b365635c6cab Mon Sep 17 00:00:00 2001 From: Hendrik Ranocha Date: Fri, 23 Feb 2024 13:47:49 +0100 Subject: [PATCH 44/63] set development version to v0.7.1-pre --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 2fb8e196829..800c7b4c0fa 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "Trixi" uuid = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb" authors = ["Michael Schlottke-Lakemper ", "Gregor Gassner ", "Hendrik Ranocha ", "Andrew R. Winters ", "Jesse Chan "] -version = "0.7.0" +version = "0.7.1-pre" [deps] CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2" From 4ee60e7973ff78d553dad65f7f4760443891bdb6 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Sat, 24 Feb 2024 05:57:09 +0100 Subject: [PATCH 45/63] CompatHelper: bump compat for Trixi to 0.7 for package benchmark, (keep existing compat) (#1853) Co-authored-by: CompatHelper Julia --- benchmark/Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/benchmark/Project.toml b/benchmark/Project.toml index e94144cfd15..51d271e65fc 100644 --- a/benchmark/Project.toml +++ b/benchmark/Project.toml @@ -8,4 +8,4 @@ Trixi = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb" BenchmarkTools = "0.5, 0.7, 1.0" OrdinaryDiffEq = "5.65, 6" PkgBenchmark = "0.2.10" -Trixi = "0.4, 0.5, 0.6" +Trixi = "0.4, 0.5, 0.6, 0.7" From e205b0637d72341041f59cc740933a2bc5835687 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Fri, 1 Mar 2024 17:30:44 +0100 Subject: [PATCH 46/63] Bump crate-ci/typos from 1.18.0 to 1.18.2 (#1856) Bumps [crate-ci/typos](https://github.com/crate-ci/typos) from 1.18.0 to 1.18.2. - [Release notes](https://github.com/crate-ci/typos/releases) - [Changelog](https://github.com/crate-ci/typos/blob/master/CHANGELOG.md) - [Commits](https://github.com/crate-ci/typos/compare/v1.18.0...v1.18.2) --- updated-dependencies: - dependency-name: crate-ci/typos dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --- .github/workflows/SpellCheck.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/SpellCheck.yml b/.github/workflows/SpellCheck.yml index b242b6e811e..87e34cb50f3 100644 --- a/.github/workflows/SpellCheck.yml +++ b/.github/workflows/SpellCheck.yml @@ -10,4 +10,4 @@ jobs: - name: Checkout Actions Repository uses: actions/checkout@v4 - name: Check spelling - uses: crate-ci/typos@v1.18.0 + uses: crate-ci/typos@v1.18.2 From 8cdb93892dead6e33ae581e60fd8199aec4ee19e Mon Sep 17 00:00:00 2001 From: Andrew Winters Date: Wed, 6 Mar 2024 13:24:50 +0100 Subject: [PATCH 47/63] Upwind SBP on curved meshes (#1857) * baseline implementation of the curvilinear USBP for testing * working version of curvilinear upwind solver. Needs significant cleanup of debugging statements and different variants of the rotated flux vector splittings * cleanup of the fdsbp_2d file * clean-up FVS routines in the compressible Euler file * cleanup and remove unnecessary containers * add tests for the new solver * remove extra space * run formatter * Apply suggestions from code review Co-authored-by: Hendrik Ranocha * add specialized calc_metric_terms function for upwind type * revert change to the surface integral function * add reference for curvilinear van Leer splitting * new splitting_drikakis_tsangaris in Cartesian and generalized coordinates * added test for Cartesian splitting_drikakis_tsangaris * run formatter * Update src/equations/compressible_euler_2d.jl * remove orientation_or_normal from Steger-Warming --------- Co-authored-by: Hendrik Ranocha --- .../elixir_euler_free_stream_upwind.jl | 86 ++++++ .../elixir_euler_source_terms_upwind.jl | 87 ++++++ src/Trixi.jl | 3 +- src/equations/compressible_euler_2d.jl | 290 +++++++++++++++++- src/equations/numerical_fluxes.jl | 12 +- src/solvers/dgsem_unstructured/dg_2d.jl | 2 +- src/solvers/fdsbp_tree/fdsbp_2d.jl | 2 +- .../fdsbp_unstructured/containers_2d.jl | 10 +- src/solvers/fdsbp_unstructured/fdsbp_2d.jl | 99 +++++- test/test_tree_2d_fdsbp.jl | 26 ++ test/test_unstructured_2d.jl | 70 +++++ 11 files changed, 659 insertions(+), 28 deletions(-) create mode 100644 examples/unstructured_2d_fdsbp/elixir_euler_free_stream_upwind.jl create mode 100644 examples/unstructured_2d_fdsbp/elixir_euler_source_terms_upwind.jl diff --git a/examples/unstructured_2d_fdsbp/elixir_euler_free_stream_upwind.jl b/examples/unstructured_2d_fdsbp/elixir_euler_free_stream_upwind.jl new file mode 100644 index 00000000000..2a1956f9d10 --- /dev/null +++ b/examples/unstructured_2d_fdsbp/elixir_euler_free_stream_upwind.jl @@ -0,0 +1,86 @@ +# !!! warning "Experimental implementation (upwind SBP)" +# This is an experimental feature and may change in future releases. + +using OrdinaryDiffEq +using Trixi + +############################################################################### +# semidiscretization of the compressible Euler equations + +equations = CompressibleEulerEquations2D(1.4) + +initial_condition = initial_condition_constant + +# Boundary conditions for free-stream preservation test +boundary_condition_free_stream = BoundaryConditionDirichlet(initial_condition) + +boundary_conditions = Dict(:outerCircle => boundary_condition_free_stream, + :cone1 => boundary_condition_free_stream, + :cone2 => boundary_condition_free_stream, + :iceCream => boundary_condition_free_stream) + +############################################################################### +# Get the Upwind FDSBP approximation space + +# TODO: FDSBP +# Note, one must set `xmin=-1` and `xmax=1` due to the reuse +# of interpolation routines from `calc_node_coordinates!` to create +# the physical coordinates in the mappings. +D_upw = upwind_operators(SummationByPartsOperators.Mattsson2017, + derivative_order = 1, + accuracy_order = 8, + xmin = -1.0, xmax = 1.0, + N = 17) + +flux_splitting = splitting_vanleer_haenel +solver = FDSBP(D_upw, + surface_integral = SurfaceIntegralStrongForm(FluxUpwind(flux_splitting)), + volume_integral = VolumeIntegralUpwind(flux_splitting)) + +############################################################################### +# Get the curved quad mesh from a file (downloads the file if not available locally) + +# Mesh with second-order boundary polynomials requires an upwind SBP operator +# with (at least) 4th order boundary closure to guarantee the approximation is +# free-stream preserving +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/ec9a345f09199ebe471d35d5c1e4e08f/raw/15975943d8642e42f8292235314b6f1b30aa860d/mesh_inner_outer_boundaries.mesh", + joinpath(@__DIR__, "mesh_inner_outer_boundaries.mesh")) + +mesh = UnstructuredMesh2D(mesh_file) + +############################################################################### +# create the semi discretization object + +semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver, + boundary_conditions = boundary_conditions) + +############################################################################### +# ODE solvers, callbacks etc. + +tspan = (0.0, 5.0) +ode = semidiscretize(semi, tspan) + +summary_callback = SummaryCallback() + +analysis_interval = 1000 +analysis_callback = AnalysisCallback(semi, interval = analysis_interval) + +alive_callback = AliveCallback(analysis_interval = analysis_interval) + +save_solution = SaveSolutionCallback(interval = 1000, + save_initial_solution = true, + save_final_solution = true) + +callbacks = CallbackSet(summary_callback, + analysis_callback, + save_solution, + alive_callback) + +############################################################################### +# run the simulation + +# set small tolerances for the free-stream preservation test +sol = solve(ode, SSPRK43(), abstol = 1.0e-12, reltol = 1.0e-12, + save_everystep = false, callback = callbacks) + +summary_callback() # print the timer summary diff --git a/examples/unstructured_2d_fdsbp/elixir_euler_source_terms_upwind.jl b/examples/unstructured_2d_fdsbp/elixir_euler_source_terms_upwind.jl new file mode 100644 index 00000000000..9bd2afa5749 --- /dev/null +++ b/examples/unstructured_2d_fdsbp/elixir_euler_source_terms_upwind.jl @@ -0,0 +1,87 @@ +# !!! warning "Experimental implementation (upwind SBP)" +# This is an experimental feature and may change in future releases. + +using OrdinaryDiffEq +using Trixi + +############################################################################### +# semidiscretization of the compressible Euler equations + +equations = CompressibleEulerEquations2D(1.4) + +initial_condition = initial_condition_convergence_test + +source_term = source_terms_convergence_test + +boundary_condition_eoc = BoundaryConditionDirichlet(initial_condition) + +boundary_conditions = Dict(:Top => boundary_condition_eoc, + :Bottom => boundary_condition_eoc, + :Right => boundary_condition_eoc, + :Left => boundary_condition_eoc) + +############################################################################### +# Get the Upwind FDSBP approximation space + +# TODO: FDSBP +# Note, one must set `xmin=-1` and `xmax=1` due to the reuse +# of interpolation routines from `calc_node_coordinates!` to create +# the physical coordinates in the mappings. +D_upw = upwind_operators(SummationByPartsOperators.Mattsson2017, + derivative_order = 1, + accuracy_order = 4, + xmin = -1.0, xmax = 1.0, + N = 9) + +flux_splitting = splitting_drikakis_tsangaris +solver = FDSBP(D_upw, + surface_integral = SurfaceIntegralStrongForm(FluxUpwind(flux_splitting)), + volume_integral = VolumeIntegralUpwind(flux_splitting)) + +############################################################################### +# Get the curved quad mesh from a file (downloads the file if not available locally) + +# Mesh with first-order boundary polynomials requires an upwind SBP operator +# with (at least) 2nd order boundary closure to guarantee the approximation is +# free-stream preserving +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/a4f4743008bf3233957a9ea6ac7a62e0/raw/8b36cc6649153fe0a5723b200368a210a1d74eaf/mesh_refined_box.mesh", + joinpath(@__DIR__, "mesh_refined_box.mesh")) + +mesh = UnstructuredMesh2D(mesh_file) + +############################################################################### +# create the semidiscretization object + +semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver, + source_terms = source_term, + boundary_conditions = boundary_conditions) + +############################################################################### +# ODE solvers, callbacks etc. + +tspan = (0.0, 1.0) +ode = semidiscretize(semi, tspan) + +summary_callback = SummaryCallback() + +analysis_interval = 1000 +analysis_callback = AnalysisCallback(semi, interval = analysis_interval) + +alive_callback = AliveCallback(analysis_interval = analysis_interval) + +save_solution = SaveSolutionCallback(interval = 1000, + save_initial_solution = true, + save_final_solution = true) + +callbacks = CallbackSet(summary_callback, + analysis_callback, + save_solution, + alive_callback) + +############################################################################### +# run the simulation + +sol = solve(ode, SSPRK43(), abstol = 1.0e-6, reltol = 1.0e-6, + save_everystep = false, callback = callbacks) + +summary_callback() # print the timer summary diff --git a/src/Trixi.jl b/src/Trixi.jl index 5f8cd9cae8e..da7359999c5 100644 --- a/src/Trixi.jl +++ b/src/Trixi.jl @@ -191,7 +191,8 @@ export flux, flux_central, flux_lax_friedrichs, flux_hll, flux_hllc, flux_hlle, FluxUpwind export splitting_steger_warming, splitting_vanleer_haenel, - splitting_coirier_vanleer, splitting_lax_friedrichs + splitting_coirier_vanleer, splitting_lax_friedrichs, + splitting_drikakis_tsangaris export initial_condition_constant, initial_condition_gauss, diff --git a/src/equations/compressible_euler_2d.jl b/src/equations/compressible_euler_2d.jl index f5a632723cf..43f15a3cfb9 100644 --- a/src/equations/compressible_euler_2d.jl +++ b/src/equations/compressible_euler_2d.jl @@ -689,7 +689,9 @@ end orientation::Integer, equations::CompressibleEulerEquations2D) -Splitting of the compressible Euler flux of Steger and Warming. +Splitting of the compressible Euler flux of Steger and Warming. For +curvilinear coordinates use the improved Steger-Warming-type splitting +[`splitting_drikakis_tsangaris`](@ref). Returns a tuple of the fluxes "minus" (associated with waves going into the negative axis direction) and "plus" (associated with waves going into the @@ -809,6 +811,174 @@ end return SVector(f1m, f2m, f3m, f4m) end +""" + splitting_drikakis_tsangaris(u, orientation_or_normal_direction, + equations::CompressibleEulerEquations2D) + splitting_drikakis_tsangaris(u, which::Union{Val{:minus}, Val{:plus}} + orientation_or_normal_direction, + equations::CompressibleEulerEquations2D) + +Improved variant of the Steger-Warming flux vector splitting +[`splitting_steger_warming`](@ref) for generalized coordinates. +This splitting also reformulates the energy +flux as in Hänel et al. to obtain conservation of the total temperature +for inviscid flows. + +Returns a tuple of the fluxes "minus" (associated with waves going into the +negative axis direction) and "plus" (associated with waves going into the +positive axis direction). If only one of the fluxes is required, use the +function signature with argument `which` set to `Val{:minus}()` or `Val{:plus}()`. + +!!! warning "Experimental implementation (upwind SBP)" + This is an experimental feature and may change in future releases. + +## References + +- D. Drikakis and S. Tsangaris (1993) + On the solution of the compressible Navier-Stokes equations using + improved flux vector splitting methods + [DOI: 10.1016/0307-904X(93)90054-K](https://doi.org/10.1016/0307-904X(93)90054-K) +- D. Hänel, R. Schwane and G. Seider (1987) + On the accuracy of upwind schemes for the solution of the Navier-Stokes equations + [DOI: 10.2514/6.1987-1105](https://doi.org/10.2514/6.1987-1105) +""" +@inline function splitting_drikakis_tsangaris(u, orientation_or_normal_direction, + equations::CompressibleEulerEquations2D) + fm = splitting_drikakis_tsangaris(u, Val{:minus}(), orientation_or_normal_direction, + equations) + fp = splitting_drikakis_tsangaris(u, Val{:plus}(), orientation_or_normal_direction, + equations) + return fm, fp +end + +@inline function splitting_drikakis_tsangaris(u, ::Val{:plus}, orientation::Integer, + equations::CompressibleEulerEquations2D) + rho, rho_v1, rho_v2, rho_e = u + v1 = rho_v1 / rho + v2 = rho_v2 / rho + p = (equations.gamma - 1) * (rho_e - 0.5 * (rho_v1 * v1 + rho_v2 * v2)) + a = sqrt(equations.gamma * p / rho) + H = (rho_e + p) / rho + + if orientation == 1 + lambda1 = v1 + a + lambda2 = v1 - a + + lambda1_p = positive_part(lambda1) # Same as (lambda_i + abs(lambda_i)) / 2, but faster :) + lambda2_p = positive_part(lambda2) + + rhoa_2gamma = 0.5 * rho * a / equations.gamma + f1p = 0.5 * rho * (lambda1_p + lambda2_p) + f2p = f1p * v1 + rhoa_2gamma * (lambda1_p - lambda2_p) + f3p = f1p * v2 + f4p = f1p * H + else # orientation == 2 + lambda1 = v2 + a + lambda2 = v2 - a + + lambda1_p = positive_part(lambda1) # Same as (lambda_i + abs(lambda_i)) / 2, but faster :) + lambda2_p = positive_part(lambda2) + + rhoa_2gamma = 0.5 * rho * a / equations.gamma + f1p = 0.5 * rho * (lambda1_p + lambda2_p) + f2p = f1p * v1 + f3p = f1p * v2 + rhoa_2gamma * (lambda1_p - lambda2_p) + f4p = f1p * H + end + return SVector(f1p, f2p, f3p, f4p) +end + +@inline function splitting_drikakis_tsangaris(u, ::Val{:minus}, orientation::Integer, + equations::CompressibleEulerEquations2D) + rho, rho_v1, rho_v2, rho_e = u + v1 = rho_v1 / rho + v2 = rho_v2 / rho + p = (equations.gamma - 1) * (rho_e - 0.5 * (rho_v1 * v1 + rho_v2 * v2)) + a = sqrt(equations.gamma * p / rho) + H = (rho_e + p) / rho + + if orientation == 1 + lambda1 = v1 + a + lambda2 = v1 - a + + lambda1_m = negative_part(lambda1) # Same as (lambda_i - abs(lambda_i)) / 2, but faster :) + lambda2_m = negative_part(lambda2) + + rhoa_2gamma = 0.5 * rho * a / equations.gamma + f1m = 0.5 * rho * (lambda1_m + lambda2_m) + f2m = f1m * v1 + rhoa_2gamma * (lambda1_m - lambda2_m) + f3m = f1m * v2 + f4m = f1m * H + else # orientation == 2 + lambda1 = v2 + a + lambda2 = v2 - a + + lambda1_m = negative_part(lambda1) # Same as (lambda_i - abs(lambda_i)) / 2, but faster :) + lambda2_m = negative_part(lambda2) + + rhoa_2gamma = 0.5 * rho * a / equations.gamma + f1m = 0.5 * rho * (lambda1_m + lambda2_m) + f2m = f1m * v1 + f3m = f1m * v2 + rhoa_2gamma * (lambda1_m - lambda2_m) + f4m = f1m * H + end + return SVector(f1m, f2m, f3m, f4m) +end + +@inline function splitting_drikakis_tsangaris(u, ::Val{:plus}, + normal_direction::AbstractVector, + equations::CompressibleEulerEquations2D) + rho, rho_v1, rho_v2, rho_e = u + v1 = rho_v1 / rho + v2 = rho_v2 / rho + p = (equations.gamma - 1) * (rho_e - 0.5 * (rho_v1 * v1 + rho_v2 * v2)) + a = sqrt(equations.gamma * p / rho) + H = (rho_e + p) / rho + + v_n = normal_direction[1] * v1 + normal_direction[2] * v2 + + lambda1 = v_n + a + lambda2 = v_n - a + + lambda1_p = positive_part(lambda1) # Same as (lambda_i + abs(lambda_i)) / 2, but faster :) + lambda2_p = positive_part(lambda2) + + rhoa_2gamma = 0.5 * rho * a / equations.gamma + f1p = 0.5 * rho * (lambda1_p + lambda2_p) + f2p = f1p * v1 + rhoa_2gamma * normal_direction[1] * (lambda1_p - lambda2_p) + f3p = f1p * v2 + rhoa_2gamma * normal_direction[2] * (lambda1_p - lambda2_p) + f4p = f1p * H + + return SVector(f1p, f2p, f3p, f4p) +end + +@inline function splitting_drikakis_tsangaris(u, ::Val{:minus}, + normal_direction::AbstractVector, + equations::CompressibleEulerEquations2D) + rho, rho_v1, rho_v2, rho_e = u + v1 = rho_v1 / rho + v2 = rho_v2 / rho + p = (equations.gamma - 1) * (rho_e - 0.5 * (rho_v1 * v1 + rho_v2 * v2)) + a = sqrt(equations.gamma * p / rho) + H = (rho_e + p) / rho + + v_n = normal_direction[1] * v1 + normal_direction[2] * v2 + + lambda1 = v_n + a + lambda2 = v_n - a + + lambda1_m = negative_part(lambda1) # Same as (lambda_i - abs(lambda_i)) / 2, but faster :) + lambda2_m = negative_part(lambda2) + + rhoa_2gamma = 0.5 * rho * a / equations.gamma + f1m = 0.5 * rho * (lambda1_m + lambda2_m) + f2m = f1m * v1 + rhoa_2gamma * normal_direction[1] * (lambda1_m - lambda2_m) + f3m = f1m * v2 + rhoa_2gamma * normal_direction[2] * (lambda1_m - lambda2_m) + f4m = f1m * H + + return SVector(f1m, f2m, f3m, f4m) +end + """ FluxLMARS(c)(u_ll, u_rr, orientation_or_normal_direction, equations::CompressibleEulerEquations2D) @@ -902,10 +1072,10 @@ end end """ - splitting_vanleer_haenel(u, orientation::Integer, + splitting_vanleer_haenel(u, orientation_or_normal_direction, equations::CompressibleEulerEquations2D) splitting_vanleer_haenel(u, which::Union{Val{:minus}, Val{:plus}} - orientation::Integer, + orientation_or_normal_direction, equations::CompressibleEulerEquations2D) Splitting of the compressible Euler flux from van Leer. This splitting further @@ -913,7 +1083,8 @@ contains a reformulation due to Hänel et al. where the energy flux uses the enthalpy. The pressure splitting is independent from the splitting of the convective terms. As such there are many pressure splittings suggested across the literature. We implement the 'p4' variant suggested by Liou and Steffen as -it proved the most robust in practice. +it proved the most robust in practice. For details on the curvilinear variant +of this flux vector splitting see Anderson et al. Returns a tuple of the fluxes "minus" (associated with waves going into the negative axis direction) and "plus" (associated with waves going into the @@ -934,11 +1105,16 @@ function signature with argument `which` set to `Val{:minus}()` or `Val{:plus}() - Meng-Sing Liou and Chris J. Steffen, Jr. (1991) High-Order Polynomial Expansions (HOPE) for Flux-Vector Splitting [NASA Technical Memorandum](https://ntrs.nasa.gov/citations/19910016425) +- W. Kyle Anderson, James L. Thomas, and Bram van Leer (1986) + Comparison of Finite Volume Flux Vector Splittings for the Euler Equations + [DOI: 10.2514/3.9465](https://doi.org/10.2514/3.9465) """ -@inline function splitting_vanleer_haenel(u, orientation::Integer, +@inline function splitting_vanleer_haenel(u, orientation_or_normal_direction, equations::CompressibleEulerEquations2D) - fm = splitting_vanleer_haenel(u, Val{:minus}(), orientation, equations) - fp = splitting_vanleer_haenel(u, Val{:plus}(), orientation, equations) + fm = splitting_vanleer_haenel(u, Val{:minus}(), orientation_or_normal_direction, + equations) + fp = splitting_vanleer_haenel(u, Val{:plus}(), orientation_or_normal_direction, + equations) return fm, fp end @@ -1002,11 +1178,57 @@ end return SVector(f1m, f2m, f3m, f4m) end +@inline function splitting_vanleer_haenel(u, ::Val{:plus}, + normal_direction::AbstractVector, + equations::CompressibleEulerEquations2D) + rho, rho_v1, rho_v2, rho_e = u + v1 = rho_v1 / rho + v2 = rho_v2 / rho + p = (equations.gamma - 1) * (rho_e - 0.5 * (rho_v1 * v1 + rho_v2 * v2)) + + a = sqrt(equations.gamma * p / rho) + H = (rho_e + p) / rho + + v_n = normal_direction[1] * v1 + normal_direction[2] * v2 + M = v_n / a + p_plus = 0.5 * (1 + equations.gamma * M) * p + + f1p = 0.25 * rho * a * (M + 1)^2 + f2p = f1p * v1 + normal_direction[1] * p_plus + f3p = f1p * v2 + normal_direction[2] * p_plus + f4p = f1p * H + + return SVector(f1p, f2p, f3p, f4p) +end + +@inline function splitting_vanleer_haenel(u, ::Val{:minus}, + normal_direction::AbstractVector, + equations::CompressibleEulerEquations2D) + rho, rho_v1, rho_v2, rho_e = u + v1 = rho_v1 / rho + v2 = rho_v2 / rho + p = (equations.gamma - 1) * (rho_e - 0.5 * (rho_v1 * v1 + rho_v2 * v2)) + + a = sqrt(equations.gamma * p / rho) + H = (rho_e + p) / rho + + v_n = normal_direction[1] * v1 + normal_direction[2] * v2 + M = v_n / a + p_minus = 0.5 * (1 - equations.gamma * M) * p + + f1m = -0.25 * rho * a * (M - 1)^2 + f2m = f1m * v1 + normal_direction[1] * p_minus + f3m = f1m * v2 + normal_direction[2] * p_minus + f4m = f1m * H + + return SVector(f1m, f2m, f3m, f4m) +end + """ - splitting_lax_friedrichs(u, orientation::Integer, + splitting_lax_friedrichs(u, orientation_or_normal_direction, equations::CompressibleEulerEquations2D) splitting_lax_friedrichs(u, which::Union{Val{:minus}, Val{:plus}} - orientation::Integer, + orientation_or_normal_direction, equations::CompressibleEulerEquations2D) Naive local Lax-Friedrichs style flux splitting of the form `f⁺ = 0.5 (f + λ u)` @@ -1021,10 +1243,12 @@ function signature with argument `which` set to `Val{:minus}()` or `Val{:plus}() !!! warning "Experimental implementation (upwind SBP)" This is an experimental feature and may change in future releases. """ -@inline function splitting_lax_friedrichs(u, orientation::Integer, +@inline function splitting_lax_friedrichs(u, orientation_or_normal_direction, equations::CompressibleEulerEquations2D) - fm = splitting_lax_friedrichs(u, Val{:minus}(), orientation, equations) - fp = splitting_lax_friedrichs(u, Val{:plus}(), orientation, equations) + fm = splitting_lax_friedrichs(u, Val{:minus}(), orientation_or_normal_direction, + equations) + fp = splitting_lax_friedrichs(u, Val{:plus}(), orientation_or_normal_direction, + equations) return fm, fp end @@ -1082,6 +1306,48 @@ end return SVector(f1m, f2m, f3m, f4m) end +@inline function splitting_lax_friedrichs(u, ::Val{:plus}, + normal_direction::AbstractVector, + equations::CompressibleEulerEquations2D) + rho_e = last(u) + rho, v1, v2, p = cons2prim(u, equations) + + a = sqrt(equations.gamma * p / rho) + H = (rho_e + p) / rho + lambda = 0.5 * (sqrt(v1^2 + v2^2) + a) + + v_normal = v1 * normal_direction[1] + v2 * normal_direction[2] + rho_v_normal = rho * v_normal + + f1p = 0.5 * rho_v_normal + lambda * u[1] + f2p = 0.5 * rho_v_normal * v1 + 0.5 * p * normal_direction[1] + lambda * u[2] + f3p = 0.5 * rho_v_normal * v2 + 0.5 * p * normal_direction[2] + lambda * u[3] + f4p = 0.5 * rho_v_normal * H + lambda * u[4] + + return SVector(f1p, f2p, f3p, f4p) +end + +@inline function splitting_lax_friedrichs(u, ::Val{:minus}, + normal_direction::AbstractVector, + equations::CompressibleEulerEquations2D) + rho_e = last(u) + rho, v1, v2, p = cons2prim(u, equations) + + a = sqrt(equations.gamma * p / rho) + H = (rho_e + p) / rho + lambda = 0.5 * (sqrt(v1^2 + v2^2) + a) + + v_normal = v1 * normal_direction[1] + v2 * normal_direction[2] + rho_v_normal = rho * v_normal + + f1m = 0.5 * rho_v_normal - lambda * u[1] + f2m = 0.5 * rho_v_normal * v1 + 0.5 * p * normal_direction[1] - lambda * u[2] + f3m = 0.5 * rho_v_normal * v2 + 0.5 * p * normal_direction[2] - lambda * u[3] + f4m = 0.5 * rho_v_normal * H - lambda * u[4] + + return SVector(f1m, f2m, f3m, f4m) +end + # Calculate maximum wave speed for local Lax-Friedrichs-type dissipation as the # maximum velocity magnitude plus the maximum speed of sound @inline function max_abs_speed_naive(u_ll, u_rr, orientation::Integer, diff --git a/src/equations/numerical_fluxes.jl b/src/equations/numerical_fluxes.jl index 6794c71a32b..e3e798381ae 100644 --- a/src/equations/numerical_fluxes.jl +++ b/src/equations/numerical_fluxes.jl @@ -415,7 +415,8 @@ flux vector splitting. The [`SurfaceIntegralUpwind`](@ref) with a given `splitting` is equivalent to the [`SurfaceIntegralStrongForm`](@ref) with `FluxUpwind(splitting)` -as numerical flux (up to floating point differences). +as numerical flux (up to floating point differences). Note, that +[`SurfaceIntegralUpwind`](@ref) is only available on [`TreeMesh`](@ref). !!! warning "Experimental implementation (upwind SBP)" This is an experimental feature and may change in future releases. @@ -431,5 +432,14 @@ end return fm + fp end +@inline function (numflux::FluxUpwind)(u_ll, u_rr, + normal_direction::AbstractVector, + equations::AbstractEquations{2}) + @unpack splitting = numflux + f_tilde_m = splitting(u_rr, Val{:minus}(), normal_direction, equations) + f_tilde_p = splitting(u_ll, Val{:plus}(), normal_direction, equations) + return f_tilde_m + f_tilde_p +end + Base.show(io::IO, f::FluxUpwind) = print(io, "FluxUpwind(", f.splitting, ")") end # @muladd diff --git a/src/solvers/dgsem_unstructured/dg_2d.jl b/src/solvers/dgsem_unstructured/dg_2d.jl index b12a96c4c31..988e995d6b7 100644 --- a/src/solvers/dgsem_unstructured/dg_2d.jl +++ b/src/solvers/dgsem_unstructured/dg_2d.jl @@ -77,7 +77,7 @@ function rhs!(du, u, t, end # Apply Jacobian from mapping to reference element - # Note! this routine is reused from dg_curved/dg_2d.jl + # Note! this routine is reused from dgsem_structured/dg_2d.jl @trixi_timeit timer() "Jacobian" apply_jacobian!(du, mesh, equations, dg, cache) # Calculate source terms diff --git a/src/solvers/fdsbp_tree/fdsbp_2d.jl b/src/solvers/fdsbp_tree/fdsbp_2d.jl index 09d18cecd75..36afbbc022f 100644 --- a/src/solvers/fdsbp_tree/fdsbp_2d.jl +++ b/src/solvers/fdsbp_tree/fdsbp_2d.jl @@ -19,7 +19,7 @@ function create_cache(mesh::Union{TreeMesh{2}, UnstructuredMesh2D}, equations, return (; f_threaded) end -function create_cache(mesh::TreeMesh{2}, equations, +function create_cache(mesh::Union{TreeMesh{2}, UnstructuredMesh2D}, equations, volume_integral::VolumeIntegralUpwind, dg, uEltype) u_node = SVector{nvariables(equations), uEltype}(ntuple(_ -> zero(uEltype), Val{nvariables(equations)}())) diff --git a/src/solvers/fdsbp_unstructured/containers_2d.jl b/src/solvers/fdsbp_unstructured/containers_2d.jl index 3857c2d8a20..f68b1e00f59 100644 --- a/src/solvers/fdsbp_unstructured/containers_2d.jl +++ b/src/solvers/fdsbp_unstructured/containers_2d.jl @@ -9,7 +9,7 @@ #! format: noindent # initialize all the values in the container of a general FD block (either straight sided or curved) -# OBS! Requires the SBP derivative matrix in order to compute metric terms that are free-stream preserving +# OBS! Requires the SBP derivative matrix in order to compute metric terms. function init_element!(elements, element, basis::AbstractDerivativeOperator, corners_or_surface_curves) calc_node_coordinates!(elements.node_coordinates, element, get_nodes(basis), @@ -29,9 +29,15 @@ function init_element!(elements, element, basis::AbstractDerivativeOperator, return elements end +# Specialization to pass the central differencing matrix from an upwind SBP operator +function calc_metric_terms!(jacobian_matrix, element, + D_SBP::SummationByPartsOperators.UpwindOperators, + node_coordinates) + calc_metric_terms!(jacobian_matrix, element, D_SBP.central, node_coordinates) +end + # construct the metric terms for a FDSBP element "block". Directly use the derivative matrix # applied to the node coordinates. -# TODO: FD; How to make this work for the upwind solver because basis has three available derivative matrices function calc_metric_terms!(jacobian_matrix, element, D_SBP::AbstractDerivativeOperator, node_coordinates) diff --git a/src/solvers/fdsbp_unstructured/fdsbp_2d.jl b/src/solvers/fdsbp_unstructured/fdsbp_2d.jl index b459f4c42cc..c35772cdf18 100644 --- a/src/solvers/fdsbp_unstructured/fdsbp_2d.jl +++ b/src/solvers/fdsbp_unstructured/fdsbp_2d.jl @@ -25,8 +25,6 @@ function create_cache(mesh::UnstructuredMesh2D, equations, dg::FDSBP, RealT, uEl return cache end -# TODO: FD; Upwind versions of surface / volume integral - # 2D volume integral contributions for `VolumeIntegralStrongForm` # OBS! This is the standard (not de-aliased) form of the volume integral. # So it is not provably stable for variable coefficients due to the the metric terms. @@ -86,6 +84,91 @@ end return nothing end +# 2D volume integral contributions for `VolumeIntegralUpwind`. +# Note that the plus / minus notation of the operators does not refer to the +# upwind / downwind directions of the fluxes. +# Instead, the plus / minus refers to the direction of the biasing within +# the finite difference stencils. Thus, the D^- operator acts on the positive +# part of the flux splitting f^+ and the D^+ operator acts on the negative part +# of the flux splitting f^-. +function calc_volume_integral!(du, u, + mesh::UnstructuredMesh2D, + nonconservative_terms::False, equations, + volume_integral::VolumeIntegralUpwind, + dg::FDSBP, cache) + # Assume that + # dg.basis isa SummationByPartsOperators.UpwindOperators + D_minus = dg.basis.minus # Upwind SBP D^- derivative operator + D_plus = dg.basis.plus # Upwind SBP D^+ derivative operator + @unpack f_minus_plus_threaded, f_minus_threaded, f_plus_threaded = cache + @unpack splitting = volume_integral + @unpack contravariant_vectors = cache.elements + + # SBP operators from SummationByPartsOperators.jl implement the basic interface + # of matrix-vector multiplication. Thus, we pass an "array of structures", + # packing all variables per node in an `SVector`. + if nvariables(equations) == 1 + # `reinterpret(reshape, ...)` removes the leading dimension only if more + # than one variable is used. + u_vectors = reshape(reinterpret(SVector{nvariables(equations), eltype(u)}, u), + nnodes(dg), nnodes(dg), nelements(dg, cache)) + du_vectors = reshape(reinterpret(SVector{nvariables(equations), eltype(du)}, + du), + nnodes(dg), nnodes(dg), nelements(dg, cache)) + else + u_vectors = reinterpret(reshape, SVector{nvariables(equations), eltype(u)}, u) + du_vectors = reinterpret(reshape, SVector{nvariables(equations), eltype(du)}, + du) + end + + # Use the tensor product structure to compute the discrete derivatives of + # the fluxes line-by-line and add them to `du` for each element. + @threaded for element in eachelement(dg, cache) + # f_minus_plus_element wraps the storage provided by f_minus_element and + # f_plus_element such that we can use a single assignment below. + # f_minus_element and f_plus_element are updated whenever we update + # `f_minus_plus_element[i, j] = ...` below. + f_minus_plus_element = f_minus_plus_threaded[Threads.threadid()] + f_minus_element = f_minus_threaded[Threads.threadid()] + f_plus_element = f_plus_threaded[Threads.threadid()] + u_element = view(u_vectors, :, :, element) + + # x direction + # We use flux vector splittings in the directions of the contravariant + # basis vectors. Thus, we do not use a broadcasting operation like + # @. f_minus_plus_element = splitting(u_element, 1, equations) + # in the Cartesian case but loop over all nodes. + for j in eachnode(dg), i in eachnode(dg) + # contravariant vectors computed with central D matrix + Ja1 = get_contravariant_vector(1, contravariant_vectors, i, j, element) + f_minus_plus_element[i, j] = splitting(u_element[i, j], Ja1, equations) + end + + for j in eachnode(dg) + mul!(view(du_vectors, :, j, element), D_minus, view(f_plus_element, :, j), + one(eltype(du)), one(eltype(du))) + mul!(view(du_vectors, :, j, element), D_plus, view(f_minus_element, :, j), + one(eltype(du)), one(eltype(du))) + end + + # y direction + for j in eachnode(dg), i in eachnode(dg) + # contravariant vectors computed with central D matrix + Ja2 = get_contravariant_vector(2, contravariant_vectors, i, j, element) + f_minus_plus_element[i, j] = splitting(u_element[i, j], Ja2, equations) + end + + for i in eachnode(dg) + mul!(view(du_vectors, i, :, element), D_minus, view(f_plus_element, i, :), + one(eltype(du)), one(eltype(du))) + mul!(view(du_vectors, i, :, element), D_plus, view(f_minus_element, i, :), + one(eltype(du)), one(eltype(du))) + end + end + + return nothing +end + # Note! The local side numbering for the unstructured quadrilateral element implementation differs # from the structured TreeMesh or StructuredMesh local side numbering: # @@ -114,8 +197,7 @@ function calc_surface_integral!(du, u, mesh::UnstructuredMesh2D, # surface at -x u_node = get_node_vars(u, equations, dg, 1, l, element) # compute internal flux in normal direction on side 4 - outward_direction = get_node_coords(normal_directions, equations, dg, l, 4, - element) + outward_direction = get_surface_normal(normal_directions, l, 4, element) f_node = flux(u_node, outward_direction, equations) f_num = get_node_vars(surface_flux_values, equations, dg, l, 4, element) multiply_add_to_node_vars!(du, inv_weight_left, (f_num - f_node), @@ -124,8 +206,7 @@ function calc_surface_integral!(du, u, mesh::UnstructuredMesh2D, # surface at +x u_node = get_node_vars(u, equations, dg, nnodes(dg), l, element) # compute internal flux in normal direction on side 2 - outward_direction = get_node_coords(normal_directions, equations, dg, l, 2, - element) + outward_direction = get_surface_normal(normal_directions, l, 2, element) f_node = flux(u_node, outward_direction, equations) f_num = get_node_vars(surface_flux_values, equations, dg, l, 2, element) multiply_add_to_node_vars!(du, inv_weight_right, (f_num - f_node), @@ -134,8 +215,7 @@ function calc_surface_integral!(du, u, mesh::UnstructuredMesh2D, # surface at -y u_node = get_node_vars(u, equations, dg, l, 1, element) # compute internal flux in normal direction on side 1 - outward_direction = get_node_coords(normal_directions, equations, dg, l, 1, - element) + outward_direction = get_surface_normal(normal_directions, l, 1, element) f_node = flux(u_node, outward_direction, equations) f_num = get_node_vars(surface_flux_values, equations, dg, l, 1, element) multiply_add_to_node_vars!(du, inv_weight_left, (f_num - f_node), @@ -144,8 +224,7 @@ function calc_surface_integral!(du, u, mesh::UnstructuredMesh2D, # surface at +y u_node = get_node_vars(u, equations, dg, l, nnodes(dg), element) # compute internal flux in normal direction on side 3 - outward_direction = get_node_coords(normal_directions, equations, dg, l, 3, - element) + outward_direction = get_surface_normal(normal_directions, l, 3, element) f_node = flux(u_node, outward_direction, equations) f_num = get_node_vars(surface_flux_values, equations, dg, l, 3, element) multiply_add_to_node_vars!(du, inv_weight_right, (f_num - f_node), diff --git a/test/test_tree_2d_fdsbp.jl b/test/test_tree_2d_fdsbp.jl index c0844ee5dba..d477cab0563 100644 --- a/test/test_tree_2d_fdsbp.jl +++ b/test/test_tree_2d_fdsbp.jl @@ -102,6 +102,32 @@ end end end + @trixi_testset "elixir_euler_convergence.jl with Drikakis-Tsangaris splitting" begin + @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_convergence.jl"), + l2=[ + 1.708838999643608e-6, + 1.7437997854485807e-6, + 1.7437997854741082e-6, + 5.457223460116349e-6, + ], + linf=[ + 9.796504911285808e-6, + 9.614745899888533e-6, + 9.614745899444443e-6, + 4.02610718399643e-5, + ], + tspan=(0.0, 0.1), flux_splitting=splitting_drikakis_tsangaris) + + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end + end + @trixi_testset "elixir_euler_kelvin_helmholtz_instability.jl" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_kelvin_helmholtz_instability.jl"), diff --git a/test/test_unstructured_2d.jl b/test/test_unstructured_2d.jl index 87d677e1623..8a62dcaec3c 100644 --- a/test/test_unstructured_2d.jl +++ b/test/test_unstructured_2d.jl @@ -610,6 +610,76 @@ end @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 end end + +@trixi_testset "FDSBP (upwind): elixir_euler_source_terms_upwind.jl" begin + @test_trixi_include(joinpath(pkgdir(Trixi, "examples", "unstructured_2d_fdsbp"), + "elixir_euler_source_terms_upwind.jl"), + l2=[4.085391175504837e-5, + 7.19179253772227e-5, + 7.191792537723135e-5, + 0.00021775241532855398], + linf=[0.0004054489124620808, + 0.0006164432358217731, + 0.0006164432358186644, + 0.001363103391379461], + tspan=(0.0, 0.05), + atol=1.0e-10) + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end +end + +@trixi_testset "FDSBP (upwind): elixir_euler_source_terms_upwind.jl with LF splitting" begin + @test_trixi_include(joinpath(pkgdir(Trixi, "examples", "unstructured_2d_fdsbp"), + "elixir_euler_source_terms_upwind.jl"), + l2=[3.8300267071890586e-5, + 5.295846741663533e-5, + 5.295846741663526e-5, + 0.00017564759295593478], + linf=[0.00018810716496542312, + 0.0003794187430412599, + 0.0003794187430412599, + 0.0009632958510650269], + tspan=(0.0, 0.025), + flux_splitting=splitting_lax_friedrichs, + atol=1.0e-10) + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end +end + +@trixi_testset "FDSBP (upwind): elixir_euler_free_stream_upwind.jl" begin + @test_trixi_include(joinpath(pkgdir(Trixi, "examples", "unstructured_2d_fdsbp"), + "elixir_euler_free_stream_upwind.jl"), + l2=[3.2114065566681054e-14, + 2.132488788134846e-14, + 2.106144937311659e-14, + 8.609642264224197e-13], + linf=[3.354871935812298e-11, + 7.006478730531285e-12, + 1.148153794261475e-11, + 9.041265514042607e-10], + tspan=(0.0, 0.05), + atol=1.0e-10) + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end +end end # Clean up afterwards: delete Trixi.jl output directory From 253c358243ed2a8b6f63c422b53cf09a68188f68 Mon Sep 17 00:00:00 2001 From: Hendrik Ranocha Date: Wed, 6 Mar 2024 13:25:19 +0100 Subject: [PATCH 48/63] set version to v0.7.1 --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 800c7b4c0fa..53b859a422f 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "Trixi" uuid = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb" authors = ["Michael Schlottke-Lakemper ", "Gregor Gassner ", "Hendrik Ranocha ", "Andrew R. Winters ", "Jesse Chan "] -version = "0.7.1-pre" +version = "0.7.1" [deps] CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2" From ca082c2eb1273611cf38e80c6d2dab04e8f8177f Mon Sep 17 00:00:00 2001 From: Hendrik Ranocha Date: Wed, 6 Mar 2024 13:25:37 +0100 Subject: [PATCH 49/63] set development version to v0.7.2-pre --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 53b859a422f..e8eb7c788ce 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "Trixi" uuid = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb" authors = ["Michael Schlottke-Lakemper ", "Gregor Gassner ", "Hendrik Ranocha ", "Andrew R. Winters ", "Jesse Chan "] -version = "0.7.1" +version = "0.7.2-pre" [deps] CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2" From 4bf61a0fd3abb21b457ea9d9ee2c19c835d018c3 Mon Sep 17 00:00:00 2001 From: Hendrik Ranocha Date: Wed, 6 Mar 2024 14:25:25 +0100 Subject: [PATCH 50/63] force new FFMPEG.jl version for tests (#1858) --- test/Project.toml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/Project.toml b/test/Project.toml index a376c2805ea..1a042dab44f 100644 --- a/test/Project.toml +++ b/test/Project.toml @@ -2,6 +2,7 @@ Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595" CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0" Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6" +FFMPEG = "c87230d0-a227-11e9-1b43-d7ebe4e7570a" ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210" LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e" MPI = "da04e1cc-30fd-572f-bb4f-1f8673147195" @@ -15,6 +16,7 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" Aqua = "0.8" CairoMakie = "0.10" Downloads = "1" +FFMPEG = "0.4" ForwardDiff = "0.10.24" LinearAlgebra = "1" MPI = "0.20" From 3bed8285ca2bb3857050bde4fd1408d151cb760d Mon Sep 17 00:00:00 2001 From: Daniel Doehring Date: Thu, 7 Mar 2024 10:41:56 +0100 Subject: [PATCH 51/63] Check BCs for periodicity for periodic Tree & Structured meshes (#1860) * Check BCs for periodicity for periodic meshes * default case for periodic bcs * fmt * specialize * error ant fmt * isperiodic TreeMesh * avoid if * shorten * shorten * Make meshes non-periodic * fix rti * shorten dispatch --------- Co-authored-by: Hendrik Ranocha --- .../elixir_advection_coupled.jl | 12 ++-- ...lixir_euler_rayleigh_taylor_instability.jl | 2 +- .../elixir_euler_warm_bubble.jl | 3 +- src/meshes/tree_mesh.jl | 3 + .../semidiscretization_hyperbolic.jl | 70 +++++++++++++++++++ ...semidiscretization_hyperbolic_parabolic.jl | 2 + 6 files changed, 86 insertions(+), 6 deletions(-) diff --git a/examples/structured_2d_dgsem/elixir_advection_coupled.jl b/examples/structured_2d_dgsem/elixir_advection_coupled.jl index 43b68f21b03..0002bb8d374 100644 --- a/examples/structured_2d_dgsem/elixir_advection_coupled.jl +++ b/examples/structured_2d_dgsem/elixir_advection_coupled.jl @@ -53,7 +53,8 @@ cells_per_dimension = (8, 8) coordinates_min1 = (-1.0, 0.0) # minimum coordinates (min(x), min(y)) coordinates_max1 = (0.0, 1.0) # maximum coordinates (max(x), max(y)) -mesh1 = StructuredMesh(cells_per_dimension, coordinates_min1, coordinates_max1) +mesh1 = StructuredMesh(cells_per_dimension, coordinates_min1, coordinates_max1, + periodicity = false) # Define the coupling functions coupling_function12 = (x, u, equations_other, equations_own) -> u @@ -84,7 +85,8 @@ semi1 = SemidiscretizationHyperbolic(mesh1, equations, initial_condition_converg coordinates_min2 = (0.0, 0.0) # minimum coordinates (min(x), min(y)) coordinates_max2 = (1.0, 1.0) # maximum coordinates (max(x), max(y)) -mesh2 = StructuredMesh(cells_per_dimension, coordinates_min2, coordinates_max2) +mesh2 = StructuredMesh(cells_per_dimension, coordinates_min2, coordinates_max2, + periodicity = false) # Define the coupling functions coupling_function21 = (x, u, equations_other, equations_own) -> u @@ -115,7 +117,8 @@ semi2 = SemidiscretizationHyperbolic(mesh2, equations, initial_condition_converg coordinates_min3 = (-1.0, -1.0) # minimum coordinates (min(x), min(y)) coordinates_max3 = (0.0, 0.0) # maximum coordinates (max(x), max(y)) -mesh3 = StructuredMesh(cells_per_dimension, coordinates_min3, coordinates_max3) +mesh3 = StructuredMesh(cells_per_dimension, coordinates_min3, coordinates_max3, + periodicity = false) # Define the coupling functions coupling_function34 = (x, u, equations_other, equations_own) -> u @@ -146,7 +149,8 @@ semi3 = SemidiscretizationHyperbolic(mesh3, equations, initial_condition_converg coordinates_min4 = (0.0, -1.0) # minimum coordinates (min(x), min(y)) coordinates_max4 = (1.0, 0.0) # maximum coordinates (max(x), max(y)) -mesh4 = StructuredMesh(cells_per_dimension, coordinates_min4, coordinates_max4) +mesh4 = StructuredMesh(cells_per_dimension, coordinates_min4, coordinates_max4, + periodicity = false) # Define the coupling functions coupling_function43 = (x, u, equations_other, equations_own) -> u diff --git a/examples/structured_2d_dgsem/elixir_euler_rayleigh_taylor_instability.jl b/examples/structured_2d_dgsem/elixir_euler_rayleigh_taylor_instability.jl index 6c254e8bd8b..dd0cc339b20 100644 --- a/examples/structured_2d_dgsem/elixir_euler_rayleigh_taylor_instability.jl +++ b/examples/structured_2d_dgsem/elixir_euler_rayleigh_taylor_instability.jl @@ -69,7 +69,7 @@ mapping(xi, eta) = SVector(0.25 * 0.5 * (1.0 + xi), 0.5 * (1.0 + eta)) num_elements_per_dimension = 32 cells_per_dimension = (num_elements_per_dimension, num_elements_per_dimension * 4) -mesh = StructuredMesh(cells_per_dimension, mapping) +mesh = StructuredMesh(cells_per_dimension, mapping, periodicity = false) initial_condition = initial_condition_rayleigh_taylor_instability boundary_conditions = (x_neg = boundary_condition_slip_wall, diff --git a/examples/structured_2d_dgsem/elixir_euler_warm_bubble.jl b/examples/structured_2d_dgsem/elixir_euler_warm_bubble.jl index 05c09d57530..38b9386e94e 100644 --- a/examples/structured_2d_dgsem/elixir_euler_warm_bubble.jl +++ b/examples/structured_2d_dgsem/elixir_euler_warm_bubble.jl @@ -100,7 +100,8 @@ coordinates_min = (0.0, 0.0) coordinates_max = (20_000.0, 10_000.0) cells_per_dimension = (64, 32) -mesh = StructuredMesh(cells_per_dimension, coordinates_min, coordinates_max) +mesh = StructuredMesh(cells_per_dimension, coordinates_min, coordinates_max, + periodicity = (true, false)) semi = SemidiscretizationHyperbolic(mesh, equations, warm_bubble_setup, solver, source_terms = warm_bubble_setup, diff --git a/src/meshes/tree_mesh.jl b/src/meshes/tree_mesh.jl index 05699d17d16..1092fc54cc1 100644 --- a/src/meshes/tree_mesh.jl +++ b/src/meshes/tree_mesh.jl @@ -228,5 +228,8 @@ function total_volume(mesh::TreeMesh) return mesh.tree.length_level_0^ndims(mesh) end +isperiodic(mesh::TreeMesh) = isperiodic(mesh.tree) +isperiodic(mesh::TreeMesh, dimension) = isperiodic(mesh.tree, dimension) + include("parallel_tree_mesh.jl") end # @muladd diff --git a/src/semidiscretization/semidiscretization_hyperbolic.jl b/src/semidiscretization/semidiscretization_hyperbolic.jl index 7ebd758de37..f61378a7dca 100644 --- a/src/semidiscretization/semidiscretization_hyperbolic.jl +++ b/src/semidiscretization/semidiscretization_hyperbolic.jl @@ -72,6 +72,8 @@ function SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver _boundary_conditions = digest_boundary_conditions(boundary_conditions, mesh, solver, cache) + check_periodicity_mesh_boundary_conditions(mesh, _boundary_conditions) + SemidiscretizationHyperbolic{typeof(mesh), typeof(equations), typeof(initial_condition), typeof(_boundary_conditions), typeof(source_terms), @@ -210,6 +212,74 @@ function digest_boundary_conditions(boundary_conditions::AbstractArray, mesh, so throw(ArgumentError("Please use a (named) tuple instead of an (abstract) array to supply multiple boundary conditions (to improve performance).")) end +# No checks for these meshes yet available +function check_periodicity_mesh_boundary_conditions(mesh::Union{P4estMesh, + UnstructuredMesh2D, + T8codeMesh, + DGMultiMesh}, + boundary_conditions) +end + +# No actions needed for periodic boundary conditions +function check_periodicity_mesh_boundary_conditions(mesh::Union{TreeMesh, + StructuredMesh}, + boundary_conditions::BoundaryConditionPeriodic) +end + +function check_periodicity_mesh_boundary_conditions_x(mesh, x_neg, x_pos) + if isperiodic(mesh, 1) && + (x_neg != BoundaryConditionPeriodic() || + x_pos != BoundaryConditionPeriodic()) + @error "For periodic mesh non-periodic boundary conditions in x-direction are supplied." + end +end + +function check_periodicity_mesh_boundary_conditions_y(mesh, y_neg, y_pos) + if isperiodic(mesh, 2) && + (y_neg != BoundaryConditionPeriodic() || + y_pos != BoundaryConditionPeriodic()) + @error "For periodic mesh non-periodic boundary conditions in y-direction are supplied." + end +end + +function check_periodicity_mesh_boundary_conditions_z(mesh, z_neg, z_pos) + if isperiodic(mesh, 3) && + (z_neg != BoundaryConditionPeriodic() || + z_pos != BoundaryConditionPeriodic()) + @error "For periodic mesh non-periodic boundary conditions in z-direction are supplied." + end +end + +function check_periodicity_mesh_boundary_conditions(mesh::Union{TreeMesh{1}, + StructuredMesh{1}}, + boundary_conditions::Union{NamedTuple, + Tuple}) + check_periodicity_mesh_boundary_conditions_x(mesh, boundary_conditions[1], + boundary_conditions[2]) +end + +function check_periodicity_mesh_boundary_conditions(mesh::Union{TreeMesh{2}, + StructuredMesh{2}}, + boundary_conditions::Union{NamedTuple, + Tuple}) + check_periodicity_mesh_boundary_conditions_x(mesh, boundary_conditions[1], + boundary_conditions[2]) + check_periodicity_mesh_boundary_conditions_y(mesh, boundary_conditions[3], + boundary_conditions[4]) +end + +function check_periodicity_mesh_boundary_conditions(mesh::Union{TreeMesh{3}, + StructuredMesh{3}}, + boundary_conditions::Union{NamedTuple, + Tuple}) + check_periodicity_mesh_boundary_conditions_x(mesh, boundary_conditions[1], + boundary_conditions[2]) + check_periodicity_mesh_boundary_conditions_y(mesh, boundary_conditions[3], + boundary_conditions[4]) + check_periodicity_mesh_boundary_conditions_z(mesh, boundary_conditions[5], + boundary_conditions[6]) +end + function Base.show(io::IO, semi::SemidiscretizationHyperbolic) @nospecialize semi # reduce precompilation time diff --git a/src/semidiscretization/semidiscretization_hyperbolic_parabolic.jl b/src/semidiscretization/semidiscretization_hyperbolic_parabolic.jl index 0f44941390a..57724374acb 100644 --- a/src/semidiscretization/semidiscretization_hyperbolic_parabolic.jl +++ b/src/semidiscretization/semidiscretization_hyperbolic_parabolic.jl @@ -136,6 +136,8 @@ function SemidiscretizationHyperbolicParabolic(mesh, equations, equations_parabo _boundary_conditions_parabolic = digest_boundary_conditions(boundary_conditions_parabolic, mesh, solver, cache) + check_periodicity_mesh_boundary_conditions(mesh, _boundary_conditions) + cache_parabolic = (; create_cache_parabolic(mesh, equations, equations_parabolic, solver, solver_parabolic, RealT, From b8b34ea21cfa22f93daa131c7ef77d8ed8f3f789 Mon Sep 17 00:00:00 2001 From: Hendrik Ranocha Date: Thu, 7 Mar 2024 10:45:17 +0100 Subject: [PATCH 52/63] set version to v0.7.2 --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index e8eb7c788ce..9a6e8e0d9a2 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "Trixi" uuid = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb" authors = ["Michael Schlottke-Lakemper ", "Gregor Gassner ", "Hendrik Ranocha ", "Andrew R. Winters ", "Jesse Chan "] -version = "0.7.2-pre" +version = "0.7.2" [deps] CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2" From b6bc7c8cae92cf6877fca90c5ef100771a7781a8 Mon Sep 17 00:00:00 2001 From: Hendrik Ranocha Date: Thu, 7 Mar 2024 10:45:30 +0100 Subject: [PATCH 53/63] set development version to v0.7.3-pre --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 9a6e8e0d9a2..6b44af4a3fa 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "Trixi" uuid = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb" authors = ["Michael Schlottke-Lakemper ", "Gregor Gassner ", "Hendrik Ranocha ", "Andrew R. Winters ", "Jesse Chan "] -version = "0.7.2" +version = "0.7.3-pre" [deps] CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2" From b11bc10d8ac68798ae2e53f9db3d5c4f824af5fa Mon Sep 17 00:00:00 2001 From: Benedict <135045760+bgeihe@users.noreply.github.com> Date: Thu, 7 Mar 2024 13:04:19 +0100 Subject: [PATCH 54/63] add warning (#1863) --- src/solvers/dgsem/basis_lobatto_legendre.jl | 1 + 1 file changed, 1 insertion(+) diff --git a/src/solvers/dgsem/basis_lobatto_legendre.jl b/src/solvers/dgsem/basis_lobatto_legendre.jl index 6a92fd1c066..9e21b88dfa1 100644 --- a/src/solvers/dgsem/basis_lobatto_legendre.jl +++ b/src/solvers/dgsem/basis_lobatto_legendre.jl @@ -12,6 +12,7 @@ Create a nodal Lobatto-Legendre basis for polynomials of degree `polydeg`. For the special case `polydeg=0` the DG method reduces to a finite volume method. Therefore, this function sets the center point of the cell as single node. +This exceptional case is currently only supported for TreeMesh! """ struct LobattoLegendreBasis{RealT <: Real, NNODES, VectorT <: AbstractVector{RealT}, From c4bf3df8a4d4e3920b0f774960d129a4af6ee287 Mon Sep 17 00:00:00 2001 From: Benedict <135045760+bgeihe@users.noreply.github.com> Date: Thu, 7 Mar 2024 13:06:20 +0100 Subject: [PATCH 55/63] Update parallelization.md (#1864) MPI support in T8code came with #1803 --- docs/src/parallelization.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/src/parallelization.md b/docs/src/parallelization.md index f599eb5fafe..2114f30fb87 100644 --- a/docs/src/parallelization.md +++ b/docs/src/parallelization.md @@ -69,8 +69,7 @@ installations. Follow the steps described [here](https://github.com/DLR-AMR/T8co [here](https://github.com/trixi-framework/P4est.jl/blob/main/README.md#installation) for the configuration. The paths that point to `libp4est.so` (and potentially to `libsc.so`) need to be the same for P4est.jl and T8code.jl. This could, e.g., be `libp4est.so` that usually can be found -in `lib/` or `local/lib/` in the installation directory of `t8code`. Note that the `T8codeMesh`, however, -does not support MPI yet. +in `lib/` or `local/lib/` in the installation directory of `t8code`. The preferences for [HDF5.jl](https://github.com/JuliaIO/HDF5.jl) always need to be set, even if you do not want to use `HDF5` from Trixi.jl, see also [issue #1079 in HDF5.jl](https://github.com/JuliaIO/HDF5.jl/issues/1079). To set the preferences for HDF5.jl, follow the instructions described From 1ca37cf2271806d203a832d3d99bfa2c14d3226f Mon Sep 17 00:00:00 2001 From: Benedict <135045760+bgeihe@users.noreply.github.com> Date: Fri, 8 Mar 2024 07:48:24 +0100 Subject: [PATCH 56/63] set capacity also when using MPI (#1862) Co-authored-by: Hendrik Ranocha --- src/meshes/mesh_io.jl | 1 + 1 file changed, 1 insertion(+) diff --git a/src/meshes/mesh_io.jl b/src/meshes/mesh_io.jl index 337e33e6969..28e6efa8c57 100644 --- a/src/meshes/mesh_io.jl +++ b/src/meshes/mesh_io.jl @@ -74,6 +74,7 @@ function save_mesh_file(mesh::TreeMesh, output_directory, timestep, attributes(file)["mesh_type"] = get_name(mesh) attributes(file)["ndims"] = ndims(mesh) attributes(file)["n_cells"] = n_cells + attributes(file)["capacity"] = mesh.tree.capacity attributes(file)["n_leaf_cells"] = count_leaf_cells(mesh.tree) attributes(file)["minimum_level"] = minimum_level(mesh.tree) attributes(file)["maximum_level"] = maximum_level(mesh.tree) From f235619a49dbc8bd7d84a77269558a64b21a155f Mon Sep 17 00:00:00 2001 From: Daniel Doehring Date: Fri, 8 Mar 2024 12:20:45 +0100 Subject: [PATCH 57/63] Mention hyphen/dash caveat for boundary symbols (#1866) * Mention hyphen/dash caveat for boundary symbols * typo * elaborate --- docs/src/meshes/p4est_mesh.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/docs/src/meshes/p4est_mesh.md b/docs/src/meshes/p4est_mesh.md index 3b35ffcad6f..a14551b3f46 100644 --- a/docs/src/meshes/p4est_mesh.md +++ b/docs/src/meshes/p4est_mesh.md @@ -256,6 +256,8 @@ By doing so, only nodesets with a label present in `boundary_symbols` are treate Other nodesets that could be used for diagnostics are not treated as external boundaries. Note that there is a leading colon `:` compared to the label in the `.inp` mesh file. This is required to turn the label into a [`Symbol`](https://docs.julialang.org/en/v1/manual/metaprogramming/#Symbols). +**Important**: In Julia, a symbol _cannot_ contain a hyphen/dash `-`, i.e., `:BC-1` is _not_ a valid symbol. +Keep this in mind when importing boundaries, you might have to convert hyphens/dashes `-` to underscores `_` in the `.inp` mesh file, i.e., `BC_1` instead of `BC-1`. A 2D example for this mesh, which is read-in for an unstructured mesh file created with `gmsh`, is presented in `examples/p4est_2d_dgsem/elixir_euler_NACA6412airfoil_mach2.jl`. From bd060b6d140b2c4f8f717a89899e867593e141c1 Mon Sep 17 00:00:00 2001 From: Andrew Winters Date: Thu, 14 Mar 2024 15:49:16 +0100 Subject: [PATCH 58/63] Add functionality for `TimeSeries` callback on `UnstructuredMesh2D` (#1855) * add functionality for TimeSeries callback on UnstructuredMesh2D * Update src/callbacks_step/time_series_dg.jl Co-authored-by: Hendrik Ranocha * Apply suggestions from code review Co-authored-by: Daniel Doehring * add strategy to correctly locate a gauge point within a curvilinear element * add sanity check that the Newton solution is correct * run formatter * implement a more general approach that also works on curved element without issue * run formatter * forgot to format the examples * Apply suggestions from code review Co-authored-by: Hendrik Ranocha Co-authored-by: Daniel Doehring * working version of the element finding routine * run formatter * add new elixir for the time series callback * add additional test for the time series callback on an unstructured mesh * add appropriate test * update docstring * add comment about the barycenter computation * add simplifications and comments from code review * adjust variable name to avoid ugly formatting * Apply suggestions from code review Co-authored-by: Hendrik Ranocha * fix variable name * remove Experimental status from the TimeSeriesCallback * move new TimeSeries test into the unit testing * add output_directory creation if not already done. Necessary if this callback is used without the SaveSolution callback * formatting * update test mesh to have one straight-sided element to trigger inverse bi-linear interpolation * update test values * add news item * forgot to update all new test values on the new mesh * update tests and use coverage override to avoid redundancy --------- Co-authored-by: Hendrik Ranocha Co-authored-by: Daniel Doehring --- NEWS.md | 12 +- .../elixir_euler_time_series.jl | 115 ++++++++ src/callbacks_step/time_series.jl | 9 +- src/callbacks_step/time_series_dg.jl | 6 +- src/callbacks_step/time_series_dg2d.jl | 279 +++++++++++++++++- test/test_unit.jl | 1 + test/test_unstructured_2d.jl | 33 +++ 7 files changed, 443 insertions(+), 12 deletions(-) create mode 100644 examples/unstructured_2d_dgsem/elixir_euler_time_series.jl diff --git a/NEWS.md b/NEWS.md index d70504d8c85..5b08d51ab89 100644 --- a/NEWS.md +++ b/NEWS.md @@ -4,13 +4,19 @@ Trixi.jl follows the interpretation of [semantic versioning (semver)](https://ju used in the Julia ecosystem. Notable changes will be documented in this file for human readability. +## Changes in the v0.7 lifecycle + +#### Added +- Implementation of `TimeSeriesCallback` for curvilinear meshes on `UnstructuredMesh2D`. + + ## Changes when updating to v0.7 from v0.6.x #### Added #### Changed -- The default wave speed estimate used within `flux_hll` is now `min_max_speed_davis` +- The default wave speed estimate used within `flux_hll` is now `min_max_speed_davis` instead of `min_max_speed_naive`. #### Deprecated @@ -26,7 +32,7 @@ for human readability. #### Added - AMR for hyperbolic-parabolic equations on 3D `P4estMesh` - `flux_hllc` on non-cartesian meshes for `CompressibleEulerEquations{2,3}D` -- Different boundary conditions for quad/hex meshes in Abaqus format, even if not generated by HOHQMesh, +- Different boundary conditions for quad/hex meshes in Abaqus format, even if not generated by HOHQMesh, can now be digested by Trixi in 2D and 3D. - Subcell (positivity) limiting support for nonlinear variables in 2D for `TreeMesh` - Added Lighthill-Whitham-Richards (LWR) traffic model @@ -40,7 +46,7 @@ for human readability. #### Changed - The wave speed estimates for `flux_hll`, `FluxHLL()` are now consistent across equations. - In particular, the functions `min_max_speed_naive`, `min_max_speed_einfeldt` are now + In particular, the functions `min_max_speed_naive`, `min_max_speed_einfeldt` are now conceptually identical across equations. Users, who have been using `flux_hll` for MHD have now to use `flux_hlle` in order to use the Einfeldt wave speed estimate. diff --git a/examples/unstructured_2d_dgsem/elixir_euler_time_series.jl b/examples/unstructured_2d_dgsem/elixir_euler_time_series.jl new file mode 100644 index 00000000000..13233cdadbc --- /dev/null +++ b/examples/unstructured_2d_dgsem/elixir_euler_time_series.jl @@ -0,0 +1,115 @@ +# An elixir that has an alternative convergence test that uses +# the `TimeSeriesCallback` on several gauge points. Many of the +# gauge points are selected as "stress tests" for the element +# identification, e.g., a gauge point that lies on an +# element corner of a curvilinear mesh + +using OrdinaryDiffEq +using Trixi + +############################################################################### +# semidiscretization of the compressible Euler equations + +equations = CompressibleEulerEquations2D(1.4) + +# Modify the manufactured solution test to use `L = sqrt(2)` +# in the initial condition and source terms +function initial_condition_convergence_shifted(x, t, + equations::CompressibleEulerEquations2D) + c = 2 + A = 0.1 + L = sqrt(2) + f = 1 / L + ω = 2 * pi * f + ini = c + A * sin(ω * (x[1] + x[2] - t)) + + rho = ini + rho_v1 = ini + rho_v2 = ini + rho_e = ini^2 + + return SVector(rho, rho_v1, rho_v2, rho_e) +end + +@inline function source_terms_convergence_shifted(u, x, t, + equations::CompressibleEulerEquations2D) + # Same settings as in `initial_condition` + c = 2 + A = 0.1 + L = sqrt(2) + f = 1 / L + ω = 2 * pi * f + γ = equations.gamma + + x1, x2 = x + si, co = sincos(ω * (x1 + x2 - t)) + rho = c + A * si + rho_x = ω * A * co + # Note that d/dt rho = -d/dx rho = -d/dy rho. + + tmp = (2 * rho - 1) * (γ - 1) + + du1 = rho_x + du2 = rho_x * (1 + tmp) + du3 = du2 + du4 = 2 * rho_x * (rho + tmp) + + return SVector(du1, du2, du3, du4) +end + +initial_condition = initial_condition_convergence_shifted + +source_term = source_terms_convergence_shifted + +############################################################################### +# Get the DG approximation space + +solver = DGSEM(polydeg = 6, surface_flux = flux_lax_friedrichs) + +############################################################################### +# Get the curved quad mesh from a file (downloads the file if not available locally) + +mesh_file = Trixi.download("https://gist.githubusercontent.com/andrewwinters5000/b434e724e3972a9c4ee48d58c80cdcdb/raw/55c916cd8c0294a2d4a836e960dac7247b7c8ccf/mesh_multiple_flips.mesh", + joinpath(@__DIR__, "mesh_multiple_flips.mesh")) + +mesh = UnstructuredMesh2D(mesh_file, periodicity = true) + +############################################################################### +# create the semi discretization object + +semi = SemidiscretizationHyperbolic(mesh, equations, initial_condition, solver, + source_terms = source_term) + +############################################################################### +# ODE solvers, callbacks etc. + +tspan = (0.0, 1.0) +ode = semidiscretize(semi, tspan) + +summary_callback = SummaryCallback() + +analysis_interval = 1000 +analysis_callback = AnalysisCallback(semi, interval = analysis_interval) + +alive_callback = AliveCallback(analysis_interval = analysis_interval) + +time_series = TimeSeriesCallback(semi, + [(0.75, 0.7), (1.23, 0.302), (0.8, 1.0), + (0.353553390593274, 0.353553390593274), + (0.505, 1.125), (1.37, 0.89), (0.349, 0.7153), + (0.883883476483184, 0.406586401289607), + (sqrt(2), sqrt(2))]; + interval = 10) + +callbacks = CallbackSet(summary_callback, + analysis_callback, + time_series, + alive_callback) + +############################################################################### +# run the simulation + +sol = solve(ode, RDPK3SpFSAL49(); abstol = 1.0e-6, reltol = 1.0e-6, + ode_default_options()..., callback = callbacks); + +summary_callback() # print the timer summary diff --git a/src/callbacks_step/time_series.jl b/src/callbacks_step/time_series.jl index 7baa6b9c5a1..f6d76f0fb15 100644 --- a/src/callbacks_step/time_series.jl +++ b/src/callbacks_step/time_series.jl @@ -23,8 +23,8 @@ After the last time step, the results are stored in an HDF5 file `filename` in d The real data type `RealT` and data type for solution variables `uEltype` default to the respective types used in the solver and the cache. -!!! warning "Experimental implementation" - This is an experimental feature and may change in future releases. +Currently this callback is only implemented for [`TreeMesh`](@ref) in 2D +and [`UnstructuredMesh2D`](@ref). """ mutable struct TimeSeriesCallback{RealT <: Real, uEltype <: Real, SolutionVariables, VariableNames, Cache} @@ -96,6 +96,11 @@ function TimeSeriesCallback(mesh, equations, solver, cache, point_coordinates; throw(ArgumentError("`point_coordinates` must be a matrix of size n_points × ndims")) end + # create the output folder if it does not exist already + if mpi_isroot() && !isdir(output_directory) + mkpath(output_directory) + end + # Transpose point_coordinates to our usual format [ndims, n_points] # Note: They are accepted in a different format to allow direct input from `readdlm` point_coordinates_ = permutedims(point_coordinates) diff --git a/src/callbacks_step/time_series_dg.jl b/src/callbacks_step/time_series_dg.jl index 1b63979d579..ae394afbbfd 100644 --- a/src/callbacks_step/time_series_dg.jl +++ b/src/callbacks_step/time_series_dg.jl @@ -5,8 +5,10 @@ @muladd begin #! format: noindent -# Store time series file for a TreeMesh with a DG solver -function save_time_series_file(time_series_callback, mesh::TreeMesh, equations, dg::DG) +# Store time series file for a DG solver +function save_time_series_file(time_series_callback, + mesh::Union{TreeMesh, UnstructuredMesh2D}, + equations, dg::DG) @unpack (interval, solution_variables, variable_names, output_directory, filename, point_coordinates, point_data, time, step, time_series_cache) = time_series_callback diff --git a/src/callbacks_step/time_series_dg2d.jl b/src/callbacks_step/time_series_dg2d.jl index c15945d6e16..ad7c6851c80 100644 --- a/src/callbacks_step/time_series_dg2d.jl +++ b/src/callbacks_step/time_series_dg2d.jl @@ -6,7 +6,9 @@ #! format: noindent # Creates cache for time series callback -function create_cache_time_series(point_coordinates, mesh::TreeMesh{2}, dg, cache) +function create_cache_time_series(point_coordinates, + mesh::Union{TreeMesh{2}, UnstructuredMesh2D}, + dg, cache) # Determine element ids for point coordinates element_ids = get_elements_by_coordinates(point_coordinates, mesh, dg, cache) @@ -68,6 +70,144 @@ function get_elements_by_coordinates!(element_ids, coordinates, mesh::TreeMesh, return element_ids end +# Elements on an `UnstructuredMesh2D` are possibly curved. Assume that each +# element is convex, i.e., all interior angles are less than 180 degrees. +# This routine computes the shortest distance from a given point to each element +# surface in the mesh. These distances then indicate possible candidate elements. +# From these candidates we (essentially) apply a ray casting strategy and identify +# the element in which the point lies by comparing the ray formed by the point to +# the nearest boundary to the rays cast by the candidate element barycenters to the +# boundary. If these rays point in the same direction, then we have identified the +# desired element location. +function get_elements_by_coordinates!(element_ids, coordinates, + mesh::UnstructuredMesh2D, + dg, cache) + if length(element_ids) != size(coordinates, 2) + throw(DimensionMismatch("storage length for element ids does not match the number of coordinates")) + end + + # Reset element ids - 0 indicates "not (yet) found" + element_ids .= 0 + + # Compute and save the barycentric coordinate on each element + bary_centers = zeros(eltype(mesh.corners), 2, mesh.n_elements) + calc_bary_centers!(bary_centers, dg, cache) + + # Iterate over coordinates + distances = zeros(eltype(mesh.corners), mesh.n_elements) + indices = zeros(Int, mesh.n_elements, 2) + for index in 1:length(element_ids) + # Grab the current point for which the element needs found + point = SVector(coordinates[1, index], + coordinates[2, index]) + + # Compute the minimum distance between the `point` and all the element surfaces + # saved into `distances`. The point in `node_coordinates` that gives said minimum + # distance on each element is saved in `indices` + distances, indices = calc_minimum_surface_distance(point, + cache.elements.node_coordinates, + dg, mesh) + + # Get the candidate elements where the `point` might live + candidates = findall(abs.(minimum(distances) .- distances) .< + 500 * eps(eltype(point))) + + # The minimal surface point is on a boundary so it plays no role which candidate + # we use to grab it. So just use the first one + surface_point = SVector(cache.elements.node_coordinates[1, + indices[candidates[1], + 1], + indices[candidates[1], + 2], + candidates[1]], + cache.elements.node_coordinates[2, + indices[candidates[1], + 1], + indices[candidates[1], + 2], + candidates[1]]) + + # Compute the vector pointing from the current `point` toward the surface + P = surface_point - point + + # If the vector `P` is the zero vector then this `point` is at an element corner or + # on a surface. In this case the choice of a candidate element is ambiguous and + # we just use the first candidate. However, solutions might differ at discontinuous + # interfaces such that this choice may influence the result. + if sum(P .* P) < 500 * eps(eltype(point)) + element_ids[index] = candidates[1] + continue + end + + # Loop through all the element candidates until we find a vector from the barycenter + # to the surface that points in the same direction as the current `point` vector. + # This then gives us the correct element. + for element in 1:length(candidates) + bary_center = SVector(bary_centers[1, candidates[element]], + bary_centers[2, candidates[element]]) + # Vector pointing from the barycenter toward the minimal `surface_point` + B = surface_point - bary_center + if sum(P .* B) > zero(eltype(bary_center)) + element_ids[index] = candidates[element] + break + end + end + end + + return element_ids +end + +# Use the available `node_coordinates` on each element to compute and save the barycenter. +# In essence, the barycenter is like an average where all the x and y node coordinates are +# summed and then we divide by the total number of degrees of freedom on the element, i.e., +# the value of `n^2` in two spatial dimensions. +@inline function calc_bary_centers!(bary_centers, dg, cache) + n = nnodes(dg) + @views for element in eachelement(dg, cache) + bary_centers[1, element] = sum(cache.elements.node_coordinates[1, :, :, + element]) / n^2 + bary_centers[2, element] = sum(cache.elements.node_coordinates[2, :, :, + element]) / n^2 + end + return nothing +end + +# Compute the shortest distance from a `point` to the surface of each element +# using the available `node_coordinates`. Also return the index pair of this +# minimum surface point location. We compute and store in `min_distance` +# the squared norm to avoid computing computationally more expensive square roots. +# Note! Could be made more accurate if the `node_coordinates` were super-sampled +# and reinterpolated onto a higher polynomial degree before this computation. +function calc_minimum_surface_distance(point, node_coordinates, + dg, mesh::UnstructuredMesh2D) + n = nnodes(dg) + min_distance2 = Inf * ones(eltype(mesh.corners), length(mesh)) + indices = zeros(Int, length(mesh), 2) + for k in 1:length(mesh) + # used to ensure that only boundary points are used + on_surface = MVector(false, false) + for j in 1:n + on_surface[2] = (j == 1) || (j == n) + for i in 1:n + on_surface[1] = (i == 1) || (i == n) + if !any(on_surface) + continue + end + node = SVector(node_coordinates[1, i, j, k], + node_coordinates[2, i, j, k]) + distance2 = sum(abs2, node - point) + if distance2 < min_distance2[k] + min_distance2[k] = distance2 + indices[k, 1] = i + indices[k, 2] = j + end + end + end + end + + return min_distance2, indices +end + function get_elements_by_coordinates(coordinates, mesh, dg, cache) element_ids = Vector{Int}(undef, size(coordinates, 2)) get_elements_by_coordinates!(element_ids, coordinates, mesh, dg, cache) @@ -106,8 +246,137 @@ function calc_interpolating_polynomials!(interpolating_polynomials, coordinates, return interpolating_polynomials end -function calc_interpolating_polynomials(coordinates, element_ids, mesh::TreeMesh, dg, - cache) +function calc_interpolating_polynomials!(interpolating_polynomials, coordinates, + element_ids, + mesh::UnstructuredMesh2D, dg::DGSEM, cache) + @unpack nodes = dg.basis + + wbary = barycentric_weights(nodes) + + # Helper array for a straight-sided quadrilateral element + corners = zeros(eltype(mesh.corners), 4, 2) + + for index in 1:length(element_ids) + # Construct point + x = SVector(ntuple(i -> coordinates[i, index], ndims(mesh))) + + # Convert to unit coordinates; procedure differs for straight-sided + # versus curvilinear elements + element = element_ids[index] + if !mesh.element_is_curved[element] + for j in 1:2, i in 1:4 + # Pull the (x,y) values of the element corners from the global corners array + corners[i, j] = mesh.corners[j, mesh.element_node_ids[i, element]] + end + # Compute coordinates in reference system + unit_coordinates = invert_bilinear_interpolation(mesh, x, corners) + + # Sanity check that the computed `unit_coordinates` indeed recover the desired point `x` + x_check = straight_side_quad_map(unit_coordinates[1], unit_coordinates[2], + corners) + if !isapprox(x[1], x_check[1]) || !isapprox(x[2], x_check[2]) + error("failed to compute computational coordinates for the time series point $(x), closet candidate was $(x_check)") + end + else # mesh.element_is_curved[element] + unit_coordinates = invert_transfinite_interpolation(mesh, x, + view(mesh.surface_curves, + :, element)) + + # Sanity check that the computed `unit_coordinates` indeed recover the desired point `x` + x_check = transfinite_quad_map(unit_coordinates[1], unit_coordinates[2], + view(mesh.surface_curves, :, element)) + if !isapprox(x[1], x_check[1]) || !isapprox(x[2], x_check[2]) + error("failed to compute computational coordinates for the time series point $(x), closet candidate was $(x_check)") + end + end + + # Calculate interpolating polynomial for each dimension, making use of tensor product structure + for d in 1:ndims(mesh) + interpolating_polynomials[:, d, index] .= lagrange_interpolating_polynomials(unit_coordinates[d], + nodes, + wbary) + end + end + + return interpolating_polynomials +end + +# Use a Newton iteration to determine the computational coordinates +# (xi, eta) of an (x,y) `point` that is given in physical coordinates +# by inverting the transformation. For straight-sided elements this +# amounts to inverting a bi-linear interpolation. For curved +# elements we invert the transfinite interpolation with linear blending. +# The residual function for the Newton iteration is +# r(xi, eta) = X(xi, eta) - point +# and the Jacobian entries are computed accordingly from either +# `straight_side_quad_map_metrics` or `transfinite_quad_map_metrics`. +# We exploit the 2x2 nature of the problem and directly compute the matrix +# inverse to make things faster. The implementations below are inspired by +# an answer on Stack Overflow (https://stackoverflow.com/a/18332009) where +# the author explicitly states that their code is released to the public domain. +@inline function invert_bilinear_interpolation(mesh::UnstructuredMesh2D, point, + element_corners) + # Initial guess for the point (center of the reference element) + xi = zero(eltype(point)) + eta = zero(eltype(point)) + for k in 1:5 # Newton's method should converge quickly + # Compute current x and y coordinate and the Jacobian matrix + # J = (X_xi, X_eta; Y_xi, Y_eta) + x, y = straight_side_quad_map(xi, eta, element_corners) + J11, J12, J21, J22 = straight_side_quad_map_metrics(xi, eta, element_corners) + + # Compute residuals for the Newton teration for the current (x, y) coordinate + r1 = x - point[1] + r2 = y - point[2] + + # Newton update that directly applies the inverse of the 2x2 Jacobian matrix + inv_detJ = inv(J11 * J22 - J12 * J21) + + # Update with explicitly inverted Jacobian + xi = xi - inv_detJ * (J22 * r1 - J12 * r2) + eta = eta - inv_detJ * (-J21 * r1 + J11 * r2) + + # Ensure updated point is in the reference element + xi = min(max(xi, -1), 1) + eta = min(max(eta, -1), 1) + end + + return SVector(xi, eta) +end + +@inline function invert_transfinite_interpolation(mesh::UnstructuredMesh2D, point, + surface_curves::AbstractVector{<:CurvedSurface}) + # Initial guess for the point (center of the reference element) + xi = zero(eltype(point)) + eta = zero(eltype(point)) + for k in 1:5 # Newton's method should converge quickly + # Compute current x and y coordinate and the Jacobian matrix + # J = (X_xi, X_eta; Y_xi, Y_eta) + x, y = transfinite_quad_map(xi, eta, surface_curves) + J11, J12, J21, J22 = transfinite_quad_map_metrics(xi, eta, surface_curves) + + # Compute residuals for the Newton teration for the current (x,y) coordinate + r1 = x - point[1] + r2 = y - point[2] + + # Newton update that directly applies the inverse of the 2x2 Jacobian matrix + inv_detJ = inv(J11 * J22 - J12 * J21) + + # Update with explicitly inverted Jacobian + xi = xi - inv_detJ * (J22 * r1 - J12 * r2) + eta = eta - inv_detJ * (-J21 * r1 + J11 * r2) + + # Ensure updated point is in the reference element + xi = min(max(xi, -1), 1) + eta = min(max(eta, -1), 1) + end + + return SVector(xi, eta) +end + +function calc_interpolating_polynomials(coordinates, element_ids, + mesh::Union{TreeMesh, UnstructuredMesh2D}, + dg, cache) interpolating_polynomials = Array{real(dg), 3}(undef, nnodes(dg), ndims(mesh), length(element_ids)) @@ -121,8 +390,8 @@ end # Record the solution variables at each given point function record_state_at_points!(point_data, u, solution_variables, n_solution_variables, - mesh::TreeMesh{2}, equations, dg::DG, - time_series_cache) + mesh::Union{TreeMesh{2}, UnstructuredMesh2D}, + equations, dg::DG, time_series_cache) @unpack element_ids, interpolating_polynomials = time_series_cache old_length = length(first(point_data)) new_length = old_length + n_solution_variables diff --git a/test/test_unit.jl b/test/test_unit.jl index 1907a281718..03a78f6918a 100644 --- a/test/test_unit.jl +++ b/test/test_unit.jl @@ -600,6 +600,7 @@ end end @timed_testset "TimeSeriesCallback" begin + # Test the 2D TreeMesh version of the callback and some warnings @test_nowarn_mod trixi_include(@__MODULE__, joinpath(examples_dir(), "tree_2d_dgsem", "elixir_acoustics_gaussian_source.jl"), diff --git a/test/test_unstructured_2d.jl b/test/test_unstructured_2d.jl index 8a62dcaec3c..6814250dd47 100644 --- a/test/test_unstructured_2d.jl +++ b/test/test_unstructured_2d.jl @@ -198,6 +198,39 @@ end end end +@trixi_testset "elixir_euler_time_series.jl" begin + @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_euler_time_series.jl"), + l2=[ + 6.984024099236519e-5, + 6.289022520363763e-5, + 6.550951878107466e-5, + 0.00016222767700879948, + ], + linf=[ + 0.0005367823248620951, + 0.000671293180158461, + 0.0005656680962440319, + 0.0013910024779804075, + ], + tspan=(0.0, 0.2), + # With the default `maxiters = 1` in coverage tests, + # there would be no time series to check against. + coverage_override=(maxiters = 20,)) + # Extra test that the `TimeSeries` callback creates reasonable data + point_data_1 = time_series.affect!.point_data[1] + @test all(isapprox.(point_data_1[1:4], + [1.9546882708551676, 1.9547149531788077, + 1.9547142161310154, 3.821066781119142])) + # Ensure that we do not have excessive memory allocations + # (e.g., from type instabilities) + let + t = sol.t[end] + u_ode = sol.u[end] + du_ode = similar(u_ode) + @test (@allocated Trixi.rhs!(du_ode, u_ode, semi, t)) < 1000 + end +end + @trixi_testset "elixir_acoustics_gauss_wall.jl" begin @test_trixi_include(joinpath(EXAMPLES_DIR, "elixir_acoustics_gauss_wall.jl"), l2=[0.029330394861252995, 0.029345079728907965, From 9323c2ae47300ce83976fcdaba8f5801e82e41a5 Mon Sep 17 00:00:00 2001 From: Hendrik Ranocha Date: Thu, 14 Mar 2024 15:54:43 +0100 Subject: [PATCH 59/63] set version to v0.7.3 --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index 6b44af4a3fa..f2f8a10626a 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "Trixi" uuid = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb" authors = ["Michael Schlottke-Lakemper ", "Gregor Gassner ", "Hendrik Ranocha ", "Andrew R. Winters ", "Jesse Chan "] -version = "0.7.3-pre" +version = "0.7.3" [deps] CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2" From a528083a1c41d9fd131fc972816881d3276f718e Mon Sep 17 00:00:00 2001 From: Hendrik Ranocha Date: Thu, 14 Mar 2024 15:54:55 +0100 Subject: [PATCH 60/63] set development version to v0.7.4-pre --- Project.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Project.toml b/Project.toml index f2f8a10626a..97da4aec51b 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "Trixi" uuid = "a7f1ee26-1774-49b1-8366-f1abc58fbfcb" authors = ["Michael Schlottke-Lakemper ", "Gregor Gassner ", "Hendrik Ranocha ", "Andrew R. Winters ", "Jesse Chan "] -version = "0.7.3" +version = "0.7.4-pre" [deps] CodeTracking = "da1fd8a2-8d9e-5ec2-8556-3022fb5608a2" From aa9ea20342e3d02445ec2dc53e380c405da3b683 Mon Sep 17 00:00:00 2001 From: Benedict <135045760+bgeihe@users.noreply.github.com> Date: Fri, 15 Mar 2024 10:20:43 +0100 Subject: [PATCH 61/63] reset n_boundaries_per_direction (#1870) --- src/solvers/dgsem_tree/containers_2d.jl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/src/solvers/dgsem_tree/containers_2d.jl b/src/solvers/dgsem_tree/containers_2d.jl index 4bfbddead9a..7048739a226 100644 --- a/src/solvers/dgsem_tree/containers_2d.jl +++ b/src/solvers/dgsem_tree/containers_2d.jl @@ -421,6 +421,8 @@ end function init_boundaries!(boundaries, elements, mesh::TreeMesh2D) # Exit early if there are no boundaries to initialize if nboundaries(boundaries) == 0 + # In this case n_boundaries_per_direction still needs to be reset! + boundaries.n_boundaries_per_direction = SVector(0, 0, 0, 0) return nothing end From 38a9a5234cb2e5588fced11c7bac5d9441142014 Mon Sep 17 00:00:00 2001 From: Hendrik Ranocha Date: Fri, 15 Mar 2024 10:21:54 +0100 Subject: [PATCH 62/63] remove some minor allocations for threaded FDSBP (#1868) * do not inline calc_volume_integral! for FDSBP * avoid allocations in unstructured prolong2interfaces! * avoid allocations in unstructured prolong2boundaries! --- src/solvers/dgsem_unstructured/dg_2d.jl | 40 ++++++++++++---------- src/solvers/fdsbp_unstructured/fdsbp_2d.jl | 10 +++--- 2 files changed, 27 insertions(+), 23 deletions(-) diff --git a/src/solvers/dgsem_unstructured/dg_2d.jl b/src/solvers/dgsem_unstructured/dg_2d.jl index 988e995d6b7..ce602e178d8 100644 --- a/src/solvers/dgsem_unstructured/dg_2d.jl +++ b/src/solvers/dgsem_unstructured/dg_2d.jl @@ -95,49 +95,51 @@ function prolong2interfaces!(cache, u, mesh::UnstructuredMesh2D, equations, surface_integral, dg::DG) @unpack interfaces = cache + @unpack element_ids, element_side_ids = interfaces + interfaces_u = interfaces.u @threaded for interface in eachinterface(dg, cache) - primary_element = interfaces.element_ids[1, interface] - secondary_element = interfaces.element_ids[2, interface] + primary_element = element_ids[1, interface] + secondary_element = element_ids[2, interface] - primary_side = interfaces.element_side_ids[1, interface] - secondary_side = interfaces.element_side_ids[2, interface] + primary_side = element_side_ids[1, interface] + secondary_side = element_side_ids[2, interface] if primary_side == 1 for i in eachnode(dg), v in eachvariable(equations) - interfaces.u[1, v, i, interface] = u[v, i, 1, primary_element] + interfaces_u[1, v, i, interface] = u[v, i, 1, primary_element] end elseif primary_side == 2 for i in eachnode(dg), v in eachvariable(equations) - interfaces.u[1, v, i, interface] = u[v, nnodes(dg), i, primary_element] + interfaces_u[1, v, i, interface] = u[v, nnodes(dg), i, primary_element] end elseif primary_side == 3 for i in eachnode(dg), v in eachvariable(equations) - interfaces.u[1, v, i, interface] = u[v, i, nnodes(dg), primary_element] + interfaces_u[1, v, i, interface] = u[v, i, nnodes(dg), primary_element] end else # primary_side == 4 for i in eachnode(dg), v in eachvariable(equations) - interfaces.u[1, v, i, interface] = u[v, 1, i, primary_element] + interfaces_u[1, v, i, interface] = u[v, 1, i, primary_element] end end if secondary_side == 1 for i in eachnode(dg), v in eachvariable(equations) - interfaces.u[2, v, i, interface] = u[v, i, 1, secondary_element] + interfaces_u[2, v, i, interface] = u[v, i, 1, secondary_element] end elseif secondary_side == 2 for i in eachnode(dg), v in eachvariable(equations) - interfaces.u[2, v, i, interface] = u[v, nnodes(dg), i, + interfaces_u[2, v, i, interface] = u[v, nnodes(dg), i, secondary_element] end elseif secondary_side == 3 for i in eachnode(dg), v in eachvariable(equations) - interfaces.u[2, v, i, interface] = u[v, i, nnodes(dg), + interfaces_u[2, v, i, interface] = u[v, i, nnodes(dg), secondary_element] end else # secondary_side == 4 for i in eachnode(dg), v in eachvariable(equations) - interfaces.u[2, v, i, interface] = u[v, 1, i, secondary_element] + interfaces_u[2, v, i, interface] = u[v, 1, i, secondary_element] end end end @@ -278,26 +280,28 @@ function prolong2boundaries!(cache, u, mesh::UnstructuredMesh2D, equations, surface_integral, dg::DG) @unpack boundaries = cache + @unpack element_id, element_side_id = boundaries + boundaries_u = boundaries.u @threaded for boundary in eachboundary(dg, cache) - element = boundaries.element_id[boundary] - side = boundaries.element_side_id[boundary] + element = element_id[boundary] + side = element_side_id[boundary] if side == 1 for l in eachnode(dg), v in eachvariable(equations) - boundaries.u[v, l, boundary] = u[v, l, 1, element] + boundaries_u[v, l, boundary] = u[v, l, 1, element] end elseif side == 2 for l in eachnode(dg), v in eachvariable(equations) - boundaries.u[v, l, boundary] = u[v, nnodes(dg), l, element] + boundaries_u[v, l, boundary] = u[v, nnodes(dg), l, element] end elseif side == 3 for l in eachnode(dg), v in eachvariable(equations) - boundaries.u[v, l, boundary] = u[v, l, nnodes(dg), element] + boundaries_u[v, l, boundary] = u[v, l, nnodes(dg), element] end else # side == 4 for l in eachnode(dg), v in eachvariable(equations) - boundaries.u[v, l, boundary] = u[v, 1, l, element] + boundaries_u[v, l, boundary] = u[v, 1, l, element] end end end diff --git a/src/solvers/fdsbp_unstructured/fdsbp_2d.jl b/src/solvers/fdsbp_unstructured/fdsbp_2d.jl index c35772cdf18..cbe11ac6ac9 100644 --- a/src/solvers/fdsbp_unstructured/fdsbp_2d.jl +++ b/src/solvers/fdsbp_unstructured/fdsbp_2d.jl @@ -28,11 +28,11 @@ end # 2D volume integral contributions for `VolumeIntegralStrongForm` # OBS! This is the standard (not de-aliased) form of the volume integral. # So it is not provably stable for variable coefficients due to the the metric terms. -@inline function calc_volume_integral!(du, u, - mesh::UnstructuredMesh2D, - nonconservative_terms::False, equations, - volume_integral::VolumeIntegralStrongForm, - dg::FDSBP, cache) +function calc_volume_integral!(du, u, + mesh::UnstructuredMesh2D, + nonconservative_terms::False, equations, + volume_integral::VolumeIntegralStrongForm, + dg::FDSBP, cache) D = dg.basis # SBP derivative operator @unpack f_threaded = cache @unpack contravariant_vectors = cache.elements From 2dfde7faf3cc74f066d86148ae6c99ed9e58fa79 Mon Sep 17 00:00:00 2001 From: Daniel Doehring Date: Fri, 15 Mar 2024 13:55:10 +0100 Subject: [PATCH 63/63] Docstrings for some methods in basis Lobatto-Legendre (#1874) * Docstrings for some methods in basis LL * double back slash --- .../src/files/scalar_linear_advection_1d.jl | 2 +- src/solvers/dgsem/basis_lobatto_legendre.jl | 77 +++++++++++++++++-- 2 files changed, 72 insertions(+), 7 deletions(-) diff --git a/docs/literate/src/files/scalar_linear_advection_1d.jl b/docs/literate/src/files/scalar_linear_advection_1d.jl index 77ba7b087cc..9b48f29d341 100644 --- a/docs/literate/src/files/scalar_linear_advection_1d.jl +++ b/docs/literate/src/files/scalar_linear_advection_1d.jl @@ -115,7 +115,7 @@ integral = sum(nodes.^3 .* weights) # To approximate the solution, we need to get the polynomial coefficients $\{u_j^{Q_l}\}_{j=0}^N$ # for every element $Q_l$. -# After defining all nodes, we can implement the spatial coordinate $x$ and its initial value $u0$ +# After defining all nodes, we can implement the spatial coordinate $x$ and its initial value $u0 = u(t_0)$ # for every node. x = Matrix{Float64}(undef, length(nodes), n_elements) for element in 1:n_elements diff --git a/src/solvers/dgsem/basis_lobatto_legendre.jl b/src/solvers/dgsem/basis_lobatto_legendre.jl index 9e21b88dfa1..cac1dba9c74 100644 --- a/src/solvers/dgsem/basis_lobatto_legendre.jl +++ b/src/solvers/dgsem/basis_lobatto_legendre.jl @@ -404,7 +404,8 @@ function calc_dsplit(nodes, weights) return dsplit end -# Calculate the polynomial derivative matrix D +# Calculate the polynomial derivative matrix D. +# This implements algorithm 37 "PolynomialDerivativeMatrix" from Kopriva's book. function polynomial_derivative_matrix(nodes) n_nodes = length(nodes) d = zeros(n_nodes, n_nodes) @@ -421,6 +422,7 @@ function polynomial_derivative_matrix(nodes) end # Calculate and interpolation matrix (Vandermonde matrix) between two given sets of nodes +# See algorithm 32 "PolynomialInterpolationMatrix" from Kopriva's book. function polynomial_interpolation_matrix(nodes_in, nodes_out, baryweights_in = barycentric_weights(nodes_in)) n_nodes_in = length(nodes_in) @@ -433,6 +435,7 @@ function polynomial_interpolation_matrix(nodes_in, nodes_out, return vandermonde end +# This implements algorithm 32 "PolynomialInterpolationMatrix" from Kopriva's book. function polynomial_interpolation_matrix!(vandermonde, nodes_in, nodes_out, baryweights_in) @@ -463,7 +466,19 @@ function polynomial_interpolation_matrix!(vandermonde, return vandermonde end -# Calculate the barycentric weights for a given node distribution. +""" + barycentric_weights(nodes) + +Calculate the barycentric weights for a given node distribution, i.e., +```math +w_j = \\frac{1}{ \\prod_{k \\neq j} \\left( x_j - x_k \\right ) } +``` + +For details, see (especially Section 3) +- Jean-Paul Berrut and Lloyd N. Trefethen (2004). + Barycentric Lagrange Interpolation. + [DOI:10.1137/S0036144502417715](https://doi.org/10.1137/S0036144502417715) +""" function barycentric_weights(nodes) n_nodes = length(nodes) weights = ones(n_nodes) @@ -494,12 +509,31 @@ function calc_lhat(x, nodes, weights) return lhat end -# Calculate Lagrange polynomials for a given node distribution. +""" + lagrange_interpolating_polynomials(x, nodes, wbary) + +Calculate Lagrange polynomials for a given node distribution with +associated barycentric weights `wbary` at a given point `x` on the +reference interval ``[-1, 1]``. + +This returns all ``l_j(x)``, i.e., the Lagrange polynomials for each node ``x_j``. +Thus, to obtain the interpolating polynomial ``p(x)`` at ``x``, one has to +multiply the Lagrange polynomials with the nodal values ``u_j`` and sum them up: +``p(x) = \\sum_{j=1}^{n} u_j l_j(x)``. + +For details, see e.g. Section 2 of +- Jean-Paul Berrut and Lloyd N. Trefethen (2004). + Barycentric Lagrange Interpolation. + [DOI:10.1137/S0036144502417715](https://doi.org/10.1137/S0036144502417715) +""" function lagrange_interpolating_polynomials(x, nodes, wbary) n_nodes = length(nodes) polynomials = zeros(n_nodes) for i in 1:n_nodes + # Avoid division by zero when `x` is close to node by using + # the Kronecker-delta property at nodes + # of the Lagrange interpolation polynomials. if isapprox(x, nodes[i], rtol = eps(x)) polynomials[i] = 1 return polynomials @@ -518,6 +552,17 @@ function lagrange_interpolating_polynomials(x, nodes, wbary) return polynomials end +""" + gauss_lobatto_nodes_weights(n_nodes::Integer) + +Computes nodes ``x_j`` and weights ``w_j`` for the (Legendre-)Gauss-Lobatto quadrature. +This implements algorithm 25 "GaussLobattoNodesAndWeights" from the book + +- David A. Kopriva, (2009). + Implementing spectral methods for partial differential equations: + Algorithms for scientists and engineers. + [DOI:10.1007/978-90-481-2261-5](https://doi.org/10.1007/978-90-481-2261-5) +""" # From FLUXO (but really from blue book by Kopriva) function gauss_lobatto_nodes_weights(n_nodes::Integer) # From Kopriva's book @@ -585,7 +630,7 @@ function gauss_lobatto_nodes_weights(n_nodes::Integer) return nodes, weights end -# From FLUXO (but really from blue book by Kopriva) +# From FLUXO (but really from blue book by Kopriva, algorithm 24) function calc_q_and_l(N::Integer, x::Float64) L_Nm2 = 1.0 L_Nm1 = x @@ -609,7 +654,17 @@ function calc_q_and_l(N::Integer, x::Float64) end calc_q_and_l(N::Integer, x::Real) = calc_q_and_l(N, convert(Float64, x)) -# From FLUXO (but really from blue book by Kopriva) +""" + gauss_nodes_weights(n_nodes::Integer) + +Computes nodes ``x_j`` and weights ``w_j`` for the Gauss-Legendre quadrature. +This implements algorithm 23 "LegendreGaussNodesAndWeights" from the book + +- David A. Kopriva, (2009). + Implementing spectral methods for partial differential equations: + Algorithms for scientists and engineers. + [DOI:10.1007/978-90-481-2261-5](https://doi.org/10.1007/978-90-481-2261-5) +""" function gauss_nodes_weights(n_nodes::Integer) # From Kopriva's book n_iterations = 10 @@ -666,7 +721,17 @@ function gauss_nodes_weights(n_nodes::Integer) end end -# From FLUXO (but really from blue book by Kopriva) +""" + legendre_polynomial_and_derivative(N::Int, x::Real) + +Computes the Legendre polynomial of degree `N` and its derivative at `x`. +This implements algorithm 22 "LegendrePolynomialAndDerivative" from the book + +- David A. Kopriva, (2009). + Implementing spectral methods for partial differential equations: + Algorithms for scientists and engineers. + [DOI:10.1007/978-90-481-2261-5](https://doi.org/10.1007/978-90-481-2261-5) +""" function legendre_polynomial_and_derivative(N::Int, x::Real) if N == 0 poly = 1.0