Adding a tutorial on adding new parabolic terms #1209

jlchan · 2022-08-25T18:27:08Z

This includes a description of the operators Gradient and Divergence used for dispatch in the boundary conditions.

jlchan · 2022-08-25T21:23:06Z

@ranocha this is now ready to review (should have no more commits). I built the docs preview on my laptop and it looks good.

@sloede this includes some documentation of the Gradient and Divergence boundary conditions (#1147). I remember you were asking about documentation of these BCs previously.

ranocha

Great, thanks! I have one question below.

docs/literate/src/files/adding_new_parabolic_terms.jl

ranocha · 2022-08-26T05:02:41Z

docs/literate/src/files/adding_new_parabolic_terms.jl

+u_left = 1.0
+u_bottom = 2.0
+
+boundary_conditions_hyperbolic = (; x_neg = BoundaryConditionDirichlet((x, t, equations) -> SVector(u_left)),
+                                    y_neg = BoundaryConditionDirichlet((x, t, equations) -> SVector(u_bottom)),
+                                    y_pos = boundary_condition_do_nothing,
+                                    x_pos = boundary_condition_do_nothing)
+
+boundary_conditions_parabolic = (; x_neg = BoundaryConditionConstantDirichlet(u_left),
+                                   y_neg = BoundaryConditionConstantDirichlet(u_bottom),


If users copy this directly to their code, they will run into type instabilities with non-constant globals. What about adding const qualifiers to u_left and u_bottom or copying their values directly into the corresponding lines?
It doesn't really matter for this demonstration of the behavior, but it would probably be nice to follow best practices in the tutorials in general (when it's not too complex).

Done - removed u_left, u_bottom.

Is the type instability due to the use of u_left in the anonymous function?

Yes - it picks up a global variable from there and the global variable is neither typed nor const

sloede

LGTM - thanks for doing this! I just left a few minor suggestions which may or may not be applied; either way this PR can be merged afterwards.

docs/literate/src/files/adding_new_parabolic_terms.jl

andrewwinters5000

Thanks for adding this @jlchan ! It looks quite nice. I just added two minor suggestions.

docs/literate/src/files/adding_new_parabolic_terms.jl

Co-authored-by: Andrew Winters <[email protected]> Co-authored-by: Michael Schlottke-Lakemper <[email protected]>

jlchan · 2022-08-26T13:41:31Z

Thanks for the reviews @ranocha, @sloede, @andrewwinters5000! I've addressed the comments now

ranocha

Thanks!

docs/literate/src/files/adding_new_parabolic_terms.jl

Co-authored-by: Andrew Winters <[email protected]>

@threaded

* Parabolic terms for DGMulti (#1136) * minor formatting * adding multi-term semidiscretization * fixing bug and adding test * changing name * changing name, importing SplitODEFunction * fixing test by adding norm * trying another test fix * adding norm back * adjusting tol * try to fix test again * syntax error * removing norm frm test * adding cache to parabolic terms (enable reuse of inviscid cache) * generalize dgmulti iterators * fix typo * generalizing reset_du! for dgmulti * WIP gradient and divergence computations * fix name * more generalization * divergence + remove repeated code * adding cache * remove test * update diffusion test * update diffusion rhs * moving routines around * fix multiple includes * removing time dependence for now from viscous rhs * export ScalarDiffusion2D * fix test * working periodic advection RHS * cleanup and comments * making periodic advection-diffusion example * trim whitespace * adding t back in to parabolic rhs add t back in * refactoring boundary condition code * update elixir with BCs * change default DGMulti interface flux behavior same as in #1139 * cleanup * renaming variables * BC prepping * cleanup of elixir * more name fixing * Update src/semidiscretization/semidiscretization_hyperbolic_parabolic.jl Co-authored-by: Hendrik Ranocha <[email protected]> * adding Neumann BCs * switching to weak form weak form more weak form weak form * fixing cache variable names * simplified parabolic boundary flux treatement * updated elixir with different types of BCs * Update src/semidiscretization/semidiscretization_hyperbolic_parabolic.jl Co-authored-by: Michael Schlottke-Lakemper <[email protected]> * Update src/semidiscretization/semidiscretization_hyperbolic_parabolic.jl Co-authored-by: Michael Schlottke-Lakemper <[email protected]> * Update src/equations/equations.jl Co-authored-by: Michael Schlottke-Lakemper <[email protected]> * rhs! -> rhs_parabolic! * move Gradient/Divergence types * add "no boundary condition" BC * rename ScalarDiffusion -> LaplaceDiffusion r r * rhs -> rhs_parabolic! again * comments * moving tests around * scalarDiffusion -> LaplaceDiffusion * tuple-based constructor * updating examples * add ScalarPlotData2D docstring (#1145) Co-authored-by: Jesse Chan <[email protected]> * Apply suggestions from code review Co-authored-by: Michael Schlottke-Lakemper <[email protected]> Co-authored-by: Hendrik Ranocha <[email protected]> * renaming for consistency parabolic_equations -> equations_parabolic no_boundary_condition -> boundary_condition_do_nothing * move Neumann BCs into equations.jl * renaming, e.g., ParabolicEquations -> EquationsParabolic, etc * rename test module * generalize LaplaceDiffusion2D to any number of variables * removing saveat times and standardizing `tol` names * parabolic_cache -> cache_parabolic cache * renaming `create_cache` -> `create_cache_parabolic` avoids conflicts when using dg::DGMultiFluxDiff * Update examples/dgmulti_2d/elixir_advection_diffusion.jl Co-authored-by: Michael Schlottke-Lakemper <[email protected]> * Update src/equations/equations.jl Co-authored-by: Michael Schlottke-Lakemper <[email protected]> * Update src/semidiscretization/semidiscretization_hyperbolic_parabolic.jl Co-authored-by: Michael Schlottke-Lakemper <[email protected]> * parabolic_boundary_conditions -> boundary_conditions_parabolic similarly for hyperbolic d * Update src/semidiscretization/semidiscretization_hyperbolic_parabolic.jl Co-authored-by: Michael Schlottke-Lakemper <[email protected]> * add equations as field to LaplaceDiffusion2D * moving Neumann BCs into equations.jl and adding default BC behavior * running parabolic tests, adding integration test * adding parabolic tests to ci * missing comma * Update src/equations/laplace_diffusion_2d.jl Co-authored-by: Hendrik Ranocha <[email protected]> * fix test * fix test typo * fix tests (for real this time) * improve test coverage Co-authored-by: Jesse Chan <[email protected]> Co-authored-by: Hendrik Ranocha <[email protected]> Co-authored-by: Michael Schlottke-Lakemper <[email protected]> * Additional work on parabolic terms (#1148) * make "do nothing BC" a struct, move it to basic_types * add varnames for LaplaceDiffusion * add forgotten @threaded * update comment * Revert "add forgotten @threaded" This reverts commit 1564501. * add @threaded (without enumerate) * remove periodic advection diffusion elixir (redundant) * adding test * one more test * Update src/basic_types.jl Co-authored-by: Hendrik Ranocha <[email protected]> Co-authored-by: Jesse Chan <[email protected]> Co-authored-by: Hendrik Ranocha <[email protected]> * Reorganization of boundary conditions (#1152) * moving "default" boundary conditions back into equations file * add periodic advection_diffusion back in * updating test * update test * Apply suggestions from code review Co-authored-by: Jesse Chan <[email protected]> Co-authored-by: Hendrik Ranocha <[email protected]> Co-authored-by: Hendrik Ranocha <[email protected]> * Adding parabolic solver option (#1153) * adding parabolic solver types * incorporating parabolic solver types into dg_parabolic penalties * specializing parabolic solver options in LaplaceDiffusion2D * moving things around to fix CI * dropped arg in test * Apply suggestions from code review Co-authored-by: Hendrik Ranocha <[email protected]> * renaming files and ViscousFlux solvers renaming files rename rename * Added TODO note for penalty term * ViscousFlux___ -> ViscousFormulation___ * move function def around Co-authored-by: Jesse Chan <[email protected]> Co-authored-by: Hendrik Ranocha <[email protected]> * rearrange include order * Add support for hyperbolic-parabolic systems to TreeMesh2D (#1156) * Add prototype for advection-diffusion elixir for TreeMesh2D * Initial implementation of `calc_gradient!` for TreeMesh{2} * First complete implementation of the parabolic rhs operator for TreeMesh * Make it work * Add first elixir that works * Clean up elixir * first draft of container for Navier-Stokes constants and fluxes * remove unneeded temperature computation * draft of elixir with possible boundary condition structure * added manufactured solution and source term * fix typo in function name for MMS * update variable names for consistency. improve comments * fix dumb typos in new equation system name * actually export new equations * add comment near variable_mapping declaration. * Apply suggestions from code review Co-authored-by: Hendrik Ranocha <[email protected]> * parabolic equations now exported separately * change name to CompressibleNavierStokesEquations2D * export NS with proper name * explicitly require compressible Euler in the type parameter * name kinematic viscosity nu for consistency with Lattice-Boltzmann * add promotion in constructor * make Reynolds, Prandtl, Mach, and kappa keyword arguments * update constructor call in elixir * reduce computation by exploiting stress tensor symmetry * fix unpacking of flux * modifying parabolic cache creation in cache, we assume we take the gradient of all hyperbolic variables. since the number of parabolic variables can differ from the number of hyperbolic variables, we pass in the hyperbolic equations to `create_cache_parabolic` now * comments * comments * formatting and renaming equations to equations_hyperbolic formatting comments * fix unpacking of gradients in flux * adding CNS BCs * adding lid-driven cavity elixir * adding variable transform, editing cons2prim for CNS * add prim2cons for NS (inconsistent right now) * add draft of DGMulti Navier Stokes convergence elixir * converging solution using elixir for TreeMesh with BCs * fixing DGMulti advection diffusion elixir convergence * naming equations as parabolic/hyperbolic * generalizing transform_variables * add TODO more todos * additional checks on get_unsigned_normal * adding isothermal BC * commenting out unused CNS functions for now * fix call to transform_variables * comments and cleanup * changing default solver and Re for cavity * adding more advection diffusion tests * label tests * add gradient_variables field to SemidiscretizationHyperbolicParabolic * Revert "add gradient_variables field to SemidiscretizationHyperbolicParabolic" This reverts commit 063b602. * allowing for specialization in transform_variables adding a function `gradient_variable_transformation` which should get specialized if the gradient variables are not conservative variables * formatting and comments * reverting elixir * comments * standardizing time tol * minor fix to CNS boundary flux for convenience make it so that the density state is computed correctly, even though it's not used * formatting + comments * using primitive variables in viscous flux instead of conservative * minor formatting * add CNS tests * fix test * testing if scoping issues fix TreeMesh tests * decreasing timestep tol for TreeMesh parabolic test * enabling periodic BCs for TreeMesh + more tests * fix density BC flux (unused, but could be useful) * adding non-working TreeMesh elixirs * adding AD checks * standardizing parameters in convergence elixirs * minor cleanup * revert DGMulti CNS elixir setup back to the one used in tests * adding TreeMesh CNS convergence test * removing redundant elixir * add more tests * add more test * Apply suggestions from code review Co-authored-by: Hendrik Ranocha <[email protected]> * set version to v0.4.43 * set development version to v0.4.44-pre * add YouTube links to JuliaCon presentations (#1192) * add YouTube links to JuliaCon presentations * Apply suggestions from code review Co-authored-by: Michael Schlottke-Lakemper <[email protected]> Co-authored-by: Michael Schlottke-Lakemper <[email protected]> * improved readability of equation docstrings in compressible Euler files * Navier-Stokes in 2D on DGMulti and TreeMesh (#1165) * first draft of container for Navier-Stokes constants and fluxes * remove unneeded temperature computation * draft of elixir with possible boundary condition structure * added manufactured solution and source term * fix typo in function name for MMS * update variable names for consistency. improve comments * fix dumb typos in new equation system name * actually export new equations * add comment near variable_mapping declaration. * Apply suggestions from code review Co-authored-by: Hendrik Ranocha <[email protected]> * parabolic equations now exported separately * change name to CompressibleNavierStokesEquations2D * export NS with proper name * explicitly require compressible Euler in the type parameter * name kinematic viscosity nu for consistency with Lattice-Boltzmann * add promotion in constructor * make Reynolds, Prandtl, Mach, and kappa keyword arguments * update constructor call in elixir * reduce computation by exploiting stress tensor symmetry * fix unpacking of flux * modifying parabolic cache creation in cache, we assume we take the gradient of all hyperbolic variables. since the number of parabolic variables can differ from the number of hyperbolic variables, we pass in the hyperbolic equations to `create_cache_parabolic` now * comments * comments * formatting and renaming equations to equations_hyperbolic formatting comments * fix unpacking of gradients in flux * adding CNS BCs * adding lid-driven cavity elixir * adding variable transform, editing cons2prim for CNS * add prim2cons for NS (inconsistent right now) * add draft of DGMulti Navier Stokes convergence elixir * converging solution using elixir for TreeMesh with BCs * fixing DGMulti advection diffusion elixir convergence * naming equations as parabolic/hyperbolic * generalizing transform_variables * add TODO more todos * additional checks on get_unsigned_normal * adding isothermal BC * commenting out unused CNS functions for now * fix call to transform_variables * comments and cleanup * changing default solver and Re for cavity * adding more advection diffusion tests * label tests * add gradient_variables field to SemidiscretizationHyperbolicParabolic * Revert "add gradient_variables field to SemidiscretizationHyperbolicParabolic" This reverts commit 063b602. * allowing for specialization in transform_variables adding a function `gradient_variable_transformation` which should get specialized if the gradient variables are not conservative variables * formatting and comments * reverting elixir * comments * standardizing time tol * minor fix to CNS boundary flux for convenience make it so that the density state is computed correctly, even though it's not used * formatting + comments * using primitive variables in viscous flux instead of conservative * minor formatting * add CNS tests * fix test * testing if scoping issues fix TreeMesh tests * decreasing timestep tol for TreeMesh parabolic test * enabling periodic BCs for TreeMesh + more tests * fix density BC flux (unused, but could be useful) * adding non-working TreeMesh elixirs * adding AD checks * standardizing parameters in convergence elixirs * minor cleanup * revert DGMulti CNS elixir setup back to the one used in tests * adding TreeMesh CNS convergence test * removing redundant elixir * add more tests * add more test * Apply suggestions from code review Co-authored-by: Hendrik Ranocha <[email protected]> * add docstrings Co-authored-by: Hendrik Ranocha <[email protected]> Co-authored-by: Hendrik Ranocha <[email protected]> Co-authored-by: Jesse Chan <[email protected]> * add docstring for CNS equations * removing some addressed TODOs * adjust definition of the kappa constant * avoid overwriting u_grad with viscous_flux results * remove old TODOs * clarify TODOs for later * removing let statements * rearrange main docstring. Fix typos in math environment causing it to not parse * update TODO notes * Apply suggestions from code review Co-authored-by: Andrew Winters <[email protected]> * update TODO notes * Apply suggestions from code review Co-authored-by: Andrew Winters <[email protected]> * update TODO notes * changing diffusivity names Auto stash before merge of "parabolic-treemesh" and "origin/parabolic-treemesh" * Reynolds/Prandtl number name changes for consistency * Apply suggestions from code review Co-authored-by: Hendrik Ranocha <[email protected]> Co-authored-by: Michael Schlottke-Lakemper <[email protected]> Co-authored-by: Andrew Winters <[email protected]> * fixing bug introduced by GH code review * moving manufactured solution into the CNS equations file * fix allocation issue * get_diffusivity -> diffusivity * removing cruft code, adding comment on messy prim2cons routine * moving manufactured solution back into elixirs * Update examples/dgmulti_2d/elixir_advection_diffusion_nonperiodic.jl * TODO -> Todo, and .6 -> 0.6 d * Update src/solvers/dgsem_tree/dg_2d_parabolic.jl Co-authored-by: Hendrik Ranocha <[email protected]> * adding note to Adiabatic/Isothermal BCs * replacing CompressibleNavierStokesEquations with ...Diffusion * Update src/solvers/dgsem_tree/dg_2d_parabolic.jl Co-authored-by: Hendrik Ranocha <[email protected]> * Update src/solvers/dgsem_tree/dg_2d_parabolic.jl Co-authored-by: Hendrik Ranocha <[email protected]> * documenting Jacobian sign flip * remove extra arg to `gradient_variable_transformation` * Update src/solvers/dgsem_tree/dg_2d_parabolic.jl Co-authored-by: Michael Schlottke-Lakemper <[email protected]> * change warning to error * fix bug introduced by search/replace * dg_parabolic -> parabolic_scheme * BoundaryConditionViscousWall -> BoundaryConditionNavierStokesWall * u_grad -> gradients * fix test * renaming * update comment * converting to signature `flux(u, gradients, orientation, equations)` * using prolong2interfaces/boundaries * unpacking `gradients` and `flux_viscous` * using calc_surface_integral! * adding @muladd * Apply suggestions from code review * update comments * Rename grad_u -> gradients * Update src/equations/compressible_navier_stokes_2d.jl Co-authored-by: Michael Schlottke-Lakemper <[email protected]> * Rename remaining grad_u/u_grad -> gradients * Refactor into prolong2interfaces! * Refactor calc_volume_integral! * Refactor calc_interface_flux * Refactor prolong2boundaries! * Refactor calc_divergence! * Formatting consistency * Remove dispatch on volume integral type * Add comment on why surface_integral is passed to prolong2interfaces! * Explicitly use weak form volume integral to allow easy overriding in test * Add flux differencing test for CNS test * Remove erroneous P4estMesh{2} dispatch * Remove non-cons terms from parabolic solver Co-authored-by: Andrew Winters <[email protected]> Co-authored-by: Hendrik Ranocha <[email protected]> Co-authored-by: Hendrik Ranocha <[email protected]> Co-authored-by: Jesse Chan <[email protected]> Co-authored-by: Jesse Chan <[email protected]> * Add commentary on reuse of interfaces/boundaries data structures (#1199) * Add comments on storing flux values in `u` * Rearrange function names for consistency * Update src/solvers/dgsem_tree/dg_2d_parabolic.jl Co-authored-by: Hendrik Ranocha <[email protected]> * Update src/solvers/dgsem_tree/dg_2d_parabolic.jl Co-authored-by: Andrew Winters <[email protected]> Co-authored-by: Hendrik Ranocha <[email protected]> Co-authored-by: Andrew Winters <[email protected]> * Adding parabolic term description to NEWS.md (#1207) * Add Literate docs for advection-diffusion (#1208) * adding literate docs for advection-diffusion * Apply suggestions from code review Co-authored-by: Hendrik Ranocha <[email protected]> * rename "adding parabolic terms" -> "parabolic terms" Co-authored-by: Hendrik Ranocha <[email protected]> * Adding a tutorial on adding new parabolic terms (#1209) * Viscous terms from entropy gradients (#1202) * first draft of entropy stable gradients * update TODOs * added elixir with discontinuous solution for ES testing * forgot one TODO marker * adding GradientVariables**** type parameter * fix bug (missing type param in constructor) * add elixir with periodic CNS manufactured solution * fix gradient conversion * fix entropy variables w/BCs * updating elixirs with `gradient_variables=GradientVariablesPrimitive()` * Update src/equations/compressible_navier_stokes_2d.jl Co-authored-by: Michael Schlottke-Lakemper <[email protected]> * removing unused routines * removing specialized entropy2cons and cons2entropy routines * adding more tests * removing unused elixirs * Apply suggestions from code review Co-authored-by: Hendrik Ranocha <[email protected]> * adding docs/warning for gradient variable type * extracting w_inner[4] into a more clearly named variable Co-authored-by: Hendrik Ranocha <[email protected]> Co-authored-by: Jesse Chan <[email protected]> Co-authored-by: Jesse Chan <[email protected]> Co-authored-by: Michael Schlottke-Lakemper <[email protected]> Co-authored-by: Jesse Chan <[email protected]> Co-authored-by: Hendrik Ranocha <[email protected]> * adding some minor documentation (#1214) * fix parabolic PID (#1224) * fix parabolic PID * activate analysis_callback in Navier-Stokes convergence test * fix typo * Rescale compressible Navier-Stokes (#1230) * remove the nondimensionalization and update the docstring for CNS * update TreeMesh elixirs and test values * update the elixirs and test values for DGMulti * fix unbalanced parentheses * file renaming for consistency * update file names in the parabolic test script * remove the gas constant as a parameter and update comments * rename viscosity to dynamic_viscosity * add comment about units in the docstring * Update src/equations/compressible_navier_stokes_2d.jl Co-authored-by: Michael Schlottke-Lakemper <[email protected]> * unify notation to call the viscosity mu * fix undefined variable Co-authored-by: Michael Schlottke-Lakemper <[email protected]> * improve type stability of semidiscretize for parabolic semi (#1231) * Apply suggestions from code review Co-authored-by: Hendrik Ranocha <[email protected]> Co-authored-by: Michael Schlottke-Lakemper <[email protected]> Co-authored-by: Hendrik Ranocha <[email protected]> Co-authored-by: Andrew Winters <[email protected]>

jlchan added 5 commits August 25, 2022 13:25

fixing a BC in parabolic tutorial

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"adding new parabolic terms" tutorial

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import SMatrix

8807e2a

fix using Trixi

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add extra header

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jlchan requested a review from ranocha August 25, 2022 21:14

fix some math

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jlchan and others added 3 commits August 26, 2022 08:33

Apply suggestions from code review

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Co-authored-by: Andrew Winters <[email protected]> Co-authored-by: Michael Schlottke-Lakemper <[email protected]>

removing u_left, u_bottom

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Merge remote-tracking branch 'Trixi_fork/jc/bc_docs' into jc/bc_docs

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jlchan merged commit f79183c into trixi-framework:dev Aug 27, 2022

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Adding a tutorial on adding new parabolic terms #1209

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Adding a tutorial on adding new parabolic terms #1209

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