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] 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 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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 Schlottke-Lakemper * Update docs/literate/src/files/getting_started.jl Co-authored-by: Michael Schlottke-Lakemper * Update 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Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/getting_started.jl Co-authored-by: Michael Schlottke-Lakemper * new plot in Modifying an existing setup * 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 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 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 * julia/shell-formatting * Update getting_started.jl * Update getting_started.jl * Correction of Modifying part * Usage update * Update getting_started.jl * add Visualize the solution * spell check * correction * correction * add picture paraview * divide in two parts & correction * divide in 3 parts * Update docs/literate/src/files/getting_started.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/create_first_setup.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/create_first_setup.jl Co-authored-by: Michael Schlottke-Lakemper * Update docs/literate/src/files/create_first_setup.jl Co-authored-by: Michael 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<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",