Document and unify C and Fortran examples (#133)

* rename all examples to trixi_controller_*.(c|f90) * increase buffer size (was not enough for all julia packages) * add MPI to Fotran example trixi_controller_mpi.(c|f90) should not be comparable * explain contents of examples * update docs corresponding to README.md * get data several times in trixi_controller_data (relevant for AMR) * make trixi_controller_data also work for just one variable * test t8code elixir * rename elixir in CI * adapt to C version * touch-up * same libelexir for C and Fortran * missed renaming * more missing * make t8code amr example more lightweight * not too lightweight * Update LibTrixi.jl/examples/libelixir_t8code_2d_dgsem_advection_amr.jl Co-authored-by: Michael Schlottke-Lakemper <[email protected]> * Update examples/.gitignore Co-authored-by: Michael Schlottke-Lakemper <[email protected]> * Fortran awareness * free data --------- Co-authored-by: Michael Schlottke-Lakemper <[email protected]>
trixi-framework · Oct 20, 2023 · a47d01e · a47d01e
1 parent d232781
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -154,7 +154,7 @@ jobs:
               --force
           cp ../install/share/libtrixi/LibTrixi.jl/examples/libelixir_tree1d_dgsem_advection_basic.jl .
           cp ../install/share/libtrixi/LibTrixi.jl/examples/libelixir_p4est2d_dgsem_euler_sedov.jl .
-          cp ../install/share/libtrixi/LibTrixi.jl/examples/libelixir_t8code_2d_dgsem_advection_basic.jl .
+          cp ../install/share/libtrixi/LibTrixi.jl/examples/libelixir_t8code_2d_dgsem_advection_amr.jl .
 
       - name: Initialize project directory
         if: ${{ matrix.test_type == 'package-compiler' }}
@@ -194,7 +194,7 @@ jobs:
         run: |
           cd examples/external
           ./build.sh
-          mpirun -n 2 ./build/simple_trixi_controller_c \
+          mpirun -n 2 ./build/trixi_controller_simple_c \
               ../../libtrixi-julia \
               ../../LibTrixi.jl/examples/libelixir_p4est2d_dgsem_euler_sedov.jl
         env:
@@ -221,21 +221,21 @@ jobs:
         if: ${{ matrix.test_type == 'regular' || matrix.test_type == 'coverage' }}
         run: |
           cd libtrixi-julia
-          ../build/examples/simple_trixi_controller_c . libelixir_tree1d_dgsem_advection_basic.jl
-          ../build/examples/simple_trixi_controller_f . libelixir_tree1d_dgsem_advection_basic.jl
-          ../build/examples/simple_trixi_controller_c . libelixir_p4est2d_dgsem_euler_sedov.jl
-          ../build/examples/simple_trixi_controller_f . libelixir_p4est2d_dgsem_euler_sedov.jl
-          ../build/examples/trixi_controller_data_c . libelixir_p4est2d_dgsem_euler_sedov.jl
-          ../build/examples/trixi_controller_data_f . libelixir_p4est2d_dgsem_euler_sedov.jl
-          ../build/examples/simple_t8code_c . libelixir_t8code_2d_dgsem_advection_basic.jl
+          ../build/examples/trixi_controller_simple_c . libelixir_tree1d_dgsem_advection_basic.jl
+          ../build/examples/trixi_controller_simple_f . libelixir_tree1d_dgsem_advection_basic.jl
+          ../build/examples/trixi_controller_simple_c . libelixir_p4est2d_dgsem_euler_sedov.jl
+          ../build/examples/trixi_controller_simple_f . libelixir_p4est2d_dgsem_euler_sedov.jl
+          ../build/examples/trixi_controller_data_c . libelixir_t8code_2d_dgsem_advection_amr.jl
+          ../build/examples/trixi_controller_data_f . libelixir_t8code_2d_dgsem_advection_amr.jl
+          ../build/examples/trixi_controller_t8code_c . libelixir_t8code_2d_dgsem_advection_amr.jl
         env:
           LIBTRIXI_DEBUG: all
 
       - name: Run examples
         if: ${{ matrix.test_type == 'package-compiler' }}
         run: |
           cd build/examples
-          mpirun -n 2 simple_trixi_controller_c \
+          mpirun -n 2 trixi_controller_simple_c \
               ../../libtrixi-julia \
               ../../LibTrixi.jl/examples/libelixir_p4est2d_dgsem_euler_sedov.jl
         env:
@@ -246,16 +246,16 @@ jobs:
         run: |
           cd libtrixi-julia
           set +e  # disable early exit on non-zero exit code
-          for command in "../build/examples/simple_trixi_controller_c"   \
-                         "../build/examples/simple_trixi_controller_c ." \
-                         "../build/examples/simple_trixi_controller_f"   \
-                         "../build/examples/simple_trixi_controller_f ." \
+          for command in "../build/examples/trixi_controller_simple_c"   \
+                         "../build/examples/trixi_controller_simple_c ." \
+                         "../build/examples/trixi_controller_simple_f"   \
+                         "../build/examples/trixi_controller_simple_f ." \
                          "../build/examples/trixi_controller_data_c"     \
                          "../build/examples/trixi_controller_data_c ."   \
                          "../build/examples/trixi_controller_data_f"     \
                          "../build/examples/trixi_controller_data_f ."   \
-                         "../build/examples/simple_t8code_c"             \
-                         "../build/examples/simple_t8code_c ."
+                         "../build/examples/trixi_controller_t8code_c"             \
+                         "../build/examples/trixi_controller_t8code_c ."
             do
               $command
               if [ $? -ne 2 ]; then

diff --git a/...elixir_t8code_2d_dgsem_advection_basic.jl → ...ibelixir_t8code_2d_dgsem_advection_amr.jl b/...elixir_t8code_2d_dgsem_advection_basic.jl → ...ibelixir_t8code_2d_dgsem_advection_amr.jl
@@ -19,7 +19,7 @@ function init_simstate()
 
     mapping = Trixi.coordinates2mapping(coordinates_min, coordinates_max)
 
-    trees_per_dimension = (4, 4)
+    trees_per_dimension = (2, 2)
 
     mesh = T8codeMesh(trees_per_dimension, polydeg=3,
                       mapping=mapping,
@@ -32,8 +32,8 @@ function init_simstate()
     ###############################################################################
     # ODE solvers, callbacks etc.
 
-    # Create ODE problem with time span from 0.0 to 1.0
-    ode = semidiscretize(semi, (0.0, 1.0));
+    # Create ODE problem with time span from 0.0 to 0.2
+    ode = semidiscretize(semi, (0.0, 0.2));
 
     # At the beginning of the main loop, the SummaryCallback prints a summary of the simulation setup
     # and resets the timers
@@ -48,10 +48,21 @@ function init_simstate()
     # The StepsizeCallback handles the re-calculation of the maximum Δt after each time step
     stepsize_callback = StepsizeCallback(cfl=0.5)
 
+    # The AMRCallback triggers adaptive mesh refinement
+    amr_controller = ControllerThreeLevel(semi, IndicatorMax(semi, variable=first),
+                                          base_level=2,
+                                          med_level=3, med_threshold=0.1,
+                                          max_level=4, max_threshold=0.6)
+    amr_callback = AMRCallback(semi, amr_controller,
+                               interval=10,
+                               adapt_initial_condition=true,
+                               adapt_initial_condition_only_refine=true)
+
     # Create a CallbackSet to collect all callbacks such that they can be passed to the ODE solver
     callbacks = CallbackSet(summary_callback,
                             analysis_callback,
                             alive_callback,
+                            amr_callback,
                             stepsize_callback)
 
 

diff --git a/LibTrixi.jl/test/test_t8code.jl b/LibTrixi.jl/test/test_t8code.jl
@@ -6,7 +6,7 @@ using Trixi
 
 
 libelixir = joinpath(dirname(pathof(LibTrixi)),
-                     "../examples/libelixir_t8code_2d_dgsem_advection_basic.jl")
+                     "../examples/libelixir_t8code_2d_dgsem_advection_amr.jl")
 
 # initialize a simulation via API, receive a handle
 handle = trixi_initialize_simulation(libelixir)

diff --git a/README.md b/README.md
@@ -111,7 +111,7 @@ Go to some directory from where you want to run a Trixi simulation.
 
 ```shell
 LIBTRIXI_DEBUG=all \
-    <install_directory>/bin/simple_trixi_controller_c \
+    <install_directory>/bin/trixi_controller_simple_c \
     <libtrixi-julia_directory> \
     <install_directory>/share/libtrixi/LibTrixi.jl/examples/libelixir_tree1d_dgsem_advection_basic.jl
 ```
@@ -207,20 +207,25 @@ Current time step length: 0.050000
  ────────────────────────────────────────────────────────────────────────────────────
 ```
 
-If you change the executable name from `simple_trixi_controller_c` to
-`simple_trixi_controller_f`, you will get a near identical output. The corresponding source
-files `simple_trixi_controller.c` and `simple_trixi_controller.f90` give you an idea on how
-to use the C and Fortran APIs of libtrixi, and can be found in the
-[`examples/`](examples/) folder.
+If you change the executable name from `trixi_controller_simple_c` to
+`trixi_controller_simple_f`, you will get a near identical output. The corresponding source
+files can be found in the [`examples/`](examples/) folder. The examples demonstrate different
+aspects on how to use the C and Fortran APIs of libtrixi:
+
+- `trixi_controller_simple.(c|f90)`: basic usage
+- `trixi_controller_mpi.(c|f90)`: usage in the presence of MPI
+- `trixi_controller_data.(c|f90)`: simulation data access
+- `trixi_controller_t8code.c`: interacting with t8code
+  (there is no Fortran example yet as the Fortran interface of t8code is still under development)
 
 If you just want to test the Julia part of libtrixi, i.e., LibTrixi.jl, you can also run
-everything from Julia.
+`trixi_controller_simple.jl` from Julia.
 
 ```shell
 JULIA_DEPOT_PATH=<julia-depot_directory> \
 LIBTRIXI_DEBUG=all \
     julia --project=<libtrixi-julia_directory>
-    <install_directory>/share/libtrixi/examples/simple_trixi_controller.jl
+    <install_directory>/share/libtrixi/examples/trixi_controller_simple.jl
     <install_directory>/share/libtrixi/LibTrixi.jl/examples/libelixir_tree1d_dgsem_advection_basic.jl
 ```
 
@@ -247,7 +252,7 @@ the `examples/` directory as
 ```shell
 make -f MakefileExternal LIBTRIXI_PREFIX=path/to/libtrixi/prefix
 ```
-to build `simple_trixi_controller_f`.
+to build `trixi_controller_simple_f`.
 
 #### CMake
 
@@ -289,12 +294,12 @@ To try this out, perform the following steps:
       make
       ```
     - Go to the `examples` folder in the repository root and compile
-      `simple_trixi_controller_c`:
+      `trixi_controller_simple_c`:
       ```shell
       cd examples
       make -f MakefileCompiled LIBTRIXI_PREFIX=$PWD/../LibTrixi.jl/lib/build
       ```
-      This will create a `simple_trixi_controller_c` file.
+      This will create a `trixi_controller_simple_c` file.
 
     *using cmake*
     - Add
@@ -305,7 +310,7 @@ To try this out, perform the following steps:
 3. From inside the `examples` folder you should be able to run the example (in parallel)
    with the following command:
    ```shell
-   mpirun -n 2 simple_trixi_controller_c \
+   mpirun -n 2 trixi_controller_simple_c \
        ../libtrixi-julia \
        ../LibTrixi.jl/examples/libelixir_p4est2d_dgsem_euler_sedov.jl
    ```

diff --git a/docs/src/index.md b/docs/src/index.md
@@ -113,7 +113,7 @@ Go to some directory from where you want to run a Trixi simulation.
 
 ```shell
 LIBTRIXI_DEBUG=all \
-    <install_directory>/bin/simple_trixi_controller_c \
+    <install_directory>/bin/trixi_controller_simple_c \
     <libtrixi-julia_directory> \
     <install_directory>/share/libtrixi/LibTrixi.jl/examples/libelixir_tree1d_dgsem_advection_basic.jl
 ```
@@ -209,18 +209,27 @@ Current time step length: 0.050000
  ────────────────────────────────────────────────────────────────────────────────────
 ```
 
-If you change the executable name from `simple_trixi_controller_c` to
-`simple_trixi_controller_f`, you will get a near identical output. The corresponding source
-files `simple_trixi_controller.c` and `simple_trixi_controller.f90` give you an idea on how
-to use the C and Fortran APIs of libtrixi, and can be found in the
-[`examples/`](https://github.com/trixi-framework/libtrixi/tree/main/examples/) folder.
+If you change the executable name from `trixi_controller_simple_c` to
+`trixi_controller_simple_f`, you will get a near identical output. The corresponding source
+files can be found in the
+[`examples/`](https://github.com/trixi-framework/libtrixi/tree/main/examples/) folder. The
+examples demonstrate different aspects on how to use the C and Fortran APIs of libtrixi:
+
+- `trixi_controller_simple.(c|f90)`: basic usage
+- `trixi_controller_mpi.(c|f90)`: usage in the presence of MPI
+- `trixi_controller_data.(c|f90)`: simulation data access
+- `trixi_controller_t8code.c`: interacting with t8code
+  (there is no Fortran example yet as the Fortran interface of t8code is still under development)
 
 If you just want to test the Julia part of libtrixi, i.e., LibTrixi.jl, you can also run
-everything from Julia. From the repository root, execute
+`trixi_controller_simple.jl` from Julia.
+
 ```shell
-JULIA_DEPOT_PATH=$PWD/libtrixi-julia/julia-depot \
+JULIA_DEPOT_PATH=<julia-depot_directory> \
+LIBTRIXI_DEBUG=all \
     julia --project=<libtrixi-julia_directory>
-    <install_directory>/share/libtrixi/LibTrixi.jl/examples/simple_trixi_controller.jl
+    <install_directory>/share/libtrixi/examples/trixi_controller_simple.jl
+    <install_directory>/share/libtrixi/LibTrixi.jl/examples/libelixir_tree1d_dgsem_advection_basic.jl
 ```
 
 Note: Most auxiliary output is hidden unless the environment variable `LIBTRIXI_DEBUG` is
@@ -246,7 +255,7 @@ which can be invoked from inside the `examples/` directory as
 ```shell
 make -f MakefileExternal LIBTRIXI_PREFIX=path/to/libtrixi/prefix
 ```
-to build `simple_trixi_controller_f`.
+to build `trixi_controller_simple_f`.
 
 #### CMake
 
@@ -289,12 +298,12 @@ To try this out, perform the following steps:
       make
       ```
     - Go to the `examples` folder in the repository root and compile
-      `simple_trixi_controller_c`:
+      `trixi_controller_simple_c`:
       ```shell
       cd examples
       make -f MakefileCompiled LIBTRIXI_PREFIX=$PWD/../LibTrixi.jl/lib/build
       ```
-      This will create a `simple_trixi_controller_c` file.
+      This will create a `trixi_controller_simple_c` file.
 
     *using cmake*
     - Add
@@ -305,7 +314,7 @@ To try this out, perform the following steps:
 3. From inside the `examples` folder you should be able to run the example (in parallel)
    with the following command:
    ```shell
-   mpirun -n 2 simple_trixi_controller_c \
+   mpirun -n 2 trixi_controller_simple_c \
        ../libtrixi-julia \
        ../LibTrixi.jl/examples/libelixir_p4est2d_dgsem_euler_sedov.jl
    ```

diff --git a/examples/.gitignore b/examples/.gitignore
@@ -1,2 +1,8 @@
-simple_trixi_controller_c
-simple_trixi_controller_f
+trixi_controller_simple_c
+trixi_controller_simple_f
+trixi_controller_mpi_c
+trixi_controller_mpi_f
+trixi_controller_data_c
+trixi_controller_data_f
+trixi_controller_t8code_c
+trixi_controller_t8code_f
diff --git a/examples/CMakeLists.txt b/examples/CMakeLists.txt
@@ -1,9 +1,11 @@
 set ( EXAMPLES
-      simple_trixi_controller.c
-      simple_trixi_controller.f90
-      simple_t8code.c 
+      trixi_controller_simple.c
+      trixi_controller_simple.f90
+      trixi_controller_mpi.c
+      trixi_controller_mpi.f90
       trixi_controller_data.c
-      trixi_controller_data.f90 )
+      trixi_controller_data.f90
+      trixi_controller_t8code.c )
 
 if ( NOT T8CODE_FOUND )
     list( FILTER EXAMPLES EXCLUDE REGEX ".*(t|T)8(c|C)(o|O)(d|D)(e|E).*" )
@@ -67,4 +69,4 @@ foreach ( EXAMPLE ${EXAMPLES} )
 endforeach()
 
 # install the julia controller example as well
-install( FILES simple_trixi_controller.jl DESTINATION share/libtrixi/examples/ )
+install( FILES trixi_controller_simple.jl DESTINATION share/libtrixi/examples/ )
diff --git a/examples/MakefileCompiled b/examples/MakefileCompiled
@@ -14,5 +14,5 @@ CFLAGS ?= -fPIC
 LDFLAGS ?= -L$(libdir) -Wl,-rpath,$(libdir) -L$(MPI_PREFIX)/lib -Wl,-rpath,$(MPI_PREFIX)/lib
 LIBS ?= -ltrixi -lmpi
 
-simple_trixi_controller_c: simple_trixi_controller.c
+trixi_controller_simple_c: trixi_controller_simple.c
 	$(CC) $< -o $@ $(CFLAGS) $(CPPFLAGS) $(LDFLAGS) $(LIBS)
diff --git a/examples/MakefileExternal b/examples/MakefileExternal
@@ -6,5 +6,5 @@ FC ?= f95
 libdir := $(LIBTRIXI_PREFIX)/lib
 incdir := $(LIBTRIXI_PREFIX)/include
 
-simple_trixi_controller_f: simple_trixi_controller.f90
+trixi_controller_simple_f: trixi_controller_simple.f90
 	$(FC) $< -o $@ -fPIC -I$(incdir) -L$(libdir) -Wl,-rpath,$(libdir) -ltrixi $(libdir)/libtrixi_tls.o
diff --git a/examples/external/CMakeLists.txt b/examples/external/CMakeLists.txt
@@ -14,8 +14,8 @@ find_package( MPI REQUIRED )
 find_package( LibTrixi REQUIRED )
 
 # Set sources
-set ( TARGET_NAME simple_trixi_controller_c )
-add_executable ( ${TARGET_NAME} ${CMAKE_SOURCE_DIR}/../simple_trixi_controller.c )
+set ( TARGET_NAME trixi_controller_simple_c )
+add_executable ( ${TARGET_NAME} ${CMAKE_SOURCE_DIR}/../trixi_controller_simple.c )
 
 # Set libraries to link
 target_link_libraries(

diff --git a/examples/trixi_controller_data.c b/examples/trixi_controller_data.c
@@ -24,32 +24,38 @@ int main ( int argc, char *argv[] ) {
     printf("\n*** Trixi controller ***   Set up Trixi simulation\n");
     int handle = trixi_initialize_simulation( argv[2] );
 
+    // Get number of variables
+    int nvariables = trixi_nvariables( handle );
+    printf("\n*** Trixi controller ***   nvariables %d\n", nvariables);
+
     // Main loop
+    int steps = 0;
+    int nelements = 0;
+    double* data = NULL;
+
     printf("\n*** Trixi controller ***   Entering main loop\n");
     while ( !trixi_is_finished( handle ) ) {
 
         trixi_step( handle );
-    }
+        steps++;
 
-    // get number of elements
-    int nelements = trixi_nelements( handle );
-    printf("\n*** Trixi controller ***   nelements %d\n", nelements);
+        if (steps % 10 == 0) {
 
-    // get number of variables
-    int nvariables = trixi_nvariables( handle );
-    printf("\n*** Trixi controller ***   nvariables %d\n", nvariables);
-
-    // allocate memory
-    double* data = malloc( sizeof(double) * nelements * nvariables );
+            // Get number of elements
+            nelements = trixi_nelements( handle );
+            printf("\n*** Trixi controller ***   nelements %d\n", nelements);
 
-    // get averaged cell values for each variable
-    trixi_load_cell_averages(data, handle);
+            // Allocate memory
+            data = realloc( data, sizeof(double) * nelements * nvariables );
 
-    // compute temperature
-    const double gas_constant = 0.287;
+            // Get averaged cell values for each variable
+            trixi_load_cell_averages(data, handle);
+        }
+    }
 
+    // Print first variable
     for (int i = 0; i < nelements; ++i) {
-        printf("T[cell %3d] = %f\n", i, data[i+3*nelements] / (gas_constant * data[i]) );
+        printf("u[cell %3d] = %f\n", i, data[i]);
     }
 
     // Finalize Trixi simulation
@@ -60,5 +66,7 @@ int main ( int argc, char *argv[] ) {
     printf("\n*** Trixi controller ***   Finalize Trixi\n");
     trixi_finalize();
 
+    free(data);
+
     return 0;
 }