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commit 1abe268 Merge: 6990c76 977ae30 Author: HanneThienpondt <[email protected]> Date: Thu Feb 27 10:44:53 2025 +0100 Merge branch 'master' of ssh://github.com/stellaGK/stella commit 6990c76 Author: HanneThienpondt <[email protected]> Date: Thu Feb 27 10:44:40 2025 +0100 Ignore pyrokinetics version file. commit 977ae30 Author: HanneThienpondt <[email protected]> Date: Thu Feb 27 10:42:32 2025 +0100 Auto-check whether pyrokinetics can load a stella output. (#197) * Automatically tests if stella is compatible with the pyrokinetics module. commit 69f5343 Author: HanneThienpondt <[email protected]> Date: Wed Feb 26 17:58:17 2025 +0100 Move utils folder into STELLA_CODE folder. (#193) commit ea4e3e5 Author: HanneThienpondt <[email protected]> Date: Tue Feb 25 15:46:14 2025 +0100 Add plotting scripts for potential(x,y) and B(X,Y,Z) to stellapy. (#192) * Add plotting scripts for potential(x,y) and B(X,Y,Z) commit b78d868 Author: valentin-seitz <[email protected]> Date: Tue Feb 25 10:47:59 2025 +0100 Adding include guards for response matrix (#190) Prevent definition of the subroutine, which uses an undefined symbol from the mp module in case ISO_C_BINDING is not available. commit 7f9b2a5 Author: HanneThienpondt <[email protected]> Date: Tue Feb 25 10:47:06 2025 +0100 Write apar(kx,ky,z) and bpar(kx,ky,z) (#191) * Write apar(kx,ky,z,t) and bpar(kx,ky,z,t) to the netcdf file. * Include write_apar2_vs_kxky and write_bpar2_vs_kxky * Print bpar to the output files. commit 7131981 Author: HanneThienpondt <[email protected]> Date: Wed Feb 19 14:58:46 2025 +0100 Add compilation files for Xula and Marenostrum (#188) * Add compilation files for Xula * Add compilation files for Marenostrum * Add load modules file for Marconi * Add load modules files for Dirac and Stellar * Add a ReadMe to help compile stella on an HPC system. * Clean-up indents and add LAPACK_LIB and LAPACK_INC * And a makefile for the GCC (GNU gfortran) compile commit 159d687 Author: HanneThienpondt <[email protected]> Date: Thu Feb 13 13:17:44 2025 +0100 Change the -J flag to $(MODULE_FLAG) commit 19fb404 Author: HanneThienpondt <[email protected]> Date: Thu Feb 13 11:31:55 2025 +0100 183 Ensure that <nzed> is always an even integer. (#187) * Clean up zgrid module. * Make sure <nzed> is an even integer. commit 6fbdda4 Author: HanneThienpondt <[email protected]> Date: Thu Feb 13 10:52:25 2025 +0100 Clean up compilation, and add makefile for Stellar (#186) * Clean up compilation of stella. - Split the Makefile into smaller parts - Added a flag "MODULE_FLAG" which can be set from the system dependent makefile, since some systems need "MODULE_FLAG = -J" while other systems need "MODULE_FLAG = -module" * Add makefile for stellar. commit 3942f40 Author: HanneThienpondt <[email protected]> Date: Thu Feb 13 10:18:58 2025 +0100 Since january 2025 the macos system on GitHub can not find the hdf5 libraries anymore during the compilation of stella. (#185) * Fix stella compilation on MacOs on GitHub.
stellaGK · Feb 27, 2025 · 7803eee · 7803eee
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diff --git a/.github/workflows/check_pyrokinetics.yml b/.github/workflows/check_pyrokinetics.yml
@@ -0,0 +1,62 @@
+# Run these tests automatically on Github on every push and pull request.
+name: Check Pyrokinetics
+on: [push, pull_request]
+
+# We always run in a bash shell
+defaults:
+  run:
+    shell: bash
+
+# First build stella, and then perform pyrokinetics tests
+jobs:
+
+#-----------------------------------------------------------------------
+#                              Quick build                              
+#-----------------------------------------------------------------------
+
+  # Build stella to perform pyrokinetics tests
+  pyrokinetics-tests: 
+    name: Check Pyrokinetics
+    runs-on: ubuntu-22.04
+    env:
+      OMPI_MCA_rmaps_base_oversubscribe: yes
+      MPIRUN: mpiexec -np
+      STELLA_SYSTEM: gnu_ubuntu
+
+    steps:
+
+      # Check-out repository under $GITHUB_WORKSPACE
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      # Install dependencies
+      - name: Install dependencies
+        run: |
+          sudo apt update
+          sudo apt install -y gfortran make libfftw3-dev libnetcdf-dev libnetcdff-dev 
+          sudo apt install -y netcdf-bin python3 python3-pip openmpi-bin libopenmpi-dev
+
+      # Build stella executable
+      - name: Build stella
+        run: |
+          git submodule update --init --recursive
+          make -j 12
+          chmod +x stella
+          
+      # Install dependencies
+      - name: Install dependencies and python virtual environment
+        run: |
+          sudo apt update
+          sudo apt install -y gfortran make libfftw3-dev libnetcdf-dev libnetcdff-dev 
+          sudo apt install -y netcdf-bin python3 python3-pip openmpi-bin libopenmpi-dev
+          pip3 install --upgrade pip
+          pip3 install --user -r AUTOMATIC_TESTS/requirements.txt
+          pip3 install EXTERNALS/pyrokinetics/.
+          sed -i 's/nproc = 16/nproc = 1/g' AUTOMATIC_TESTS/config.ini
+          
+      # Perform pyrokinetics tests
+      - name: Pyrokinetics tests
+        run: make pyrokinetics-tests
+
+
+
diff --git a/.github/workflows/check_stella.yml b/.github/workflows/check_stella.yml
@@ -22,10 +22,11 @@ jobs:
       MPIRUN: mpiexec -np
 
     # Run the same set-up multiple times
+    # Note that macos-12 has been deprecated on GitHub in 2025 
     strategy:
       fail-fast: false
       matrix:
-        os: [macos-12, macos-13, macos-14, ubuntu-20.04, ubuntu-22.04, ubuntu-24.04]
+        os: [macos-13, macos-14, ubuntu-20.04, ubuntu-22.04, ubuntu-24.04]
         compiler: [Make, CMake]
 
     # Operating system
@@ -45,21 +46,21 @@ jobs:
             echo "FFTW_LIB_DIR=/usr/local/Cellar/fftw/3.3.10_1/lib/" >> $GITHUB_ENV
             echo "Set FFTW_INC_DIR = /usr/local/include/" 
             echo "FFTW_INC_DIR=/usr/local/include/" >> $GITHUB_ENV
-            echo "Set NETCDF_LIB_DIR = /usr/local/lib -L/usr/local/Cellar/netcdf-fortran/4.6.1/lib/"
-            echo "NETCDF_LIB_DIR=/usr/local/lib -L/usr/local/Cellar/netcdf-fortran/4.6.1/lib/" >> $GITHUB_ENV
-            echo "Set NETCDF_INC_DIR = /usr/local/Cellar/netcdf-fortran/4.6.1/include/"
-            echo "NETCDF_INC_DIR=/usr/local/Cellar/netcdf-fortran/4.6.1/include/" >> $GITHUB_ENV 
+            echo "Set NETCDF_LIB_DIR = /usr/local/lib -L/usr/local/Cellar/netcdf-fortran/4.6.1_1/lib/"
+            echo "NETCDF_LIB_DIR=/usr/local/lib -L/usr/local/Cellar/netcdf-fortran/4.6.1_1/lib/" >> $GITHUB_ENV
+            echo "Set NETCDF_INC_DIR = /usr/local/Cellar/netcdf-fortran/4.6.1_1/include/"
+            echo "NETCDF_INC_DIR=/usr/local/Cellar/netcdf-fortran/4.6.1_1/include/" >> $GITHUB_ENV
           elif [ ${{ matrix.os }} == 'macos-14' ]; then 
             echo "Set STELLA_SYSTEM = macos"
             echo "STELLA_SYSTEM=macos" >> $GITHUB_ENV 
             echo "Set FFTW_LIB_DIR = /opt/homebrew/Cellar/fftw/3.3.10_1/lib/"
             echo "FFTW_LIB_DIR=/opt/homebrew/Cellar/fftw/3.3.10_1/lib/" >> $GITHUB_ENV
             echo "Set FFTW_INC_DIR = /opt/homebrew/include/" 
             echo "FFTW_INC_DIR=/opt/homebrew/include/" >> $GITHUB_ENV
-            echo "Set NETCDF_LIB_DIR = /opt/homebrew/lib -L/opt/homebrew/Cellar/netcdf-fortran/4.6.1/lib/"
-            echo "NETCDF_LIB_DIR=/opt/homebrew/lib -L/opt/homebrew/Cellar/netcdf-fortran/4.6.1/lib/" >> $GITHUB_ENV
-            echo "Set NETCDF_INC_DIR = /opt/homebrew/Cellar/netcdf-fortran/4.6.1/include/"
-            echo "NETCDF_INC_DIR=/opt/homebrew/Cellar/netcdf-fortran/4.6.1/include/" >> $GITHUB_ENV 
+            echo "Set NETCDF_LIB_DIR = /opt/homebrew/lib -L/opt/homebrew/Cellar/netcdf-fortran/4.6.1_1/lib/"
+            echo "NETCDF_LIB_DIR=/opt/homebrew/lib -L/opt/homebrew/Cellar/netcdf-fortran/4.6.1_1/lib/" >> $GITHUB_ENV
+            echo "Set NETCDF_INC_DIR = /opt/homebrew/Cellar/netcdf-fortran/4.6.1_1/include/"
+            echo "NETCDF_INC_DIR=/opt/homebrew/Cellar/netcdf-fortran/4.6.1_1/include/" >> $GITHUB_ENV
           elif ${{ contains(matrix.os, 'ubuntu') }}; then  
             echo "Set STELLA_SYSTEM = gnu_ubuntu"
             echo "STELLA_SYSTEM=gnu_ubuntu" >> $GITHUB_ENV
@@ -87,6 +88,22 @@ jobs:
       # Check-out repository under $GITHUB_WORKSPACE
       - name: Check-out repository
         uses: actions/checkout@v4 
+
+      # Print system information
+      - name: System information
+        run: |
+          if ${{ contains(matrix.os, 'macos') }}; then  
+            echo " "; echo "System information:"; echo "$(system_profiler SPHardwareDataType | sed 's/^/  /')"
+            echo " "; echo "Gfortran version:"; echo "$(gfortran --version | sed 's/^/  /')"
+            echo " "; echo "Clang version:"; echo "$(clang --version | sed 's/^/  /')"
+            make numerical-tests-system
+          elif ${{ contains(matrix.os, 'ubuntu') }}; then  
+            echo " "; echo "System information:"; echo "$(cat /etc/*release | sed 's/^/  /')"
+            echo " "; echo "Number of cores:"; echo "$(lscpu | egrep 'Model name|Socket|Thread|NUMA|CPU\(s\)' | sed 's/^/  /')"
+            echo " "; echo "Gfortran version:"; echo "$(gfortran --version | sed 's/^/  /')"
+            echo " "; echo "Netcdf version:"; echo "$(nf-config --all | sed 's/^/  /')"
+            make numerical-tests-system
+          fi
           
       # Build stella executable
       - name: Build stella
@@ -114,31 +131,29 @@ jobs:
              cmake . -B COMPILATION/build_cmake
              cmake --build COMPILATION/build_cmake -j 4
           fi
-
-      # Print system information
-      - name: System information
-        run: |
-          if ${{ contains(matrix.os, 'macos') }}; then  
-            echo " "; echo "System information:"; echo "$(system_profiler SPHardwareDataType | sed 's/^/  /')"
-            echo " "; echo "Gfortran version:"; echo "$(gfortran --version | sed 's/^/  /')"
-            echo " "; echo "Clang version:"; echo "$(clang --version | sed 's/^/  /')"
-            make numerical-tests-system
-          elif ${{ contains(matrix.os, 'ubuntu') }}; then  
-            echo " "; echo "System information:"; echo "$(cat /etc/*release | sed 's/^/  /')"
-            echo " "; echo "Number of cores:"; echo "$(lscpu | egrep 'Model name|Socket|Thread|NUMA|CPU\(s\)' | sed 's/^/  /')"
-            echo " "; echo "Gfortran version:"; echo "$(gfortran --version | sed 's/^/  /')"
-            echo " "; echo "Netcdf version:"; echo "$(nf-config --all | sed 's/^/  /')"
-            make numerical-tests-system
-          fi
           
       # Check $GITHUB_WORKSPACE
       - name: Check Github Workspace
+        if: success() || failure()
         run: | 
           echo " "; echo "Running directory:"; echo "  $(pwd)"
           echo " "; echo "Files in directory:"; echo "$(ls -la | sed 's/^/  /')"
           
+      # Location of packages
+      - name: Location of packages
+        if: success() || failure()
+        run: |
+          if [ ${{ matrix.compiler }} == 'CMake' ]; then 
+             echo " "; echo "--------- DIRECTORIES OF PACKAGES ----------"
+             cat COMPILATION/build_cmake/CMakeCache.txt
+          fi
+          if [ ${{ matrix.compiler }} == 'Make' ]; then 
+             echo " "; echo "Check the CMake compilation for the location of the packages." 
+          fi
+          
       # Install python environment
       - name: Install python virtual environment
+        if: success() || failure()
         run: |
           if [ ${{ matrix.os }} == 'ubuntu-24.04' ] || [ ${{ matrix.os }} == 'macos-14' ]; then 
             python3 -m venv AUTOMATIC_TESTS/venv
@@ -187,7 +202,7 @@ jobs:
           if [ ${{ matrix.os }} == 'ubuntu-24.04' ] || [ ${{ matrix.os }} == 'macos-14' ]; then source AUTOMATIC_TESTS/venv/bin/activate; fi
           make numerical-tests-6
           
-      - name: Python tests 7 - Electromagnetic effects"
+      - name: Python tests 7 - Electromagnetic effects
         if: success() || failure() 
         run: |
           if [ ${{ matrix.os }} == 'ubuntu-24.04' ] || [ ${{ matrix.os }} == 'macos-14' ]; then source AUTOMATIC_TESTS/venv/bin/activate; fi
@@ -225,7 +240,7 @@ jobs:
           git submodule update --init --recursive
           make -j 12
           
-          # Stella is bugged when compiling without the falg debug = on
+          # Stella is bugged when compiling without the flag debug = on
           # So the python tests will break when compiling with CMake
           #cmake . -B COMPILATION/build_cmake
           #cmake --build COMPILATION/build_cmake -j 4

diff --git a/.gitignore b/.gitignore
@@ -38,6 +38,8 @@ system_fortran.f90
 
 # Stellapy
 !stellapy/data/stella
+*.pickle
+stellapy_figures/
 
 # Fortran tests
 automated-fortran-tests
@@ -76,6 +78,9 @@ share/python-wheels/
 *.egg
 MANIFEST
 
+# External modules
+EXTERNALS/pyrokinetics/src/pyrokinetics/_version.py
+
 # PyInstaller
 #  Usually these files are written by a python script from a template
 #  before PyInstaller builds the exe, so as to inject date/other infos into it.

diff --git a/.gitmodules b/.gitmodules
@@ -7,3 +7,6 @@
 [submodule "externals/neasyf"]
 	path = EXTERNALS/neasyf
 	url = https://github.com/PlasmaFAIR/neasy-f.git
+[submodule "EXTERNALS/pyrokinetics"]
+	path = EXTERNALS/pyrokinetics
+	url = https://github.com/pyro-kinetics/pyrokinetics
diff --git a/AUTOMATIC_TESTS/Makefile b/AUTOMATIC_TESTS/Makefile
@@ -53,6 +53,11 @@ numerical-tests-system:
 test-tools: check-tests-dependencies $(PROJECT_DIR)/stella
 	@echo "Running: test stella tools"
 	@python3 -m pytest -v -rF -W ignore::DeprecationWarning $(TEST_DIR)/test_tools/
+
+# Run the automated stella tests (the -r flag shows the full stella output and -rf shows extra info about the failed outputs)
+pyrokinetics-tests: check-tests-dependencies $(PROJECT_DIR)/stella
+	@echo "Running: automated stella tests for pyrokinetics"
+	@python3 -m pytest -v -rF -W ignore::DeprecationWarning $(TEST_DIR)/pyrokinetics_tests/
 
 # Run the automated stella tests (the -r flag shows the full stella output)
 # -rA shows all outputs, -rf shows only failed outputs 

diff --git a/AUTOMATIC_TESTS/check_automated_stella_tests_requirements.py b/AUTOMATIC_TESTS/check_automated_stella_tests_requirements.py
@@ -14,7 +14,10 @@
 for line in contents:
     if line.startswith("#"):
         continue
+    if line.replace(' ','').replace('\n','').replace('\t','')=='':
+        continue
     module = line.split("=")[0]
+    if 'pyrokinetics' in line: module = 'pyrokinetics'
     requirements.append(module.replace(">", "").replace("~", "").replace("\n", ""))
 
 failed_modules = []
@@ -33,6 +36,7 @@
             Run:
                 make create-test-virtualenv
                 source AUTOMATIC_TESTS/venv/bin/activate
+                pip install EXTERNALS/pyrokinetics/.
             to install and activate test dependencies
             """
         )

diff --git a/AUTOMATIC_TESTS/pyrokinetics_tests/test_1_whether_pyrokinetics_loads/empty.in b/AUTOMATIC_TESTS/pyrokinetics_tests/test_1_whether_pyrokinetics_loads/empty.in
@@ -0,0 +1,38 @@
+
+! Smallest possible input file that runs without errors
+! and that runs fast, hence we set (nkx,nky,nzed,nmu,nvpa)
+
+&parameters_numerical
+  nstep=10
+/
+&stella_diagnostics_knobs
+  nwrite = 1
+/
+&species_parameters_1 
+/
+&kt_grids_knobs
+  grid_option='range'
+/
+&kt_grids_range_parameters
+  naky = 10
+  aky_min = 0.1
+  aky_max = 1.0
+  nakx = 1
+  akx_min = 0.0
+  akx_max = 0.0
+/
+&zgrid_parameters 
+  nzed = 8
+/
+&vpamu_grids_parameters
+  nmu = 4 
+  nvgrid = 6 
+/
+&millergeo_parameters
+  rhoc = 0.5
+  shat = 0.796
+  qinp = 1.4
+  rmaj = 2.77778
+  rgeo = 2.77778
+  kappa = 1.0
+/ 
diff --git a/AUTOMATIC_TESTS/pyrokinetics_tests/test_1_whether_pyrokinetics_loads/miller_linear_CBC.in b/AUTOMATIC_TESTS/pyrokinetics_tests/test_1_whether_pyrokinetics_loads/miller_linear_CBC.in
@@ -0,0 +1,97 @@
+
+! Simple linear example using CBC
+
+&parameters_physics
+  adiabatic_option = 'iphi00=2'
+  full_flux_surface = .false.
+  include_apar = .false.
+  nonlinear = .false.
+  vnew_ref = 0.01
+/
+&parameters_numerical
+  delt = 0.05 
+  nstep = 10
+  print_extra_info_to_terminal = .false.
+/
+&stella_diagnostics_knobs
+  nsave = 10
+  nwrite = 1
+  save_for_restart = .false.
+  write_all = .true.
+/
+&species_knobs
+  nspec = 2
+  species_option = 'stella'
+/
+&species_parameters_1
+  dens = 1.0
+  fprim = 1.0
+  mass = 1.0
+  temp = 1.0
+  tprim = 3.0
+  type = 'ion'
+  z = 1.0
+/
+&species_parameters_2
+  dens = 1.0
+  fprim = 1.0
+  mass = 0.0005446
+  temp = 1.0
+  tprim = 3.0
+  type = 'electron'
+  z = -1.0
+/
+&kt_grids_knobs
+  grid_option='range'
+/
+&kt_grids_range_parameters
+  naky = 10
+  aky_min = 0.1
+  aky_max = 1.0
+  nakx = 1
+  akx_min = 0.0
+  akx_max = 0.0
+/
+&zgrid_parameters
+  boundary_option = 'zero'
+  nperiod = 1
+  nzed = 8
+/
+&vpamu_grids_parameters
+  nmu = 4 
+  nvgrid = 6 
+/
+&init_g_knobs
+  ginit_option = 'noise'
+  phiinit = 0.01
+/
+&dissipation
+  hyper_dissipation = .true.
+/
+&geo_knobs
+  geo_option = 'miller'
+/
+&time_advance_knobs 
+  explicit_option = 'rk2'
+/
+&layouts_knobs
+  vms_layout = 'vms'
+  xyzs_layout = 'yxzs'
+/
+&millergeo_parameters
+  nzed_local = 128
+  rhoc = 0.5
+  shat = 0.796
+  qinp = 1.4
+  rmaj = 2.77778
+  rgeo = 2.77778
+  shift = 0.0
+  kappa = 1.0
+  kapprim = 0.0
+  tri = 0.0
+  triprim = 0.0
+  betaprim = 0.0
+  d2qdr2 = 0.0
+  d2psidr2 = 0.0
+  betadbprim = 0.0
+/