Run automatic stella tests on old stella releases

.github/workflows/old_stella_releases.yml

@@ -0,0 +1,193 @@
+# Run these tests automatically on Github on every push and pull request.
+# Use the macOS operating system, which has 4 cores.
+name: Check old stella releases
+on: [push]
+
+# We always run in a bash shell
+defaults:
+  run:
+    shell: bash
+
+# First build stella, and then perform python tests
+jobs:
+
+#-----------------------------------------------------------------------
+#                             Python tests                              
+#-----------------------------------------------------------------------
+
+  # Perform python tests one by one
+  stella-v5: 
+    runs-on: ubuntu-22.04
+    env:
+      OMPI_MCA_rmaps_base_oversubscribe: yes
+      MPIRUN: mpiexec -np
+      STELLA_SYSTEM: gnu_ubuntu
+
+    # Run the same set-up multiple times
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - name: "1 - Does stella run "
+          #- name: "2 - Geometry"
+          #- name: "3 - Gyrokinetic equation"
+          #- name: "4 - Flux tube"
+          #- name: "5 - Diagnostics"
+          #- name: "6 - Full Flux Surface"
+          #- name: "7 - Electromagnetic effects"
+
+    steps:
+
+      # Check-out repository under $GITHUB_WORKSPACE
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      # 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 --user -r AUTOMATIC_TESTS/requirements.txt
+          sed -i 's/nproc = 16/nproc = 4/g' AUTOMATIC_TESTS/config.ini 
+
+      # Check $GITHUB_WORKSPACE
+      - name: Check Github Workspace
+        run: | 
+          echo " "; echo "Running directory:"; echo "  $(pwd)"
+          echo " "; echo "Files in directory:"; echo "$(ls -la | sed 's/^/  /')"
+          echo " "; echo "Files in directory:"; echo "$(ls AUTOMATIC_TESTS/numerical_tests -la | sed 's/^/  /')"
+          echo " "; echo "Files in directory:"; echo "$(ls AUTOMATIC_TESTS/numerical_tests/stella_releases -la | sed 's/^/  /')"
+
+      # Coppy stella executable from AUTOMATIC_TESTS/numerical_tests/stella_releases
+      - name: Copy stella executable
+        run: |
+          cp AUTOMATIC_TESTS/numerical_tests/stella_releases/stella_v0.7 stella
+
+      # Perform python tests  
+      - name: Numerical python tests
+        run: |
+          # Make stella executable
+          chmod +x stella
+
+          # Run one of the python tests
+          if ${{ contains(matrix.config.name, '1 -') }}; then make numerical-tests-1; fi
+          if ${{ contains(matrix.config.name, '2 -') }}; then make numerical-tests-2; fi
+          if ${{ contains(matrix.config.name, '3 -') }}; then make numerical-tests-3; fi
+          if ${{ contains(matrix.config.name, '4 -') }}; then make numerical-tests-4; fi
+          if ${{ contains(matrix.config.name, '5 -') }}; then make numerical-tests-5; fi
+          if ${{ contains(matrix.config.name, '6 -') }}; then make numerical-tests-6; fi
+          if ${{ contains(matrix.config.name, '7 -') }}; then make numerical-tests-7; fi
+
+  # Perform python tests one by one
+  stella-v6: 
+    runs-on: ubuntu-22.04
+    env:
+      OMPI_MCA_rmaps_base_oversubscribe: yes
+      MPIRUN: mpiexec -np
+      STELLA_SYSTEM: gnu_ubuntu
+
+    # Run the same set-up multiple times
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - name: "1 - Does stella run "
+          #- name: "2 - Geometry"
+          #- name: "3 - Gyrokinetic equation"
+          #- name: "4 - Flux tube"
+          #- name: "5 - Diagnostics"
+          #- name: "6 - Full Flux Surface"
+          #- name: "7 - Electromagnetic effects"
+
+    steps:
+
+      # Check-out repository under $GITHUB_WORKSPACE
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      # 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 --user -r AUTOMATIC_TESTS/requirements.txt
+          sed -i 's/nproc = 16/nproc = 4/g' AUTOMATIC_TESTS/config.ini 
+
+      # Coppy stella executable from AUTOMATIC_TESTS/numerical_tests/stella_releases
+      - name: Download stella 
+        run: |
+          cp AUTOMATIC_TESTS/numerical_tests/stella_releases/stella_v0.6 stella
+
+      # Perform python tests  
+      - name: Numerical python tests
+        run: |
+          # Make stella executable
+          chmod +x stella
+
+          # Run one of the python tests
+          if ${{ contains(matrix.config.name, '1 -') }}; then make numerical-tests-1; fi
+          if ${{ contains(matrix.config.name, '2 -') }}; then make numerical-tests-2; fi
+          if ${{ contains(matrix.config.name, '3 -') }}; then make numerical-tests-3; fi
+          if ${{ contains(matrix.config.name, '4 -') }}; then make numerical-tests-4; fi
+          if ${{ contains(matrix.config.name, '5 -') }}; then make numerical-tests-5; fi
+          if ${{ contains(matrix.config.name, '6 -') }}; then make numerical-tests-6; fi
+          if ${{ contains(matrix.config.name, '7 -') }}; then make numerical-tests-7; fi
+
+
+  # Perform python tests one by one
+  stella-v7: 
+    runs-on: ubuntu-22.04
+    env:
+      OMPI_MCA_rmaps_base_oversubscribe: yes
+      MPIRUN: mpiexec -np
+      STELLA_SYSTEM: gnu_ubuntu
+
+    # Run the same set-up multiple times
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - name: "1 - Does stella run "
+          #- name: "2 - Geometry"
+          #- name: "3 - Gyrokinetic equation"
+          #- name: "4 - Flux tube"
+          #- name: "5 - Diagnostics"
+          #- name: "6 - Full Flux Surface"
+          #- name: "7 - Electromagnetic effects"
+
+    steps:
+
+      # Check-out repository under $GITHUB_WORKSPACE
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      # 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 --user -r AUTOMATIC_TESTS/requirements.txt
+          sed -i 's/nproc = 16/nproc = 4/g' AUTOMATIC_TESTS/config.ini 
+
+      # Coppy stella executable from AUTOMATIC_TESTS/numerical_tests/stella_releases
+      - name: Download stella 
+        run: |
+          cp AUTOMATIC_TESTS/numerical_tests/stella_releases/stella_v0.7 stella
+
+      # Perform python tests  
+      - name: Numerical python tests
+        run: |
+          # Make stella executable
+          chmod +x stella
+
+          # Run one of the python tests
+          if ${{ contains(matrix.config.name, '1 -') }}; then make numerical-tests-1; fi
+          if ${{ contains(matrix.config.name, '2 -') }}; then make numerical-tests-2; fi
+          if ${{ contains(matrix.config.name, '3 -') }}; then make numerical-tests-3; fi
+          if ${{ contains(matrix.config.name, '4 -') }}; then make numerical-tests-4; fi
+          if ${{ contains(matrix.config.name, '5 -') }}; then make numerical-tests-5; fi
+          if ${{ contains(matrix.config.name, '6 -') }}; then make numerical-tests-6; fi
+          if ${{ contains(matrix.config.name, '7 -') }}; then make numerical-tests-7; fi

.gitignore

@@ -7,6 +7,7 @@
 *.swp
 *.so
 stella
+update-input-file
 .DS_Store
 geo/vmec_interface/test_vmec_to_geometry_interface
 post_processing/clean_hist

AUTOMATIC_TESTS/Makefile

@@ -49,6 +49,11 @@ numerical-tests-7: check-tests-dependencies $(PROJECT_DIR)/stella
 numerical-tests-system:
 	@python3 $(TEST_DIR)/system_information.py
 
+# Test tools
+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)
 # -rA shows all outputs, -rf shows only failed outputs 
 numerical-tests-verbose: check-tests-dependencies $(PROJECT_DIR)/stella

AUTOMATIC_TESTS/numerical_tests/common_input_files/geometry_CBC.in

@@ -0,0 +1,24 @@
+
+! Miller geometry corresponding to the Cyclone Base Case (CBC)
+! See [2000 - Dimits - Comparisons and physics basis of tokamak transport models and turbulence simulations]
+
+&geo_knobs
+  geo_option = 'miller'
+/
+&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
+/ 

AUTOMATIC_TESTS/numerical_tests/common_input_files/init_distribution_noise.in

@@ -0,0 +1,6 @@
+
+&init_g_knobs
+  ginit_option = 'noise'
+  phiinit = 0.01
+/
+

AUTOMATIC_TESTS/numerical_tests/common_input_files/kinetic_electrons_and_ions.in

@@ -0,0 +1,23 @@
+
+&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
+/

AUTOMATIC_TESTS/numerical_tests/common_input_files/low_resolution_kxky_box.in

@@ -0,0 +1,11 @@
+
+
+&kt_grids_knobs
+  grid_option = 'box'
+/
+&kt_grids_box_parameters
+  jtwist = 5
+  nx = 6
+  ny = 9
+  y0 = 15
+/

AUTOMATIC_TESTS/numerical_tests/common_input_files/low_resolution_zvpamu_linked.in

@@ -0,0 +1,10 @@
+
+&zgrid_parameters
+  boundary_option = 'linked'
+  nperiod = 1
+  nzed = 12
+/
+&vpamu_grids_parameters
+  nmu = 2 
+  nvgrid = 3 
+/

AUTOMATIC_TESTS/numerical_tests/common_input_files/other_knobs.in

@@ -0,0 +1,8 @@
+
+&dissipation
+  hyper_dissipation = .true.
+/
+&layouts_knobs
+  vms_layout = 'vms'
+  xyzs_layout = 'yxzs'
+/

AUTOMATIC_TESTS/numerical_tests/common_input_files/short_time_trace_nstep10.in

@@ -0,0 +1,17 @@
+
+&time_advance_knobs
+  explicit_option = 'rk2'
+/
+&knobs
+  delt = 0.01 
+  nstep = 10
+  fapar = 0.0
+  fbpar = 0.0
+  fphi = 1.0
+/
+&parameters_numerical
+  delt = 0.01 
+  nstep = 10
+  print_extra_info_to_terminal = .false.
+  explicit_option = 'rk2'
+/

AUTOMATIC_TESTS/numerical_tests/common_input_files/short_time_trace_nstep100.in

@@ -0,0 +1,19 @@
+
+&time_advance_knobs
+  explicit_option = 'rk2'
+/
+&knobs
+  delt = 0.01 
+  nstep = 100
+  fapar = 0.0
+  fbpar = 0.0
+  fphi = 1.0
+  rng_seed = 1
+/
+&parameters_numerical
+  delt = 0.01 
+  nstep = 100
+  print_extra_info_to_terminal = .false.
+  explicit_option = 'rk2'
+  rng_seed = 1
+/

AUTOMATIC_TESTS/numerical_tests/common_input_files/write_all_diagnostics.in

@@ -0,0 +1,25 @@
+
+! Write all diagnostics
+
+&stella_diagnostics_knobs
+  nsave = 10
+  nwrite = 1
+  save_for_restart = .false.
+  write_phi_vs_time = .true.
+  write_gvmus = .true.
+  write_gzvs = .true.
+  write_omega = .true.
+  write_kspectra = .true.
+  write_moments = .true.
+  write_radial_fluxes = .true.
+  write_radial_moments = .true.
+  write_fluxes_kxkyz = .true.
+  flux_norm = .true.
+/
+&diagnostics 
+  nsave = 10
+  nwrite = 1
+  save_for_restart = .false.
+  flux_norm = .true.
+  write_all = .true.
+/