Update the input file so it contains all default variables.

.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.
+/

AUTOMATIC_TESTS/numerical_tests/common_input_files/write_all_diagnostics_nwrite10.in

@@ -0,0 +1,27 @@
+
+! Write all diagnostics
+
+&stella_diagnostics_knobs
+  nsave = 100
+  nwrite = 10
+  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.
+  write_apar_vs_time = .true. 
+  write_bpar_vs_time = .true.
+/
+&diagnostics 
+  nsave = 100
+  nwrite = 10
+  save_for_restart = .false.
+  flux_norm = .true.
+  write_all = .true.
+/

AUTOMATIC_TESTS/numerical_tests/test_1_whether_stella_runs/miller_nonlinear_CBC.in

@@ -1,94 +1,21 @@
 
 ! Simple nonlinear example using CBC
 
+!include common_input_files/geometry_CBC.in
+!include common_input_files/kinetic_electrons_and_ions.in
+!include common_input_files/low_resolution_kxky_box.in
+!include common_input_files/low_resolution_zvpamu_linked.in
+!include common_input_files/init_distribution_noise.in
+!include common_input_files/write_all_diagnostics.in
+!include common_input_files/short_time_trace_nstep10.in
+!include common_input_files/other_knobs.in
+
 &physics_flags
-  adiabatic_option = 'iphi00=2'
-  full_flux_surface = .false.
-  include_apar = .false.
   nonlinear = .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_box_parameters
-  jtwist = 5
-  nx = 6
-  ny = 9
-  y0 = 15
-/
-&zgrid_parameters
-  boundary_option = 'linked'
-  nperiod = 1
-  nzed = 12
-/
-&vpamu_grids_parameters
-  nmu = 2 
-  nvgrid = 3 
-/
-&knobs
-  delt = 0.01 
-  nstep = 10
-  print_extra_info_to_terminal = .false.  
-/
-&stella_diagnostics_knobs
-  nsave = 10
-  nwrite = 1
-  save_for_restart = .false.
-  write_all = .true.
-/
-&init_g_knobs
-  ginit_option = 'noise'
-  phiinit = 0.01
-/
-&dissipation
-  hyper_dissipation = .true.
-/
-&geo_knobs
-  geo_option = 'miller'
-/
-&kt_grids_knobs
-  grid_option = 'box'
-/
-&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
-/ 
+
+
+
+
+
+