Merge pull request #114 from n-claes/refactor/settings

Major change in behaviour of settings

.github/workflows/legolas.yml

@@ -6,27 +6,25 @@ on:
   pull_request:
     branches: [master, develop]
 
-env:
-  CC: /usr/bin/gcc-10
-  FC: /usr/bin/gfortran-10
-  PFUNIT_DIR: /home/runner/work/legolas/legolas/tests/pFUnit/build/installed
-  LEGOLASDIR: /home/runner/work/legolas/legolas
-  ARPACK_ROOT: /home/runner/work/legolas/legolas/tests/arpack-ng
-
 jobs:
   test:
-    name: "${{ matrix.name }}"
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
 
     strategy:
       fail-fast: false
       matrix:
-        include:
-          - name: unit-tests
-            coverage: true
-          - name: regression
-            coverage: true
-
+        name: [unit-tests, regression]
+        os: [ubuntu-latest]
+        compiler: [gfortran-11]
+        coverage: [true]
+
+    env:
+      FC: ${{ matrix.compiler }}
+      PFUNIT_DIR: /home/runner/work/legolas/legolas/tests/pFUnit/build/installed
+      LEGOLASDIR: /home/runner/work/legolas/legolas
+      ARPACK_ROOT: /home/runner/work/legolas/legolas/tests/arpack-ng
+
+    name: ${{ matrix.name }}
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python 3.9
@@ -39,16 +37,17 @@ jobs:
       with:
         cmake-version: "3.24.x"
 
-    - name: Install dependencies
+    - name: Install Legolas dependencies
       run: |
         sudo apt-get update
+        sudo apt-get install ${{ matrix.compiler }}
         sudo apt-get install libblas-dev
         sudo apt-get install liblapack-dev
         sudo apt-get install lcov
-        gfortran-10 --version
+        ${FC} --version
         cmake --version
-        which gcov
-        which gcov-10
+        gcov --version
+
     - name: Install Python dependencies & Pylbo
       run: |
         python -m pip install --upgrade pip
@@ -61,7 +60,7 @@ jobs:
       uses: actions/cache@v1
       with:
         path: tests/pFUnit/
-        key: ${{ runner.os }}-pfunitv1
+        key: ${{ runner.os }}-pfunitv2
 
     - name: Build pFUnit
       if: steps.pfunit-cache.outputs.cache-hit != 'true'
@@ -80,7 +79,7 @@ jobs:
       uses: actions/cache@v1
       with:
         path: tests/arpack-ng/
-        key: ${{ runner.os }}-arpackv2
+        key: ${{ runner.os }}-arpackv3
 
     - name: Build ARPACK
       if: steps.arpack-cache.outputs.cache-hit != 'true'
@@ -128,7 +127,7 @@ jobs:
         cd coverage
         lcov --capture --directory $LEGOLASDIR/build \
             --output-file ${{ matrix.name }}.info \
-            --gcov-tool /usr/bin/gcov-10
+            --gcov-tool /usr/bin/gcov-11
         # filter out coverage files
         find $LEGOLASDIR/build -name '*.gc*' -delete
 

post_processing/pylbo/automation/defaults.py

@@ -6,20 +6,13 @@
         ("x_start", (int, np.integer, float)),
         ("x_end", (int, np.integer, float)),
         ("gridpoints", (int, np.integer)),
-        ("mesh_accumulation", bool),
-        ("ev_1", (int, np.integer, float)),
-        ("ev_2", (int, np.integer, float)),
-        ("sigma_1", (int, np.integer, float)),
-        ("sigma_2", (int, np.integer, float)),
         ("force_r0", bool),
         ("coaxial", bool),
     ],
     "equilibriumlist": [
         ("equilibrium_type", str),
         ("boundary_type", str),
         ("use_defaults", bool),
-        ("remove_spurious_eigenvalues", bool),
-        ("nb_spurious_eigenvalues", (int, np.integer)),
     ],
     "savelist": [
         ("write_matrices", bool),
@@ -29,32 +22,30 @@
         ("write_derived_eigenfunctions", bool),
         ("show_results", bool),
         ("basename_datfile", str),
-        ("basename_logfile", str),
         ("output_folder", str),
         ("logging_level", (int, np.integer)),
-        ("dry_run", bool),
         ("write_eigenfunction_subset", bool),
         ("eigenfunction_subset_center", complex),
         ("eigenfunction_subset_radius", (int, np.integer, float)),
     ],
     "physicslist": [
+        ("physics_type", str),
         ("mhd_gamma", float),
+        ("incompressible", bool),
+        ("dropoff_edge_dist", (int, np.integer, float)),
+        ("dropoff_width", (int, np.integer, float)),
         ("flow", bool),
         ("radiative_cooling", bool),
         ("ncool", (int, np.integer)),
         ("cooling_curve", str),
         ("external_gravity", bool),
-        ("thermal_conduction", bool),
-        ("use_fixed_tc_para", bool),
+        ("parallel_conduction", bool),
+        ("perpendicular_conduction", bool),
         ("fixed_tc_para_value", (int, np.integer, float)),
-        ("use_fixed_tc_perp", bool),
         ("fixed_tc_perp_value", (int, np.integer, float)),
         ("resistivity", bool),
-        ("use_fixed_resistivity", bool),
-        ("fixed_eta_value", (int, np.integer, float)),
+        ("fixed_resistivity_value", (int, np.integer, float)),
         ("use_eta_dropoff", bool),
-        ("dropoff_edge_dist", (int, np.integer, float)),
-        ("dropoff_width", (int, np.integer, float)),
         ("viscosity", bool),
         ("viscosity_value", (int, np.integer, float)),
         ("viscous_heating", bool),
@@ -64,10 +55,8 @@
         ("elec_inertia", bool),
         ("inertia_dropoff", bool),
         ("electron_fraction", (int, np.integer, float)),
-        ("incompressible", bool),
     ],
     "unitslist": [
-        ("cgs_units", bool),
         ("unit_density", (int, np.integer, float)),
         ("unit_temperature", (int, np.integer, float)),
         ("unit_magneticfield", (int, np.integer, float)),

src/CMakeLists.txt

@@ -5,6 +5,22 @@ set (sources
         mod_equilibrium_params.f08
         dataIO/mod_exceptions.f08
         dataIO/mod_logging.f08
+        dataIO/mod_console.f08
+        settings/physics/mod_flow_settings.f08
+        settings/physics/mod_cooling_settings.f08
+        settings/physics/mod_gravity_settings.f08
+        settings/physics/mod_resistivity_settings.f08
+        settings/physics/mod_viscosity_settings.f08
+        settings/physics/mod_conduction_settings.f08
+        settings/physics/mod_hall_settings.f08
+        settings/mod_settings.f08
+        settings/mod_dims.f08
+        settings/mod_io_settings.f08
+        settings/mod_solver_settings.f08
+        settings/mod_physics_settings.f08
+        settings/mod_grid_settings.f08
+        settings/mod_equilibrium_settings.f08
+        settings/mod_units.f08
         mod_physical_constants.f08
         utils/mod_get_indices.f08
         matrices/datastructure/mod_matrix_node.f08
@@ -14,7 +30,6 @@ set (sources
         matrices/datastructure/mod_banded_matrix_hermitian.f08
         matrices/datastructure/mod_banded_operations.f08
         matrices/datastructure/mod_transform_matrix.f08
-        mod_units.f08
         mod_grid.f08
         mod_types.f08
         mod_check_values.f08

src/boundaries/mod_boundary_manager.f08

@@ -1,7 +1,8 @@
 module mod_boundary_manager
-  use mod_global_variables, only: dp, dim_quadblock
+  use mod_global_variables, only: dp
   use mod_logging, only: log_message, str
   use mod_matrix_structure, only: matrix_t
+  use mod_settings, only: settings_t
   implicit none
 
   private
@@ -14,70 +15,73 @@ module mod_boundary_manager
   logical, save, protected :: apply_noslip_bounds_right
 
   interface
-    module subroutine apply_essential_boundaries_left(matrix)
+    module subroutine apply_essential_boundaries_left(matrix, settings)
       type(matrix_t), intent(inout) :: matrix
+      type(settings_t), intent(in) :: settings
     end subroutine apply_essential_boundaries_left
 
-    module subroutine apply_essential_boundaries_right(matrix)
+    module subroutine apply_essential_boundaries_right(matrix, settings)
       type(matrix_t), intent(inout) :: matrix
+      type(settings_t), intent(in) :: settings
     end subroutine apply_essential_boundaries_right
 
-    module subroutine apply_natural_boundaries_left(matrix)
+    module subroutine apply_natural_boundaries_left(matrix, settings)
       type(matrix_t), intent(inout) :: matrix
+      type(settings_t), intent(in) :: settings
     end subroutine apply_natural_boundaries_left
 
-    module subroutine apply_natural_boundaries_right(matrix)
+    module subroutine apply_natural_boundaries_right(matrix, settings)
       type(matrix_t), intent(inout) :: matrix
+      type(settings_t), intent(in) :: settings
     end subroutine apply_natural_boundaries_right
   end interface
 
   public :: apply_boundary_conditions
 
 contains
 
-  subroutine apply_boundary_conditions(matrix_A, matrix_B)
+  subroutine apply_boundary_conditions(matrix_A, matrix_B, settings)
     !> the A-matrix with boundary conditions imposed on exit
     type(matrix_t), intent(inout) :: matrix_A
     !> the B-matrix with boundary conditions imposed on exit
     type(matrix_t), intent(inout) :: matrix_B
+    !> the settings object
+    type(settings_t), intent(in) :: settings
 
-    call set_boundary_flags()
+    call set_boundary_flags(settings)
 
     ! handle left side boundary conditions B-matrix
-    call apply_natural_boundaries_left(matrix_B)
-    call apply_essential_boundaries_left(matrix_B)
+    call apply_natural_boundaries_left(matrix_B, settings)
+    call apply_essential_boundaries_left(matrix_B, settings)
     ! handle left side boundary conditions A-matrix
-    call apply_natural_boundaries_left(matrix_A)
-    call apply_essential_boundaries_left(matrix_A)
+    call apply_natural_boundaries_left(matrix_A, settings)
+    call apply_essential_boundaries_left(matrix_A, settings)
     ! handle right side boundary conditions B-matrix
-    call apply_natural_boundaries_right(matrix_B)
-    call apply_essential_boundaries_right(matrix_B)
+    call apply_natural_boundaries_right(matrix_B, settings)
+    call apply_essential_boundaries_right(matrix_B, settings)
     ! handle right side boundary conditions A-matrix
-    call apply_natural_boundaries_right(matrix_A)
-    call apply_essential_boundaries_right(matrix_A)
+    call apply_natural_boundaries_right(matrix_A, settings)
+    call apply_essential_boundaries_right(matrix_A, settings)
   end subroutine apply_boundary_conditions
 
 
-  subroutine set_boundary_flags()
-    use mod_equilibrium, only: kappa_field
-    use mod_global_variables, only: &
-      thermal_conduction, viscosity, coaxial, dp_LIMIT, geometry
+  subroutine set_boundary_flags(settings)
+    type(settings_t), intent(in) :: settings
+
 
     apply_T_bounds = .false.
     apply_noslip_bounds_left = .false.
     apply_noslip_bounds_right = .false.
 
     ! check if we need regularity conditions on T, this is the case if we have
     ! perpendicular thermal conduction
-    if (thermal_conduction .and. any(abs(kappa_field % kappa_perp) > dp_LIMIT)) then
-      apply_T_bounds = .true.
-    end if
+    apply_T_bounds = settings%physics%conduction%has_perpendicular_conduction()
 
     ! for viscosity, check if we need a no-slip condition.
-    if (viscosity) then
+    if (settings%physics%viscosity%is_enabled()) then
       apply_noslip_bounds_right = .true.
       ! does not apply on-axis for cylindrical, unless two coaxial walls are present
-      if (coaxial .or. geometry == "Cartesian") then
+      if (settings%grid%coaxial .or. settings%grid%get_geometry() == "Cartesian") then
         apply_noslip_bounds_left = .true.
       end if
     end if