musica 0.7.2__tar.gz → 0.7.3__tar.gz

{musica-0.7.2 → musica-0.7.3}/.github/workflows/release.yml

@@ -2,10 +2,9 @@ name: Publish Python Package
 
 on:
   workflow_dispatch:
-  push:
-  # release:
-  #   types:
-  #     - published
+  release:
+    types:
+      - published
 
 jobs:
   build_sdist:
@@ -67,7 +66,7 @@ jobs:
     runs-on: ubuntu-latest
     environment:
       name: pypi
-      url: https://pypi.org/p/<your-pypi-project-name>
+      url: https://pypi.org/p/musica
     permissions:
       id-token: write
 

{musica-0.7.2 → musica-0.7.3}/CITATION.cff

@@ -64,4 +64,4 @@ number: 10
 page: "E1743 - E1760"
 doi: "10.1175/BAMS-D-19-0331.1"
 url: "https://journals.ametsoc.org/view/journals/bams/101/10/bamsD190331.xml"
-version: 0.7.0
+version: 0.7.3

{musica-0.7.2 → musica-0.7.3}/CMakeLists.txt

@@ -1,7 +1,7 @@
 cmake_minimum_required(VERSION 3.21)
 
 # must be on the same line so that pyproject.toml can correctly identify the version
-project(musica-distribution VERSION 0.7.2)
+project(musica-distribution VERSION 0.7.3)
 
 set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH};${PROJECT_SOURCE_DIR}/cmake)
 set(CMAKE_USER_MAKE_RULES_OVERRIDE ${CMAKE_MODULE_PATH}/SetDefaults.cmake)

{musica-0.7.2 → musica-0.7.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: musica
-Version: 0.7.2
+Version: 0.7.3
 Summary: MUSICA is a Python library for performing computational simulations in atmospheric chemistry.
 Home-page: https://wiki.ucar.edu/display/MUSICA/MUSICA+Home
 Author-Email: Matthew Dawsom <mattdawson@ucar.edu>, Jiwon Gim <jiwongim@ucar.edu>, David Fillmore <fillmore@ucar.edu>, Kyle Shores <kshores@ucar.edu>

{musica-0.7.2 → musica-0.7.3}/cmake/dependencies.cmake

@@ -51,7 +51,7 @@ endif()
 if (MUSICA_ENABLE_MICM AND MUSICA_BUILD_C_CXX_INTERFACE)
 
   set_git_default(MICM_GIT_REPOSITORY https://github.com/NCAR/micm.git)
-  set_git_default(MICM_GIT_TAG v3.5.0)
+  set_git_default(MICM_GIT_TAG 6b1c58a9be14095e3f3c6df403c91c4e800f23de)
 
   FetchContent_Declare(micm
       GIT_REPOSITORY ${MICM_GIT_REPOSITORY}
@@ -75,7 +75,7 @@ if (MUSICA_ENABLE_TUVX AND MUSICA_BUILD_C_CXX_INTERFACE)
   set(TUVX_INSTALL_INCLUDE_DIR ${MUSICA_INSTALL_INCLUDE_DIR} CACHE STRING "" FORCE)
 
   set_git_default(TUVX_GIT_REPOSITORY https://github.com/NCAR/tuv-x.git)
-  set_git_default(TUVX_GIT_TAG 80f896a0fb591987c2a79209377bd6f599b4fb6f)
+  set_git_default(TUVX_GIT_TAG 674ee1e72853bb44d23c36602fa73c955b2f021d)
 
   FetchContent_Declare(tuvx
     GIT_REPOSITORY ${TUVX_GIT_REPOSITORY}

{musica-0.7.2 → musica-0.7.3}/configs/chapman/species.json

@@ -3,7 +3,7 @@
         {
             "name": "M",
             "type": "CHEM_SPEC",
-            "tracer type": "CONSTANT"
+            "tracer type": "THIRD_BODY"
         },
         {
             "name": "O2",

{musica-0.7.2 → musica-0.7.3}/docker/Dockerfile

@@ -9,7 +9,6 @@ RUN dnf -y update \
         gfortran \
         gdb \
         git \
-        lapack-devel \
         lcov \
         make \
         netcdf-fortran-devel \

{musica-0.7.2 → musica-0.7.3}/docker/Dockerfile.fortran-gcc

@@ -13,7 +13,6 @@ RUN dnf -y update \
     git \
     hdf5-devel \
     json-devel \
-    lapack-devel \
     lcov \
     libcurl-devel \
     m4 \
@@ -38,6 +37,7 @@ RUN cd musica \
     && cmake -S . \
              -B build \
              -D CMAKE_BUILD_TYPE=${BUILD_TYPE} \
+             -D MUSICA_GIT_TAG=${MUSICA_GIT_TAG} \
              -D MUSICA_BUILD_FORTRAN_INTERFACE=ON \
              -D MUSICA_ENABLE_MEMCHECK=ON \
     && cd build \

{musica-0.7.2 → musica-0.7.3}/docker/Dockerfile.fortran-gcc.integration

@@ -14,7 +14,6 @@ RUN dnf -y update \
     git \
     hdf5-devel \
     json-devel \
-    lapack-devel \
     lcov \
     libcurl-devel \
     m4 \

{musica-0.7.2 → musica-0.7.3}/docker/Dockerfile.memcheck

@@ -9,7 +9,6 @@ RUN dnf -y update \
         gfortran \
         gdb \
         git \
-        lapack-devel \
         lcov \
         make \
         netcdf-fortran-devel \

{musica-0.7.2 → musica-0.7.3}/docker/Dockerfile.mpi

@@ -16,7 +16,6 @@ RUN sudo dnf -y install \
         gcc-c++ \
         gfortran \
         git \
-        lapack-devel \
         lcov \
         make \
         netcdf-fortran-devel \

{musica-0.7.2 → musica-0.7.3}/docker/Dockerfile.mpi_openmp

@@ -16,7 +16,6 @@ RUN sudo dnf -y install \
         gcc-c++ \
         gfortran \
         git \
-        lapack-devel \
         lcov \
         make \
         netcdf-fortran-devel \

{musica-0.7.2 → musica-0.7.3}/docker/Dockerfile.openmp

@@ -16,7 +16,6 @@ RUN sudo dnf -y install \
         gcc-c++ \
         gfortran \
         git \
-        lapack-devel \
         lcov \
         make \
         netcdf-fortran-devel \

{musica-0.7.2 → musica-0.7.3}/docker/Dockerfile.python

@@ -9,7 +9,6 @@ RUN dnf -y update \
         gcc-fortran \
         gdb \
         git \
-        lapack-devel \
         make \
         netcdf-fortran-devel \
         pip \

{musica-0.7.2 → musica-0.7.3}/fortran/test/fetch_content_integration/CMakeLists.txt

@@ -116,4 +116,4 @@ if (MUSICA_ENABLE_TUVX)
     copy_tuvx_data_dir ALL ${CMAKE_COMMAND} -E copy_directory
     ${CMAKE_CURRENT_SOURCE_DIR}/../../../build/_deps/tuvx-src/data ${CMAKE_BINARY_DIR}/data
   )
-endif()
+endif()

{musica-0.7.2 → musica-0.7.3}/fortran/test/fetch_content_integration/test_micm_api.F90

@@ -30,7 +30,7 @@ contains
     real(c_double)                :: pressure
     real(c_double)                :: air_density
     integer(c_int)                :: num_concentrations, num_user_defined_reaction_rates
-    real(c_double), dimension(5)  :: concentrations 
+    real(c_double), dimension(4)  :: concentrations 
     real(c_double), dimension(3)  :: user_defined_reaction_rates 
     character(len=256)            :: config_path
     integer(c_int)                :: solver_type
@@ -52,8 +52,8 @@ contains
     temperature = 272.5
     pressure = 101253.4
     air_density = pressure / ( GAS_CONSTANT * temperature )
-    num_concentrations = 5
-    concentrations = (/ 0.75, 0.4, 0.8, 0.01, 0.02 /)
+    num_concentrations = 4
+    concentrations = (/ 0.4, 0.8, 0.01, 0.02 /)
     num_user_defined_reaction_rates = 3
     user_defined_reaction_rates = (/ 0.1, 0.2, 0.3 /)
 
@@ -109,21 +109,16 @@ contains
     ASSERT( logical( bool_value ) )
 
     string_value = micm%get_species_property_string( "O3", "missing property", error )
-    ASSERT( error%is_error( MICM_ERROR_CATEGORY_SPECIES, \
-                      MICM_SPECIES_ERROR_CODE_PROPERTY_NOT_FOUND ) )
+    ASSERT( error%is_error( MICM_ERROR_CATEGORY_SPECIES, MICM_SPECIES_ERROR_CODE_PROPERTY_NOT_FOUND ) )
     double_value = micm%get_species_property_double( "O3", "missing property", error )
-    ASSERT( error%is_error( MICM_ERROR_CATEGORY_SPECIES, \
-                      MICM_SPECIES_ERROR_CODE_PROPERTY_NOT_FOUND ) )
+    ASSERT( error%is_error( MICM_ERROR_CATEGORY_SPECIES, MICM_SPECIES_ERROR_CODE_PROPERTY_NOT_FOUND ) )
     int_value = micm%get_species_property_int( "O3", "missing property", error )
-    ASSERT( error%is_error( MICM_ERROR_CATEGORY_SPECIES, \
-                      MICM_SPECIES_ERROR_CODE_PROPERTY_NOT_FOUND ) )
+    ASSERT( error%is_error( MICM_ERROR_CATEGORY_SPECIES, MICM_SPECIES_ERROR_CODE_PROPERTY_NOT_FOUND ) )
     bool_value = micm%get_species_property_bool( "O3", "missing property", error )
-    ASSERT( error%is_error( MICM_ERROR_CATEGORY_SPECIES, \
-                      MICM_SPECIES_ERROR_CODE_PROPERTY_NOT_FOUND ) )
+    ASSERT( error%is_error( MICM_ERROR_CATEGORY_SPECIES, MICM_SPECIES_ERROR_CODE_PROPERTY_NOT_FOUND ) )
     deallocate( micm )
     micm => micm_t( "configs/invalid", solver_type, num_grid_cells, error )
-    ASSERT( error%is_error( MICM_ERROR_CATEGORY_CONFIGURATION, \
-                      MICM_CONFIGURATION_ERROR_CODE_INVALID_FILE_PATH ) )
+    ASSERT( error%is_error( MICM_ERROR_CATEGORY_CONFIGURATION, MICM_CONFIGURATION_ERROR_CODE_INVALID_FILE_PATH ) )
     ASSERT( .not. associated( micm ) )
 
     write(*,*) "[test micm fort api] Finished."

{musica-0.7.2 → musica-0.7.3}/fortran/test/fetch_content_integration/test_tuvx_api.F90

@@ -3,7 +3,8 @@
 !
 program combined_tuvx_tests
   use iso_c_binding
-  use musica_tuvx, only: tuvx_t, grid_map_t, grid_t, profile_map_t, profile_t
+  use musica_tuvx, only: tuvx_t, grid_map_t, grid_t, profile_map_t, profile_t, &
+                         radiator_map_t, radiator_t
   use musica_util, only: assert, error_t
 
   implicit none
@@ -55,22 +56,36 @@ contains
 
   subroutine test_tuvx_solve()
 
-    type(tuvx_t),        pointer :: tuvx
-    type(error_t)                :: error
-    type(grid_map_t),    pointer :: grids
-    character(len=256)           :: config_path
-    type(grid_t),        pointer :: grid
-    type(profile_map_t), pointer :: profiles
-    type(profile_t),     pointer :: profile, profile_copy
-    real*8, dimension(5), target :: edges, edge_values, temp_edge
-    real*8, dimension(4), target :: midpoints, midpoint_values, layer_densities, temp_midpoint
-    real*8                       :: temp_real
+    type(tuvx_t),         pointer    :: tuvx
+    type(error_t)                    :: error
+    character(len=256)               :: config_path
+    type(grid_map_t),     pointer    :: grids
+    type(grid_t),         pointer    :: grid, height_grid, wavelength_grid
+    type(profile_map_t),  pointer    :: profiles
+    type(profile_t),      pointer    :: profile, profile_copy
+    type(radiator_map_t), pointer    :: radiators
+    type(radiator_t),     pointer    :: radiator, radiator_copy
+    real*8, dimension(5), target     :: edges, edge_values, temp_edge
+    real*8, dimension(4), target     :: midpoints, midpoint_values, layer_densities, temp_midpoint
+    real*8                           :: temp_real
+    integer                          :: num_vertical_layers, num_wavelength_bins
+    real*8, dimension(3,2), target   :: optical_depths, temp_od
+    real*8, dimension(3,2), target   :: single_scattering_albedos, temp_ssa
+    real*8, dimension(3,2,1), target :: asymmetry_factors, temp_asym
 
     edges = (/ 1.0, 2.0, 3.0, 4.0, 5.0 /)
     midpoints = (/ 15.0, 25.0, 35.0, 45.0 /)  
     edge_values = (/ 10.0, 20.0, 30.0, 40.0, 50.0 /)
     midpoint_values = (/ 15.0, 25.0, 35.0, 45.0 /)
     layer_densities = (/ 2.0, 4.0, 1.0, 7.0 /)
+    num_vertical_layers = 3
+    num_wavelength_bins = 2
+    optical_depths(:,1) = (/ 30.0, 20.0, 10.0 /)
+    optical_depths(:,2) = (/ 70.0, 80.0, 90.0 /)
+    single_scattering_albedos(:,1) = (/ 300.0, 200.0, 100.0 /)
+    single_scattering_albedos(:,2) = (/ 700.0, 800.0, 900.0 /)
+    asymmetry_factors(:,1,1) = (/ 3.0, 2.0, 1.0 /)
+    asymmetry_factors(:,2,1) = (/ 7.0, 8.0, 9.0 /)
 
     config_path = "examples/ts1_tsmlt.json"
 
@@ -312,12 +327,146 @@ contains
     ASSERT_EQ( temp_edge(3), 36.0 )
     ASSERT_EQ( temp_edge(4), 38.0 )
     ASSERT_EQ( temp_edge(5), 40.0 )
-    
+
+    radiators => tuvx%get_radiators( error )
+    ASSERT( error%is_success() )
+
+    radiator => radiators%get( "foo_radiator", error )
+    ASSERT( .not. error%is_success() )
+    deallocate( radiator )
+    deallocate( radiators )
+
+    radiators =>radiator_map_t( error )
+    ASSERT( error%is_success() )
+
+    height_grid => grid_t( "height", "km", num_vertical_layers, error )
+    wavelength_grid => grid_t( "wavelength", "nm", num_wavelength_bins, error )
+    radiator => radiator_t( "foo_radiator", height_grid, wavelength_grid, error )
+    ASSERT( error%is_success() )
+
+    call radiator%set_optical_depths( optical_depths, error )
+    ASSERT( error%is_success() )
+
+    call radiator%get_optical_depths( temp_od, error )
+    ASSERT( error%is_success() )
+    ASSERT_EQ( temp_od(1,1), 30.0 )
+    ASSERT_EQ( temp_od(2,1), 20.0 )
+    ASSERT_EQ( temp_od(3,1), 10.0 )
+    ASSERT_EQ( temp_od(1,2), 70.0 )
+    ASSERT_EQ( temp_od(2,2), 80.0 )
+    ASSERT_EQ( temp_od(3,2), 90.0 )
+
+    call radiator%set_single_scattering_albedos( single_scattering_albedos, error )
+    ASSERT( error%is_success() )
+
+    call radiator%get_single_scattering_albedos( temp_ssa, error )
+    ASSERT( error%is_success() )
+    ASSERT_EQ( temp_ssa(1,1), 300.0 )
+    ASSERT_EQ( temp_ssa(2,1), 200.0 )
+    ASSERT_EQ( temp_ssa(3,1), 100.0 )
+    ASSERT_EQ( temp_ssa(1,2), 700.0 )
+    ASSERT_EQ( temp_ssa(2,2), 800.0 )
+    ASSERT_EQ( temp_ssa(3,2), 900.0 )
+
+    call radiator%set_asymmetry_factors( asymmetry_factors, error )
+    ASSERT( error%is_success() )
+
+    call radiator%get_asymmetry_factors( temp_asym, error )
+    ASSERT( error%is_success() )
+    ASSERT_EQ( temp_asym(1,1,1), 3.0 )
+    ASSERT_EQ( temp_asym(2,1,1), 2.0 )
+    ASSERT_EQ( temp_asym(3,1,1), 1.0 )
+    ASSERT_EQ( temp_asym(1,2,1), 7.0 )
+    ASSERT_EQ( temp_asym(2,2,1), 8.0 )
+    ASSERT_EQ( temp_asym(3,2,1), 9.0 )
+!
+    call radiators%add( radiator, error )
+    radiator_copy => radiators%get( "foo_radiator", error )
+
+    optical_depths(:,:) = 0.0
+    single_scattering_albedos(:,:) = 0.0
+    asymmetry_factors(:,:,:) = 0.0
+
+    call radiator_copy%get_optical_depths( optical_depths, error )
+    ASSERT( error%is_success() )
+    ASSERT_EQ( optical_depths(1,1), 30.0 )
+    ASSERT_EQ( optical_depths(2,1), 20.0 )
+    ASSERT_EQ( optical_depths(3,1), 10.0 )
+    ASSERT_EQ( optical_depths(1,2), 70.0 )
+    ASSERT_EQ( optical_depths(2,2), 80.0 )
+    ASSERT_EQ( optical_depths(3,2), 90.0 )
+
+    call radiator_copy%get_single_scattering_albedos( single_scattering_albedos, error )
+    ASSERT( error%is_success() )
+    ASSERT_EQ( single_scattering_albedos(1,1), 300.0 )
+    ASSERT_EQ( single_scattering_albedos(2,1), 200.0 )
+    ASSERT_EQ( single_scattering_albedos(3,1), 100.0 )
+    ASSERT_EQ( single_scattering_albedos(1,2), 700.0 )
+    ASSERT_EQ( single_scattering_albedos(2,2), 800.0 )
+    ASSERT_EQ( single_scattering_albedos(3,2), 900.0 )
+
+    call radiator_copy%get_asymmetry_factors( asymmetry_factors, error )
+    ASSERT( error%is_success() )
+    ASSERT_EQ( asymmetry_factors(1,1,1), 3.0 )
+    ASSERT_EQ( asymmetry_factors(2,1,1), 2.0 )
+    ASSERT_EQ( asymmetry_factors(3,1,1), 1.0 )
+    ASSERT_EQ( asymmetry_factors(1,2,1), 7.0 )
+    ASSERT_EQ( asymmetry_factors(2,2,1), 8.0 )
+    ASSERT_EQ( asymmetry_factors(3,2,1), 9.0 )
+
+    optical_depths(:,1) = (/ 90.0, 80.0, 70.0 /)
+    optical_depths(:,2) = (/ 75.0, 85.0, 95.0 /)
+    single_scattering_albedos(:,1) = (/ 900.0, 800.0, 700.0 /)
+    single_scattering_albedos(:,2) = (/ 750.0, 850.0, 950.0 /)
+    asymmetry_factors(:,1,1) = (/ 9.0, 8.0, 7.0 /)
+    asymmetry_factors(:,2,1) = (/ 5.0, 4.0, 3.0 /)
+
+    call radiator_copy%set_optical_depths( optical_depths, error )
+    call radiator_copy%set_single_scattering_albedos( single_scattering_albedos, error )
+    call radiator_copy%set_asymmetry_factors( asymmetry_factors, error )
+    ASSERT( error%is_success() )
+
+    optical_depths(:,:) = 0.0
+    single_scattering_albedos(:,:) = 0.0
+    asymmetry_factors(:,:,:) = 0.0
+
+    call radiator%get_optical_depths( optical_depths, error )
+    ASSERT( error%is_success() )
+    ASSERT_EQ( optical_depths(1,1), 90.0 )
+    ASSERT_EQ( optical_depths(2,1), 80.0 )
+    ASSERT_EQ( optical_depths(3,1), 70.0 )
+    ASSERT_EQ( optical_depths(1,2), 75.0 )
+    ASSERT_EQ( optical_depths(2,2), 85.0 )
+    ASSERT_EQ( optical_depths(3,2), 95.0 )
+
+    call radiator%get_single_scattering_albedos( single_scattering_albedos, error )
+    ASSERT( error%is_success() )
+    ASSERT_EQ( single_scattering_albedos(1,1), 900.0 )
+    ASSERT_EQ( single_scattering_albedos(2,1), 800.0 )
+    ASSERT_EQ( single_scattering_albedos(3,1), 700.0 )
+    ASSERT_EQ( single_scattering_albedos(1,2), 750.0 )
+    ASSERT_EQ( single_scattering_albedos(2,2), 850.0 )
+    ASSERT_EQ( single_scattering_albedos(3,2), 950.0 )
+
+    call radiator%get_asymmetry_factors( asymmetry_factors, error )
+    ASSERT( error%is_success() )
+    ASSERT_EQ( asymmetry_factors(1,1,1), 9.0 )
+    ASSERT_EQ( asymmetry_factors(2,1,1), 8.0 )
+    ASSERT_EQ( asymmetry_factors(3,1,1), 7.0 )
+    ASSERT_EQ( asymmetry_factors(1,2,1), 5.0 )
+    ASSERT_EQ( asymmetry_factors(2,2,1), 4.0 )
+    ASSERT_EQ( asymmetry_factors(3,2,1), 3.0 )
+
     deallocate( grid )
     deallocate( grids )
     deallocate( profile )
     deallocate( profile_copy )
     deallocate( profiles )
+    deallocate( radiator_copy )
+    deallocate( radiator )
+    deallocate( radiators )
+    deallocate( height_grid )
+    deallocate( wavelength_grid )
     deallocate( tuvx )
 
   end subroutine test_tuvx_solve

{musica-0.7.2 → musica-0.7.3}/fortran/tuvx/CMakeLists.txt

@@ -4,5 +4,7 @@ target_sources(musica-fortran
     grid_map.F90
     profile.F90
     profile_map.F90
+    radiator.F90
+    radiator_map.F90
     tuvx.F90
 )

{musica-0.7.2 → musica-0.7.3}/fortran/tuvx/grid.F90

@@ -82,7 +82,7 @@ module musica_tuvx_grid
     procedure :: set_edges
     ! Get grid edges
     procedure :: get_edges
-    ! Set the grid edges and midpoints
+    ! Set the grid midpoints
     procedure :: set_midpoints
     ! Get the grid midpoints
     procedure :: get_midpoints

{musica-0.7.2 → musica-0.7.3}/fortran/tuvx/profile.F90

@@ -16,7 +16,7 @@ module musica_tuvx_profile
   interface
     function create_profile_c(profile_name, profile_units, grid, error) &
       bind(C, name="CreateProfile")
-      use iso_c_binding, only: c_ptr, c_char, c_size_t
+      use iso_c_binding, only: c_ptr, c_char
       use musica_util, only: error_t_c
       character(len=1, kind=c_char), intent(in) :: profile_name(*)
       character(len=1, kind=c_char), intent(in) :: profile_units(*)