Add radiator from NetCDF file

cmake/dependencies.cmake

@@ -73,7 +73,7 @@ else()
 
   FetchContent_Declare(musicacore
     GIT_REPOSITORY https://github.com/NCAR/musica-core.git
-    GIT_TAG v0.4.0
+    GIT_TAG v0.4.1
     FIND_PACKAGE_ARGS NAMES musicacore
   )
 

docs/source/user_guide.rst

@@ -721,6 +721,52 @@ the provided units that is present in the list of
 These profiles should describe the concentration of
 the constituent on the ``height`` grid.
 
+
+From NetCDF file
+~~~~~~~~~~~~~~~~
+This radiator type allows loading the optical properties of
+a radiator from a NetCDF file. The optical properties will
+remain constant throughout the calculations.
+
+.. code-block:: JSON
+
+    {
+      "name": "foo",
+      "type": "from netcdf file",
+      "file path": "path/to/file.nc"
+    }
+
+
+============================    ==============
+keys                            Required/Optional
+============================    ==============
+``name``                        required
+``type``                        required
+``file path``                   required 
+============================    ==============
+
+The ``file path`` should be a string containing the absolute
+or relative path to the NetCDF file containing the optical
+properties.
+
+The NetCDF file should be structured as follows::
+
+   dimensions:
+      heights = NUMBER_OF_VERTICAL_LAYERS ;
+      wavelengths = NUMBER_OF_WAVELENGTH_BINS ;
+   variables:
+      double optical_depth(wavelengths, heights) ;
+      double single_scattering_albedo(wavelengths, heights) ;
+      double asymmetry_factor(wavelengths, heights) ;
+
+
+The ``NUMBER_OF_VERTICAL_LAYERS`` and ``NUMBER_OF_WAVELENGTH_BINS``
+must correspond to the number of bins in the ``height`` and
+``wavelength`` grids specified in the TUV-x configuration file.
+(Note that these optical properties are per grid section and not at
+grid edges.) No interpolation is performed on this data set.
+
+
 Aerosols
 ~~~~~~~~
 A special radiator type exists for aerosols, which
@@ -762,7 +808,7 @@ keys                            Required/Optional
 ``enable diagnostics``          optional
 ============================    ==============
 
-The regressoin tests compare the new version of TUV-x to the old version. One
+The regression tests compare the new version of TUV-x to the old version. One
 way is by directly comparing output. The `enable diagnostics` allows for this
 ouptut to be disabled. If this is enabled, a folder named `output` will be 
 created in the same directory TUV-x is run from.

etc/modeling2/build_tuvx_modeling2_gnu.sh

@@ -23,7 +23,6 @@ export LD_LIBRARY_PATH="/opt/local/lib64:/opt/local/lib:/usr/bin:/usr/lib:usr/li
 cd ${TUVX_HOME}
 curl -LO https://github.com/jacobwilliams/json-fortran/archive/8.2.1.tar.gz
 git clone https://github.com/NCAR/tuv-x.git
-git clone https://github.com/NCAR/musica-core.git
 
 # extract
 cd ${TUVX_HOME}
@@ -39,35 +38,21 @@ cd $JSON_FORTRAN_ROOT
 sed -i 's/\-C $<CONFIG>//' CMakeLists.txt
 mkdir -p build
 cd build
-cmake3 -D CMAKE_Fortran_COMPILER=/opt/local/bin/gfortran \
+cmake -D CMAKE_Fortran_COMPILER=/opt/local/bin/gfortran \
        -D SKIP_DOC_GEN:BOOL=TRUE \
        -D CMAKE_INSTALL_PREFIX=$INSTALL_ROOT \
        ..
 make -j4 install
 mkdir -p $JSON_FORTRAN_HOME/lib/shared
 mv $JSON_FORTRAN_HOME/lib/*.so* $JSON_FORTRAN_HOME/lib/shared
 
-# musica-core
-MUSICA_CORE_ROOT=${TUVX_HOME}/musica-core
-export MUSICA_CORE_HOME=${INSTALL_ROOT}/musica-core-0.1.0
-export MUSICA_CORE_PACKAGE=${INSTALL_ROOT}/musicacore-0.1.0/cmake/musicacore-0.1.0
-cd ${MUSICA_CORE_ROOT}
-mkdir -p build
-cd build
-cmake3 -D CMAKE_Fortran_COMPILER=gfortran \
-      -D CMAKE_BUILD_TYPE=release \
-      -D CMAKE_INSTALL_PREFIX=${INSTALL_ROOT} \
-      ..
-make -j4 install
-
 # TUV-x
 TUVX_ROOT=$TUVX_HOME/tuv-x
 cd $TUVX_ROOT
 mkdir -p build
 cd build
-cmake3 -D CMAKE_Fortran_COMPILER=/opt/local/bin/gfortran \
+cmake -D CMAKE_Fortran_COMPILER=/opt/local/bin/gfortran \
        -D CMAKE_BUILD_TYPE=release \
-       -D musicacore_DIR=${MUSICA_CORE_PACKAGE} \
        -D ENABLE_COVERAGE=OFF \
        -D ENABLE_MEMCHECK=OFF \
        -D CMAKE_INSTALL_PREFIX=${TUVX_HOME} \

src/radiative_transfer/radiator_factory.F90

@@ -8,6 +8,7 @@ module tuvx_radiator_factory
   use tuvx_radiator,                   only : radiator_t
   use tuvx_radiator_aerosol,           only : radiator_aerosol_t
   use tuvx_radiator_from_host,         only : radiator_from_host_t
+  use tuvx_radiator_from_netcdf_file,  only : radiator_from_netcdf_file_t
 
   implicit none
 
@@ -49,6 +50,9 @@ function radiator_builder( config, grid_warehouse, profile_warehouse,       &
       case( 'aerosol' )
         new_radiator => radiator_aerosol_t( config, grid_warehouse,           &
                                             profile_warehouse )
+      case( 'from netcdf file' )
+        new_radiator => radiator_from_netcdf_file_t( config, grid_warehouse,  &
+                                                     profile_warehouse )
       case default
         call die_msg( 460768245, "Invalid radiator type: '"//                 &
                                  radiator_type%to_char()//"'" )
@@ -73,6 +77,8 @@ type(string_t) function radiator_type_name( radiator ) result( name )
         name = "radiator_aerosol_t"
       type is( radiator_from_host_t )
         name = "radiator_from_host_t"
+      type is( radiator_from_netcdf_file_t )
+        name = "radiator_from_netcdf_file_t"
       class default
         call die( 365718517 )
     end select
@@ -99,6 +105,8 @@ function radiator_allocate( type_name ) result( radiator )
         allocate( radiator_aerosol_t :: radiator )
       case( 'radiator_from_host_t' )
         allocate( radiator_from_host_t :: radiator )
+      case( 'radiator_from_netcdf_file_t' )
+        allocate( radiator_from_netcdf_file_t :: radiator )
       case default
         call die_msg( 670539061, "Invalid radiator type: '"//                 &
                                  type_name//"'" )

src/radiative_transfer/radiators/CMakeLists.txt

@@ -5,6 +5,7 @@ target_sources(tuvx_object
   PRIVATE
     aerosol.F90
     from_host.F90
+    from_netcdf_file.F90
 )
 
 ################################################################################

src/radiative_transfer/radiators/from_netcdf_file.F90

@@ -0,0 +1,116 @@
+! Copyright (C) 2023 National Center for Atmospheric Research
+! SPDX-License-Identifier: Apache-2.0
+module tuvx_radiator_from_netcdf_file
+
+  use musica_constants,                only : dk => musica_dk
+  use musica_string,                   only : string_t
+  use tuvx_radiator,                   only : radiator_t
+
+  implicit none
+
+  private
+  public :: radiator_from_netcdf_file_t
+
+  !> User-specified radiator
+  !!
+  !! User-specified radiators have fixed optical properties that are read
+  !! in from a NetCDF file.
+  type, extends(radiator_t) :: radiator_from_netcdf_file_t
+  contains
+    !> Update the radiator for new environmental conditions
+    procedure :: update_state
+  end type radiator_from_netcdf_file_t
+
+  !> User-specified radiator constructor
+  interface radiator_from_netcdf_file_t
+    module procedure constructor
+  end interface radiator_from_netcdf_file_t
+
+contains
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+  !> Initialize a user-specified radiator
+  function constructor( config, grid_warehouse, profile_warehouse )           &
+      result ( this )
+
+    use musica_assert,                 only : assert_msg
+    use musica_config,                 only : config_t
+    use musica_string,                 only : string_t
+    use tuvx_grid,                     only : grid_t
+    use tuvx_grid_warehouse,           only : grid_warehouse_t
+    use musica_io_netcdf,              only : io_netcdf_t
+    use tuvx_profile_warehouse,        only : profile_warehouse_t
+
+    class(radiator_from_netcdf_file_t), pointer       :: this ! The constructor radiator
+    type(config_t),                     intent(inout) :: config ! configuration for the radiator
+    type(grid_warehouse_t),             intent(inout) :: grid_warehouse ! Configured grids
+    type(profile_warehouse_t),          intent(inout) :: profile_warehouse ! Configured profiles
+
+    character(len=*),  parameter :: Iam =                                     &
+                                    "radiator from NetCDF file constructor"
+    class(grid_t), pointer :: heights, wavelengths
+    type(string_t) :: file_path, variable
+    type(io_netcdf_t), pointer :: netcdf_file
+    real(kind=dk), allocatable :: temp_G(:,:)
+    integer :: i_wl, i_height
+    type(string_t) :: required_keys(3), optional_keys(0)
+
+    required_keys(1) = "type"
+    required_keys(2) = "name"
+    required_keys(3) = "file path"
+    call assert_msg( 723245326,                                               &
+                     config%validate( required_keys, optional_keys ),         &
+                     "Bad configuration data format for radiator from NetCDF" )
+
+    allocate(this)
+
+    call config%get( "name", this%handle_, Iam )
+    call config%get( "type", this%type_,   Iam )
+
+    heights => grid_warehouse%get_grid( "height", "km" )
+    wavelengths => grid_warehouse%get_grid( "wavelength", "nm" )
+
+    allocate( this%state_%layer_OD_(  heights%ncells_, wavelengths%ncells_ ) )
+    allocate( this%state_%layer_SSA_( heights%ncells_, wavelengths%ncells_ ) )
+    allocate( this%state_%layer_G_( heights%ncells_, wavelengths%ncells_, 1 ) )
+    allocate( temp_G( heights%ncells_, wavelengths%ncells_ ) )
+
+    call config%get( "file path", file_path, Iam )
+    netcdf_file => io_netcdf_t( file_path, read_only = .true. )
+    variable = "optical_depth"
+    call netcdf_file%read_2D_double( variable, this%state_%layer_OD_,  Iam )
+    variable = "single_scattering_albedo"
+    call netcdf_file%read_2D_double( variable, this%state_%layer_SSA_, Iam )
+    variable = "asymmetry_factor"
+    call netcdf_file%read_2D_double( variable, temp_G, Iam )
+    this%state_%layer_G_(:,:,1) = temp_G(:,:)
+
+    deallocate( netcdf_file )
+    deallocate( heights )
+    deallocate( wavelengths )
+
+  end function constructor
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+  !> Update the radiator state for current conditions
+  subroutine update_state( this, grid_warehouse, profile_warehouse,           &
+      cross_section_warehouse )
+
+    use tuvx_cross_section_warehouse,  only : cross_section_warehouse_t
+    use tuvx_grid_warehouse,           only : grid_warehouse_t
+    use tuvx_profile_warehouse,        only : profile_warehouse_t
+
+    class(radiator_from_netcdf_file_t), intent(inout) :: this ! Radiator to update
+    type(grid_warehouse_t),             intent(inout) :: grid_warehouse ! Current grids
+    type(profile_warehouse_t),          intent(inout) :: profile_warehouse ! Current profiles
+    type(cross_section_warehouse_t),    intent(inout) :: cross_section_warehouse ! Current cross-sections
+
+    ! nothing to update - radiator properties for this type are fixed
+
+  end subroutine update_state
+
+!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+
+end module tuvx_radiator_from_netcdf_file

test/data/radiators.from_netcdf_file.config.json

@@ -0,0 +1,23 @@
+{
+  "grids": [
+    {
+      "name" : "height",
+      "type" : "from config file",
+      "units" : "km",
+      "values" : [ 0.0, 10.0, 20.0, 30.0 ]
+    },
+    {
+      "name" : "wavelength",
+      "type" : "from config file",
+      "units" : "nm",
+      "values" : [ 550.0, 600.0, 650.0, 700.0, 720.0 ]
+    }
+  ],
+  "radiators": [
+    {
+      "name" : "foo",
+      "type" : "from netcdf file",
+      "file path" : "test/data/radiator.nc"
+    }
+  ]
+}

test/unit/radiator/CMakeLists.txt

@@ -9,5 +9,6 @@ include(test_util)
 create_standard_test(NAME radiator SOURCES radiator_core.F90
                                            radiator_test.F90)
 create_standard_test(NAME radiator_from_host SOURCES from_host.F90)
+create_standard_test(NAME radiator_from_netcdf_file SOURCES from_netcdf_file.F90)
 
 ################################################################################