Add TUV-x height grid updates

.github/workflows/test.yaml

@@ -12,4 +12,14 @@ jobs:
     - name: build Docker image
       run: docker build -t musica -f test/docker/Dockerfile.musica .
     - name: run tests in container
-      run: docker run --name test-container -t musica bash -c 'make test ARGS="--rerun-failed --output-on-failure -j8"'
+      run: docker run --name test-container -t musica bash -c 'make test ARGS="--rerun-failed --output-on-failure -j8"'
+  test_musica_api_no_install:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+    - name: build Docker image
+      run: docker build -t musica-no-install -f test/docker/Dockerfile.musica.no_install .
+    - name: run tests in container
+      run: docker run --name test-container -t musica-no-install bash -c 'make test ARGS="--rerun-failed --output-on-failure -j8"'

schemes/musica/micm/musica_ccpp_micm.F90

@@ -1,5 +1,4 @@
 module musica_ccpp_micm
-  use iso_c_binding
 
   ! Note: "micm_t" is included in an external pre-built MICM library that the host
   ! model is responsible for linking to during compilation
@@ -17,50 +16,52 @@ module musica_ccpp_micm
 
 contains
 
-  !> Register MICM constituents with the CCPP
-  subroutine micm_register(constituents, solver_type, num_grid_cells, errmsg, errcode)
+  !> Register MICM constituent properties with the CCPP
+  subroutine micm_register(solver_type, num_grid_cells, constituent_props, errmsg, errcode)
     use ccpp_constituent_prop_mod, only: ccpp_constituent_properties_t
-    use musica_micm, only: Rosenbrock, RosenbrockStandardOrder
-    use musica_util, only: error_t
+    use musica_micm,               only: Rosenbrock, RosenbrockStandardOrder
+    use musica_util,               only: error_t
+    use iso_c_binding,             only: c_int
 
-    type(ccpp_constituent_properties_t), allocatable, intent(out) :: constituents(:)
     integer(c_int),                                   intent(in)  :: solver_type
     integer(c_int),                                   intent(in)  :: num_grid_cells
+    type(ccpp_constituent_properties_t), allocatable, intent(out) :: constituent_props(:)
     character(len=512),                               intent(out) :: errmsg
     integer,                                          intent(out) :: errcode
 
     ! local variables
-    type(error_t)        :: error
-    real(kind=kind_phys) :: molar_mass
-    logical              :: is_advected
-    integer              :: i
-
-    errcode = 0
-    errmsg = ''
+    type(error_t)                 :: error
+    real(kind=kind_phys)          :: molar_mass
+    character(len=:), allocatable :: species_name
+    logical                       :: is_advected
+    integer                       :: i, species_index
 
     micm => micm_t(filename_of_micm_configuration, solver_type, num_grid_cells, error)
     if (has_error_occurred(error, errmsg, errcode)) return
 
-    allocate(constituents(size(micm%species_ordering)), stat=errcode)
+    allocate(constituent_props(micm%species_ordering%size()), stat=errcode)
     if (errcode /= 0) then
-      errmsg = "[MUSICA Error] Failed to allocate memory for constituents."
+      errmsg = "[MUSICA Error] Failed to allocate memory for constituent properties."
       return
     end if
 
-    do i = 1, size(micm%species_ordering)
-    associate( map => micm%species_ordering(i) )
-      molar_mass = micm%get_species_property_double(map%name(), &
+    do i = 1, micm%species_ordering%size()
+    associate( map => micm%species_ordering )
+      species_name = map%name(i)
+      species_index = map%index(i)
+
+      molar_mass = micm%get_species_property_double(species_name, &
                                                     "molecular weight [kg mol-1]", &
                                                     error)
       if (has_error_occurred(error, errmsg, errcode)) return
-      is_advected = micm%get_species_property_bool(map%name(), &
-                                                      "__is advected", &
-                                                      error)
+      is_advected = micm%get_species_property_bool(species_name, &
+                                                   "__is advected", &
+                                                   error)
       if (has_error_occurred(error, errmsg, errcode)) return
 
-      call constituents(map%index())%instantiate( &
-        std_name = map%name(), &
-        long_name = map%name(), &
+      call constituent_props(species_index)%instantiate( &
+        std_name = species_name, &
+        long_name = species_name, &
         units = 'kg kg-1', &
         vertical_dim = 'vertical_layer_dimension', &
         default_value = 0.0_kind_phys, &
@@ -78,25 +79,26 @@ end subroutine micm_register
   !> Intitialize MICM
   subroutine micm_init(errmsg, errcode)
     character(len=512), intent(out) :: errmsg
-    integer, intent(out)            :: errcode
+    integer,            intent(out) :: errcode
 
-    errcode = 0
     errmsg = ''
+    errcode = 0
 
   end subroutine micm_init
 
   !> Solve chemistry at the current time step
-  subroutine micm_run(time_step, temperature, pressure, dry_air_density, constituents, &
-                      rate_params, errmsg, errcode)
-    use musica_micm, only: solver_stats_t
-    use musica_util, only: string_t, error_t
+  subroutine micm_run(time_step, temperature, pressure, dry_air_density, &
+              user_defined_rate_parameters, constituents, errmsg, errcode)
+    use musica_micm,   only: solver_stats_t
+    use musica_util,   only: string_t, error_t
+    use iso_c_binding, only: c_double
 
     real(kind_phys),        intent(in)    :: time_step          ! s
     real(c_double), target, intent(in)    :: temperature(:)     ! K
     real(c_double), target, intent(in)    :: pressure(:)        ! Pa
     real(c_double), target, intent(in)    :: dry_air_density(:) ! kg m-3
+    real(c_double), target, intent(in)    :: user_defined_rate_parameters(:) ! various units
     real(c_double), target, intent(inout) :: constituents(:)    ! mol m-3
-    real(c_double), target, intent(inout) :: rate_params(:)
     character(len=512),     intent(out)   :: errmsg
     integer,                intent(out)   :: errcode
 
@@ -107,18 +109,16 @@ subroutine micm_run(time_step, temperature, pressure, dry_air_density, constitue
     real(c_double)       :: c_time_step
     integer              :: i_elem
 
-    errcode = 0
-    errmsg = ''
     c_time_step = real(time_step, c_double) 
 
-    call micm%solve(c_time_step,     &
-                    temperature,     &
-                    pressure,        &
-                    dry_air_density, &
-                    constituents,    &
-                    rate_params,     &
-                    solver_state,    &
-                    solver_stats,    &
+    call micm%solve(c_time_step,                  &
+                    temperature,                  &
+                    pressure,                     &
+                    dry_air_density,              &
+                    constituents,                 &
+                    user_defined_rate_parameters, &
+                    solver_state,                 &
+                    solver_stats,                 &
                     error)
     if (has_error_occurred(error, errmsg, errcode)) return
 
@@ -127,10 +127,10 @@ end subroutine micm_run
   !> Finalize MICM
   subroutine micm_final(errmsg, errcode)
     character(len=512), intent(out) :: errmsg
-    integer, intent(out)            :: errcode
+    integer,            intent(out) :: errcode
 
-    errcode = 0
     errmsg = ''
+    errcode = 0
 
   end subroutine micm_final
 

schemes/musica/micm/micm_util.F90 → schemes/musica/micm/musica_ccpp_micm_util.F90

@@ -1,4 +1,4 @@
-module micm_util
+module musica_ccpp_micm_util
   implicit none
 
   private
@@ -7,94 +7,69 @@ module micm_util
 
 contains
 
+  !> Reshape array (2D/3D -> 1D) and convert type (kind_phys -> c_double)
   subroutine reshape_into_micm_arr(temperature, pressure, dry_air_density, constituents, &
-      rate_params, m_temperature, m_pressure, m_dry_air_density, m_constituents, m_rate_params)
+      micm_temperature, micm_pressure, micm_dry_air_density, micm_constituents)
     use iso_c_binding, only: c_double
     use ccpp_kinds,    only: kind_phys
 
-    real(kind_phys), target, intent(in)  :: temperature(:,:)     ! K
-    real(kind_phys), target, intent(in)  :: pressure(:,:)        ! Pa
-    real(kind_phys), target, intent(in)  :: dry_air_density(:,:) ! kg m-3
-    real(kind_phys), target, intent(in)  :: constituents(:,:,:)  ! kg kg-1
-    real(kind_phys), target, intent(in)  :: rate_params(:,:,:)
-    real(c_double),  target, intent(out) :: m_temperature(:)     ! K
-    real(c_double),  target, intent(out) :: m_pressure(:)        ! Pa
-    real(c_double),  target, intent(out) :: m_dry_air_density(:) ! kg m-3
-    real(c_double),  target, intent(out) :: m_constituents(:)    ! kg kg-1
-    real(c_double),  target, intent(out) :: m_rate_params(:)
+    real(kind_phys), target, intent(in)  :: temperature(:,:)        ! K
+    real(kind_phys), target, intent(in)  :: pressure(:,:)           ! Pa
+    real(kind_phys), target, intent(in)  :: dry_air_density(:,:)    ! kg m-3
+    real(kind_phys), target, intent(in)  :: constituents(:,:,:)     ! kg kg-1
+    real(c_double),  target, intent(out) :: micm_temperature(:)     ! K
+    real(c_double),  target, intent(out) :: micm_pressure(:)        ! Pa
+    real(c_double),  target, intent(out) :: micm_dry_air_density(:) ! kg m-3
+    real(c_double),  target, intent(out) :: micm_constituents(:)    ! kg kg-1
 
     ! local variables
-    integer :: num_columns, num_layers
-    integer :: num_constituents, num_rate_params
-    integer :: i_column, i_layer, i_elem, i_constituents, i_rate_params
+    integer :: num_columns, num_layers, num_constituents
+    integer :: i_column, i_layer, i_elem, i_constituents
 
     num_columns = size(constituents, dim=1)
     num_layers = size(constituents, dim=2)
     num_constituents = size(constituents, dim=3)
-    num_rate_params = size(rate_params, dim=3)
 
-    ! Reshape into 1-D arry in species-column first order
-    ! refers to: state.variables_[i_cell][i_species] = concentrations[i_species_elem++]
+    ! Reshape into 1-D arry in species-column first order, referring to
+    ! state.variables_[i_cell][i_species] = concentrations[i_species_elem++]
     i_elem = 1
     i_constituents = 1
-    i_rate_params = 1
     do i_layer = 1, num_layers
       do i_column = 1, num_columns
-        m_temperature(i_elem) = real(temperature(i_column, i_layer), c_double)
-        m_pressure(i_elem) = real(pressure(i_column, i_layer), c_double)
-        m_dry_air_density(i_elem) = real(dry_air_density(i_column, i_layer), c_double)
-        m_constituents(i_constituents : i_constituents + num_constituents - 1) &
+        micm_temperature(i_elem) = real(temperature(i_column, i_layer), c_double)
+        micm_pressure(i_elem) = real(pressure(i_column, i_layer), c_double)
+        micm_dry_air_density(i_elem) = real(dry_air_density(i_column, i_layer), c_double)
+        micm_constituents(i_constituents : i_constituents + num_constituents - 1) &
                             = real(constituents(i_column, i_layer, :), c_double)
-        m_rate_params(i_rate_params : i_rate_params + num_rate_params - 1) &
-                            = real(rate_params(i_column, i_layer, :), c_double)
         i_elem = i_elem + 1
         i_constituents = i_constituents + num_constituents
-        i_rate_params = i_rate_params + num_rate_params
       end do
     end do
 
   end subroutine reshape_into_micm_arr
 
-  subroutine reshape_into_ccpp_arr(temperature, pressure, dry_air_density, constituents, &
-      rate_params, m_temperature, m_pressure, m_dry_air_density, m_constituents, m_rate_params)
+  !> Reshape array (1D -> 3D) and convert type (c_double -> kind_phys)
+  subroutine reshape_into_ccpp_arr(micm_constituents, constituents)
     use iso_c_binding, only: c_double
     use ccpp_kinds,    only: kind_phys
-    real(kind_phys), intent(out) :: temperature(:,:)     ! K
-    real(kind_phys), intent(out) :: pressure(:,:)        ! Pa
-    real(kind_phys), intent(out) :: dry_air_density(:,:) ! kg m-3
-    real(kind_phys), intent(out) :: constituents(:,:,:)  ! kg kg-1
-    real(kind_phys), intent(out) :: rate_params(:,:,:)
-    real(c_double),  intent(in)  :: m_temperature(:)     ! K
-    real(c_double),  intent(in)  :: m_pressure(:)        ! Pa
-    real(c_double),  intent(in)  :: m_dry_air_density(:) ! kg m-3
-    real(c_double),  intent(in)  :: m_constituents(:)    ! kg kg-1
-    real(c_double),  intent(in)  :: m_rate_params(:)
+
+    real(c_double),  intent(in)    :: micm_constituents(:) ! kg kg-1
+    real(kind_phys), intent(inout) :: constituents(:,:,:)  ! kg kg-1
 
     ! local variables
-    integer :: num_columns, num_layers
-    integer :: num_constituents, num_rate_params
-    integer :: i_column, i_layer, i_elem, i_constituents, i_rate_params
+    integer :: num_columns, num_layers, num_constituents
+    integer :: i_column, i_layer, i_constituents
 
     num_columns = size(constituents, dim=1)
     num_layers = size(constituents, dim=2)
     num_constituents = size(constituents, dim=3)
-    num_rate_params = size(rate_params, dim=3)
 
-    i_elem = 1
     i_constituents = 1
-    i_rate_params = 1
     do i_layer = 1, num_layers
       do i_column = 1, num_columns
-        temperature(i_column, i_layer) = real(m_temperature(i_elem), kind_phys)
-        pressure(i_column, i_layer) = real(m_pressure(i_elem), kind_phys)
-        dry_air_density(i_column, i_layer) = real(m_dry_air_density(i_elem), kind_phys)
         constituents(i_column, i_layer, :) &
-            = real(m_constituents(i_constituents : i_constituents + num_constituents - 1), kind_phys)
-        rate_params(i_column, i_layer, :) &
-            = real(m_rate_params(i_rate_params : i_rate_params + num_rate_params - 1), kind_phys)
-        i_elem = i_elem + 1
+            = real(micm_constituents(i_constituents : i_constituents + num_constituents - 1), kind_phys)
         i_constituents = i_constituents + num_constituents
-        i_rate_params = i_rate_params + num_rate_params
       end do
     end do
 
@@ -156,4 +131,4 @@ subroutine convert_to_mass_mixing_ratio(dry_air_density, molar_mass_arr, constit
 
   end subroutine convert_to_mass_mixing_ratio
 
-end module micm_util
+end module musica_ccpp_micm_util