initialize_species Subroutine

public subroutine initialize_species(mesh, params, species)

Populates species fields with initial mass fractions and handles naming.

Performs name-based matching between the transport registry and namelist initial conditions. Normalizes the initial mixture to ensure the physical constraint is met at .

Arguments

Type IntentOptional Attributes Name
type(mesh_t), intent(in) :: mesh

The computational mesh.
type(case_params_t), intent(in) :: params

Input configuration.
type(species_fields_t), intent(inout) :: species

The fields to initialize.

Calls

proc~~initialize_species~~CallsGraph proc~initialize_species mod_species::initialize_species proc~finalize_species mod_species::finalize_species proc~initialize_species->proc~finalize_species proc~lowercase mod_kinds::lowercase proc~initialize_species->proc~lowercase

Called by

proc~~initialize_species~~CalledByGraph proc~initialize_species mod_species::initialize_species program~lowmach_react_hex lowmach_react_hex program~lowmach_react_hex->proc~initialize_species

Source Code

   subroutine initialize_species(mesh, params, species)
      type(mesh_t), intent(in) :: mesh
      type(case_params_t), intent(in) :: params
      type(species_fields_t), intent(inout) :: species

      integer :: c, k, j
      real(rk) :: sum_Y
      real(rk) :: init_mixture(params%nspecies)
      character(len=name_len) :: target_name

      call finalize_species(species)

      species%nspecies = params%nspecies
      if (species%nspecies <= 0) return

      allocate(species%Y(species%nspecies, mesh%ncells))
      allocate(species%Y_old(species%nspecies, mesh%ncells))
      allocate(species%names(species%nspecies))

      species%names = params%species_name(1:species%nspecies)

      ! Match namelist initial conditions by species name
      init_mixture = zero
      
      do j = 1, params%namelist_nspecies
         target_name = trim(lowercase(params%namelist_species_name(j)))
         if (len_trim(target_name) == 0) cycle
         
         do k = 1, species%nspecies
            if (trim(lowercase(species%names(k))) == target_name) then
               init_mixture(k) = params%initial_Y(j)
               exit
            end if
         end do
      end do

      ! Normalize the initial mixture vector
      sum_Y = sum(init_mixture)
      if (sum_Y > zero) then
         init_mixture = init_mixture / sum_Y
      else
         ! Fallback: If no IC specified, set the mixture to 100% of the first species.
         if (species%nspecies > 0) init_mixture(1) = one
      end if

      do c = 1, mesh%ncells
         species%Y(:, c) = init_mixture
      end do

      species%Y_old = species%Y
   end subroutine initialize_species