Rxns with layers

.gitignore

@@ -1,3 +1,5 @@
+**/*.d
+**/*.dSym
 **/.DS_Store
 **/*.pyc
 CMakeCache.txt

src/aero_rep_data.F90

@@ -74,6 +74,10 @@ module camp_aero_rep_data
     !! functions of the aerosol representation that cannot be obtained
     !! from the camp_camp_state::camp_state_t object. (integer)
     integer(kind=i_kind), allocatable, public ::  condensed_data_int(:)
+    !> Array of booleans indicating if phase exists at the surface of a
+    !! particle. Used in SIMPOL and HL reactions for single particle 
+    !! representation. 
+    logical, allocatable, public :: aero_phase_is_at_surface(:)
     !> Number of environment-dependent parameters
     !! These are parameters that need updated when environmental conditions
     !! change
@@ -489,26 +493,50 @@ end function get_name
 
   !> Get a set of ids for all instances of a phase in this aerosol
   !! representation for use during solving
-  function phase_ids(this, phase_name)
+  function phase_ids(this, phase_name, is_at_surface)
 
     !> List of phase ids
     integer(kind=i_kind), allocatable :: phase_ids(:)
     !> Aerosol representation data
     class(aero_rep_data_t), intent(in) :: this
     !> Aerosol phase name
     character(len=*), intent(in) :: phase_name
+    !> Indicates if aerosol phase is at the surface of particle
+    logical, intent(in), optional :: is_at_surface
 
     integer(kind=i_kind) :: num_instances, i_instance, i_phase
 
     num_instances = this%num_phase_instances(phase_name)
     allocate(phase_ids(num_instances))
-    i_instance = 1
-    do i_phase = 1, size(this%aero_phase)
-      if (this%aero_phase(i_phase)%val%name().eq.phase_name) then
-        phase_ids(i_instance) = i_phase
-        i_instance = i_instance + 1
+    if (present(is_at_surface)) then
+      if (is_at_surface) then
+        i_instance = 1
+        do i_phase = 1, size(this%aero_phase)
+          if (this%aero_phase(i_phase)%val%name().eq. phase_name .and. &
+              this%aero_phase_is_at_surface(i_phase)) then
+            phase_ids(i_instance) = i_phase
+            i_instance = i_instance + 1
+          end if
+        end do
+      else
+        i_instance = 1
+        do i_phase = 1, size(this%aero_phase)
+          if (this%aero_phase(i_phase)%val%name().eq. phase_name .and. &
+              .not. this%aero_phase_is_at_surface(i_phase)) then
+            phase_ids(i_instance) = i_phase
+            i_instance = i_instance + 1
+          end if
+        end do
       end if
-    end do
+    else
+      i_instance = 1
+      do i_phase = 1, size(this%aero_phase)
+        if (this%aero_phase(i_phase)%val%name().eq.phase_name) then
+          phase_ids(i_instance) = i_phase
+          i_instance = i_instance + 1
+        end if
+      end do
+    end if
 
   end function phase_ids
 

src/aero_reps/aero_rep_modal_binned_mass.F90

@@ -477,6 +477,7 @@ subroutine initialize(this, aero_phase_set, spec_state_id)
 
     ! Allocate space for the aerosol phases and species state ids
     allocate(this%aero_phase(num_phase))
+    allocate(this%aero_phase_is_at_surface(num_phase))
     allocate(this%phase_state_id(size(this%aero_phase)))
 
     ! Allocate condensed data arrays
@@ -616,6 +617,9 @@ subroutine initialize(this, aero_phase_set, spec_state_id)
 
               ! Add the aerosol phase to the list
               this%aero_phase(i_phase) = aero_phase_set(k_phase)
+
+              ! No species exist at surface 
+              this%aero_phase_is_at_surface(i_phase) = .true.
 
               ! Save the starting id for this phase on the state array
               this%phase_state_id(i_phase) = curr_spec_state_id

src/aero_reps/aero_rep_single_particle.F90

@@ -358,6 +358,7 @@ subroutine initialize(this, aero_phase_set, spec_state_id)
     ! each layer in each particle, and set PHASE_STATE_ID and
     ! PHASE_MODEL_DATA_ID for each phase
     allocate(this%aero_phase(num_phases * num_particles))
+    allocate(this%aero_phase_is_at_surface(num_phases * num_particles))
     curr_phase = 1
     do i_layer = 1, size(ordered_layer_id)
       j_layer = ordered_layer_id(i_layer)
@@ -395,6 +396,13 @@ subroutine initialize(this, aero_phase_set, spec_state_id)
             do i_particle = 0, num_particles-1
               this%aero_phase(i_particle*num_phases + curr_phase) = &
                 aero_phase_set(j_phase)
+              if (i_layer .eq. NUM_LAYERS_) then
+                this%aero_phase_is_at_surface(i_particle*num_phases + curr_phase) = &
+                  .true.
+                else
+                  this%aero_phase_is_at_surface(i_particle*num_phases + curr_phase) = &
+                    .false.
+              end if
             end do
             PHASE_STATE_ID_(i_layer,i_phase) = curr_id
             PHASE_MODEL_DATA_ID_(i_layer,i_phase) = j_phase

src/aero_reps/aero_rep_single_particle.c

@@ -437,8 +437,9 @@ void aero_rep_single_particle_print(int *aero_rep_int_data,
   printf("\nAerosol representation id: %d", AERO_REP_ID_);
   printf("\nMax computational particles: %d", MAX_PARTICLES_);
   printf("\nParticle state size: %d", PARTICLE_STATE_SIZE_);
-  printf("\n\n   - Phases -");
   for(int i_layer = 0; i_layer < NUM_LAYERS_; ++i_layer){
+    printf("\nLayer: %d", i_layer);
+    printf("\n\n   - Phases -");
     for (int i_phase = 0; i_phase < NUM_PHASES_(i_layer); ++i_phase) {
       printf("\n  state id: %d model data id: %d num Jac elements: %d",
              PHASE_STATE_ID_(i_layer,i_phase), PHASE_MODEL_DATA_ID_(i_layer,i_phase),

src/rxns/rxn_HL_phase_transfer.F90

@@ -257,7 +257,7 @@ subroutine initialize(this, chem_spec_data, aero_rep, n_cells)
 
       ! Get the number of Jacobian elements for calculations of mass, volume,
       ! number, etc. for this partitioning into this phase
-      phase_ids = aero_rep(i_aero_rep)%val%phase_ids(phase_name)
+      phase_ids = aero_rep(i_aero_rep)%val%phase_ids(phase_name,is_at_surface=.true.)
       do i_phase = 1, size(phase_ids)
         n_aero_jac_elem = n_aero_jac_elem + &
                 aero_rep(i_aero_rep)%val%num_jac_elem(phase_ids(i_phase))
@@ -316,7 +316,7 @@ subroutine initialize(this, chem_spec_data, aero_rep, n_cells)
               phase_name = phase_name, spec_name = water_name)
 
       ! Get the phase ids for this aerosol phase
-      phase_ids = aero_rep(i_aero_rep)%val%phase_ids(phase_name)
+      phase_ids = aero_rep(i_aero_rep)%val%phase_ids(phase_name,is_at_surface=.true.)
 
       ! Add the species concentration and activity coefficient ids to
       ! the condensed data, and set the number of jacobian elements for

src/rxns/rxn_SIMPOL_phase_transfer.F90

@@ -255,7 +255,7 @@ subroutine initialize(this, chem_spec_data, aero_rep, n_cells)
 
       ! Get the number of Jacobian elements for calculations of mass, volume,
       ! number, etc. for this partitioning into this phase
-      phase_ids = aero_rep(i_aero_rep)%val%phase_ids(phase_name)
+      phase_ids = aero_rep(i_aero_rep)%val%phase_ids(phase_name,is_at_surface=.true.)
       do i_phase = 1, size(phase_ids)
         n_aero_jac_elem = n_aero_jac_elem + &
                 aero_rep(i_aero_rep)%val%num_jac_elem(phase_ids(i_phase))
@@ -319,8 +319,7 @@ subroutine initialize(this, chem_spec_data, aero_rep, n_cells)
       end if
 
       ! Get the phase ids for this aerosol phase
-      phase_ids = aero_rep(i_aero_rep)%val%phase_ids(phase_name)
-
+      phase_ids = aero_rep(i_aero_rep)%val%phase_ids(phase_name,is_at_surface=.true.)
       ! Add the species concentration and activity coefficient ids to
       ! the condensed data, and set the number of Jacobian elements for
       ! the aerosol representations and the locations of the real data

test/unit_aero_rep_data/test_aero_rep_single_particle.F90

@@ -192,6 +192,21 @@ subroutine test_config_read()
         call assert(603635677, aero_rep%phase_state_size(layer=2,phase=2) .eq. 2)
         call assert(768528274, aero_rep%phase_state_size(layer=3,phase=1) .eq. 3)
 
+        ! check boolean surface array 
+        call assert(438901931, aero_rep%aero_phase_is_at_surface(1) .eqv. .false.)
+        call assert(545268641, aero_rep%aero_phase_is_at_surface(2) .eqv. .false.)
+        call assert(450505920, aero_rep%aero_phase_is_at_surface(3) .eqv. .false.)
+        call assert(160921440, aero_rep%aero_phase_is_at_surface(4) .eqv. .true.)
+        call assert(013254644, aero_rep%aero_phase_is_at_surface(5) .eqv. .false.)
+        call assert(691645657, aero_rep%aero_phase_is_at_surface(6) .eqv. .false.)
+        call assert(916896739, aero_rep%aero_phase_is_at_surface(7) .eqv. .false.)
+        call assert(668436322, aero_rep%aero_phase_is_at_surface(8) .eqv. .true.)
+        call assert(952270724, aero_rep%aero_phase_is_at_surface(9) .eqv. .false.)
+        call assert(410924438, aero_rep%aero_phase_is_at_surface(10) .eqv. .false.)
+        call assert(266324037, aero_rep%aero_phase_is_at_surface(11) .eqv. .false.)
+        call assert(008760891, aero_rep%aero_phase_is_at_surface(12) .eqv. .true.)
+
+        call assert(768528274, aero_rep%phase_state_size(layer=3,phase=1) .eq. 3)
         ! test num_phase_instances funtion
         phase_name_test = "bread"
         num_bread = 2