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Suggests path sedimentations diags #63

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19 changes: 17 additions & 2 deletions src/aed_pathogens.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -101,9 +101,10 @@ MODULE aed_pathogens

! Diagnostic IDs for processes
INTEGER,ALLOCATABLE :: id_growth(:), id_mortality(:), id_sunlight(:), id_grazing(:), id_total(:)
INTEGER,ALLOCATABLE :: id_pth_f_sed(:), id_pth_d_sed(:)

INTEGER :: id_oxy, id_pH, id_doc, id_tss ! Dependency ID
INTEGER :: id_tem, id_sal ! Environmental IDs (3D)
INTEGER :: id_tem, id_sal, id_dz ! Environmental IDs (3D)
INTEGER :: id_par, id_nir, id_uva, id_uvb ! Environmental IDs (3D)
INTEGER :: id_I_0 ! Environmental ID (2D)
INTEGER :: resuspension
Expand Down Expand Up @@ -253,6 +254,7 @@ SUBROUTINE aed_define_pathogens(data, namlst)
data%id_uva = aed_locate_global('uva')
data%id_uvb = aed_locate_global('uvb')
data%id_I_0 = aed_locate_sheet_global('par_sf')
data%id_dz = aed_locate_global('layer_ht')
IF ( resuspension > 0 ) &
data%id_taub = aed_locate_sheet_global('taub')

Expand Down Expand Up @@ -403,6 +405,8 @@ SUBROUTINE aed_pathogens_load_params(data, dbase, count, list)
ALLOCATE(data%id_growth(count))
ALLOCATE(data%id_sunlight(count))
ALLOCATE(data%id_mortality(count))
ALLOCATE(data%id_pth_f_sed(count))
ALLOCATE(data%id_pth_d_sed(count))
ENDIF

DO i=1,count
Expand Down Expand Up @@ -456,6 +460,8 @@ SUBROUTINE aed_pathogens_load_params(data, dbase, count, list)
data%id_growth(i) = aed_define_diag_variable( TRIM(data%pathogens(i)%p_name)//'_g', 'orgs/m3/day', 'growth')
data%id_sunlight(i) = aed_define_diag_variable( TRIM(data%pathogens(i)%p_name)//'_l', 'orgs/m3/day', 'sunlight')
data%id_mortality(i) = aed_define_diag_variable( TRIM(data%pathogens(i)%p_name)//'_m', 'orgs/m3/day', 'mortality')
data%id_pth_f_sed(i) = aed_define_diag_variable( TRIM(data%pathogens(i)%p_name)//'_f_set', 'orgs/m3/d', 'alive sedimentation') !PRequest
data%id_pth_d_sed(i) = aed_define_diag_variable( TRIM(data%pathogens(i)%p_name)//'_d_set', 'orgs/m3/d', 'dead sedimentation') !PRequest
ENDIF
ENDDO
DEALLOCATE(pd)
Expand Down Expand Up @@ -526,6 +532,7 @@ SUBROUTINE aed_calculate_pathogens(data,column,layer_idx)
IF (data%pathogens(pth_i)%coef_sett_fa > zero_) THEN
pth_a = _STATE_VAR_(data%id_pa(pth_i))
END IF
pth_d = _STATE_VAR_(data%id_pd(pth_i)) ! BMT pull request

growth = zero_
predation = zero_
Expand Down Expand Up @@ -761,16 +768,24 @@ SUBROUTINE aed_mobility_pathogens(data,column,layer_idx,mobility)
AED_REAL,INTENT(inout) :: mobility(:)
!
!LOCALS
AED_REAL :: temp, vel
AED_REAL :: temp, vel, dz
INTEGER :: ss_i,pth_i
!
!-------------------------------------------------------------------------------
!BEGIN
temp = _STATE_VAR_(data%id_tem)
dz = _STATE_VAR_(data%id_dz)

_DIAG_VAR_(data%id_pth_f_sed) = zero_
_DIAG_VAR_(data%id_pth_d_sed) = zero_

! First set velocity for free pathogen groups
DO pth_i=1,data%num_pathogens
mobility(data%id_pf(pth_i)) = data%pathogens(pth_i)%coef_sett_w_path
IF ( diag_level >= 10 ) THEN
_DIAG_VAR_(data%id_pth_f_sed(pth_i)) = (mobility(data%id_pf(pth_i))/dz) * _STATE_VAR_(data%id_pf(pth_i)) * secs_per_day ! orgs/m3/d !PRequest
_DIAG_VAR_(data%id_pth_d_sed(pth_i)) = (mobility(data%id_pd(pth_i))/dz) * _STATE_VAR_(data%id_pd(pth_i)) * secs_per_day ! orgs/m3/d !PRequest
END IF
ENDDO

! Compute settling rate of particles
Expand Down