Merge pull request #65 from MichaelBarryBMT/pathogens-attach-diag

Adds additional attachment diag
AquaticEcoDynamics · Mar 22, 2023 · 6fd233d · 6fd233d
2 parents e4eab46 + 136ab4a
commit 6fd233d
Showing 1 changed file with 20 additions and 4 deletions.
diff --git a/src/aed_pathogens.F90 b/src/aed_pathogens.F90
@@ -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(:), id_pth_a_sed(:), id_attachment(:)
 
  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
@@ -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')
 
@@ -403,6 +405,10 @@ 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))
+ ALLOCATE(data%id_pth_a_sed(count))
+ ALLOCATE(data%id_attachment(count))
  ENDIF
 
  DO i=1,count
@@ -456,6 +462,12 @@ 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')
+ data%id_pth_d_sed(i) = aed_define_diag_variable( TRIM(data%pathogens(i)%p_name)//'_d_set', 'orgs/m3/d', 'dead sedimentation')
+ IF (data%pathogens(i)%coef_sett_fa > zero_) THEN
+ data%id_pth_a_sed(i) = aed_define_diag_variable( TRIM(data%pathogens(i)%p_name)//'_a_set', 'orgs/m3/d', 'attached sedimentation') 
+ data%id_attachment(i) = aed_define_diag_variable( TRIM(data%pathogens(i)%p_name)//'_att', 'orgs/m3/d', 'attachment rate') 
+ END IF
  ENDIF
  ENDDO
  DEALLOCATE(pd)
@@ -619,9 +631,13 @@ SUBROUTINE aed_calculate_pathogens(data,column,layer_idx)
  ! SET DIAGNOSTICS
  _DIAG_VAR_(data%id_total(pth_i)) = pth_f + pth_a + pth_d ! orgs/m3/s
  IF ( diag_level >= 10 ) THEN
- _DIAG_VAR_(data%id_growth(pth_i)) = growth*(pth_f + pth_a) ! orgs/m3/s
- _DIAG_VAR_(data%id_sunlight(pth_i)) = light*pth_f + (light/2.)*pth_a ! orgs/m3/s
- _DIAG_VAR_(data%id_mortality(pth_i)) = mortality*(pth_f + pth_a) ! orgs/m3/s
+ _DIAG_VAR_(data%id_growth(pth_i)) = growth*(pth_f + pth_a) * secs_per_day ! orgs/m3/d
+ _DIAG_VAR_(data%id_sunlight(pth_i)) = (light*pth_f + (light/2.)*pth_a) * secs_per_day ! orgs/m3/d
+ _DIAG_VAR_(data%id_mortality(pth_i)) = mortality*(pth_f + pth_a) * secs_per_day ! orgs/m3/d
+ ! Attached
+ IF (data%pathogens(pth_i)%coef_sett_fa > zero_) THEN
+ _DIAG_VAR_(data%id_attachment(pth_i)) = attachment * secs_per_day ! orgs/m3/d
+ END IF
  ENDIF
  ENDDO
 END SUBROUTINE aed_calculate_pathogens