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Particle bioshade and cdom light extinction #1

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Particle bioshade and cdom light extinction #1

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330b5f7
Refactor particle BGC logic and light update
rqthomas Oct 23, 2025
14f1a28
minor formating
rqthomas Oct 23, 2025
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26 changes: 19 additions & 7 deletions src/aed_api.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -1404,6 +1404,14 @@ SUBROUTINE aed_run_model(nCols, nLevs, doSurface)
!----------------------------------------------------------------------
!# Pre flux integration tasks
CALL pre_kinetics(all_cols(:,col), col, nLevs)

!----------------------------------------------------------------------
!# Particle BGC is needed BEFORE aed_run_column so bioshade works
IF (do_particle_bgc) THEN
CALL Particles(nLevs)
CALL aed_calculate_particles(all_cols(:,col), col, nLevs)
ENDIF


!----------------------------------------------------------------------
!# Main time-step tasks
Expand All @@ -1413,14 +1421,14 @@ SUBROUTINE aed_run_model(nCols, nLevs, doSurface)

!----------------------------------------------------------------------------
!# Particle tracking tasks
IF (do_particle_bgc) THEN
!IF (do_particle_bgc) THEN
! print *,'Particle BGC', call_count, nLevs
CALL Particles(nLevs)
DO col=1, nCols
IF (.NOT. data(col)%active) CYCLE !# skip this column if dry
CALL aed_calculate_particles(all_cols(:,col), col, nLevs)
ENDDO
ENDIF
! CALL Particles(nLevs)
! DO col=1, nCols
! IF (.NOT. data(col)%active) CYCLE !# skip this column if dry
! CALL aed_calculate_particles(all_cols(:,col), col, nLevs)
! ENDDO
!ENDIF

!-------------------------------------------------------------------------------
CONTAINS
Expand Down Expand Up @@ -1526,6 +1534,10 @@ SUBROUTINE aed_run_column(icolm, col, nlev, doSurface)
!# Time-integrate one biological time step
CALL calculate_fluxes(icolm, col, nlev, doSurface)

!# Update light needs to be called again so that any diagnostics that
!# influence like (e.g., cdom) have values from calculate_fluxes.
CALL update_light(icolm, col, nlev)

!# Update the water column layers
data(col)%cc(:, bot:top) = data(col)%cc(:, bot:top) + dt_eff*flux_pel(:, bot:top)

Expand Down