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Njeffery debug zbgc3 d #207

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merged 17 commits into from
Oct 26, 2018
Merged

Njeffery debug zbgc3 d #207

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a5fe6f0
Corrects icepack initialization for bgc.
njeffery Aug 14, 2018
44474a2
Debugged zbgc on gx1 for bgcgx1 test.
njeffery Oct 12, 2018
7535243
Updating debugZbgc3D branch to CICE master
eclare108213 Oct 17, 2018
abd1d66
env and nml options files for dyn alloc
eclare108213 Oct 17, 2018
d0d46ed
set nslyr=1
eclare108213 Oct 17, 2018
dfebc28
add bgc tests to base_suite
eclare108213 Oct 18, 2018
de13aee
alignment in namelists
eclare108213 Oct 18, 2018
1c6dacb
data dir and filenames for bgc
eclare108213 Oct 18, 2018
06c8a87
rename bgc testing options
eclare108213 Oct 18, 2018
8599bbc
expanding bgc options
eclare108213 Oct 19, 2018
100d6c9
remove ISPOL and NICE bgc options for CICE
eclare108213 Oct 19, 2018
cdf2081
correct doc
eclare108213 Oct 19, 2018
31d18de
add apostrophes to doc
eclare108213 Oct 19, 2018
acbd01a
Add two missing parameters to bgc initialization.
njeffery Oct 23, 2018
1c0012d
resolve conflicts
eclare108213 Oct 23, 2018
85cdedb
Get bgc code running on 4 compilers on conrad.
apcraig Oct 26, 2018
9f47dac
Merge branch 'njeffery_debugZbgc3D' of https://github.com/njeffery/ci…
apcraig Oct 26, 2018
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259 changes: 166 additions & 93 deletions cicecore/cicedynB/general/ice_forcing_bgc.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -72,9 +72,10 @@ end subroutine alloc_forcing_bgc

subroutine get_forcing_bgc

use ice_blocks, only: block, get_block
use ice_domain, only: nblocks, blocks_ice
use ice_arrays_column, only: ocean_bio_all
use ice_calendar, only: yday
use ice_domain, only: nblocks
use ice_flux, only: sss
use ice_flux_bgc, only: sil, nit
use ice_forcing, only: trestore, trest, fyear, &
Expand All @@ -84,6 +85,7 @@ subroutine get_forcing_bgc

integer (kind=int_kind) :: &
i, j, iblk, & ! horizontal indices
ilo,ihi,jlo,jhi, & ! beginning and end of physical domain
ixm,ixp, ixx, & ! record numbers for neighboring months
maxrec , & ! maximum record number
recslot , & ! spline slot for current record
Expand Down Expand Up @@ -111,6 +113,9 @@ subroutine get_forcing_bgc
nit_file , & ! nitrate input file
sil_file ! silicate input file

type (block) :: &
this_block ! block information for current block

character(len=*), parameter :: subname = '(get_forcing_bgc)'

call icepack_query_parameters(secday_out=secday)
Expand All @@ -125,11 +130,14 @@ subroutine get_forcing_bgc
if (trim(nit_data_type) == 'clim'.or. &
trim(sil_data_type) == 'clim') then

nit_file = trim(bgc_data_dir)//'nitrate_climatologyWOA_gx1v6f.nc'
nit_file = 'nitrate_climatologyWOA_gx1v6f_20150107.nc'
!'nitrate_WOA2005_surface_monthly' ! gx1 only
sil_file = trim(bgc_data_dir)//'silicate_climatologyWOA_gx1v6f.nc'
sil_file = 'silicate_climatologyWOA_gx1v6f_20150107.nc'
!'silicate_WOA2005_surface_monthly' ! gx1 only

nit_file = trim(bgc_data_dir)//'/'//trim(nit_file)
sil_file = trim(bgc_data_dir)//'/'//trim(sil_file)

if (my_task == master_task .and. istep == 1) then
if (trim(sil_data_type)=='clim' .AND. tr_bgc_Sil) then
write (nu_diag,*) ' '
Expand Down Expand Up @@ -194,43 +202,70 @@ subroutine get_forcing_bgc
call interpolate_data (sil_data, sildat)

if (istep == 1 .or. .NOT. restore_bgc) then
!$OMP PARALLEL DO PRIVATE(iblk,i,j)
do iblk = 1, nblocks
do j = 1, ny_block
do i = 1, nx_block
sil(i,j,iblk) = sildat(i,j,iblk)
ks = 2*icepack_max_algae + icepack_max_doc + 3 + icepack_max_dic
ocean_bio_all(i,j,ks,iblk) = sil(i,j,iblk) !Sil
enddo
enddo

!$OMP PARALLEL DO PRIVATE(iblk,ilo,ihi,jlo,jhi,this_block)
do iblk = 1, nblocks

this_block = get_block(blocks_ice(iblk),iblk)
ilo = this_block%ilo
ihi = this_block%ihi
jlo = this_block%jlo
jhi = this_block%jhi

do j = jlo, jhi
do i = ilo, ihi

sil(i,j,iblk) = sildat(i,j,iblk)
ks = 2*icepack_max_algae + icepack_max_doc + 3 + icepack_max_dic
ocean_bio_all(i,j,ks,iblk) = sil(i,j,iblk) !Sil
enddo
enddo
enddo

!$OMP END PARALLEL DO
elseif (restore_bgc) then
!$OMP PARALLEL DO PRIVATE(iblk,i,j)
do iblk = 1, nblocks
do j = 1, ny_block
do i = 1, nx_block
sil(i,j,iblk) = sil(i,j,iblk) &

!$OMP PARALLEL DO PRIVATE(iblk,ilo,ihi,jlo,jhi,this_block)
do iblk = 1, nblocks

this_block = get_block(blocks_ice(iblk),iblk)
ilo = this_block%ilo
ihi = this_block%ihi
jlo = this_block%jlo
jhi = this_block%jhi

do j = jlo, jhi
do i = ilo, ihi

sil(i,j,iblk) = sil(i,j,iblk) &
+ (sildat(i,j,iblk)-sil(i,j,iblk))*dt/trest
ks = 2*icepack_max_algae + icepack_max_doc + 3 + icepack_max_dic
ocean_bio_all(i,j,ks,iblk) = sil(i,j,iblk) !Sil
enddo
ks = 2*icepack_max_algae + icepack_max_doc + 3 + icepack_max_dic
ocean_bio_all(i,j,ks,iblk) = sil(i,j,iblk) !Sil
enddo
enddo
enddo
enddo
!$OMP END PARALLEL DO
!$OMP END PARALLEL DO
endif !restore
elseif (tr_bgc_Sil) then
!$OMP PARALLEL DO PRIVATE(iblk,i,j)
do iblk = 1, nblocks
do j = 1, ny_block
do i = 1, nx_block
sil(i,j,iblk) = 25.0_dbl_kind
ks = 2*icepack_max_algae + icepack_max_doc + 3 + icepack_max_dic
ocean_bio_all(i,j,ks,iblk) = sil(i,j,iblk) !Sil
enddo
!$OMP PARALLEL DO PRIVATE(iblk,ilo,ihi,jlo,jhi,this_block)
do iblk = 1, nblocks

this_block = get_block(blocks_ice(iblk),iblk)
ilo = this_block%ilo
ihi = this_block%ihi
jlo = this_block%jlo
jhi = this_block%jhi

do j = jlo, jhi
do i = ilo, ihi

sil(i,j,iblk) = 25.0_dbl_kind
ks = 2*icepack_max_algae + icepack_max_doc + 3 + icepack_max_dic
ocean_bio_all(i,j,ks,iblk) = sil(i,j,iblk) !Sil
enddo
enddo
enddo
enddo
!$OMP END PARALLEL DO
!$OMP END PARALLEL DO

endif !tr_bgc_Sil
!-------------------------------------------------------------------
Expand All @@ -249,67 +284,97 @@ subroutine get_forcing_bgc
call interpolate_data (nit_data, nitdat)

if (istep == 1 .or. .NOT. restore_bgc) then
!$OMP PARALLEL DO PRIVATE(iblk,i,j)
do iblk = 1, nblocks
do j = 1, ny_block
do i = 1, nx_block
nit(i,j,iblk) = nitdat(i,j,iblk)
ks = icepack_max_algae + 1
ocean_bio_all(i,j,ks,iblk) = nit(i,j,iblk) !nit
ks = 2*icepack_max_algae + icepack_max_doc + 7 + icepack_max_dic
ocean_bio_all(i,j,ks,iblk) = nit(i,j,iblk) !PON
!$OMP PARALLEL DO PRIVATE(iblk,ilo,ihi,jlo,jhi,this_block)
do iblk = 1, nblocks

this_block = get_block(blocks_ice(iblk),iblk)
ilo = this_block%ilo
ihi = this_block%ihi
jlo = this_block%jlo
jhi = this_block%jhi

do j = jlo, jhi
do i = ilo, ihi

nit(i,j,iblk) = nitdat(i,j,iblk)
ks = icepack_max_algae + 1
ocean_bio_all(i,j,ks,iblk) = nit(i,j,iblk) !nit
ks = 2*icepack_max_algae + icepack_max_doc + 7 + icepack_max_dic
ocean_bio_all(i,j,ks,iblk) = nit(i,j,iblk) !PON
enddo
enddo
enddo
enddo
enddo
!$OMP END PARALLEL DO
!$OMP END PARALLEL DO
elseif (restore_bgc ) then
!$OMP PARALLEL DO PRIVATE(iblk,i,j)
do iblk = 1, nblocks
do j = 1, ny_block
do i = 1, nx_block
nit(i,j,iblk) = nit(i,j,iblk) &
!$OMP PARALLEL DO PRIVATE(iblk,ilo,ihi,jlo,jhi,this_block)
do iblk = 1, nblocks

this_block = get_block(blocks_ice(iblk),iblk)
ilo = this_block%ilo
ihi = this_block%ihi
jlo = this_block%jlo
jhi = this_block%jhi

do j = jlo, jhi
do i = ilo, ihi

nit(i,j,iblk) = nit(i,j,iblk) &
+ (nitdat(i,j,iblk)-nit(i,j,iblk))*dt/trest
ks = icepack_max_algae + 1
ocean_bio_all(i,j,ks,iblk) = nit(i,j,iblk) !nit
ks = 2*icepack_max_algae + icepack_max_doc + 7 + icepack_max_dic
ocean_bio_all(i,j,ks,iblk) = nit(i,j,iblk) !PON
ks = icepack_max_algae + 1
ocean_bio_all(i,j,ks,iblk) = nit(i,j,iblk) !nit
ks = 2*icepack_max_algae + icepack_max_doc + 7 + icepack_max_dic
ocean_bio_all(i,j,ks,iblk) = nit(i,j,iblk) !PON
enddo
enddo
enddo
enddo
enddo
!$OMP END PARALLEL DO
!$OMP END PARALLEL DO
endif !restore_bgc

elseif (trim(nit_data_type) == 'sss' .AND. tr_bgc_Nit) then

!$OMP PARALLEL DO PRIVATE(iblk,i,j)
do iblk = 1, nblocks
do j = 1, ny_block
do i = 1, nx_block
nit(i,j,iblk) = sss(i,j,iblk)
ks = icepack_max_algae + 1
ocean_bio_all(i,j,ks,iblk) = nit(i,j,iblk) !nit
ks = 2*icepack_max_algae + icepack_max_doc + 7 + icepack_max_dic
ocean_bio_all(i,j,ks,iblk) = nit(i,j,iblk) !PON
!$OMP PARALLEL DO PRIVATE(iblk,ilo,ihi,jlo,jhi,this_block)
do iblk = 1, nblocks

this_block = get_block(blocks_ice(iblk),iblk)
ilo = this_block%ilo
ihi = this_block%ihi
jlo = this_block%jlo
jhi = this_block%jhi

do j = jlo, jhi
do i = ilo, ihi

nit(i,j,iblk) = sss(i,j,iblk)
ks = icepack_max_algae + 1
ocean_bio_all(i,j,ks,iblk) = nit(i,j,iblk) !nit
ks = 2*icepack_max_algae + icepack_max_doc + 7 + icepack_max_dic
ocean_bio_all(i,j,ks,iblk) = nit(i,j,iblk) !PON
enddo
enddo
enddo
enddo
enddo
!$OMP END PARALLEL DO

elseif (tr_bgc_Nit) then
!$OMP PARALLEL DO PRIVATE(iblk,ilo,ihi,jlo,jhi,this_block)
do iblk = 1, nblocks

this_block = get_block(blocks_ice(iblk),iblk)
ilo = this_block%ilo
ihi = this_block%ihi
jlo = this_block%jlo
jhi = this_block%jhi

do j = jlo, jhi
do i = ilo, ihi

!$OMP PARALLEL DO PRIVATE(iblk,i,j)
do iblk = 1, nblocks
do j = 1, ny_block
do i = 1, nx_block
nit(i,j,iblk) = 12.0_dbl_kind
ks = icepack_max_algae + 1
ocean_bio_all(i,j,ks,iblk) = nit(i,j,iblk) !nit
ks = 2*icepack_max_algae + icepack_max_doc + 7 + icepack_max_dic
ocean_bio_all(i,j,ks,iblk) = nit(i,j,iblk) !PON
enddo
nit(i,j,iblk) = 12.0_dbl_kind
ks = icepack_max_algae + 1
ocean_bio_all(i,j,ks,iblk) = nit(i,j,iblk) !nit
ks = 2*icepack_max_algae + icepack_max_doc + 7 + icepack_max_dic
ocean_bio_all(i,j,ks,iblk) = nit(i,j,iblk) !PON
enddo
enddo
enddo
enddo
!$OMP END PARALLEL DO
!$OMP END PARALLEL DO

endif !tr_bgc_Nit

Expand Down Expand Up @@ -381,20 +446,28 @@ subroutine get_forcing_bgc
+ c2intp * nit_data_p(2)
endif

!$OMP PARALLEL DO PRIVATE(iblk,i,j)
do iblk = 1, nblocks
do j = 1, ny_block
do i = 1, nx_block
ks = 2*icepack_max_algae + icepack_max_doc + 3 + icepack_max_dic
ocean_bio_all(i,j,ks,iblk) = sil(i,j,iblk) !Sil
ks = icepack_max_algae + 1
ocean_bio_all(i,j,ks,iblk) = nit(i,j,iblk) !nit
ks = 2*icepack_max_algae + icepack_max_doc + 7 + icepack_max_dic
ocean_bio_all(i,j,ks,iblk) = nit(i,j,iblk) !PON
enddo
!$OMP PARALLEL DO PRIVATE(iblk,ilo,ihi,jlo,jhi,this_block)
do iblk = 1, nblocks

this_block = get_block(blocks_ice(iblk),iblk)
ilo = this_block%ilo
ihi = this_block%ihi
jlo = this_block%jlo
jhi = this_block%jhi

do j = jlo, jhi
do i = ilo, ihi

ks = 2*icepack_max_algae + icepack_max_doc + 3 + icepack_max_dic
ocean_bio_all(i,j,ks,iblk) = sil(i,j,iblk) !Sil
ks = icepack_max_algae + 1
ocean_bio_all(i,j,ks,iblk) = nit(i,j,iblk) !nit
ks = 2*icepack_max_algae + icepack_max_doc + 7 + icepack_max_dic
ocean_bio_all(i,j,ks,iblk) = nit(i,j,iblk) !PON
enddo
enddo
enddo
enddo
!$OMP END PARALLEL DO
!$OMP END PARALLEL DO

! Save record number for next time step
bgcrecnum = recnum
Expand Down
7 changes: 3 additions & 4 deletions cicecore/drivers/cesm/CICE_InitMod.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -105,7 +105,6 @@ subroutine cice_init(mpicom_ice)

call input_data ! namelist variables
if (trim(runid) == 'bering') call check_finished_file
call init_zbgc ! vertical biogeochemistry namelist

call init_domain_blocks ! set up block decomposition
call init_grid1 ! domain distribution
Expand All @@ -118,6 +117,7 @@ subroutine cice_init(mpicom_ice)
call init_ice_timers ! initialize all timers
call ice_timer_start(timer_total) ! start timing entire run
call init_grid2 ! grid variables
call init_zbgc ! vertical biogeochemistry namelist

call init_calendar ! initialize some calendar stuff
call init_hist (dt) ! initialize output history file
Expand Down Expand Up @@ -149,6 +149,8 @@ subroutine cice_init(mpicom_ice)
call init_state ! initialize the ice state
call init_transport ! initialize horizontal transport
call ice_HaloRestore_init ! restored boundary conditions
call icepack_query_parameters(skl_bgc_out=skl_bgc, z_tracers_out=z_tracers)
if (skl_bgc .or. z_tracers) call alloc_forcing_bgc ! allocate biogeochemistry arrays

call init_restart ! initialize restart variables

Expand All @@ -157,7 +159,6 @@ subroutine cice_init(mpicom_ice)
call init_history_dyn ! initialize dynamic history variables

call icepack_query_tracer_flags(tr_aero_out=tr_aero, tr_zaero_out=tr_zaero)
call icepack_query_parameters(skl_bgc_out=skl_bgc, z_tracers_out=z_tracers)
call icepack_warnings_flush(nu_diag)
if (icepack_warnings_aborted()) call abort_ice(error_message=subname, &
file=__FILE__, line=__LINE__)
Expand Down Expand Up @@ -186,8 +187,6 @@ subroutine cice_init(mpicom_ice)
! if (tr_aero) call faero_data ! data file
! if (tr_zaero) call fzaero_data ! data file (gx1)
if (tr_aero .or. tr_zaero) call faero_default ! default values

if (skl_bgc .or. z_tracers) call alloc_forcing_bgc ! allocate biogeochemistry arrays
if (skl_bgc .or. z_tracers) call get_forcing_bgc ! biogeochemistry
#endif
#endif
Expand Down
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