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Ying et al. 2024 #255

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32d8869
ecogem source codes (merged with latest master branch)
ruiying-ocean Aug 23, 2024
18bfb14
add user-config files
ruiying-ocean Aug 23, 2024
b383a0e
add forcings, LGM basic configs, and definition.xml
ruiying-ocean Aug 23, 2024
b09a177
update readme.txt
ruiying-ocean Aug 23, 2024
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18 changes: 14 additions & 4 deletions genie-ecogem/src/fortran/ecogem.f90
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Expand Up @@ -84,8 +84,8 @@ subroutine ecogem( &
REAL,DIMENSION(iomax,npmax) ::AP_uptake ! Auto uptake for each plankton
REAL,DIMENSION(iomax,npmax) ::HP_uptake ! Auto uptake for each plankton
!REAL,DIMENSION(npmax) ::diameter !ckc for size dependent fractionation

REAL,DIMENSION(npmax) ::mortality,respiration
REAL,DIMENSION(npmax) ::mort_loss, respir_loss, eaten_loss ! real-time carbon biomass loss
REAL,DIMENSION(npmax) ::beta_mort_1,beta_graz_1
REAL,DIMENSION(iomax+iChl,npmax) ::assimilated,unassimilated
REAL,DIMENSION(npmax) ::BioC,PP
Expand Down Expand Up @@ -323,7 +323,7 @@ subroutine ecogem( &
PAR_out = PAR_in * exp(-k_tot*layerthick) ! light leaving bottom of layer
PAR_in = PAR_out
endif

! ?
up_inorg(:,:) = 0.0 ! (iomax,npmax)
qreg(:,:) = 0.0 ! (iomax,npmax)
Expand All @@ -347,7 +347,7 @@ subroutine ecogem( &
call quota_limitation(quota,limit,VLlimit,qreg,qreg_h)

call t_limitation(templocal,gamma_TP,gamma_TK)

call nutrient_uptake(qreg(:,:),loc_nuts(:),gamma_TK,up_inorg(:,:))

call photosynthesis(PAR_layer,loc_biomass,limit,VLlimit,up_inorg,gamma_TP,up_inorg(iDIC,:),chlsynth,totPP)
Expand All @@ -373,7 +373,7 @@ subroutine ecogem( &
! mortality(:) = mortality(:) * gamma_TK ! temp adjusted?

! calculate respiration
respiration(:) = respir(:) !* (1.0 - exp(-1.0e10 * loc_biomass(iCarb,:))) ! reduce respiration at very low biomass
respiration(:) = respir(:) * gamma_TK !* (1.0 - exp(-1.0e10 * loc_biomass(iCarb,:))) ! reduce respiration at very low biomass

! calculate assimilation efficiency based on quota status
!BAW: zoolimit should be optional Totzoolimit(:) = 0.0 !total food limitation - Maria May 2019 !!! Need to check if consistent!!!
Expand Down Expand Up @@ -458,6 +458,9 @@ subroutine ecogem( &
do io=1,iomax
AP_uptake(io,:) = dbiomassdt(io,:)
HP_uptake(io,:) = GrazPredEat(io,:) * assimilated(io,:)
mort_loss(:) = mortality(:) * BioC(:)
respir_loss(:) = respiration(:) * BioC(:)
eaten_loss(:)= GrazPreyEaten(iCarb, :)
enddo
endif

Expand Down Expand Up @@ -627,6 +630,10 @@ subroutine ecogem( &
if (eco_uptake_fluxes) then
AP_flux(io,:,i,j,k) = AP_uptake(io,:) ! mmol/m^3/s
HP_flux(io,:,i,j,k) = HP_uptake(io,:) ! mmol/m^3/s
! save the global biomass loss fluxes
plankton_mort(:,i,j,k) = mort_loss(:)
plankton_eaten(:,i,j,k) = eaten_loss(:)
plankton_respir(:,i,j,k) = respir_loss(:)
end if
enddo

Expand Down Expand Up @@ -914,6 +921,9 @@ SUBROUTINE diag_ecogem_timeslice( &
if (eco_uptake_fluxes) then
int_AP_timeslice(:,:,:,:,:) = int_AP_timeslice(:,:,:,:,:) + loc_dtyr * AP_flux(:,:,:,:,:) * pday ! mmol m^-3 d^-1 autotrophic flux in each plankton
int_HP_timeslice(:,:,:,:,:) = int_HP_timeslice(:,:,:,:,:) + loc_dtyr * HP_flux(:,:,:,:,:) * pday ! mmol m^-3 d^-1 heterotrophic flux in each plankton
int_pmort_timeslice(:,:,:,:) = int_pmort_timeslice(:,:,:,:) + loc_dtyr * plankton_mort(:,:,:,:) * pday ! mmol C m^-3 d^-1 plankton mortality flux in each plankton
int_peaten_timeslice(:,:,:,:) = int_peaten_timeslice(:,:,:,:) + loc_dtyr * plankton_eaten(:,:,:,:) * pday ! mmol C m^-3 d^-1 plankton grazing flux in each plankton
int_prespir_timeslice(:,:,:,:) = int_prespir_timeslice(:,:,:,:) + loc_dtyr * plankton_respir(:,:,:,:) * pday ! mmol C m^-3 d^-1 plankton respiration flux in each plankton
end if
end if

Expand Down
521 changes: 410 additions & 111 deletions genie-ecogem/src/fortran/ecogem_data.f90
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35 changes: 33 additions & 2 deletions genie-ecogem/src/fortran/ecogem_data_netCDF.f90
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Expand Up @@ -488,6 +488,7 @@ SUBROUTINE sub_save_netcdf_2d()
real::shannon(n_i,n_j),simpson(n_i,n_j),nthresh(n_i,n_j),berger(n_i,n_j)
real::picochl(n_i,n_j),nanochl(n_i,n_j),microchl(n_i,n_j)
real::nphyto

!-----------------------------------------------------------------------
! INITIALIZE LOCAL VARIABLES
!-----------------------------------------------------------------------
Expand Down Expand Up @@ -551,8 +552,38 @@ SUBROUTINE sub_save_netcdf_2d()
write (longstrng, "(A,A31,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Heterotrophic Uptake - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
call sub_adddef_netcdf(loc_iou,3,'eco2D'//shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
call sub_putvar2d('eco2D'//shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))
endif
endif
endif

! only export carbon loss
if (io .eq. iCarb) then

loc_ij(:,:) = int_peaten_timeslice(jp,:,:,n_k)
! short string: eco2D_Eaten_C_001
! unit formatter: A2,A,A8,A,A1
write (shrtstrng, "(A5, A7, A, A1, I3.3)") 'eco2D','_Eaten_',trim(adjustl(quotastrng(io))),'_',jp
write (longstrng, "(A, A16,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Grazed - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
call sub_adddef_netcdf(loc_iou,3,shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
call sub_putvar2d(shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))

!short string: eco2D_Mortality_C_001
loc_ij(:,:) = int_pmort_timeslice(jp,:,:,n_k)
write (shrtstrng, "(A5, A11, A, A1, I3.3)") 'eco2D','_Mortality_',trim(adjustl(quotastrng(io))),'_',jp
write (longstrng, "(A, A20,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Mortality - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
call sub_adddef_netcdf(loc_iou,3,shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
call sub_putvar2d(shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))

!short string: eco2D_Respiration_C_001
loc_ij(:,:) = int_prespir_timeslice(jp,:,:,n_k)
write (shrtstrng, "(A5, A13, A, A1, I3.3)") 'eco2D','_Respiration_',trim(adjustl(quotastrng(io))),'_',jp
write (longstrng, "(A,A22,I3.3,A2,A,A8,A,A1)") trim(adjustl(quotastrng(io))),' Respiration - Popn. #',jp,' (',trim(adjustl(diamtr)),' micron ',trim(pft(jp)),')'
call sub_adddef_netcdf(loc_iou,3,shrtstrng,longstrng,trim(quotaunits(io))//' d^-1',loc_c0,loc_c0)
call sub_putvar2d(shrtstrng,loc_iou,n_i,n_j,loc_ntrec,loc_ij(:,:),loc_mask(:,:))

endif
endif



end do
! Write community total biomasses and inorganic resource fluxes
write (shrtstrng, "(A10,A,A6)") "_Plankton_",trim(adjustl(quotastrng(io))),"_Total"
Expand Down
20 changes: 18 additions & 2 deletions genie-ecogem/src/fortran/ecogem_lib.f90
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Expand Up @@ -150,6 +150,13 @@ MODULE ecogem_lib
! Mixotrophy parameters
real :: trophic_tradeoff
namelist/ini_ecogem_nml/trophic_tradeoff
! foramecogenie parameters (11)
logical::ctrl_use_foramecogenie
real :: foram_auto_cost, foram_hetero_cost
real :: foram_spine_scale, foram_symbiont_esd_scale
namelist/ini_ecogem_nml/foram_auto_cost, foram_hetero_cost
namelist/ini_ecogem_nml/foram_spine_scale, foram_symbiont_esd_scale
namelist/ini_ecogem_nml/ctrl_use_foramecogenie
! Temperature dependence
real :: temp_A,temp_P,temp_K,temp_T0 !
namelist/ini_ecogem_nml/temp_A,temp_P,temp_K,temp_T0
Expand Down Expand Up @@ -290,6 +297,9 @@ MODULE ecogem_lib
REAL ,ALLOCATABLE,DIMENSION(:,:,:,:,:)::export_flux ! surface export flux for each plankton (iomax,npmax,i,j,k) Fanny/Maria - Aug19
REAL ,ALLOCATABLE,DIMENSION(:,:,:,:,:)::AP_flux ! surface autotrophic flux for each plankton (iomax,npmax,i,j,k)
REAL ,ALLOCATABLE,DIMENSION(:,:,:,:,:)::HP_flux ! surface heterotrophic flux for each plankton (iomax,npmax,i,j,k)
REAL ,ALLOCATABLE,DIMENSION(:,:,:,:):: plankton_respir ! respiration carbon flux for each plankton (npmax,i,j,k), RY, Oct 2023
REAL ,ALLOCATABLE,DIMENSION(:,:,:,:):: plankton_mort ! mortality carbon flux for each plankton (npmax,i,j,k), RY, Oct 2023
REAL ,ALLOCATABLE,DIMENSION(:,:,:,:):: plankton_eaten !grazed carbon flux for each plankton (npmax,i,j,k), RY, Oct 2023
!ckc isotope uptake flux array, to trace full food web interaction
REAL ,ALLOCATABLE,DIMENSION(:,:,:,:,:)::up_flux_iso !ckc rate of upstake isotopes (iimaxiso,npmax,i,j,k)
REAL ,ALLOCATABLE,DIMENSION(:,:,:,:) ::eco_carb ! carbonate chemistry variables
Expand All @@ -305,7 +315,7 @@ MODULE ecogem_lib
character(len=5) ,ALLOCATABLE,DIMENSION(:) ::rsrcstrng ! Inorganic resource labels
INTEGER ,ALLOCATABLE,DIMENSION(:) ::random_n ! n population replicates
INTEGER ,ALLOCATABLE,DIMENSION(:) ::nut2quota ! match nutrients to quotas
REAL ,ALLOCATABLE,DIMENSION(:) ::volume,diameter ,logvol,logesd ! Size parameters
REAL ,ALLOCATABLE,DIMENSION(:) ::volume,diameter,logvol,logesd ! Size parameters
REAL ,ALLOCATABLE,DIMENSION(:) ::autotrophy,heterotrophy ! Trophic strategy
LOGICAL ,ALLOCATABLE,DIMENSION(:) ::herbivory,carnivory ! Feeding behavior - Added by Grigoratou, Nov18
real ,ALLOCATABLE,DIMENSION(:) ::pp_opt_a_array,pp_sig_a_array,ns_array ! grazing parameters as arrays
Expand All @@ -318,6 +328,10 @@ MODULE ecogem_lib
REAL ,ALLOCATABLE,DIMENSION(:) ::qcarbon,alphachl ! Carbon quota and Photosynthesis parameters
REAL ,ALLOCATABLE,DIMENSION(:) ::graz,kg,pp_opt,pp_sig ! Grazing parameters
REAL ,ALLOCATABLE,DIMENSION(:) ::respir,biosink,mort,beta_graz,beta_mort ! Other loss parameters
REAL ,ALLOCATABLE,DIMENSION(:) ::symbiont_auto_cost, symbiont_hetero_cost ! RY, foramecogenie symbiont cost parameter
REAL ,ALLOCATABLE,DIMENSION(:) ::auto_volume, spine_esd_scale, symbiont_esd_scale ! RY, foramecogenie size parameter
REAL ,ALLOCATABLE,DIMENSION(:) ::respir_cost ! RY, foramecogenie grazing parameter

! Grazing kernel
REAL,ALLOCATABLE,DIMENSION(:,:)::gkernel,gkernelT
! netCDF and netCDF restart parameters
Expand Down Expand Up @@ -348,7 +362,6 @@ MODULE ecogem_lib
real::par_misc_t_err !
LOGICAL::par_misc_t_go = .FALSE. !
LOGICAL::par_misc_t_echo_header = .TRUE. !
!
real::par_misc_t_tseries = 0.0
real::par_misc_t_tslice = 0.0
logical::par_misc_t_intseries = .FALSE.
Expand Down Expand Up @@ -385,6 +398,9 @@ MODULE ecogem_lib
REAL ,ALLOCATABLE,DIMENSION(:,:,:,:,:) ::int_export_timeslice ! Surface export flux for each plankton (iomax,npmax,i,j,k) Fanny/Maria - Aug19
REAL ,ALLOCATABLE,DIMENSION(:,:,:,:,:) ::int_AP_timeslice ! Surface autotrophic uptake flux for each plankton (iomax,npmax,i,j,k)
REAL ,ALLOCATABLE,DIMENSION(:,:,:,:,:) ::int_HP_timeslice ! Surface heterotrophic uptake flux for each plankton (iomax,npmax,i,j,k)
REAL ,ALLOCATABLE,DIMENSION(:,:,:,:) ::int_peaten_timeslice ! Surface grazed (carbon) flux for each plankton (npmax,i,j,k)
REAL ,ALLOCATABLE,DIMENSION(:,:,:,:) ::int_pmort_timeslice ! Surface mortality (carbon) flux for each plankton (npmax,i,j,k)
REAL ,ALLOCATABLE,DIMENSION(:,:,:,:) ::int_prespir_timeslice ! Surface respiration (carbon) flux for each plankton (npmax,i,j,k)

! ### ADD ADDITIONAL TIME-SLICE ARRAY DEFINITIONS HERE ######################################################################### !

Expand Down
44 changes: 41 additions & 3 deletions genie-ecogem/src/fortran/initialise_ecogem.f90
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Expand Up @@ -150,6 +150,18 @@ SUBROUTINE initialise_ecogem( &
call check_iostat(alloc_error,__LINE__,__FILE__)
ALLOCATE(HP_flux(iomax,npmax,n_i,n_j,n_k),STAT=alloc_error) ! Hetero flux per plankton type
call check_iostat(alloc_error,__LINE__,__FILE__)
ALLOCATE(plankton_eaten(npmax,n_i,n_j,n_k),STAT=alloc_error)
call check_iostat(alloc_error,__LINE__,__FILE__)
ALLOCATE(plankton_mort(npmax,n_i,n_j,n_k),STAT=alloc_error)
call check_iostat(alloc_error,__LINE__,__FILE__)
ALLOCATE(plankton_respir(npmax,n_i,n_j,n_k),STAT=alloc_error)
call check_iostat(alloc_error,__LINE__,__FILE__)
ALLOCATE(int_pmort_timeslice(npmax,n_i,n_j,n_k),STAT=alloc_error)
call check_iostat(alloc_error,__LINE__,__FILE__)
ALLOCATE(int_prespir_timeslice(npmax,n_i,n_j,n_k),STAT=alloc_error)
call check_iostat(alloc_error,__LINE__,__FILE__)
ALLOCATE(int_peaten_timeslice(npmax,n_i,n_j,n_k),STAT=alloc_error)
call check_iostat(alloc_error,__LINE__,__FILE__)

! ecogem time-slice arrays
ALLOCATE(int_plankton_timeslice(iomax+iChl,npmax,n_i,n_j,n_k),STAT=alloc_error)
Expand Down Expand Up @@ -324,6 +336,28 @@ SUBROUTINE initialise_ecogem( &
if (useFe ) rsrcstrng(iFe) = 'Fe'
if (useSiO2 ) rsrcstrng(iSiO2) = 'SiO2'

! foramecogenie arrays allocation
if (ctrl_use_foramecogenie) then

ALLOCATE(respir_cost(npmax),STAT=alloc_error)
call check_iostat(alloc_error,__LINE__,__FILE__)

ALLOCATE(auto_volume(npmax),STAT=alloc_error)
call check_iostat(alloc_error,__LINE__,__FILE__)

ALLOCATE(spine_esd_scale(npmax),STAT=alloc_error)
call check_iostat(alloc_error,__LINE__,__FILE__)

ALLOCATE(symbiont_esd_scale(npmax),STAT=alloc_error)
call check_iostat(alloc_error,__LINE__,__FILE__)

ALLOCATE(symbiont_auto_cost(npmax),STAT=alloc_error)
call check_iostat(alloc_error,__LINE__,__FILE__)

ALLOCATE(symbiont_hetero_cost(npmax),STAT=alloc_error)
call check_iostat(alloc_error,__LINE__,__FILE__)
endif

! ---------------------------------------------------------- !
! OPEN ASCII FILES !---------------------------------------- !
! ---------------------------------------------------------- !
Expand All @@ -338,13 +372,17 @@ SUBROUTINE initialise_ecogem( &
enddo

! get explicit grazing parameters from input file
if(ctrl_grazing_explicit)then
CALL sub_init_explicit_grazing_params()
if(ctrl_grazing_explicit .AND. .NOT. ctrl_use_foramecogenie)then
CALL sub_init_explicit_grazing_params()
else if (ctrl_grazing_explicit .AND. ctrl_use_foramecogenie) then
CALL sub_init_explicit_rich_grazing_params()
endif

if (ctrl_use_foramecogenie .AND. ctrl_debug_init > 0) call sub_debug_foramecogem()

! *** initialise plankton biomass array
call sub_init_plankton()

! JDW: allocate and load temperature forcing dataset
if(ctrl_force_T)then
allocate(T_input(n_i,n_j),STAT=alloc_error)
Expand Down
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