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6 merge neccton dev #7

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45eef14
Phyto.F90 - added p_qlcmin, minimum Chl / C ratio
Jun 5, 2026
f6b1409
added p_qo2cr and p_qo2cf coefficients, O2consumed per carbon respire…
Jun 8, 2026
bec8fe3
Phyto.F90 - added partition of nutrient stress excretion / respiratio…
Jun 9, 2026
0d68d69
typo in Phyto.F90
Jun 9, 2026
dcbbeb4
fabm_multispectral_2xDetritus.yaml - with new parameters, p_pu_rn, p_…
Jun 9, 2026
1a7a466
shared.F90 - updated default (hard-coded) values of p_qo2cr (1.32) an…
Jun 9, 2026
368d11c
Potential fix for pull request finding
ggalli00 Jun 9, 2026
bcc26ca
Potential fix for pull request finding
ggalli00 Jun 9, 2026
5f43d06
Potential fix for pull request finding
ggalli00 Jun 9, 2026
89ca936
Fix p_qun typo in multispectral 2xDetritus preset
Copilot Jun 10, 2026
ee623fc
shared.F90 - typo in comment
Jun 10, 2026
03ff501
Merge branch '6-merge_neccton_dev' of github.com:inogs/bfmforfabm int…
Jun 11, 2026
3831695
Phyto.F90 - deleted unused ERSEM-II light parameters
Jun 11, 2026
3226341
fabm_V13C.yaml - new parameters, synced with EIS_2026_11 V13C run
Jun 11, 2026
5688bf1
renamed yaml file to fabm_EIS_2026_11_V13C.yaml
Jun 11, 2026
98f47a1
removed fabm_V13C.yaml
Jun 11, 2026
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4 changes: 2 additions & 2 deletions MesoZoo.F90
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Expand Up @@ -665,8 +665,8 @@ subroutine do(self,_ARGUMENTS_DO_)
!-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
prI = ONE - self%p_puI - self%p_peI
rrc = prI * rut_c + self%p_srs*et*zooc
! call flux_vector(iiPel, ppO2o, ppO2o, -rrc/MW_C)
_SET_ODE_(self%id_O2o,-(rrc/MW_C))
! call flux_vector(iiPel, ppO2o, ppO2o, -rrc/MW_C*p_qo2cr)
_SET_ODE_(self%id_O2o,-(rrc/MW_C*p_qo2cr))
! call quota_flux(iiPel, ppzooc, ppzooc, ppO3c, rrc, tfluxC)
_SET_ODE_(self%id_c,-rrc)
_SET_ODE_(self%id_O3c,rrc)
Expand Down
4 changes: 2 additions & 2 deletions MicroZoo.F90
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Expand Up @@ -571,8 +571,8 @@ subroutine do(self,_ARGUMENTS_DO_)
! call quota_flux(iiPel, ppzooc, ppzooc, ppO3c, rrtc, tfluxC)
_SET_ODE_(self%id_c, -rrtc)
_SET_ODE_(self%id_O3c,rrtc)
! call flux_vector(iiPel, ppO2o, ppO2o, -rrtc/MW_C)
_SET_ODE_(self%id_O2o,-(rrtc/MW_C))
! call flux_vector(iiPel, ppO2o, ppO2o, -rrtc/MW_C*p_qo2cr)
_SET_ODE_(self%id_O2o,-(rrtc/MW_C*p_qo2cr))

_SET_DIAGNOSTIC_(self%id_rrsc,rrsc)
_SET_DIAGNOSTIC_(self%id_rrac,rrac)
Expand Down
4 changes: 2 additions & 2 deletions PelBac.F90
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Expand Up @@ -638,8 +638,8 @@ subroutine do(self,_ARGUMENTS_DO_)
!SEAMLESS call quota_flux( iiPel, ppbacc, ppbacc, ppO3c, rrc, tfluxC)
_SET_ODE_(self%id_O3c,rrc)
_SET_ODE_(self%id_c,-rrc)
!SEAMLESS call flux_vector( iiPel, ppO2o, ppO2o, -eO2*rrc/MW_C )
_SET_ODE_(self%id_O2o,-eO2*rrc/MW_C )
!SEAMLESS call flux_vector( iiPel, ppO2o, ppO2o, -eO2*rrc/MW_C*p_qo2cr )
_SET_ODE_(self%id_O2o,-eO2*rrc/MW_C*p_qo2cr )

flN6rPBA = (ONE- eO2)*rrc/ MW_C* self%p_qro
!SEAMLESS call flux_vector( iiPel, ppN6r, ppN6r, flN6rPBA )
Expand Down
68 changes: 31 additions & 37 deletions Phyto.F90
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Expand Up @@ -108,7 +108,7 @@ module bfm_Phyto
type (type_diagnostic_variable_id) :: id_rugc ! gross primary production
type (type_diagnostic_variable_id) :: id_flPIR2c ! release to semi-labile transparent DOC
type (type_diagnostic_variable_id) :: id_flPIR2c_act ! activity release to semi-labile DOC
type (type_diagnostic_variable_id) :: id_flPIR2c_tot ! total release to semi-labile DOC
type (type_diagnostic_variable_id) :: id_flPIO3c ! extra respiration under nutrient stress
type (type_diagnostic_variable_id) :: id_f2cdom ! fraction to CDOM
type (type_diagnostic_variable_id) :: id_run ! net primary production
type (type_diagnostic_variable_id) :: id_sadap ! adaptation
Expand Down Expand Up @@ -145,12 +145,12 @@ module bfm_Phyto

! Parameters (described in subroutine initialize, below)
real(rk) :: p_q10,p_temp,p_sum,p_srs,p_sdmo,p_thdo,p_seo,p_sheo,p_pu_ea,p_pu_ra
real(rk) :: p_qun,p_lN4, p_qnlc, p_qncPPY, p_xqn, p_qup, p_qplc,p_qpcPPY, p_xqp
real(rk) :: p_qun,p_lN4, p_qnlc, p_qncPPY, p_xqn, p_qup, p_qplc, p_qpcPPY, p_xqp
real(rk) :: p_pu_rn
real(rk) :: p_chPs, p_Contois, p_qus, p_qslc ,p_qscPPY
real(rk) :: p_esNI,p_res
real(rk) :: p_caco3r
real(rk) :: p_sdchl, p_alpha_chl, p_quantum_yield, p_qlcPPY, p_epsChla, p_tochl_relt,p_EpEk_or
real(rk) :: p_iswLtyp, p_chELiPPY, p_clELiPPY, p_ruELiPPY,p_addepth
real(rk) :: p_sdchl, p_alpha_chl, p_quantum_yield, p_qlcPPY, p_qlcmin, p_epsChla, p_tochl_relt,p_EpEk_or
real(rk) :: p_rPIm
real(rk) :: p_fX1p, p_fX2p
real(rk) :: p_fR6
Expand Down Expand Up @@ -267,15 +267,10 @@ subroutine initialize(self,configunit)
call self%get_parameter(self%p_quantum_yield, 'p_quantum_yield','mgC/uE', 'Photochemical efficiency')
call self%get_parameter(self%p_Esource, 'p_Esource', '1-6', 'source of light for PP')
call self%get_parameter(self%p_qlcPPY, 'p_qlcPPY', 'mgChla/mgC','reference quotum Chla:C')
call self%get_parameter(self%p_qlcmin, 'p_qlcmin', 'mgChla/mgC','minimum quotum Chla:C')
call self%get_parameter(self%p_epsChla, 'p_epsChla', 'm2/mgChla', 'Chla-specific extinction coefficient')
call self%get_parameter(self%p_tochl_relt, 'p_tochl_relt', '1/d', 'Relaxation rate towards maximum Chla:C')
call self%get_parameter(self%p_EpEk_or, 'p_EpEk_or', '-', 'Optimal value of E_PAR/E_K')
! --------- Light parameters ERSEM-II -----------
call self%get_parameter(self%p_iswLtyp, 'p_iswLtyp', '0-6', 'Shape of the productivity function')
call self%get_parameter(self%p_chELiPPY, 'p_chELiPPY', 'W/m2', 'Maximum Iopt')
call self%get_parameter(self%p_clELiPPY, 'p_clELiPPY', 'W/m2', 'Minimum Iopt')
call self%get_parameter(self%p_ruELiPPY, 'p_ruELiPPY', '1/d', 'Maximum daily shift in Iopt (1/d)')
call self%get_parameter(self%p_addepth, 'p_addepth', 'm', 'Adaptation depth. Meaningless with high-res models')
! --------- Sinking parameters -----------
call self%get_parameter(self%p_rPIm, 'p_rPIm', 'm/d', 'Phytoplankton background sinking rate')
! --------- Calcite parameters only for P2 ------------
Expand All @@ -288,6 +283,8 @@ subroutine initialize(self,configunit)
call self%get_parameter(self%p_fR6, 'p_fR6', '-', 'fraction of lysis to R6 (small POC)', default=0.8_rk)
! --------- Optical type ------------
call self%get_parameter(self%p_OT, 'p_OT', '1-9', 'optical type label for absorption/scattering spectra')
! --------- nutrient stress respiration / excretion partition ------
call self%get_parameter(self%p_pu_rn, 'p_pu_rn', '-', 'nutrient stress respiration fraction', default=0.0_rk)


! Register state variables (handled by type_bfm_pelagic_base)
Expand Down Expand Up @@ -414,9 +411,9 @@ subroutine initialize(self,configunit)
call self%register_diagnostic_variable(self%id_rr1c, 'rr1c','mgC/m3/d','lysis fraction to labile DOC',output=output_none)
call self%register_diagnostic_variable(self%id_rrc, 'rrc', 'mgC/m3/d','total respiration',output=output_none)
call self%register_diagnostic_variable(self%id_rugc, 'rugc','mgC/m3/d','Gross primary production')
call self%register_diagnostic_variable(self%id_flPIR2c_tot,'flPIR2c_tot', 'mgC/m3/d', 'total flux to semilabile DOC',output=output_none)
call self%register_diagnostic_variable(self%id_flPIR2c_act,'flPIR2c_act', 'mgC/m3/d', 'activity flux to semilabile DOC',output=output_none)
call self%register_diagnostic_variable(self%id_flPIR2c, 'flPIR2c', 'mgC/m3/d', 'flux to transparent semilabile DOC',output=output_none)
call self%register_diagnostic_variable(self%id_flPIO3c, 'flPIO3c', 'mgC/m3/d', 'extra respiration under nutrient stress',output=output_none)
call self%register_diagnostic_variable(self%id_f2cdom, 'f2cdom', '-', 'fraction to semilabile CDOM',output=output_none)
call self%register_diagnostic_variable(self%id_run, 'run', 'mgC/m3/d','net primary production')
call self%register_diagnostic_variable(self%id_sadap, 'sadap', 'mgC/m3/d',' adaptation',output=output_none)
Expand Down Expand Up @@ -514,7 +511,7 @@ subroutine do(self,_ARGUMENTS_DO_)
real(rk) :: sdo, sea, seo
real(rk) :: pe_R6, rr1c, rr6c, rr8c
real(rk) :: sra, srs, srt, rrc
real(rk) :: rugc, slc, flPIR2c, flPIR2c_tot, f2cdom
real(rk) :: rugc, slc, flPIR2c, flPIO3c, f2cdom
real(rk) :: run, sadap
real(rk) :: cqun3, rumn3, rumn4, rumn, rump
real(rk) :: netgrowth, sunPPY
Expand Down Expand Up @@ -844,10 +841,10 @@ subroutine do(self,_ARGUMENTS_DO_)
!SEAMLESS call quota_flux( iiPel, ppphytoc, ppphytoc,ppO3c, rrc, tfluxC )
_SET_ODE_(self%id_c,-rrc)
_SET_ODE_(self%id_O3c,rrc)
!SEAMLESS call flux_vector( iiPel, ppO2o,ppO2o,-( rrc/ MW_C) )
_SET_ODE_(self%id_O2o,-(rrc/MW_C))
!SEAMLESS call flux_vector( iiPel, ppO2o,ppO2o, rugc/ MW_C )
_SET_ODE_(self%id_O2o,rugc/MW_C)
!SEAMLESS call flux_vector( iiPel, ppO2o,ppO2o,-( rrc/ MW_C * p_qo2cr) )
_SET_ODE_(self%id_O2o,-(rrc/MW_C*p_qo2cr))
!SEAMLESS call flux_vector( iiPel, ppO2o,ppO2o, rugc/ MW_C * p_qo2cf )
_SET_ODE_(self%id_O2o,rugc/MW_C*p_qo2cf)
!SEAMLESS

!-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Expand Down Expand Up @@ -881,8 +878,9 @@ subroutine do(self,_ARGUMENTS_DO_)
_SET_DIAGNOSTIC_(self%id_rumn, rumn)
_SET_DIAGNOSTIC_(self%id_rump, rump)

netgrowth = run
flPIO3c = ZERO
if (self%p_netgrowth) then
!-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
! Check which fraction of fixed C can be used for new biomass
! given the internal storage.
! N and P uptake are compared sequentially
Expand All @@ -893,31 +891,26 @@ subroutine do(self,_ARGUMENTS_DO_)
0.05_rk * rugc*( qpcPPY - self%p_qplc)))/ self%p_qplc)

!-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
! Excrete C that cannot be used for growth as carbo-hydrates:
! Excrete / respire C that cannot be used for growth as carbo-hydrates:
! Correct the net C uptake
!-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
netgrowth = max( netgrowth, ZERO)
flPIR2c_tot = flPIR2c+ run- netgrowth
flPIR2c = ((1.00D0-f2cdom)*flPIR2c) + run - netgrowth
flPIR2c = ((1.00D0 - f2cdom) * flPIR2c) + (1.00D0 - self%p_pu_rn) * (run - netgrowth)
flPIO3c = self%p_pu_rn * (run - netgrowth)
run = netgrowth
end if

_SET_DIAGNOSTIC_(self%id_netgrowth, netgrowth)

!!SEAMLESS call quota_flux( iiPel, ppphytoc, ppphytoc,ppR2c, 0.98D0 * flPIR2c, tfluxC ) ! flux to non CDOM
! _SET_ODE_(self%id_c, -(1.00D0-f2cdom) * flPIR2c_tot)
! _SET_ODE_(self%id_R2c,(1.00D0-f2cdom) * flPIR2c_tot)
!!SEAMLESS call quota_flux( iiPel, ppphytoc, ppphytoc,ppR2l, 0.02D0 * flPIR2c, tfluxC ) ! flux to CDOM
! _SET_ODE_(self%id_c, -f2cdom * flPIR2c_tot)
! _SET_ODE_(self%id_X2c,f2cdom * flPIR2c_tot)
_SET_DIAGNOSTIC_(self%id_flPIR2c, flPIR2c)
_SET_DIAGNOSTIC_(self%id_flPIO3c, flPIO3c)
_SET_DIAGNOSTIC_(self%id_netgrowth, netgrowth)

! CEA 98% of activity excretion + nutrient estress excretion produce only R2c
_SET_ODE_(self%id_c,-flPIR2c)
_SET_ODE_(self%id_R2c,flPIR2c)

_SET_DIAGNOSTIC_(self%id_flPIR2c, flPIR2c)
_SET_DIAGNOSTIC_(self%id_flPIR2c_tot, flPIR2c_tot)
_SET_ODE_(self%id_c, -flPIO3c)
_SET_ODE_(self%id_O3c, flPIO3c)
_SET_ODE_(self%id_O2o, -flPIO3c * (p_qo2cr / MW_C))
_SET_ODE_(self%id_c, -flPIR2c)
_SET_ODE_(self%id_R2c, flPIR2c)

!-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
! Specific net growth rate (d-1)
!-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
Expand Down Expand Up @@ -1148,9 +1141,10 @@ subroutine do(self,_ARGUMENTS_DO_)
photochem*( phytol+ p_small)* parEIR))
rate_Chl = rho_Chl*(sum - seo - sea - sra) * phytoc - sdo*phytol
case (2) ! OPATM-BFM
rho_Chl = self%p_qlcPPY * sum/( photochem* qlcPPY * parEIR * et + p_small)
rate_Chl = iN* rho_Chl* run- max( self%p_sdchl * ( ONE - iN), sdo)* &
phytol+ min( ZERO, sum- slc+ sdo)* max( ZERO, phytol- self%p_qlcPPY * phytoc)
rho_Chl = self%p_qlcmin + ((self%p_qlcPPY - self%p_qlcmin) * sunPPY / &
(photochem * qlcPPY * parEIR * et + p_small))
rate_Chl = iN * rho_Chl * run - max(self%p_sdchl * (ONE - iN), sdo) * &
phytol + min(ZERO, sum - slc + sdo) * max(ZERO, phytol - self%p_qlcPPY * phytoc)
case (3) ! UNIBO
rho_Chl = self%p_qlcPPY*min(ONE, &
(sum-seo-sea-sra) *phytoc / &
Expand Down
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