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Add comments for nutrient uptake #146

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Add comments for nutrient uptake
hpowley Jun 9, 2025
578426b
Merge branch 'master' into 145_documentation_nutrient_uptake
wathen Nov 3, 2025
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28 changes: 23 additions & 5 deletions src/primary_producer.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -482,14 +482,21 @@ subroutine do(self,_ARGUMENTS_DO_)
_SET_DIAGNOSTIC_(self%id_fPIRPc,fPIRPc)
! Phosphorus flux...........................................

! Lysis loss of phosphorus
! Lysis loss of phosphorus (mmol P m-3 d-1)
fPIRPp = sPIRP * min(self%qplc*cP,pP)
fPIRDp = sdo * pP - fPIRPp

! Net phosphorus uptake
! Maximum achievable uptake (mmol P m-3 d-1)
rump = self%qurp * N1pP * c

!Regulation term relaxing internal quota towards maximum quota (using nutrient luxury uptake) (mmol P m-3 d-1)
misp = self%snplux*(self%xqp * qpRPIcX*cP - pP)

!Assimilation demand at maximum quota and compensating for rest respiration (mmol P m-3 d-1)
runp = sun*c * qpRPIcX*self%xqp - srs*pP

! Uptake capped at maximum achievable uptake (mmol P m-3 d-1)
fN1PIp = MIN(rump, runp+misp)

! Source equations
Expand All @@ -511,12 +518,23 @@ subroutine do(self,_ARGUMENTS_DO_)
fPIRDn = sdo * nP - fPIRPn

! Net nitrogen uptake

! maximum acheivable uptake of nitrate (mmol NO3 m-3 d-1)
rumn3 = self%qun3 * N3nP * c

! Maximum achievable uptake of ammonium (mmol NH4 m-3 d-1)
rumn4 = self%qun4 * N4nP * c

!Total maximum achievable uptake of nitrogen (mmol NH4 m-3 d-1)
rumn = rumn3 + rumn4

!Regulation term relaxing internal quota towards maximum quota (using nutrient luxury uptake) (mmol NO3 m-3 d-1)
misn = self%snplux * (self%xqn * qnRPIcX*cP - nP)

!Assimilation demand at maximum quota and compensating for rest respiration (mmol NO3 m-3 d-1)
runn = sun*c * qnRPIcX*self%xqn - srs*nP

! Uptake capped at maximum achievable uptake of nitrogen (mmol NO3 m-3 d-1)
fNIPIn = MIN(rumn, runn + misn)

! Partitioning over NH4 and NO3 uptake
Expand Down Expand Up @@ -546,17 +564,17 @@ subroutine do(self,_ARGUMENTS_DO_)
! Silicate flux.............................................
_GET_(self%id_s,sP)

! Loss of silicate due to lysis
! Loss of silicate due to lysis (mmol Si m-3 d-1)
fPIRPs = sdo * sP

! Loss of excess silicate (qsP1c > qsc)
! Loss of excess silicate (qsP1c > qsc) (mmol Si m-3 d-1)
fPIN5s = MAX ( 0._rk, sP-self%qsc * cP) / onedayX

! Net silicate uptake
! Net silicate uptake (mmol Si m-3)
fN5PIs = MAX ( 0._rk, self%qsc*run) - fPIN5s
_SET_DIAGNOSTIC_(self%id_fN5PIs, fN5PIs)

! Source equations
! Source equations
_SET_ODE_(self%id_s,(fN5PIs - fPIRPs))
_SET_ODE_(self%id_N5s,-fN5PIs)
_SET_ODE_(self%id_RPs, fPIRPs)
Expand Down