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benw |
1.4 |
C $Header: /u/gcmpack/MITgcm_contrib/darwin2/pkg/quota/quota_plankton.F,v 1.3 2015/05/19 14:32:43 benw Exp $ |
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jahn |
1.1 |
C $Name: $ |
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#include "CPP_OPTIONS.h" |
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#include "PTRACERS_OPTIONS.h" |
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#include "DARWIN_OPTIONS.h" |
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#ifdef ALLOW_PTRACERS |
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#ifdef ALLOW_DARWIN |
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#ifdef ALLOW_QUOTA |
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c ==================================================================== |
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c SUBROUTINE QUOTA_PLANKTON |
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c 0. New version for mixotrophic QUOTA model |
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c |
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c 1. Local ecological interactions for models with many phytoplankton |
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c "functional groups" |
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c 2. Timestep plankton and nutrients locally |
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c 3. Same equations for DOM and POM |
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c 4. Remineralization of detritus also determined in routine |
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c 5. Sinking particles and plankton |
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c 6. NOT in this routine: iron chemistry |
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c |
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c Mick Follows, Scott Grant, Fall/Winter 2005 |
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c Stephanie Dutkiewicz Spring/Summer 2006 |
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c Ben Ward, 2009/10 |
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c |
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c - Dropped in initial quota version... |
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c - R* diagnostics (#define DAR_DIAG_RSTAR) |
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c - diazotrophy (#define ALLOW_DIAZ) |
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c - mutation code (#define ALLOW_MUTANTS) |
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c - new nitrogen limiting scheme (#undef OLD_NSCHEME) |
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c - diversity diagnostics |
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c - waveband dependence of light attenuation and absorption |
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c ==================================================================== |
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SUBROUTINE QUOTA_PLANKTON( |
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I biomass, orgmat, nutrient, |
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O PP, |
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benw |
1.3 |
I bioabove, |
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jahn |
1.1 |
I orgabove, |
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#ifdef FQUOTA |
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I freefelocal, inputFelocal, |
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#endif |
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benw |
1.2 |
#ifdef QUOTA_DIAG_LIMIT |
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benw |
1.3 |
O AP, HP, |
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O Rlim, Ilim, photo_Tempfunction, |
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benw |
1.2 |
#endif |
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jahn |
1.1 |
I PARlocal, Tlocal, Slocal, |
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I bottom, surface, dzlocal, |
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O dbiomassdt,dorgmatdt, dnutrientdt, |
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I debug, |
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I runtim, |
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I MyThid) |
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implicit none |
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#include "SIZE.h" |
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#include "EEPARAMS.h" |
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#include "DARWIN_PARAMS.h" |
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#include "QUOTA_SIZE.h" |
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#include "QUOTA.h" |
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C !INPUT PARAMETERS: =================================================== |
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C myThid :: thread number |
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INTEGER myThid |
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CEOP |
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c === GLOBAL VARIABLES ===================== |
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c iimax = no of nutrient species (1=Carbon,2=Nitrate, ...) |
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c npmax = no of plankton species |
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c komax = no of organic matter classes |
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c biomass = plankton biomass (auto/mixo/hetero) |
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c x_num = cell density |
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c quota = (average) cell quota |
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c nutrient = ambient inorganic nutrient concntration |
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c orgmat = organic matter biomass (dissolved and particulate) |
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_RL biomass(iomax,npmax) |
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_RL nutrient(iimax) |
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_RL orgmat(iomax-iChl,komax) |
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_RL quota(iomax-iChl,npmax) |
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_RL PP |
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_RL bioabove(iomax,npmax) |
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_RL orgabove(iomax-iChl,komax) |
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#ifdef FQUOTA |
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_RL freefelocal |
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_RL inputFelocal |
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#endif |
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benw |
1.2 |
#ifdef QUOTA_DIAG_LIMIT |
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benw |
1.3 |
_RL Rlim(iomax-iChl-1,npmax),Ilim(npmax),Tlim |
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_RL AP(iomax,npmax),HP(iomax,npmax) |
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benw |
1.2 |
#endif |
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jahn |
1.1 |
_RL m_ref(npmax) |
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_RL PARlocal |
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_RL Tlocal |
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_RL Slocal |
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INTEGER bottom |
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INTEGER surface |
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_RL dzlocal |
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INTEGER debug |
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_RL dbiomassdt(iomax,npmax) |
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_RL dchloro(npmax) |
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_RL dnutrientdt(iimax) |
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_RL dorgmatdt(iomax-iChl,komax) |
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#ifdef ALLOW_PAR_DAY |
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_RL PARdaylocal |
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#endif |
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_RL runtim |
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c LOCAL VARIABLES |
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c ------------------------------------------------------------- |
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c WORKING VARIABLES |
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c ii = nutrient element index |
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integer ii,io |
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c jp = plankton index |
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integer jp,jp2 |
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c ko = organic matter index |
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integer ko |
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c 'spare' indices |
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integer ii2, ko2 |
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integer jpred, jprey |
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integer iin |
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c variables for plankton growth rate limitation |
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_RL limit |
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_RL qlimit(npmax) |
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#ifdef FQUOTA |
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_RL felimit(npmax) |
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#endif |
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c plankton specific nutrient limitation terms |
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_RL qreg(iomax,npmax) |
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benw |
1.3 |
_RL q_reg(iomax,npmax) |
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jahn |
1.1 |
c photosynthesis light limitation term |
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_RL ilimit(npmax) |
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c temperature limitation terms |
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_RL photo_Tempfunction |
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_RL activ_Tempfunction |
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c uptake of inorganic nutrients |
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_RL up_inorg(iimax,npmax) |
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c plankton grazing rates |
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_RL grazing(iomax,npmax,npmax) |
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benw |
1.3 |
_RL food1,food2,refuge(npmax) |
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jahn |
1.1 |
_RL biomass2(npmax) |
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c plankton respiration rates (carbon only) |
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_RL C_resp(npmax) |
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c varible for mimumum phyto |
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_RL biomassmin(npmax) |
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c variables for remineralization of organic matter |
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c |
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benw |
1.3 |
c variables for sinking |
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jahn |
1.1 |
_RL bvert(iomax,npmax) |
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_RL pomsink(iomax-iChl) |
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benw |
1.3 |
_RL fSurf,fBott |
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jahn |
1.1 |
c variables for sums of plankton and organic matter |
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_RL totplankton(iomax) |
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_RL totorgmat(iomax-iChl) |
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c ? |
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_RL facpz |
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_RL kpar, kinh |
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benw |
1.3 |
_RL tmp, tmpr,tmpz, tmpgrow, tmp1, tmp2 |
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jahn |
1.1 |
integer ITEST |
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c |
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c ***************************************************************** |
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c ******************** Evaluate Quota Status ********************** |
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c ***************************************************************** |
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c qlimit --> Function of most limiting nutrient |
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c 1 = replete, 0 = no C assimilation |
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c N,Si - linear from quota |
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c P & Fe - Droop from quota |
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c |
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c qreg --> individual nutrient status for uptake regualtion |
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c 0 = quota full, 1 = quota empty |
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c linear for all elements (not needed for Si) |
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benw |
1.3 |
c qreg(C,jp) = inverse of qreg for most limiting element |
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jahn |
1.1 |
c |
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do jp = 1,npmax |
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c set diagnostic to zero |
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qlimit(jp) = 1. _d 0 |
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qreg(iCarb,jp) = 1. _d 0 |
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c |
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do io = 2,iomax-iChl ! skip carbon index; quota = X:C biomass ratio |
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c quota = nutrient biomass to carbon biomass ratio |
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if (biomass(iCarb,jp).gt.0. _d 0) then |
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quota(io,jp) = biomass(io,jp) / biomass(iCarb,jp) |
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else |
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benw |
1.3 |
quota(io,jp) = qmin(io,jp) |
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jahn |
1.1 |
endif |
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c limit ranges from 1 to 0 between qmin and qmax |
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if (quota(io,jp).le.qmin(io,jp)) then ! if quota empty... |
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limit = 0. _d 0 |
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qreg(io,jp) = 1. _d 0 |
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elseif (quota(io,jp).ge.qmax(io,jp)) then ! if quota full... |
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limit = 1. _d 0 |
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qreg(io,jp) = 0. _d 0 |
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else ! if quota somewhere in between... |
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if (io.eq.iNitr.or.io.eq.iSili) then ! linear |
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limit = (quota(io,jp) - qmin(io,jp)) |
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& / ( qmax(io,jp) - qmin(io,jp)) |
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else ! normalised Droop |
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limit = (1. _d 0 - qmin(io,jp)/quota(io,jp)) |
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& / (1. _d 0 - qmin(io,jp)/qmax(io,jp) ) |
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endif |
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! regulation term is always linear |
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qreg(io,jp) = (qmax(io,jp) - quota(io,jp)) |
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& / (qmax(io,jp) - qmin(io,jp) ) |
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endif |
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benw |
1.3 |
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benw |
1.2 |
#ifdef QUOTA_DIAG_LIMIT |
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benw |
1.3 |
if (io.eq.iNitr) Rlim(iNitr-1,jp) = limit |
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#ifdef PQUOTA |
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if (io.eq.iPhos) Rlim(iPhos-1,jp) = limit |
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#endif |
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#ifdef FQUOTA |
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if (io.eq.iIron) Rlim(iIron-1,jp) = limit |
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#endif |
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benw |
1.2 |
#endif |
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jahn |
1.1 |
#ifdef FQUOTA |
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if (io.eq.iIron) then |
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felimit(jp) = limit |
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limit = 1. _d 0 |
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endif |
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#endif |
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#ifdef SQUOTA |
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! non-diatoms are not Si limited |
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if (io.eq.iSili.and.use_Si(jp).eq.0) then |
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limit = 1. _d 0 |
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qreg(iSili,jp) = 0. _d 0 |
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biomass(iSili,jp) = 0. _d 0 |
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bioabove(iSili,jp)= 0. _d 0 |
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quota(iSili,jp) = 0. _d 0 |
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endif |
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#endif |
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qlimit(jp) = min(qlimit(jp),limit) |
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qreg(iCarb,jp) = min(qreg(iCarb,jp),1. _d 0 - qreg(io,jp)) |
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benw |
1.2 |
c |
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benw |
1.3 |
q_reg(io,jp) = qreg(io,jp) ** hill |
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jahn |
1.1 |
enddo ! io |
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benw |
1.3 |
q_reg(iCarb,jp) = qreg(iCarb,jp) ** hill |
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#ifdef QUOTA_DIAG_LIMIT |
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! use monod limitation diagnostic where types are extinct |
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if (biomass(iCarb,jp).le.0. _d 0) then |
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Rlim(iNitr-1,jp) = nutrient(iNO3)/(nutrient(iNO3)+kn(iNO3,jp)) |
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#ifdef PQUOTA |
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Rlim(iPhos-1,jp) = nutrient(iPO4)/(nutrient(iPO4)+kn(iPO4,jp)) |
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#endif |
| 244 |
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#ifdef FQUOTA |
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Rlim(iIron-1,jp) = nutrient(iFeT)/(nutrient(iFeT)+kn(iFeT,jp)) |
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#endif |
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endif |
| 248 |
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#endif |
| 249 |
jahn |
1.1 |
if (autotrophy(jp).eq. 0. _d 0) then |
| 250 |
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biomass(iChlo,jp) = 0. _d 0 ! pure heterotroph, so chl is zero |
| 251 |
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bioabove(iChlo,jp) = 0. _d 0 |
| 252 |
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endif |
| 253 |
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enddo ! jp |
| 254 |
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c |
| 255 |
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c **************************************************************** |
| 256 |
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c * Determine temperature Dependent Growth function for Plankton * |
| 257 |
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c **************************************************************** |
| 258 |
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call quota_tempfunc( |
| 259 |
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I Tlocal, |
| 260 |
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O photo_Tempfunction, |
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O activ_Tempfunction, |
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I myThid) |
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c |
| 264 |
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c ***************************************************************** |
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c ******************** Resource Acquisition *********************** |
| 266 |
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c ***************************************************************** |
| 267 |
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do jp=1,npmax |
| 268 |
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if (autotrophy(jp).gt.0.0 _d 0) then |
| 269 |
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do ii=2,iimax ! not carbon... |
| 270 |
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if (ii.eq.iNO3.or.ii.eq.iNO2.or.ii.eq.iNH4) io=iNitr |
| 271 |
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if (ii.eq.iPO4) io=iPhos |
| 272 |
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if (ii.eq.iFeT) io=iIron |
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if (ii.eq.iSi) io=iSili |
| 274 |
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c C-specific nutrient uptake, modulated by quota fullness and temperature |
| 275 |
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if (nutrient(ii).gt.0. _d 0) then |
| 276 |
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up_inorg(ii,jp) = vmaxi(ii,jp) ! maximum uptake rate |
| 277 |
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& * nutrient(ii)/(nutrient(ii)+kn(ii,jp)) ! ambient nutrients |
| 278 |
benw |
1.3 |
& * q_reg(io,jp) ! quota satiation |
| 279 |
jahn |
1.1 |
& * activ_Tempfunction ! temperature effects |
| 280 |
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#ifdef AMMON |
| 281 |
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c apply ammonium inhibition to NO3 and NO2 |
| 282 |
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if (ii.eq.iNO3.or.ii.eq.iNO2) then |
| 283 |
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up_inorg(ii,jp) = up_inorg(ii,jp) |
| 284 |
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& * exp(-amminhib*nutrient(iNH4)) |
| 285 |
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endif |
| 286 |
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#endif |
| 287 |
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else |
| 288 |
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up_inorg(ii,jp) = 0. _d 0 |
| 289 |
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endif |
| 290 |
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enddo ! ii |
| 291 |
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else ! if autotrophy(jp).eq.0 |
| 292 |
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do ii=1,iimax |
| 293 |
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up_inorg(ii,jp) = 0. _d 0 |
| 294 |
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enddo |
| 295 |
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endif ! autotrophy |
| 296 |
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enddo ! jp |
| 297 |
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c |
| 298 |
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c **************************************************************** |
| 299 |
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c ************* Photosynthetic Carbon Assimilation *************** |
| 300 |
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c **************************************************************** |
| 301 |
benw |
1.2 |
PP = 0.0 _d 0 |
| 302 |
jahn |
1.1 |
call GEIDER98( |
| 303 |
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I PARlocal, |
| 304 |
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I biomass, |
| 305 |
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I qlimit, |
| 306 |
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#ifdef FQUOTA |
| 307 |
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I felimit, |
| 308 |
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#endif |
| 309 |
benw |
1.2 |
#ifdef QUOTA_DIAG_LIMIT |
| 310 |
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O Ilim, |
| 311 |
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#endif |
| 312 |
jahn |
1.1 |
U up_inorg, |
| 313 |
benw |
1.2 |
O PP, |
| 314 |
jahn |
1.1 |
I photo_Tempfunction, |
| 315 |
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O dchloro, ! chlorophyll synthesis rate |
| 316 |
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I myThid) |
| 317 |
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c |
| 318 |
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c **************************************************************** |
| 319 |
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c ********************* Heterotrophic Grazing ******************** |
| 320 |
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c **************************************************************** |
| 321 |
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c PRE-ASSIMILATION grazing of type jpredator by type jprey |
| 322 |
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do jpred=1,npmax ! loop predators |
| 323 |
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if (autotrophy(jpred).lt.1. _d 0) then ! not for pure autotrophs |
| 324 |
benw |
1.3 |
food1 = 0.0 _d 0 |
| 325 |
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food2 = 0.0 _d 0 |
| 326 |
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do jprey=1,npmax ! sum all the prey carbon of predator, weighted by availability (preference) |
| 327 |
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if (graz_pref(jpred,jprey).gt.0.0 _d 0) then |
| 328 |
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food1 = food1 |
| 329 |
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& + graz_pref(jpred,jprey)*biomass(iCarb,jprey) |
| 330 |
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#ifdef SWITCHING |
| 331 |
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food2 = food2 |
| 332 |
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& + (graz_pref(jpred,jprey)*biomass(iCarb,jprey))**ns |
| 333 |
jahn |
1.1 |
#endif |
| 334 |
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endif |
| 335 |
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enddo |
| 336 |
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! calculate grazing effort |
| 337 |
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if (food1.gt.0. _d 0) then |
| 338 |
benw |
1.3 |
refuge(jpred) = (1.0 _d 0 - exp(Lambda * food1)) |
| 339 |
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tmp1 = activ_Tempfunction ! saturated grazing |
| 340 |
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& * food1 / (food1 + kg(jpred)) ! grazing effort |
| 341 |
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& * refuge(jpred) ! grazing refuge |
| 342 |
jahn |
1.1 |
else |
| 343 |
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tmp1 = 0. _d 0 |
| 344 |
|
|
endif |
| 345 |
|
|
do jprey=1,npmax ! loop prey carbon consumption |
| 346 |
|
|
if (food1.gt.0. _d 0) then |
| 347 |
|
|
grazing(iCarb,jpred,jprey) ! d^-1 |
| 348 |
benw |
1.3 |
& = tmp1 ! grazing effort |
| 349 |
benw |
1.4 |
#ifdef ONEGRAZER |
| 350 |
|
|
& * graz(jprey) ! prey dependent maximum rate |
| 351 |
|
|
#else |
| 352 |
benw |
1.3 |
& * graz(jpred) ! predator dependent maximum rate |
| 353 |
benw |
1.4 |
#endif |
| 354 |
benw |
1.3 |
#ifdef SWITCHING |
| 355 |
|
|
& *(graz_pref(jpred,jprey)*biomass(iCarb,jprey))**ns/food2 |
| 356 |
jahn |
1.1 |
#else |
| 357 |
benw |
1.3 |
& * graz_pref(jpred,jprey)*biomass(iCarb,jprey) /food1 |
| 358 |
jahn |
1.1 |
#endif |
| 359 |
|
|
else |
| 360 |
|
|
grazing(iCarb,jpred,jprey) = 0. _d 0 |
| 361 |
|
|
endif |
| 362 |
|
|
! other organic elements (+ chlorophyll) are grazed in stoichiometric relation to carbon |
| 363 |
|
|
if (grazing(iCarb,jpred,jprey).gt.0. _d 0 |
| 364 |
|
|
& .and.biomass(iCarb,jprey).gt.0. _d 0) then |
| 365 |
|
|
do io=2,iomax |
| 366 |
|
|
grazing(io,jpred,jprey) = grazing(iCarb,jpred,jprey) ! uptake of prey carbon |
| 367 |
|
|
& * biomass(io,jprey) ! * |
| 368 |
|
|
& / biomass(iCarb,jprey) ! biomass ratio of prey |
| 369 |
|
|
enddo |
| 370 |
|
|
else |
| 371 |
|
|
do io=1,iomax |
| 372 |
|
|
grazing(io,jpred,jprey) = 0. _d 0 |
| 373 |
|
|
enddo |
| 374 |
|
|
endif |
| 375 |
|
|
enddo ! jprey |
| 376 |
|
|
else ! if pure autotrophs (i.e. autotrophy(jpred).eq.1) |
| 377 |
|
|
do io=1,iomax |
| 378 |
|
|
do jprey=1,npmax |
| 379 |
|
|
grazing(io,jpred,jprey) = 0. _d 0 |
| 380 |
|
|
enddo |
| 381 |
|
|
enddo |
| 382 |
|
|
endif |
| 383 |
|
|
enddo ! jpred |
| 384 |
|
|
c |
| 385 |
|
|
c ************************************************************ |
| 386 |
|
|
c end evaluate biological process terms |
| 387 |
|
|
c ----------------------------------------------------------------- |
| 388 |
|
|
c |
| 389 |
|
|
c ----------------------------------------------------------------- |
| 390 |
benw |
1.3 |
c evaluate vertical sink terms |
| 391 |
jahn |
1.1 |
c ************************************************************ |
| 392 |
|
|
c biosink is +ve downwards |
| 393 |
|
|
c (upstream - downstream) * vertical velocity |
| 394 |
|
|
c bvert is a gain term |
| 395 |
benw |
1.3 |
|
| 396 |
|
|
! factors to avoid sinking into surface layer, or out of bottom |
| 397 |
|
|
fSurf=float(1-surface) |
| 398 |
|
|
fBott=float(1-bottom) |
| 399 |
|
|
! |
| 400 |
jahn |
1.1 |
do io=1,iomax |
| 401 |
benw |
1.3 |
! plankton sinking |
| 402 |
jahn |
1.1 |
do jp=1,npmax |
| 403 |
benw |
1.3 |
bvert(io,jp) = (fSurf*bioabove(io,jp)-fBott*biomass(io,jp)) |
| 404 |
jahn |
1.1 |
& * biosink(jp) / dzlocal ! + sinking in - sinking out |
| 405 |
|
|
enddo |
| 406 |
benw |
1.3 |
! organic matter sinking |
| 407 |
jahn |
1.1 |
if (io.ne.iChlo) then |
| 408 |
benw |
1.3 |
pomsink(io) = (fSurf*orgabove(io,2)-fBott*orgmat(io,2)) |
| 409 |
|
|
& * orgsink(2) / dzlocal |
| 410 |
jahn |
1.1 |
endif |
| 411 |
|
|
enddo |
| 412 |
|
|
c ************************************************************ |
| 413 |
|
|
c end evaluate vertical sink terms |
| 414 |
|
|
c ----------------------------------------------------------------- |
| 415 |
|
|
c |
| 416 |
|
|
c ------------------------------------------------------------------- |
| 417 |
|
|
c calculate tendency terms (and some diagnostics) |
| 418 |
|
|
c ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc |
| 419 |
|
|
c BIOMASS |
| 420 |
|
|
c inorganic uptake |
| 421 |
|
|
do jp=1,npmax |
| 422 |
|
|
dbiomassdt(iCarb,jp) = biomass(iCarb,jp)*up_inorg(iDIC,jp) |
| 423 |
|
|
dbiomassdt(iNitr,jp) = biomass(iCarb,jp)*up_inorg(iNO3,jp) |
| 424 |
|
|
#ifdef NITRITE |
| 425 |
|
|
& + biomass(iCarb,jp)*up_inorg(iNO2,jp) |
| 426 |
|
|
#endif |
| 427 |
|
|
#ifdef AMMON |
| 428 |
|
|
& + biomass(iCarb,jp)*up_inorg(iNH4,jp) |
| 429 |
|
|
#endif |
| 430 |
|
|
#ifdef PQUOTA |
| 431 |
|
|
dbiomassdt(iPhos,jp) = biomass(iCarb,jp)*up_inorg(iPO4,jp) |
| 432 |
|
|
#endif |
| 433 |
|
|
#ifdef SQUOTA |
| 434 |
|
|
dbiomassdt(iSili,jp) = biomass(iCarb,jp)*up_inorg(iSi,jp) |
| 435 |
|
|
#endif |
| 436 |
|
|
#ifdef FQUOTA |
| 437 |
|
|
dbiomassdt(iIron,jp) = biomass(iCarb,jp)*up_inorg(iFeT,jp) |
| 438 |
|
|
#endif |
| 439 |
benw |
1.3 |
#ifdef QUOTA_DIAG_LIMIT |
| 440 |
|
|
do io=1,iomax |
| 441 |
|
|
AP(io,jp) = dbiomassdt(io,jp) |
| 442 |
|
|
enddo |
| 443 |
|
|
#endif |
| 444 |
jahn |
1.1 |
c |
| 445 |
|
|
dbiomassdt(iChlo,jp) = dchloro(jp) |
| 446 |
|
|
c |
| 447 |
|
|
! respiration |
| 448 |
|
|
dbiomassdt(iCarb,jp) = dbiomassdt(iCarb,jp) |
| 449 |
|
|
& - respiration(jp) * biomass(iCarb,jp) |
| 450 |
|
|
& * activ_Tempfunction |
| 451 |
|
|
c |
| 452 |
|
|
c grazing uptake |
| 453 |
|
|
do io=1,iomax |
| 454 |
benw |
1.3 |
#ifdef QUOTA_DIAG_LIMIT |
| 455 |
|
|
HP(io,jp) = 0.0 _d 0 |
| 456 |
|
|
#endif |
| 457 |
jahn |
1.1 |
if (io.ne.iSili.and.io.ne.iChlo) then ! don't take up silicate or chlorophyll |
| 458 |
|
|
c Grazing uptake of everything but silicate and chlorophyll |
| 459 |
|
|
do jprey=1,npmax |
| 460 |
|
|
dbiomassdt(io,jp) = dbiomassdt(io,jp) |
| 461 |
|
|
& + biomass(iCarb,jp) ! carbon biomass of predator |
| 462 |
|
|
& * grazing(io,jp,jprey)! * carbon specific rate |
| 463 |
benw |
1.3 |
& * assim_graz(jp,jprey) * q_reg(io,jp) |
| 464 |
|
|
#ifdef QUOTA_DIAG_LIMIT |
| 465 |
|
|
HP(io,jp) = HP(io,jp) |
| 466 |
|
|
& + biomass(iCarb,jp) ! carbon biomass of predator |
| 467 |
|
|
& * grazing(io,jp,jprey)! * carbon specific rate |
| 468 |
|
|
& * assim_graz(jp,jprey) * q_reg(io,jp) |
| 469 |
|
|
#endif |
| 470 |
jahn |
1.1 |
enddo ! jprey |
| 471 |
|
|
c Exudation of elemental reservoirs |
| 472 |
benw |
1.3 |
if (io.ne.iChl.or.io.ne.iSili) then |
| 473 |
jahn |
1.1 |
dbiomassdt(io,jp) = dbiomassdt(io,jp) |
| 474 |
|
|
& - kexc(io,jp) * biomass(io,jp) |
| 475 |
|
|
endif |
| 476 |
|
|
endif |
| 477 |
|
|
! |
| 478 |
benw |
1.4 |
! calculate (temperature adjusted?) mortality rates |
| 479 |
benw |
1.2 |
m_ref(jp) = kmort(jp) !* activ_Tempfunction |
| 480 |
jahn |
1.1 |
! |
| 481 |
|
|
! Loss and sinking terms - include silicate and chlorophyll |
| 482 |
|
|
dbiomassdt(io,jp) = dbiomassdt(io,jp) |
| 483 |
|
|
& - biomass(io,jp) |
| 484 |
|
|
& * m_ref(jp) |
| 485 |
|
|
& + bvert(io,jp) |
| 486 |
|
|
do jpred=1,npmax |
| 487 |
|
|
! - losses to other predators |
| 488 |
|
|
dbiomassdt(io,jp) = dbiomassdt(io,jp) |
| 489 |
|
|
& - biomass(iCarb,jpred) ! carbon biomass of predator |
| 490 |
|
|
& * grazing(io,jpred,jp) ! * carbon specific rate |
| 491 |
|
|
enddo ! jpred |
| 492 |
|
|
enddo ! io |
| 493 |
|
|
enddo ! jp |
| 494 |
|
|
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc |
| 495 |
|
|
c NUTRIENTS |
| 496 |
|
|
! uptake by phytoplankton |
| 497 |
|
|
do ii=1,iimax |
| 498 |
|
|
dnutrientdt(ii) = 0. _d 0 |
| 499 |
|
|
do jp=1,npmax |
| 500 |
|
|
dnutrientdt(ii) = dnutrientdt(ii) |
| 501 |
|
|
& - biomass(iCarb,jp)*up_inorg(ii,jp) ! - uptake of inorganic nutrients |
| 502 |
|
|
enddo ! jp |
| 503 |
|
|
enddo ! ii |
| 504 |
|
|
c |
| 505 |
|
|
! remineralisation of organic matter |
| 506 |
|
|
do ko=1,komax |
| 507 |
|
|
dnutrientdt(iDIC) = dnutrientdt(iDIC) |
| 508 |
|
|
& + orgmat(iCarb,ko) * remin(iCarb,ko) |
| 509 |
|
|
& * activ_Tempfunction |
| 510 |
|
|
#ifndef AMMON |
| 511 |
|
|
dnutrientdt(iNO3) = dnutrientdt(iNO3) |
| 512 |
|
|
& + orgmat(iNitr,ko) * remin(iNitr,ko) ! straight to NO3, if no NH4 ... |
| 513 |
|
|
& * activ_Tempfunction |
| 514 |
|
|
#else |
| 515 |
|
|
dnutrientdt(iNH4) = dnutrientdt(iNH4) |
| 516 |
|
|
& + orgmat(iNitr,ko) * remin(iNitr,ko) ! ... or to NH4 |
| 517 |
|
|
& * activ_Tempfunction |
| 518 |
|
|
#endif |
| 519 |
|
|
#ifdef PQUOTA |
| 520 |
|
|
dnutrientdt(iPO4) = dnutrientdt(iPO4) |
| 521 |
|
|
& + orgmat(iPhos,ko) * remin(iPhos,ko) |
| 522 |
|
|
& * activ_Tempfunction |
| 523 |
|
|
#endif |
| 524 |
|
|
#ifdef SQUOTA |
| 525 |
|
|
dnutrientdt(iSi) = dnutrientdt(iSi) |
| 526 |
|
|
& + orgmat(iSili,ko) * remin(iSili,ko) |
| 527 |
|
|
& * activ_Tempfunction |
| 528 |
|
|
#endif |
| 529 |
|
|
#ifdef FQUOTA |
| 530 |
|
|
dnutrientdt(iFeT) = dnutrientdt(iFeT) |
| 531 |
|
|
& + orgmat(iIron,ko) * remin(iIron,ko) |
| 532 |
|
|
& * activ_Tempfunction |
| 533 |
|
|
#endif |
| 534 |
|
|
enddo !ko |
| 535 |
|
|
#ifdef FQUOTA |
| 536 |
|
|
dnutrientdt(iFeT) = dnutrientdt(iFeT) |
| 537 |
|
|
& - scav * freefelocal ! scavenging of free iron |
| 538 |
|
|
& + alpfe * inputFelocal/dzlocal ! atmospheric input |
| 539 |
|
|
#endif |
| 540 |
|
|
|
| 541 |
|
|
! respiration |
| 542 |
|
|
do jp=1,npmax |
| 543 |
|
|
dnutrientdt(iDIC) = dnutrientdt(iDIC) |
| 544 |
|
|
& + respiration(jp) * biomass(iCarb,jp) |
| 545 |
|
|
& * activ_Tempfunction |
| 546 |
|
|
enddo |
| 547 |
|
|
|
| 548 |
|
|
! oxidation of NH4 and NO2 compounds |
| 549 |
|
|
#ifdef AMMON |
| 550 |
|
|
dnutrientdt(iNH4) = dnutrientdt(iNH4) |
| 551 |
|
|
& - amm2nrite * nutrient(iNH4) ! ammonium to (nitrite or nitrate) |
| 552 |
|
|
#ifdef NITRITE |
| 553 |
|
|
dnutrientdt(iNO2) = dnutrientdt(iNO2) |
| 554 |
|
|
& + amm2nrite * nutrient(iNH4) ! nitrite from ammonium |
| 555 |
|
|
& - nrite2nrate * nutrient(iNO2) ! nitrite to nitrate |
| 556 |
|
|
dnutrientdt(iNO3) = dnutrientdt(iNO3) |
| 557 |
|
|
& + nrite2nrate * nutrient(iNO2) ! nitrate from nitrite |
| 558 |
|
|
#else |
| 559 |
|
|
dnutrientdt(iNO3) = dnutrientdt(iNO3) ! or |
| 560 |
benw |
1.2 |
& + amm2nrite * nutrient(iNH4) ! nitrate from ammonium |
| 561 |
jahn |
1.1 |
#endif |
| 562 |
|
|
#endif |
| 563 |
|
|
c |
| 564 |
|
|
c******************************************************************************** |
| 565 |
|
|
c organic matter |
| 566 |
|
|
do io=1,iomax-iChl |
| 567 |
|
|
dorgmatdt(io,1) = 0. _d 0 ! dissolved |
| 568 |
|
|
dorgmatdt(io,2) = pomsink(io) ! particulate |
| 569 |
|
|
do jp=1,npmax |
| 570 |
|
|
! mortality & excretion |
| 571 |
|
|
dorgmatdt(io,1) = dorgmatdt(io,1) |
| 572 |
|
|
& + biomass(io,jp) |
| 573 |
|
|
& * m_ref(jp) |
| 574 |
|
|
& * beta_mort(io,jp) |
| 575 |
|
|
if (io.eq.iCarb.or.io.eq.iNitr.or.io.eq.iPhos) then |
| 576 |
|
|
dorgmatdt(io,1) = dorgmatdt(io,1) |
| 577 |
|
|
& + kexc(io,jp) * biomass(io,jp) |
| 578 |
|
|
endif |
| 579 |
|
|
dorgmatdt(io,2) = dorgmatdt(io,2) |
| 580 |
|
|
& + biomass(io,jp) |
| 581 |
|
|
& * m_ref(jp) |
| 582 |
benw |
1.3 |
& *(1. _d 0-beta_mort(io,jp)) |
| 583 |
jahn |
1.1 |
do jprey=1,npmax |
| 584 |
|
|
! unassimilated grazing |
| 585 |
|
|
dorgmatdt(io,1) = dorgmatdt(io,1) |
| 586 |
|
|
& + biomass(iCarb,jp) |
| 587 |
|
|
& * grazing(io,jp,jprey) |
| 588 |
benw |
1.3 |
& *(1. _d 0-assim_graz(jp,jprey)*q_reg(io,jp)) |
| 589 |
jahn |
1.1 |
& * beta_graz(io,jprey) |
| 590 |
|
|
dorgmatdt(io,2) = dorgmatdt(io,2) |
| 591 |
|
|
& + biomass(iCarb,jp) |
| 592 |
|
|
& * grazing(io,jp,jprey) |
| 593 |
benw |
1.3 |
& *(1. _d 0-assim_graz(jp,jprey)*q_reg(io,jp)) |
| 594 |
|
|
& *(1. _d 0-beta_graz(io,jprey)) |
| 595 |
jahn |
1.1 |
enddo ! jprey |
| 596 |
|
|
enddo ! jp |
| 597 |
|
|
! remineralisation of organic matter |
| 598 |
|
|
do ko=1,komax |
| 599 |
|
|
dorgmatdt(io,ko) = dorgmatdt(io,ko) |
| 600 |
|
|
& - orgmat(io,ko) * remin(io,ko) |
| 601 |
|
|
& * activ_Tempfunction |
| 602 |
|
|
enddo ! ko |
| 603 |
|
|
enddo ! io |
| 604 |
|
|
c******************************************************************************** |
| 605 |
|
|
c ------------------------------------------------------------------- |
| 606 |
|
|
ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc |
| 607 |
|
|
c -------------------------------------------------------------------------- |
| 608 |
|
|
RETURN |
| 609 |
|
|
END |
| 610 |
|
|
#endif /*ALLOW_QUOTA*/ |
| 611 |
|
|
#endif /*ALLOW_DARWIN*/ |
| 612 |
|
|
#endif /*ALLOW_PTRACERS*/ |
| 613 |
|
|
c ================================================================== |
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