c c======================================================================= c Include file "cbiopnh.h" c======================================================================= c #ifdef bioMcGillic # ifndef rmdocinc c ATTH2O1 light attenuation scale of seawater (cm-1). c ATTPHY light attenuation scale of phytoplankton c (liter umole-1 cm-1). c BIOPOS switch to enforce positive biological fields: c [0] do not enforce, [1] enforce. # if defined codunlim | defined codlim # if defined codunlim c CDKP prey response coefficient. [(cm^2 m^3)/(s mmole N)] c CDKT temperature response coefficient. {cm^2/[s (deg C)^2]} c CDKZ depth response coefficient. (cm/s) # else c CDKP prey response coefficient. [(cm m^3)/(mmole N)] c CDKT temperature response coefficient. [cm/(deg C)^2] c CDKZ depth response coefficient. # endif c CDSPD maximum cod cruising speed. (cm/s) c CDTMAX maximum preferred temperature for cod. (deg C) c CDTMIN minimum preferred temperature for cod. (deg C) c CDWMAX maximum vertical swimming speed. (cm/s) c CDZMAX maximum water depth for cod (cm). c CDZMIN minimum water depth for cod (cm). # endif c CIVLEV Ivlev grazing constant (l/umoles). c ("civlev" from PNH card 6.) c EXPORT export rate (umoles liter-1 sec-1). c FAVE vertically-integrated f-ratio (non-dimensional). c GRAZRM maximum zooplankton grazing rate (1/s). c ("rm" from PNH card 6.) c HSNH4 half saturation constant for ammonium uptake (umoles/l). c HSNO3 half saturation constant for nitrate uptake (umoles/l). c IBIOUT output write switches. [0] do not write, [1] write. c INH4 index for ammonium in tracer array. c INO3 index for nitrate in tracer array. c IPHY index for phytoplankton in tracer array. c IZOO index for zooplankton in tracer array. c NH4PR recycled (NH4) production rate (umoles liter-1 sec-1). c NO3INH strength of ammonium inhibition on nitrate uptake c (l/umoles). c NO3PR new (NO3) production rate (umoles liter-1 sec-1). c PARFRAC fraction of shortwave radiation that is photosynthetically c PHOTOINH photoinhibition parameter (cm^2/cal). c PHOTOR0 initial slope of photosynthesis response to light c (cm^2/cal). c PHOTORM maximum photosynthetic rate (1/s). c Q1 nitrate nutrient limitation factor (nondimensional). c Q2 ammonium nutrient limitation factor (nondimensional). c SBLDEP depth of the "SBL" (cm). Used for computing the vertically c integrated f-ratio. c SINKFAC f-ratio sinking rate factor (cm/s). c SINKPHY sinking rate for phytoplankton (positive down) (cm/s). c ZGRPHY zooplankton grazing rate (umoles liter-1 sec-1) c ZOOEXC1 zooplankton ammonium excretion fraction (nondimensional). c ("fslop" from PNH card 6.) c ZOOEXP1 fraction of linear zooplankton loss to export (nondimen). c ZOOEXP2 fraction of quadratic zooplankton loss to export (nondim). c ZOOLR1 linear zooplankton loss rate (1/s). c ("zloss" from PNH card 6.) c ZOOLR2 quadratic zooplankton loss rate (1/s l/umoles). c ("zloss2" from PNH card 6.) c c======================================================================= c # endif common /icbiopnh/ biopos,ibiout integer biopos,ibiout(20) c common /fcbiopnh/ atth2o1,attphy,civlev,grazrm,hsno3,hsnh4,no3inh, * photorm,photor0,photoinh,sinkphy,sinkfac,parfrac,sbldep, * zoolr1,zoolr2,zooexc1,zooexp1,zooexp2,wsnkphy, * nh4pr,no3pr,zgrphy,export,q1,q2,fave # if defined codunlim | defined codlim | defined cod_ing * ,cdkp,cdkt,cdkz,cdspd,cdtmax,cdtmin,cdwmax,cdzmax,cdzmin # endif FLOAT * atth2o1,attphy,civlev,grazrm,hsno3,hsnh4,no3inh, * photorm,photor0,photoinh,sinkphy,sinkfac,parfrac,sbldep, * zoolr1,zoolr2,zooexc1,zooexp1,zooexp2,wsnkphy # if defined codunlim | defined codlim | defined cod_ing * ,cdkp,cdkt,cdkz,cdspd,cdtmax,cdtmin,cdwmax,cdzmax,cdzmin # endif FLOAT * nh4pr(imt,km),no3pr(imt,km),zgrphy(imt,km),export(imt,km), * q1(imt,km),q2(imt,km),fave(imt) c integer inh4,ino3,iphy,izoo parameter (ino3=3,iphy=4,izoo=5,inh4=6) # if defined codunlim | defined codlim | defined cod_ing integer icod parameter (icod=7) # endif #endif #ifdef bioAnder # ifndef rmdocinc c ATTPHY phytoplankton light attenuation scale (liter umole-1 cm-1). c BIOPOS switch to enforce positive biological fields: c [0] do not enforce, [1] enforce. # if defined codunlim | defined codlim # if defined codunlim c CDKP prey response coefficient. [(cm^2 m^3)/(s mmole N)] c CDKT temperature response coefficient. {cm^2/[s (deg C)^2]} c CDKZ depth response coefficient. (cm/s) # else c CDKP prey response coefficient. [(cm m^3)/(mmole N)] c CDKT temperature response coefficient. [cm/(deg C)^2] c CDKZ depth response coefficient. # endif c CDSPD maximum cod cruising speed. (cm/s) c CDTMAX maximum preferred temperature for cod. (deg C) c CDTMIN minimum preferred temperature for cod. (deg C) c CDWMAX maximum vertical swimming speed. (cm/s) c CDZMAX maximum water depth for cod (cm). c CDZMIN minimum water depth for cod (cm). # endif c CIVLEV Ivlev constant for zooplankton grazing of phytoplankton c (l/umoles). c FRACRMN fraction of the sinking phytoplankton and detritus flux c that reaches the seafloor that is remineralized in the c bottom level; the remainder is "buried" (nondimensional). c GRAZRM maximum phytoplankton grazing rate (1/sec). c HSNH4 half saturation constant for ammonium uptake (umoles/l). c HSNO3 half saturation constant for nitrate uptake (umoles/l). c IBIOUT output write switches. [0] do not write, [1] write. c IDET index for detritus in tracer array. c INH4 index for ammonium in tracer array. c INO3 index for nitrate in tracer array. c IPHY index for phytoplankton in tracer array. c IZOO index for zooplankton in tracer array. c NH4PR recycled (NH4) production rate (umoles liter-1 sec-1). c NO3INH strength of ammonium inhibition of nitrate uptake c (l/umoles). c NO3PR new (NO3) production rate (umoles liter-1 sec-1). c PARFRAC fraction of shortwave radiation that is photosynthetically c active (nondimensional). c PHOTOINH photoinhibition parameter (cm^2/cal). c PHOTOR0 initial slope of photosynthesis response to light c (cm^2/cal). c PHOTORM maximum photosynthetic rate (1/sec). c PHYLR1 linear phytoplankton mortality rate (1/sec). c PHYLR2 quadratic phytoplankton mortality rate (1/sec l/umoles). c REMNDET detritus remineralization timescale (1/sec). c REMNNH4 NH4 remineralization (nitrification) timescale (1/sec). c WSNKDET sinking rate for detritus (positive down) (cm/sec). c WSNKPHY sinking rate for phytoplankton (positive down) (cm/sec). c ZGRPHY zooplankton grazing rate (umoles liter-1 sec-1) c ZOOEXCD fraction of zooplankton grazing that is excreted as c detritus (nondimensional). c ZOOEXCN fraction of zooplankton grazing that is excreted as c ammonium (nondimensional). c ZOOLF1 fraction of linear zooplankton loss to detritus c (nondimensional). c ZOOLF2 fraction of quadratic zooplankton loss to detritus c (nondimensional). c ZOOLR1 linear zooplankton loss rate (1/sec). c ZOOLR2 quadratic zooplankton loss rate (1/sec l/umoles). c c======================================================================= c # endif common /icbiopnh/ biopos,ibiout integer biopos,ibiout(20) c common /fcbiopnh/ attphy,photorm,photor0,photoinh,hsno3,hsnh4, * no3inh,phylr1,phylr2,grazrm,civlev,zooexcn,zooexcd,zoolr1, * zoolr2,zoolf1,zoolf2,wsnkphy,wsnkdet,fracrmn,remnnh4, * remndet,parfrac, * nh4pr,no3pr,zgrphy # if defined codunlim | defined codlim | defined cod_ing * ,cdkp,cdkt,cdkz,cdspd,cdtmax,cdtmin,cdwmax,cdzmax,cdzmin # endif FLOAT * attphy,photorm,photor0,photoinh,hsno3,hsnh4, * no3inh,phylr1,phylr2,grazrm,civlev,zooexcn,zooexcd,zoolr1, * zoolr2,zoolf1,zoolf2,wsnkphy,wsnkdet,fracrmn,remnnh4, * remndet,parfrac # if defined codunlim | defined codlim | defined cod_ing * ,cdkp,cdkt,cdkz,cdspd,cdtmax,cdtmin,cdwmax,cdzmax,cdzmin # endif FLOAT * nh4pr(imt,km),no3pr(imt,km),zgrphy(imt,km) c integer idet,inh4,ino3,iphy,izoo parameter (ino3=3,iphy=4,izoo=5,inh4=6,idet=7) # if defined codunlim | defined codlim | defined cod_ing integer icod parameter (icod=8) # endif #endif #ifdef bioDuse # ifndef rmdocinc c ACHLA absorption coefficient for chl a (m^2/mg). c ACHLB absorption coefficient for chl b (m^2/mg). c ACHLC absorption coefficient for chl c (m^2/mg). c APPC absorption coefficient for photoprotectant carotenoids c (m^2/mg). c APSC absorption coefficient for photosynthetic carotenods c (m^2/mg). c ATTH2OS spectral attenuation due to water (Kw) (m-1). c ATTPHY phytoplankton light attenuation scale (liter umole-1 cm-1). c BIOPOS switch to enforce positive biological fields: c [0] do not enforce, [1] enforce. # if defined codunlim | defined codlim # if defined codunlim c CDKP prey response coefficient. [(cm^2 m^3)/(s mmole N)] c CDKT temperature response coefficient. {cm^2/[s (deg C)^2]} c CDKZ depth response coefficient. (cm/s) # else c CDKP prey response coefficient. [(cm m^3)/(mmole N)] c CDKT temperature response coefficient. [cm/(deg C)^2] c CDKZ depth response coefficient. # endif c CDSPD maximum cod cruising speed. (cm/s) c CDTMAX maximum preferred temperature for cod. (deg C) c CDTMIN minimum preferred temperature for cod. (deg C) c CDWMAX maximum vertical swimming speed. (cm/s) c CDZMAX maximum water depth for cod (cm). c CDZMIN minimum water depth for cod (cm). # endif c CHA2CHB Chl a to Chl b conversion (b:a ratio) (mg/mg). c CHA2CHC Chl a to Chl c conversion (c:a ratio) (mg/mg). c CHA2PPC Chl a to PP carotenoids (ppc:a ratio) (mg/mg). c CHA2PSC Chl a to PS carotenoids (psc:a ratio) (mg/mg). c CHIL Chi(lambda) from Morel and Antoine model of phyto c attenuation (no units, but chl in mg/m^3, K in m-1). c CHLCRATE rate constant of photoacclimation for chl:c (units???) c CHL2RAD factor for converting chl to cell size. c CHL2RADE exponent for chl-size relationship. c CIVLEV Ivlev constant for zooplankton grazing of phytoplankton c (l/ug Chl) c C2CHL Chlorophyl:Carbon ratio (mg Chl/ mg C). c C2N Nitrogen:Carbon ratio (mol N/mol C) of phytoplankton. c ELAM e(lambda) from Morel and Antoine model - see CHIL. c FRACRMN fraction of the sinking phytoplankton and detritus flux c that reaches the seafloor that is remineralized in the c bottom level; the remainder is "buried" (nondimensional). c GRAZRM maximum phytoplankton grazing rate (1/sec). c HSNH4 half saturation constant for ammonium uptake (umoles/l). c HSNO3 half saturation constant for nitrate uptake (umoles/l). c HT2QNTA conversion factor from watts to quanta/sec. (quanta/sec/ c watt). c IBIOUT output write switches. [0] do not write, [1] write. c ICHL index for chlorophyll in tracer array. c IDET index for detritus in tracer array. c INH4 index for ammonium in tracer array. c INO3 index for nitrate in tracer array. c IPMBID index identifying bidigare et al. spectral productivity c model. c IPMEXP index identifying exponential form for productivity model c IPMOD productivity model switch. c IPMTNH index identifying hyperbolic tangent form for productivity c model c IPMKM index identifying Kiefer and Mitchell (1983) model ("white c light" model) c IPMSMI index identifying Smith (1936) productivity model c IQN3 index for cellular nitrogen (from nitrate) in tracer array. c IQN4 index for cellular nitrogen (from ammonia) in tracer array. c IZOO index for zooplankton in tracer array. c LMDAMIN lower limit of light spectrum for productivity model (nm). c LMDAMAX upper limit of light spectrum for productivity model (nm). c NH4PR recycled (NH4) production rate (umoles liter-1 sec-1). c NH4URM maximum ammonium uptake rate c (umoles N / ug chl 1/day). c NO3INH strength of ammonium inhibition of nitrate uptake c (l/umoles). c NO3PR new (NO3) production rate (umoles liter-1 sec-1). c NO3URM maximum nitrate uptake rate c (umoles N / ug chl 1/day). c NQUOTA minimum nitrogen quota (Qo in Droop model) c (umoles N / ug chl). c PARFRAC fraction of shortwave radiation that is photosynthetically c active (nondimensional). c PHIM Maximum quantum yield C-based (mol C/mol photons) c PHOTOINH photoinhibition parameter c ((mgC/mgChl/sec)/(umole photonsm2/sec)). c PHOTOR0 initial slope of photosynthesis response to light c ((mgC/mgChl/sec)/(umole photonsm2/sec)). c PHOTORM maximum photosynthetic rate (mgC/mgChl/sec). c PHYLR1 linear phytoplankton mortality rate (1/sec). c PHYLR2 quadratic phytoplankton mortality rate (1/sec l/umoles). c REMNDET detritus remineralization timescale (1/sec). c REMNNH4 NH4 remineralization (nitrification) timescale (1/sec). c RHOPHY phytoplankton density (same units as density). c VISCH2O viscosity of seawater ( ). c WSJ weighting factors for irradiance (nondimensional). c WSNKDET sinking rate for detritus (positive down) (cm/sec). c WSNKPHY sinking rate for phytoplankton (positive down) (cm/sec). c ZGRPHY zooplankton grazing rate (umoles liter-1 sec-1) c ZOOEXCD fraction of zooplankton grazing that is excreted as c detritus (nondimensional). c ZOOEXCN fraction of zooplankton grazing that is excreted as c ammonium (nondimensional). c ZOOLF1 fraction of linear zooplankton loss to detritus c (nondimensional). c ZOOLF2 fraction of quadratic zooplankton loss to detritus c (nondimensional). c ZOOLR1 linear zooplankton loss rate (1/sec). c ZOOLR2 quadratic zooplankton loss rate (1/sec l/umoles). c c======================================================================= c # endif common /icbiopnh/ biopos,ipmod,ibiout integer biopos,ipmod,ibiout(20) c common /fcbiopnh/ attphy,photorm,photor0,photoinh,hsno3,hsnh4, * no3inh,phylr1,phylr2,grazrm,civlev,zooexcn,zooexcd,zoolr1, * zoolr2,zoolf1,zoolf2,wsnkphy,wsnkdet,fracrmn,remnnh4, * remndet,parfrac, * nh4pr,no3pr,zgrphy,nquota,nh4urm,no3urm,c2chl,dn2dchl, * cha2chb,cha2chc,cha2ppc,cha2psc,chlcrate,c2n,phim, * achla,achlb,achlc,appc,apsc,atth2os,chil,elam, * ht2qnta,wsj,lmdamin,lmdamax, * chlcinf # if defined codunlim | defined codlim | defined cod_ing * ,cdkp,cdkt,cdkz,cdspd,cdtmax,cdtmin,cdwmax,cdzmax,cdzmin # endif FLOAT * attphy,photorm,photor0,photoinh,hsno3,hsnh4, * no3inh,phylr1,phylr2,grazrm,civlev,zooexcn,zooexcd,zoolr1, * zoolr2,zoolf1,zoolf2,wsnkphy,wsnkdet,fracrmn,remnnh4, * remndet,parfrac,nquota,nh4urm,no3urm,c2chl,dn2dchl, * cha2chb,cha2chc,cha2ppc,cha2psc,chlcrate,c2n,phim, * ht2qnta,lmdamin,lmdamax # if defined codunlim | defined codlim | defined cod_ing * ,cdkp,cdkt,cdkz,cdspd,cdtmax,cdtmin,cdwmax,cdzmax,cdzmin # endif FLOAT * nh4pr(imt,km),no3pr(imt,km),zgrphy(imt,km), * achla(lm),achlb(lm),achlc(lm),appc(lm),apsc(lm), * atth2os(lm),chil(lm),elam(lm),wsj(lm), * chlcinf(imt,km) c integer idet,inh4,ino3,izoo,iqn3,iqn4,ichl parameter (ino3=3,iqn3=4,izoo=5,inh4=6,idet=7,ichl=8,iqn4=9) # if defined codunlim | defined codlim | defined cod_ing integer icod parameter (icod=10) # endif integer ipmexp,ipmtnh,ipmkm ,ipmsmi,ipmbid parameter (ipmexp=0,ipmtnh=1,ipmkm=2,ipmsmi=3,ipmbid=4) FLOAT * chl2rad,chl2rade,rhophy,visch2o parameter(rhophy=75.0,visch2o=9.1e-4,chl2rad=5.15*c1em12, * chl2rade=0.753) #endif #ifdef bioFasham # ifndef rmdocinc c ATTPHY light attenuation by phytoplankton (liter umole-1 cm-1). c BACFRAC bacterial ratio of NH4/DON uptake (nondimensional). c BACGRK bacteria uptake half-saturation constant (umoles/l). c BACGRR bacteria maximum growth rate (sec-1). c BEXCRR bacteria excretion rate to NH4 (sec-1). c BGRDON bacteria uptake rate of DON (umoles liter-1 sec-1) c BGRNH4 bacteria uptake rate of NH4 (umoles liter-1 sec-1) c BIOPOS switch to enforce positive biological fields: c [0] do not enforce, [1] enforce. c BRKNPON PON breakdown rate to DON (sec-1). # if defined codunlim | defined codlim # if defined codunlim c CDKP prey response coefficient. [(cm^2 m^3)/(s mmole N)] c CDKT temperature response coefficient. {cm^2/[s (deg C)^2]} c CDKZ depth response coefficient. (cm/s) # else c CDKP prey response coefficient. [(cm m^3)/(mmole N)] c CDKT temperature response coefficient. [cm/(deg C)^2] c CDKZ depth response coefficient. # endif c CDSPD maximum cod cruising speed. (cm/s) c CDTMAX maximum preferred temperature for cod. (deg C) c CDTMIN minimum preferred temperature for cod. (deg C) c CDWMAX maximum vertical swimming speed. (cm/s) c CDZMAX maximum water depth for cod (cm). c CDZMIN minimum water depth for cod (cm). # endif c FPFLUX export particle flux (10^-5 moles m-2 second-1). Note that c this is based on the zmortex*zmortr*zoo term, and does not c include the PON sinking flux. c FPREMN export remineralization rate in the euphotic zone, based on c Martin et al. (1987) carbon flux. (umoles liter-1 second-1) c GRTHPA temperature-dependent growth rate parameter "a" (sec-1). c GRTHPB temperature-dependent growth rate parameter "b" (nondimen). c GRTHPC temperature-dependent growth rate parameter "c" (degC-1). c HSNH4 half saturation constant for ammonium uptake (umoles/l). c HSNO3 half saturation constant for nitrate uptake (umoles/l). c IBAC index for bacteria in tracer array. c IBIOUT output write switches. [0] do not write, [1] write. c IDON index for dissolved organic nitrogen in tracer array. c INH4 index for ammonium in tracer array. c INO3 index for nitrate in tracer array. c IPHY index for phytoplankton in tracer array. c IPON index for particulate organic nitrogen in tracer array. c IZOO index for zooplankton in tracer array. c NH4PR recycled (NH4) production rate (umoles liter-1 sec-1). c NO3INH strength of ammonium inhibition of nitrate uptake (l/umoles) c NO3PR new (NO3) production rate (umoles liter-1 sec-1). c PARFRAC fraction of shortwave radiation that is photosynthetically c active (nondimensional). c PHYEXUD fraction of primary production exuded as DON (nondimen). c PHYGRTH initial slope of P-I curve (degC-1 cm-1). c PHYLR1 phytoplankton mortality rate (sec-1). c PREFBAC zooplankton grazing preference for bacteria (nondimen). c PREFPHY zooplankton grazing preference for phytoplankton (nondimen). c PREFPON zooplankton grazing preference for PON (nondimensional). c RMNBIO aphotic zone decay timescale for PHY, ZOO, BAC, DON (sec-1). c RMNNH4 aphotic zone decay timescale for NH4 (sec-1). c RMNPON1 linear aphotic zone decay timescale for PON (sec-1) . c RMNPON2 quadratic decay timescale for PON (liter umole-1 sec-1). c SBLDEP euphotic zone depth (cm). c WSNKPON PON sinking velocity (cm sec-1). c ZASSEFF zooplankton assimilation efficiency fraction (nondimen). c ZEXCNH4 fraction of zooplankton excretion to NH4 (nondimensional). c (The remainder goes to DON.) c ZEXCRR zooplankton excretion rate (sec-1). c ZGRAZR zooplankton maximum growth rate (sec-1). c ZGRAZK zooplankton growth half-saturation constant (umoles/l). c ZGRBAC zooplankton grazing rate of bacteria c (umoles liter-1 sec-1) c ZGRPHY zooplankton grazing rate of phytoplankton c (umoles liter-1 sec-1) c ZGRPON zooplankton grazing rate of PON (umoles liter-1 sec-1) c ZMORTEX fraction of zooplankton mortality to export (nondimen). c (The remainder goes to NH4.) c ZMORTR zooplankton mortality rate (sec-1). c c======================================================================= c # endif common /icbiopnh/ biopos,ibiout integer biopos,ibiout(20) c common /fcbiopnh/ attphy,phygrth,phyexud,phylr1,grthpa,grthpb, * grthpc,hsno3,hsnh4,no3inh,zgrazr,zgrazk,zasseff,prefphy, * prefbac,prefpon,zexcrr,zexcnh4,zmortr,zmortex,bacgrr, * bacgrk,bacfrac,bexcrr,wsnkpon,brknpon,rmnbio,rmnpon1, * rmnpon2,rmnnh4,sbldep,parfrac, * nh4pr,no3pr,zgrphy,zgrbac,zgrpon,bgrdon,bgrnh4, * fpflux,fpremn # if defined codunlim | defined codlim | defined cod_ing * ,cdkp,cdkt,cdkz,cdspd,cdtmax,cdtmin,cdwmax,cdzmax,cdzmin # endif FLOAT * attphy,phygrth,phyexud,phylr1,grthpa,grthpb, * grthpc,hsno3,hsnh4,no3inh,zgrazr,zgrazk,zasseff,prefphy, * prefbac,prefpon,zexcrr,zexcnh4,zmortr,zmortex,bacgrr, * bacgrk,bacfrac,bexcrr,wsnkpon,brknpon,rmnbio,rmnpon1, * rmnpon2,rmnnh4,sbldep,parfrac # if defined codunlim | defined codlim | defined cod_ing * ,cdkp,cdkt,cdkz,cdspd,cdtmax,cdtmin,cdwmax,cdzmax,cdzmin # endif FLOAT * nh4pr(imt,km),no3pr(imt,km),zgrphy(imt,km),zgrbac(imt,km), * zgrpon(imt,km),bgrdon(imt,km),bgrnh4(imt,km), * fpflux(imt,kmp1),fpremn(imt,km) c integer ino3,iphy,izoo,inh4,ipon,idon,ibac parameter (ino3=3,iphy=4,izoo=5,inh4=6,ipon=7,idon=8,ibac=9) # if defined codunlim | defined codlim | defined cod_ing integer icod parameter (icod=10) # endif #endif