| 1 |
stephd |
1.9 |
C $Header: /u/gcmpack/MITgcm_contrib/darwin2/pkg/monod/monod_init_fixed.F,v 1.8 2012/07/26 18:05:34 stephd Exp $ |
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stephd |
1.2 |
C $Name: $ |
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jahn |
1.1 |
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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_MONOD |
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c=============================================================================== |
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C=============================================================================== |
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CStartofinterface |
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SUBROUTINE MONOD_INIT_FIXED(myThid) |
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C =============== Global data ========================================== |
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C === Global variables === |
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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 "PARAMS.h" |
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#include "GRID.h" |
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#include "DYNVARS.h" |
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#include "GCHEM.h" |
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#include "DARWIN_PARAMS.h" |
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#include "MONOD_SIZE.h" |
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#include "MONOD.h" |
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#include "DARWIN_FLUX.h" |
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INTEGER myThid |
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C============== Local variables ============================================ |
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C msgBuf - Informational/error meesage buffer |
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CHARACTER*(MAX_LEN_MBUF) msgBuf |
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_RL pday |
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INTEGER i,j,k,bi,bj,nz |
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INTEGER tmp |
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INTEGER prec |
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CHARACTER*(MAX_LEN_MBUF) fn |
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C /--------------------------------------------------------------\ |
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C | initialise common block biochemical parameters | |
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C \--------------------------------------------------------------/ |
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WRITE(msgBuf,'(A)') |
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&'// =======================================================' |
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CALL PRINT_MESSAGE( msgBuf, standardMessageUnit, |
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& SQUEEZE_RIGHT, myThid ) |
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WRITE(msgBuf,'(A)') '// Darwin loading parameters' |
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CALL PRINT_MESSAGE( msgBuf, standardMessageUnit, |
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& SQUEEZE_RIGHT, myThid ) |
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WRITE(msgBuf,'(A)') |
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&'// =======================================================' |
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CALL PRINT_MESSAGE( msgBuf, standardMessageUnit, |
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& SQUEEZE_RIGHT, myThid ) |
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c ANNA set fixed params for WAVEBANDS |
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#ifdef WAVEBANDS |
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call wavebands_init_fixed(myThid) |
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#endif |
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c c define 1 day in seconds |
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pday = 86400.0 _d 0 |
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c attenuation coefficients |
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c ANNA only if not wavebands |
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#ifndef WAVEBANDS |
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k0= 4. _d -2 !atten coefficient water(m^-1) |
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#ifdef GEIDER |
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kc= 4. _d -2 !atten coefficient chl ((mmol chl/m3)-1) |
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#else |
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kc= 4. _d -2*16. _d 0*1. _d 0 !atten coefficient phy((uM m)-1) |
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#endif |
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#endif |
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c ANNA endif |
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c par parameters |
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parfrac= 0.4 _d 0 !fraction Qsw that is PAR |
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parconv= 1. _d 0/0.2174 _d 0 !conversion from W/m2 to uEin/m2/s |
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c for chl |
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chlpmax=40. _d 0 ! mg Chl/mmolP |
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chlpmin=16. _d 0 ! mg Chl/mmolP |
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istar=90. _d 0 ! w/m2 |
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c iron related |
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alpfe= 0.04 _d 0 !solubility of Fe dust |
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scav= 0.4 _d 0/(360. _d 0*86400. _d 0) !iron chem scavenging rate (s-1) |
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ligand_tot=1. _d -3 !total ligand (uM) |
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ligand_stab=2. _d 5 !ligand stability rate ratio |
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freefemax = .4 _d -3 ! max free fe |
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#ifdef IRON_SED_SOURCE |
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c iron sediment source |
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depthfesed=1000.0 _d 0 !depth above which to add sediment source |
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fesedflux =1.0 _d 0 * 1.0 _d -3 / (86400.0 _d 0) !iron flux (mmol/m2/s) |
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fesedflux_pcm =0.68 _d 0 * 1.0 _d -3 !iron flux (mmol/m3/s) per |
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c mmol POC/m3/s |
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#endif |
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#ifdef PART_SCAV |
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scav_rat=0.005 _d 0 /(86400.0 _d 0) |
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scav_inter=0.079 _d 0 |
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scav_exp=0.58 _d 0 |
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#endif |
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c depth for denitrification to start |
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depthdenit=185.0 _d 0 |
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c critical oxygen for O2/NO3 remineralization |
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O2crit = 6.0 _d 0 !(Lipschultz et al 1990, DSR 37, 1513-1541) |
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stephd |
1.7 |
c ratio of n to p in denitrification process |
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jahn |
1.1 |
denit_np = 120.0 _d 0 |
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stephd |
1.7 |
c ratio no3 used relative to all n in denitrification process |
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denit_no3 = 104.0 _d 0 |
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c critical nitrate below which no denit (or remin) happens |
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no3crit = 1. _d -2 |
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jahn |
1.1 |
c |
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c oxidation rates for ammonium and nitrite |
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c i.e. Knita ... NH4 -> NO2 |
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c i.e. Knitb ... NO2 -> NO3 |
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Knita = 1.0 _d 0/(.50 _d 0*pday) |
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Knitb = 1.0 _d 0/(10.0 _d 0*pday) |
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c critical light level (muEin/m2/s) after which oxidation starts |
| 122 |
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PAR0 = 10. _d 0 |
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c |
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#ifndef GEIDER |
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c set growth days ...small or big organism? |
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Smallgrow = .7 _d 0 |
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Biggrow = .4 _d 0 |
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Smallgrowrange = 0. _d 0 |
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Biggrowrange = 0. _d 0 |
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diaz_growfac = 2. _d 0 |
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#endif |
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c set mort days ...small or big organism? |
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Smallmort = 10. _d 0 |
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Bigmort = 10. _d 0 |
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Smallmortrange = 0. _d 0 |
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Bigmortrange = 0. _d 0 |
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c set export fraction ...small or big organism? |
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Smallexport = 0.2 _d 0 |
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Bigexport = 0.5 _d 0 |
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c set sinking rates (m/s)... small or big organism? |
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SmallSink = 0.0 _d 0/pday |
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BigSink = 0.5 _d 0/pday !0.5 _d 0/pday |
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c set parameters for light function for phyto growth |
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#ifndef GEIDER |
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smallksatpar = 0.12 _d 0 ! 0.8 _d 0 |
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smallksatparstd = 0.20 _d 0 ! 0.3 _d 0 |
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smallkinhib = 6.0 _d 0 ! 2.0 _d 0 |
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smallkinhibstd = 0.10 _d 0 ! 0.5 _d 0 |
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Bigksatpar = 0.12 _d 0 ! 0.35 _d 0 |
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Bigksatparstd = 0.06 _d 0 ! 0.1 _d 0 |
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Bigkinhib = 1.0 _d 0 ! 0.5 _d 0 |
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Bigkinhibstd = 0.05 _d 0 ! 0.1 _d 0 |
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#endif |
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#ifdef GEIDER |
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c for Pcm -- should be growth rates, but using old variables |
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c note these are in terms of days - converted to 1/s later |
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Smallgrow = .7 _d 0 |
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Biggrow = .4 _d 0 |
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Smallgrowrange = 0. _d 0 |
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Biggrowrange = 0. _d 0 |
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diaz_growfac = 2. _d 0 |
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c |
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smallchl2cmax = 0.2 _d 0 !mg Chl (mmol C) |
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smallchl2cmaxrange = 0.3 _d 0 !mg Chl (mmol C) |
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Bigchl2cmax = 0.5 _d 0 !mg Chl (mmol C) |
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Bigchl2cmaxrange = 0.3 _d 0 !mg Chl (mmol C) |
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c ANNA_Q units for alpha are same as expected: mmol C (mg chla)-1 (uEin)-1 (m)2 |
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c smallalphachl = 1. _d -6 !mmol C (uEin/m-2)-1 (mg Chl)-1 |
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c smallalphachlrange = 1. _d -6 !mmol C (uEin/m-2)-1 (mg Chl)-1 |
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c Bigalphachl = 6. _d -7 !mmol C (uEin/m-2)-1 (mg Chl)-1 |
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c Bigalphachlrange = 4. _d -7 !mmol C (uEin/m-2)-1 (mg Chl)-1 |
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c ANNA mQyield vals are from alphachl / aphy_chl which for now is 0.02 |
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c ANNA ranges for mQyield are same as alphachl but reduced by factor 100 |
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smallmQyield = 5. _d -5 !mmol C (uEin)-1 |
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smallmQyieldrange = 1. _d -4 !mmol C (uEin)-1 |
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BigmQyield = 3. _d -5 !mmol C (uEin)-1 |
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BigmQyieldrange = 4. _d -5 !mmol C (uEin)-1 |
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c ANNA value of aphy_chl_ave = 0.02 - its the mean of all spectras used as input data |
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aphy_chl_ave = 0.02 _d 0 !m2 (mg chla)-1 (ie. x chla gives absorption m-1) |
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c inhib for Prochl? |
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C inhibcoef_geid_val = 1.2 _d 0 !DUMMY VAL |
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inhibcoef_geid_val = 0 _d 0 !DUMMY VAL |
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#ifdef DYNAMIC_CHL |
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acclimtimescl = 1./(60. _d 0 *60. _d 0 *24. _d 0 * 20. _d 0) |
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#endif |
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#endif |
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c |
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c set temperature function |
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tempcoeff1 = 1. _d 0/3. _d 0 |
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tempcoeff2_small = 0.001 _d 0 |
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tempcoeff2_big = 0.0003 _d 0 |
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tempcoeff3 = 1.04 _d 0 |
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tempmax = 30. _d 0 ! 32. _d 0 |
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temprange = 32. _d 0 ! 30. _d 0 |
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tempnorm = 0.3 _d 0 ! 1. _d 0 |
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tempdecay = 4. _d 0 |
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c set phosphate half stauration constants .. small or big organism |
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SmallPsat=0.015 _d 0 |
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BigPsat=0.035 _d 0 |
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ProcPsat=0.01 _d 0 |
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UniDzPsat=0.012 _d 0 |
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SmallPsatrange=0.02 _d 0 |
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BigPsatrange=0.02 _d 0 |
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ProcPsatrange=0.005 _d 0 |
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UniDzPsatrange=0.02 _d 0 |
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c set NH4/NO2 frac, so that NH4/NO2 can be preferred nitrogen source |
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ksatNH4fac=.50 _d 0 |
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ksatNO2fac=1.0 _d 0 |
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c set prochl lower half-sat (used only for mutants) |
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prochlPsat=.85 _d 0 |
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c ammonia and nitrite inhibition |
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sig1 = 4.6 _d 0 |
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sig2 = 4.6 _d 0 |
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sig3 = 4.6 _d 0 |
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ngrowfac = 1. _d 0 |
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ilight = 2. _d 0 |
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c set si half sat |
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val_ksatsi=1. _d 0 |
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c set nutrient ratios for phyto |
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stephd |
1.8 |
#ifdef ONLY_P_CYCLE |
| 225 |
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val_R_SiP_diatom=0.0 _d 0 |
| 226 |
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val_R_NP=0.0 _d 0 |
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val_RFeP=0.0 _d -3 |
| 228 |
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val_R_NP_diaz=0.0 _d 0 |
| 229 |
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val_RFeP_diaz=0.0 _d 0 * val_RFeP |
| 230 |
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val_R_PC=0.0 _d 0 |
| 231 |
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val_R_PICPOC=0.0 _d 0 |
| 232 |
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#else |
| 233 |
jahn |
1.1 |
val_R_SiP_diatom=16.0 _d 0 ! 32 for Fanny's runs |
| 234 |
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val_R_NP=16.0 _d 0 |
| 235 |
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val_RFeP=1.0 _d -3 |
| 236 |
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val_R_NP_diaz=40.0 _d 0 |
| 237 |
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val_RFeP_diaz=30.0 _d 0 * val_RFeP |
| 238 |
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val_R_PC=120.0 _d 0 |
| 239 |
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val_R_PICPOC=0.8 _d 0 |
| 240 |
stephd |
1.8 |
#endif |
| 241 |
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c |
| 242 |
jahn |
1.1 |
#ifdef OLD_GRAZE |
| 243 |
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c grazing hlaf saturation |
| 244 |
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kgrazesat = 0.1 _d 0 |
| 245 |
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c set grazing rates .. small or big organism? |
| 246 |
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GrazeFast = 1.0 _d 0/(5.0 _d 0*pday) |
| 247 |
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GrazeSlow = 1.0 _d 0/(30.0 _d 0*pday) |
| 248 |
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c set grazing effeciency |
| 249 |
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GrazeEffsmall=0.6 _d 0 |
| 250 |
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GrazeEffbig =0.2 _d 0 |
| 251 |
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c set grazing of diatom factor |
| 252 |
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diatomgraz = 0.8 _d 0 |
| 253 |
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coccograz = 0.7 _d 0 |
| 254 |
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olargegraz = 0.9 _d 0 |
| 255 |
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#else |
| 256 |
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c grazing hlaf saturation |
| 257 |
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c kgrazesat = 0.1 _d 0 |
| 258 |
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kgrazesat = 0.1 _d 0 |
| 259 |
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c phygrazmin = 1 _d -5 |
| 260 |
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phygrazmin = 1 _d -10 |
| 261 |
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c set grazing rates .. small or big organism? |
| 262 |
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c GrazeFast = 1.0 _d 0/(5.0 _d 0*pday) |
| 263 |
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GrazeFast = 1.0 _d 0/(2.0 _d 0*pday) |
| 264 |
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c GrazeSlow = 1.0 _d 0/(30.0 _d 0*pday) |
| 265 |
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GrazeSlow = 1.0 _d 0/(7.0 _d 0*pday) |
| 266 |
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c set grazing effeciency |
| 267 |
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GrazeEfflow= 0.2 _d 0 |
| 268 |
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GrazeEffmod= 0.5 _d 0 |
| 269 |
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GrazeEffhi = 0.7 _d 0 |
| 270 |
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c set palatibility |
| 271 |
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palathi = 1.0 _d 0 |
| 272 |
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palatlo = 0.2 _d 0 |
| 273 |
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c set palatibilty diatom factor |
| 274 |
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diatomgraz = 0.7 _d 0 |
| 275 |
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coccograz = 0.6 _d 0 |
| 276 |
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olargegraz = 1.0 _d 0 |
| 277 |
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c set faction graz to POM |
| 278 |
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ExGrazfracbig = 0.8 _d 0 |
| 279 |
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ExGrazfracsmall = 0.8 _d 0 |
| 280 |
stephd |
1.2 |
c grazing exponential 1= holling 2, 2=holling 3 |
| 281 |
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hollexp=1.0 _d 0 |
| 282 |
jahn |
1.1 |
#endif |
| 283 |
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c set zoo mortality |
| 284 |
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ZoomortSmall = 1.0 _d 0/(30.0 _d 0*pday) |
| 285 |
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ZoomortBig = 1.0 _d 0/(30.0 _d 0*pday) |
| 286 |
stephd |
1.3 |
ZoomortSmall2 = 0. _d 0 |
| 287 |
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ZoomortBig2 = 0. _d 0 |
| 288 |
jahn |
1.1 |
c set zoo exportfrac |
| 289 |
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ZooexfacSmall = 0.2 _d 0 |
| 290 |
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ZooexfacBig = 0.7 _d 0 |
| 291 |
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c minimum phyto (below which grazing and mortality doesn't happen) |
| 292 |
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c phymin = 1 _d -10 |
| 293 |
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c phymin = 1 _d -50 |
| 294 |
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phymin = 1 _d -20 |
| 295 |
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c DOM remin rates |
| 296 |
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Kdop = 1.0 _d 0/(100.0 _d 0*pday) |
| 297 |
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Kdon = 1.0 _d 0/(100.0 _d 0*pday) |
| 298 |
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KdoFe = 1.0 _d 0/(100.0 _d 0*pday) |
| 299 |
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c Particulate detritus remin rates |
| 300 |
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c z* = wx_sink/Kremin_X |
| 301 |
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c for e-folding length scale, z* = 300 m |
| 302 |
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c choose Kremin_X = 1/30 day-1, wx_sink = 10 m day-1 |
| 303 |
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Kpremin_P = 1.0 _d 0/(50.0 _d 0*pday) |
| 304 |
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Kpremin_N = Kpremin_P |
| 305 |
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Kpremin_Fe = Kpremin_P |
| 306 |
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Kpremin_Si = 1.0 _d 0/(300.0 _d 0*pday) |
| 307 |
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c sinking rate for particulate matter (m/s) |
| 308 |
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wp_sink = 10.0 _d 0/pday |
| 309 |
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wn_sink = wp_sink |
| 310 |
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wfe_sink = wp_sink |
| 311 |
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wsi_sink = wp_sink |
| 312 |
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| 313 |
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#ifdef ALLOW_CARBON |
| 314 |
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R_OP = 170 _d 0 |
| 315 |
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Kdoc = 1.0 _d 0/(100.0 _d 0*pday) |
| 316 |
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Kpremin_C = 1.0 _d 0/(50.0 _d 0*pday) |
| 317 |
|
|
Kdissc = 1.0 _d 0/(300.0 _d 0*pday) |
| 318 |
|
|
wc_sink = wp_sink |
| 319 |
|
|
wpic_sink = 15.0 _d 0/pday |
| 320 |
|
|
permil = 1. _d 0 / 1024.5 _d 0 |
| 321 |
|
|
Pa2Atm = 1.01325 _d 5 |
| 322 |
|
|
#endif |
| 323 |
|
|
|
| 324 |
stephd |
1.5 |
#ifdef ALLOW_CDOM |
| 325 |
|
|
fraccdom=2. _d 0 / 100. _d 0 |
| 326 |
|
|
cdomdegrd= 1. _d 0 / (200 _d 0 *pday) |
| 327 |
|
|
cdombleach = 1. _d 0 / (15 _d 0 *pday) |
| 328 |
|
|
PARcdom = 20. _d 0 |
| 329 |
|
|
rnp_cdom = 16. _d 0 |
| 330 |
|
|
rfep_cdom = 1. _d -3 |
| 331 |
|
|
rcp_cdom = 120. _d 0 |
| 332 |
|
|
cdomcoeff = .1 _d -1 / 1.d -4 |
| 333 |
|
|
#endif |
| 334 |
|
|
|
| 335 |
jahn |
1.1 |
C make sure we have reserved enough space in Ptracers |
| 336 |
|
|
IF ( nCompZooMax .LT. 4 ) THEN |
| 337 |
stephd |
1.9 |
#ifndef ONLY_P_CYCLE |
| 338 |
jahn |
1.1 |
WRITE(msgBuf,'(A,A,I3)') |
| 339 |
|
|
& 'MONOD_INIT_FIXED: ERROR: 4 zooplankton components, but ', |
| 340 |
|
|
& 'nCompZooMax = ', nCompZooMax |
| 341 |
|
|
CALL PRINT_ERROR( msgBuf , 1) |
| 342 |
|
|
STOP 'ABNORMAL END: S/R MONOD_INIT_FIXED' |
| 343 |
stephd |
1.9 |
#endif |
| 344 |
jahn |
1.1 |
ENDIF |
| 345 |
|
|
DO nz = 1,nzmax |
| 346 |
|
|
iZooP (nz) = iZoo + (nz-1)*strideTypeZoo |
| 347 |
stephd |
1.6 |
#ifdef ONLY_P_CYCLE |
| 348 |
|
|
iZooN (nz) = nptot |
| 349 |
|
|
iZooFe(nz) = nptot |
| 350 |
|
|
iZooSi(nz) = nptot |
| 351 |
|
|
#else |
| 352 |
jahn |
1.1 |
iZooN (nz) = iZoo + 1*strideCompZoo + (nz-1)*strideTypeZoo |
| 353 |
|
|
iZooFe(nz) = iZoo + 2*strideCompZoo + (nz-1)*strideTypeZoo |
| 354 |
|
|
iZooSi(nz) = iZoo + 3*strideCompZoo + (nz-1)*strideTypeZoo |
| 355 |
stephd |
1.6 |
#endif |
| 356 |
jahn |
1.1 |
ENDDO |
| 357 |
|
|
#ifdef ALLOW_CARBON |
| 358 |
|
|
DO nz = 1,nzmax |
| 359 |
|
|
iZooC (nz) = iZoC + (nz-1) |
| 360 |
|
|
ENDDO |
| 361 |
|
|
#endif |
| 362 |
|
|
|
| 363 |
|
|
#ifdef DAR_DIAG_DIVER |
| 364 |
|
|
c only look at grid point with a minimum biomass |
| 365 |
|
|
diver_thresh0=1 _d -12 |
| 366 |
|
|
c diver1 - if any type greater than |
| 367 |
|
|
diver_thresh1=1 _d -8 |
| 368 |
|
|
c diver2 - if more than this proportion of total biomass |
| 369 |
|
|
diver_thresh2=1 _d -3 |
| 370 |
|
|
c diver3 - fraction of biomass to count |
| 371 |
|
|
diver_thresh3=.999 _d 0 |
| 372 |
|
|
c diver4 - fraction of maximum species |
| 373 |
|
|
diver_thresh4=1 _d -5 |
| 374 |
jahn |
1.4 |
c threshold on total biomass for contributing to Shannon and Simpson ind |
| 375 |
|
|
c (these become large at very small biomass) |
| 376 |
|
|
shannon_thresh = 1 _d -8 ! mmol P m-3 |
| 377 |
jahn |
1.1 |
#endif |
| 378 |
|
|
|
| 379 |
|
|
c set up diagnostics |
| 380 |
|
|
#ifdef ALLOW_MNC |
| 381 |
|
|
IF ( useMNC ) THEN |
| 382 |
|
|
CALL DARWIN_MNC_INIT( myThid ) |
| 383 |
|
|
#ifdef ALLOW_CARBON |
| 384 |
|
|
CALL DIC_MNC_INIT( myThid ) |
| 385 |
|
|
#endif |
| 386 |
|
|
ENDIF |
| 387 |
|
|
#endif /* ALLOW_MNC */ |
| 388 |
|
|
|
| 389 |
|
|
COJ set up diagnostics |
| 390 |
|
|
#ifdef ALLOW_DIAGNOSTICS |
| 391 |
|
|
IF ( useDIAGNOSTICS ) THEN |
| 392 |
|
|
CALL MONOD_DIAGNOSTICS_INIT( myThid ) |
| 393 |
|
|
#ifdef ALLOW_CARBON |
| 394 |
|
|
CALL DIC_DIAGNOSTICS_INIT( myThid ) |
| 395 |
|
|
#endif |
| 396 |
|
|
ENDIF |
| 397 |
|
|
#endif /* ALLOW_DIAGNOSTICS */ |
| 398 |
|
|
COJ |
| 399 |
|
|
|
| 400 |
|
|
|
| 401 |
|
|
|
| 402 |
|
|
RETURN |
| 403 |
|
|
END |
| 404 |
|
|
C============================================================================ |
| 405 |
|
|
#endif |
| 406 |
|
|
#endif |
| 407 |
|
|
|
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