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PLANK_Class.py
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import numpy as np
from numpy import zeros, array
from math import log, exp
import numba as nb
from numba.experimental import jitclass
from HSP2.ADCALC import advect
from HSP2.OXRX_Class import OXRX_Class
from HSP2.NUTRX_Class import NUTRX_Class
from HSP2.RQUTIL import sink, decbal
from HSP2.utilities import make_numba_dict, initm
spec = [
('OXRX', OXRX_Class.class_type.instance_type),
('NUTRX', NUTRX_Class.class_type.instance_type),
('aldh', nb.float64),
('aldl', nb.float64),
('alnpr', nb.float64),
('alr20', nb.float64),
('AMRFG', nb.int32),
('baco2', nb.float64),
('balbod', nb.float64),
('balcla', nb.float64[:]),
('baldep', nb.float64),
('baldox', nb.float64),
('BALFG', nb.int32),
('ballit', nb.float64),
('balno3', nb.float64),
('balorc', nb.float64),
('balorn', nb.float64),
('balorp', nb.float64),
('balpo4', nb.float64),
('balr20', nb.float64[:]),
('baltam', nb.float64),
('balvel', nb.float64),
('benal', nb.float64[:]),
('BFIXFG', nb.int32[:]),
('BINVFG', nb.int32),
('BNPFG', nb.int32),
('bpcntc', nb.float64),
('campr', nb.float64),
('cbnrbo', nb.float64),
('cfbalg', nb.float64),
('cfbalr', nb.float64),
('cflit', nb.float64),
('cfsaex', nb.float64),
('cktrb1', nb.float64),
('cktrb2', nb.float64),
('claldh', nb.float64),
('cmingr', nb.float64),
('cmmbi', nb.float64),
('cmmd1', nb.float64[:]),
('cmmd2', nb.float64[:]),
('cmmlt', nb.float64),
('cmmn', nb.float64),
('cmmnb', nb.float64[:]),
('cmmnp', nb.float64),
('cmmp', nb.float64),
('cmmpb', nb.float64[:]),
('cmmv', nb.float64),
('co2', nb.float64),
('conv', nb.float64),
('cremvl', nb.float64),
('cslit', nb.float64[:]),
('cslof1', nb.float64[:]),
('cslof2', nb.float64[:]),
('ctrbq1', nb.float64),
('ctrbq2', nb.float64),
('cvbc', nb.float64),
('cvbcl', nb.float64),
('cvbn', nb.float64),
('cvbo', nb.float64),
('cvbp', nb.float64),
('cvbpc', nb.float64),
('cvbpn', nb.float64),
('cvnrbo', nb.float64),
('cvpb', nb.float64),
('DECFG', nb.int32),
('delt', nb.float64),
('delt60', nb.float64),
('delts', nb.float64),
('dthbal', nb.float64[:]),
('dthphy', nb.float64),
('dthtba', nb.float64),
('dthzoo', nb.float64),
('errors', nb.int64[:]),
('extb', nb.float64),
('flxbal', nb.float64[:,:]),
('fravl', nb.float64),
('frrif', nb.float64),
('grobal', nb.float64[:]),
('grophy', nb.float64),
('grores', nb.float64[:]),
('grotba', nb.float64),
('grozoo', nb.float64),
('HTFG', nb.int32),
('iorc', nb.float64),
('iorn', nb.float64),
('iorp', nb.float64),
('iphyto', nb.float64),
('itorc', nb.float64),
('itorn', nb.float64),
('itorp', nb.float64),
('itotn', nb.float64),
('itotp', nb.float64),
('izoo', nb.float64),
('limbal', nb.int32[:]),
('limphy', nb.int32),
('litsed', nb.float64),
('lmingr', nb.float64),
('lsnh4', nb.float64[:]),
('lspo4', nb.float64[:]),
('malgr', nb.float64),
('mbal', nb.float64),
('mbalgr', nb.float64[:]),
('minbal', nb.float64),
('mxstay', nb.float64),
('mzoeat', nb.float64),
('naldh', nb.float64),
('nexits', nb.int32),
('nmaxfx', nb.float64),
('nminc', nb.float64),
('nmingr', nb.float64),
('nonref', nb.float64),
('NSFG', nb.int32),
('numbal', nb.int32),
('oorc', nb.float64[:]),
('oorn', nb.float64[:]),
('oorp', nb.float64[:]),
('ophyt', nb.float64[:]),
('orc', nb.float64),
('oref', nb.float64),
('orn', nb.float64),
('orp', nb.float64),
('otorc', nb.float64[:]),
('otorn', nb.float64[:]),
('otorp', nb.float64[:]),
('ototn', nb.float64[:]),
('ototp', nb.float64[:]),
('oxald', nb.float64),
('oxzd', nb.float64),
('ozoo', nb.float64[:]),
('paldh', nb.float64),
('paradf', nb.float64),
('PHFG', nb.int32),
('phybod', nb.float64),
('phycla', nb.float64),
('phydox', nb.float64),
('PHYFG', nb.int32),
('phylit', nb.float64),
('phyno3', nb.float64),
('phyorc', nb.float64),
('phyorn', nb.float64),
('phyorp', nb.float64),
('phypo4', nb.float64),
('physet', nb.float64),
('phytam', nb.float64),
('phyto', nb.float64),
('pmingr', nb.float64),
('potbod', nb.float64),
('pyco2', nb.float64),
('ratclp', nb.float64),
('refr', nb.float64),
('refset', nb.float64),
('rifcq1', nb.float64),
('rifcq2', nb.float64),
('rifcq3', nb.float64),
('rifdf', nb.float64[:]),
('rifvf', nb.float64[:]),
('roorc', nb.float64),
('roorn', nb.float64),
('roorp', nb.float64),
('rophyt', nb.float64),
('rotorc', nb.float64),
('rotorn', nb.float64),
('rotorp', nb.float64),
('rototn', nb.float64),
('rototp', nb.float64),
('rozoo', nb.float64),
('SDLTFG', nb.int32),
('seed', nb.float64),
('simlen', nb.int32),
('snkphy', nb.float64),
('snkorc', nb.float64),
('snkorn', nb.float64),
('snkorp', nb.float64),
('svol', nb.float64),
('talgrh', nb.float64),
('talgrl', nb.float64),
('talgrm', nb.float64),
('tbenal', nb.float64[:]),
('tcbalg', nb.float64[:]),
('tcbalr', nb.float64[:]),
('tcgraz', nb.float64),
('tczfil', nb.float64),
('tczres', nb.float64),
('tn', nb.float64),
('torc', nb.float64),
('torn', nb.float64),
('torp', nb.float64),
('totbod', nb.float64),
('totdox', nb.float64),
('totno3', nb.float64),
('totorc', nb.float64),
('totorn', nb.float64),
('totorp', nb.float64),
('totphy', nb.float64),
('totpo4', nb.float64),
('tottam', nb.float64),
('tottba', nb.float64),
('totzoo', nb.float64),
('tp', nb.float64),
('uunits', nb.int32),
('vol', nb.float64),
('zd', nb.float64),
('zexdel', nb.float64),
('zfil20', nb.float64),
('ZFOOD', nb.int32),
('zoco2', nb.float64),
('zomass', nb.float64),
('zoo', nb.float64),
('zoobod', nb.float64),
('zoodox', nb.float64),
('ZOOFG', nb.int32),
('zoono3', nb.float64),
('zooorc', nb.float64),
('zooorn', nb.float64),
('zooorp', nb.float64),
('zoophy', nb.float64),
('zoopo4', nb.float64),
('zootam', nb.float64),
('zres20', nb.float64),
]
@jitclass(spec)
class PLANK_Class:
#-------------------------------------------------------------------
# class initialization:
#-------------------------------------------------------------------
def __init__(self, siminfo, nexits, vol, ui_rq, ui, ts, OXRX, NUTRX):
''' Initialize instance variables for lower food web simulation '''
self.errors = zeros(int(ui['errlen']), dtype=np.int64)
'''
self.limit = array(8, type=nb.char) #np.chararray(8, itemsize=4)
self.limit[1] = 'LIT'
self.limit[2] = 'NON'
self.limit[3] = 'TEM'
self.limit[4] = 'NIT'
self.limit[5] = 'PO4'
self.limit[6] = 'NONE'
self.limit[7] = 'WAT'
'''
self.delt = siminfo['delt']
delt60 = siminfo['delt'] / 60.0 # delt60 - simulation time interval in hours
self.delt60 = delt60
self.simlen = int(siminfo['steps'])
self.delts = siminfo['delt'] * 60
self.uunits = int(siminfo['units'])
self.nexits = int(nexits)
self.vol = vol
self.svol = self.vol
# inflow/outflow conversion factor:
if self.uunits == 2: # SI conversion: (g/m3)*(m3/ivld) --> [kg/ivld]
self.conv = 1.0e-3
else: # Eng. conversion: (g/m3)*(ft3/ivld) --> [lb/ivld]
self.conv = 6.2428e-5
# flags - table-type PLNK-FLAGS
self.PHYFG = int(ui['PHYFG'])
self.ZOOFG = int(ui['ZOOFG'])
self.BALFG = int(ui['BALFG'])
self.SDLTFG = int(ui['SDLTFG'])
self.AMRFG = int(ui['AMRFG'])
self.DECFG = int(ui['DECFG'])
self.NSFG = int(ui['NSFG'])
self.ZFOOD = int(ui['ZFOOD'])
self.BNPFG = int(ui['BNPFG'])
self.HTFG = int(ui_rq['HTFG'])
self.PHFG = int(ui_rq['PHFG'])
self.bpcntc = NUTRX.bpcntc
self.cvbo = NUTRX.cvbo
self.cvbpc = NUTRX.cvbpc
self.cvbpn = NUTRX.cvbpn
if self.ZOOFG == 1 and self.PHYFG == 0:
self.errors[0] += 1
# ERRMSG: error - zooplankton cannot be simulated without phytoplankton
if self.NSFG == 1 and NUTRX.TAMFG == 0:
self.errors[1] += 1
# ERRMSG: error - ammonia cannot be included in n supply if it is not
if NUTRX.PO4FG == 0:
self.errors[2] += 1
# ERRMSG: error - phosphate must be simulated if plankton are being
self.numbal = 0
self.BFIXFG = zeros(5, dtype=np.int32)
if self.BALFG == 2: # user has selected multiple species with more complex kinetics
# additional benthic algae flags - table-type BENAL-FLAG
self.numbal = int(ui['NUMBAL'])
self.BINVFG = int(ui['BINVFG'])
for i in range(1,5):
self.BFIXFG[i] = int(ui['BFIXFG' + str(i)])
else:
self.numbal = self.BALFG # single species or none
self.cfsaex = 1.0
if self.HTFG > 0 and 'CFSAEX' in ui_rq: # via heat-parm input table
self.cfsaex = ui_rq['CFSAEX']
elif 'CFSAEX' in ui: # fraction of surface exposed - table-type surf-exposed
self.cfsaex = ui['CFSAEX']
# table-type plnk-parm1
self.ratclp = ui['RATCLP']
self.nonref = ui['NONREF']
self.litsed = ui['LITSED']
self.alnpr = ui['ALNPR']
self.extb = ui['EXTB']
self.malgr = ui['MALGR'] * self.delt60
self.paradf = ui['PARADF']
self.refr = 1.0 - self.nonref # define fraction of biomass which is refractory material
# compute derived conversion factors
self.cvbc = self.bpcntc / 100.0
self.cvnrbo = self.nonref * self.cvbo
self.cvbp = (31.0 * self.bpcntc) / (1200.0 * self.cvbpc)
self.cvbn = 14.0 * self.cvbpn * self.cvbp / 31.0
self.cvpb = 31.0 / (1000.0 * self.cvbp)
self.cvbcl = 31.0 * self.ratclp / self.cvpb
# table-type plnk-parm2
self.cmmlt = ui['CMMLT']
self.cmmn = ui['CMMN']
self.cmmnp = ui['CMMNP']
self.cmmp = ui['CMMP']
self.talgrh = ui['TALGRH']
self.talgrl = ui['TALGRL']
self.talgrm = ui['TALGRM']
if self.uunits == 1:
self.talgrh = (self.talgrh - 32.0) * 0.555
self.talgrl = (self.talgrl - 32.0) * 0.555
self.talgrm = (self.talgrm - 32.0) * 0.555
# table-type plnk-parm3
self.alr20 = ui['ALR20'] * delt60 # convert rates from 1/hr to 1/ivl
self.aldh = ui['ALDH'] * delt60
self.aldl = ui['ALDL'] * delt60
self.oxald = ui['OXALD'] * delt60
self.naldh = ui['NALDH'] * delt60
self.paldh = ui['PALDH']
# table-type plnk-parm4
self.nmingr = ui['NMINGR']
self.pmingr = ui['PMINGR']
self.cmingr = ui['CMINGR']
self.lmingr = ui['LMINGR']
self.nminc = ui['NMINC']
# phytoplankton-specific parms - table-type phyto-parm
# this table must always be input so that REFSET is read
self.seed = ui['SEED']
self.mxstay = ui['MXSTAY']
self.oref = ui['OREF']
self.claldh = ui['CLALDH']
self.physet = ui['PHYSET'] * delt60 # change settling rates to units of 1/ivl
self.refset = ui['REFSET'] * delt60 # change settling rates to units of 1/ivl
if self.PHYFG == 1 and self.ZOOFG == 1: # zooplankton-specific parameters
# table-type zoo-parm1
self.mzoeat = ui['MZOEAT'] * delt60 # convert rates from 1/hr to 1/ivl
self.zfil20 = ui['ZFIL20'] * delt60 # convert rates from 1/hr to 1/ivl
self.zres20 = ui['ZRES20'] * delt60 # convert rates from 1/hr to 1/ivl
self.zd = ui['ZD'] * delt60 # convert rates from 1/hr to 1/ivl
self.oxzd = ui['OXZD'] * delt60 # convert rates from 1/hr to 1/ivl
# table-type zoo-parm2
self.tczfil = ui['TCZFIL']
self.tczres = ui['TCZRES']
self.zexdel = ui['ZEXDEL']
self.zomass = ui['ZOMASS']
if self.BALFG >= 1: # benthic algae-specific parms; table-type benal-parm
self.mbal = ui['MBAL'] / self.cvpb # convert maximum benthic algae to micromoles of phosphorus
self.cfbalr = ui['CFBALR']
self.cfbalg = ui['CFBALG']
self.minbal = ui['MINBAL'] / self.cvpb # convert maximum benthic algae to micromoles of phosphorus
self.campr = ui['CAMPR']
self.fravl = ui['FRAVL']
self.nmaxfx = ui['NMAXFX']
self.mbalgr = zeros(self.numbal)
self.tcbalg = zeros(self.numbal)
self.cmmnb = zeros(self.numbal)
self.cmmpb = zeros(self.numbal)
self.cmmd1 = zeros(self.numbal)
self.cmmd2 = zeros(self.numbal)
self.cslit = zeros(self.numbal)
self.balr20 = zeros(self.numbal)
self.tcbalr = zeros(self.numbal)
self.cslof1 = zeros(self.numbal)
self.cslof2 = zeros(self.numbal)
self.grores = zeros(self.numbal)
if self.BALFG == 2: # user has selected multiple species with more complex kinetics
for i in range(self.numbal):
# species-specific growth parms - table type benal-grow
self.mbalgr[i] = ui['MBALGR'] * self.delt60
self.tcbalg[i] = ui['TCBALG']
self.cmmnb[i] = ui['CMMNB']
self.cmmpb[i] = ui['CMMPB']
self.cmmd1[i] = ui['CMMD1']
self.cmmd2[i] = ui['CMMD2']
self.cslit[i] = ui['CSLIT']
# species-specific resp and scour parms - table type benal-resscr
self.balr20[i] = ui['BALR20'] * self.delt60
self.tcbalr[i] = ui['TCBALR']
self.cslof1[i] = ui['CSLOF1'] * self.delt60
self.cslof2[i] = ui['CSLOF2']
self.grores[i] = ui['GRORES']
# grazing and disturbance parms - table-type benal-graze
self.cremvl = ui['CREMVL']
self.cmmbi = ui['CMMBI']
self.tcgraz = ui['TCGRAZ']
hrpyr = 8760.0 #constant
self.cremvl = (self.cremvl / self.cvpb) / hrpyr * self.delt60
if self.SDLTFG == 2: # turbidity regression parms - table-type benal-light
self.ctrbq1 = ui['CTRBQ1']
self.ctrbq2 = ui['CTRBQ2']
self.cktrb1 = ui['CKTRB1']
self.cktrb2 = ui['CKTRB2']
# table-type benal-riff1
self.frrif = ui['FRRIF']
self.cmmv = ui['CMMV']
self.rifcq1 = ui['RIFCQ1']
self.rifcq2 = ui['RIFCQ2']
self.rifcq3 = ui['RIFCQ3']
# table-type benal-riff2
self.rifvf = zeros(5); self.rifdf = zeros(5)
for i in range(1,5):
self.rifvf[i] = ui['RIFVF' + str(i)]
self.rifdf[i] = ui['RIFDF' + str(i)]
# table-type plnk-init
self.phyto = ui['PHYTO']
self.zoo = ui['ZOO']
#benal = ui['BENAL']
self.orn = ui['ORN']
self.orp = ui['ORP']
self.orc = ui['ORC']
# variable initialization:
if self.PHYFG == 0: # initialize fluxes of inactive constituent
self.rophyt = 0.0
self.ophyt[:] = 0.0 #nexits
self.phydox = self.phybod = 0.0
self.phytam = 0.0; self.phyno3 = 0.0; self.phypo4 = 0.0
self.phyorn = 0.0; self.phyorp = 0.0; self.phyorc = 0.0
self.pyco2 = 0.0
self.dthphy = 0.0; self.grophy = 0.0; self.totphy = 0.0
self.rozoo = 0.0
self.ozoo = zeros(nexits)
if self.ZOOFG == 1: # convert zoo to mg/l
self.zoo *= self.zomass
else: # zooplankton not simulated, but use default values
# initialize fluxes of inactive constituent
self.rozoo = 0.0
self.ozoo[:] = 0.0 #nexits
self.zoodox = 0.0; self.zoobod = 0.0
self.zootam = 0.0; self.zoono3 = 0.0; self.zoopo4 = 0.0
self.zooorn = 0.0; self.zooorp = 0.0; self.zooorc = 0.0
self.zoophy = 0.0
self.zoco2 = 0.0
self.grozoo = 0.0; self.dthzoo = 0.0; self.totzoo = 0.0
# benthic algae initialization:
self.benal = zeros(self.numbal)
self.flxbal = zeros((4,5))
if self.numbal == 1: # single species
self.benal[0] = ui['BENAL'] # points to table-type plnk-init above for rvals
elif self.numbal >= 2: # multiple species - table-type benal-init
for n in range(self.numbal):
self.benal[n] = ui['BENAL' + str(n+1)]
else: # no benthic algae simulated
self.baldox = 0.0; self.balbod = 0.0
self.baltam = 0.0; self.balno3 = 0.0; self.balpo4 = 0.0
self.balorn = 0.0; self.balorp = 0.0; self.balorc = 0.0
self.baco2 = 0.0
# compute derived quantities
self.phycla = self.phyto * self.cvbcl
self.balcla = zeros(self.numbal)
for i in range(self.numbal):
self.balcla[i] = self.benal[i] * self.cvbcl
self.lsnh4 = zeros(4)
self.lspo4 = zeros(4)
if self.vol > 0.0: # compute initial summary concentrations
for i in range(1, 4):
self.lsnh4[i] = NUTRX.rsnh4[i] / self.vol
self.lspo4[i] = NUTRX.rspo4[i] / self.vol
# calculate summary concentrations:
(self.torn, self.torp, self.torc, self.potbod, self.tn, self.tp) \
= self.pksums(NUTRX,self.phyto,self.zoo,self.orn,self.orp,self.orc,
NUTRX.no3,NUTRX.tam,NUTRX.no2,self.lsnh4,NUTRX.po4,self.lspo4,OXRX.bod)
return
def simulate(self, tw, phval, co2, tss, OXRX, NUTRX, iphyto, izoo, iorn, iorp, iorc,
wash, solrad, avdepe, avvele, depcor, ro, binv,
pladep_orn, pladep_orp, pladep_orc, advData):
''' '''
# hydraulics:
(nexits, vols, vol, srovol, erovol, sovol, eovol) = advData
self.vol = vol
# initialize temp. vars for DO/BOD and NUTRX states:
po4 = NUTRX.po4
no3 = NUTRX.no3
no2 = NUTRX.no2
tam = NUTRX.tam
dox = OXRX.dox
bod = OXRX.bod
self.co2 = co2
# inflows: convert from [mass/ivld] to [conc.*vol/ivld]
self.iphyto = iphyto / self.conv
self.izoo = izoo / self.conv
self.iorn = iorn / self.conv
self.iorp = iorp / self.conv
self.iorc = iorc / self.conv
#-----------------------------------------------------------
# advection:
#-----------------------------------------------------------
if self.PHYFG == 1:
# advect phytoplankton
(self.phyto, self.rophyt, self.ophyt) \
= self.advplk(self.iphyto,self.svol,srovol,self.vol,erovol,sovol,eovol,nexits,
self.oref,self.mxstay,self.seed,self.delts,self.phyto)
(self.phyto, snkphy) = sink(self.vol,avdepe,self.physet,self.phyto)
self.snkphy = -snkphy
if self.ZOOFG == 1: # zooplankton on; advect zooplankton
(self.zoo, self.rozoo, self.ozoo) \
= self.advplk(self.izoo,self.svol,srovol,vol,erovol,sovol,eovol,nexits,
self.oref,self.mxstay,self.seed,self.delts,self.zoo)
# advect organic nitrogen
inorn = self.iorn + pladep_orn
(self.orn,self.roorn,self.oorn) = advect (inorn, self.orn, nexits, self.svol, self.vol, srovol, erovol, sovol, eovol)
(self.orn, snkorn) = sink(self.vol, avdepe, self.refset, self.orn)
self.snkorn = -snkorn
# advect organic phosphorus
inorp = self.iorp + pladep_orp
(self.orp, self.roorp, self.oorp) = advect(inorp, self.orp, nexits, self.svol, self.vol, srovol, erovol, sovol, eovol)
(self.orp, snkorp) = sink(self.vol, avdepe, self.refset, self.orp)
self.snkorp = -snkorp
# advect total organic carbon
inorc = self.iorc + pladep_orc
(self.orc, self.roorc, self.oorc) = advect (inorc, self.orc, nexits, self.svol, self.vol, srovol, erovol, sovol, eovol)
(self.orc, snkorc) = sink(self.vol, avdepe, self.refset, self.orc)
self.snkorc = -snkorc
if avdepe > 0.17: # enough water to warrant computation of water quality reactions
if self.BALFG > 0:
if self.frrif < 1.0:
# make adjustments to average water velocity and depth for the
# portion of the reach that consists of riffle areas.
if ro < self.rifcq1: # below first cutoff flow
i= 1
elif ro < self.rifcq2: # below second cutoff flow
i= 2
elif ro < self.rifcq3: # below third cutoff flow
i= 3
else: # above third cutoff flow
i= 4
# calculate the adjusted velocity and depth for riffle sections
self.balvel = self.rifvf[i] * avvele
self.baldep = self.rifdf[i] * avdepe
else: # use full depth and velocity
self.balvel = avvele
self.baldep = avdepe
else:
self.balvel = 0.0
self.baldep = 0.0
# calculate solar radiation absorbed; solrad is the solar radiation at gage,
# corrected for location of reach; 0.97 accounts for surface reflection
# (assumed 3 per cent); cfsaex is the ratio of radiation incident to water
# surface to gage radiation values (accounts for regional differences, shading
# of water surface, etc); inlit is a measure of light intensity immediately below
# surface of reach/res and is expressed as ly/min, adjusted for fraction that is
# photosynthetically active.
inlit = 0.97 * self.cfsaex * solrad / self.delt * self.paradf
extsed = 0.0
if self.SDLTFG == 1: # estimate contribution of sediment to light extinction
extsed = self.litsed * tss
elif self.SDLTFG == 2: # equations from dssamt for estimating the extinction coefficient based on discharge and turbidity
# estimate turbidity based on linear regression on flow
turb = self.ctrbq1 * ro**self.ctrbq2
# estimate the portion of the extinction coefficient due to
# sediment based upon a system-wide regression of total
# extinction to turbidity, and then subtracting the
# base extinction coefficient
extsed = (self.cktrb1 * turb**self.cktrb2) - self.extb
if extsed < 0.0: # no effective sediment shading
extsed = 0.0
else: # sediment light extinction not considered
extsed = 0.0
# calculate contribution of phytoplankton to light extinction (self-shading)
extcla = 0.00452 * self.phyto * self.cvbcl
# calculate light available for algal growth, litrch only called here
(self.phylit, self.ballit, self.cflit) = self.litrch (inlit,self.extb,extcla,extsed,avdepe,self.baldep,self.PHYFG,self.BALFG)
#-----------------------------------------------------------
# sestonic algae growth & respiration
#-----------------------------------------------------------
if self.PHYFG == 1: # simulate phytoplankton, phyrx only called here
(po4,no3,tam,dox,self.orn,self.orp,self.orc,bod,self.phyto,self.limphy,self.pyco2,self.phycla,
dophy,bodphy,tamphy,no3phy,po4phy,phdth,phgro,ornphy,orpphy,orcphy) \
= self.phyrx(self.phylit,tw,self.talgrl,self.talgrh,self.talgrm,self.malgr,self.cmmp, \
self.cmmnp,NUTRX.TAMFG,self.AMRFG,self.NSFG,self.cmmn,self.cmmlt,self.delt60, \
self.cflit,self.alr20,self.cvbpn,self.PHFG,self.DECFG,self.cvbpc,self.paldh, \
self.naldh,self.claldh,self.aldl,self.aldh,NUTRX.anaer,self.oxald,self.alnpr, \
self.cvbo,self.refr,self.cvnrbo,self.cvpb,self.cvbcl,self.co2, \
self.nmingr,self.pmingr,self.cmingr,self.lmingr,self.nminc, \
po4,no3,tam,dox,self.orn,self.orp,self.orc,bod,self.phyto)
# compute associated fluxes
self.phydox = dophy * self.vol
self.phybod = bodphy * self.vol
self.phytam = tamphy * self.vol
self.phyno3 = no3phy * self.vol
self.phypo4 = po4phy * self.vol
self.dthphy = -phdth * self.vol
self.grophy = phgro * self.vol
self.phyorn = ornphy * self.vol
self.phyorp = orpphy * self.vol
self.phyorc = orcphy * self.vol
#-----------------------------------------------------------
# zooplankton growth & death:
#-----------------------------------------------------------
if self.ZOOFG == 1: # simulate zooplankton, zorx only called here
(dox,bod,self.zoo,self.orn,self.orp,self.orc,tam,no3,po4,zeat,self.zoco2,dozoo,bodzoo,nitzoo,po4zoo,zgro,zdth,zorn,zorp,zorc) \
= self.zorx(self.zfil20,self.tczfil,tw,self.phyto,self.mzoeat,self.zexdel,self.cvpb, \
self.zres20,self.tczres,NUTRX.anaer,self.zomass,NUTRX.TAMFG,self.refr, \
self.ZFOOD,self.zd,self.oxzd,self.cvbn,self.cvbp,self.cvbc,self.cvnrbo,self.cvbo, \
dox,bod,self.zoo,self.orn,self.orp,self.orc,tam,no3,po4)
# compute associated fluxes
self.zoodox = -dozoo * self.vol
self.zoobod = bodzoo * self.vol
if NUTRX.TAMFG != 0: # ammonia on, so nitrogen excretion goes to ammonia
self.zootam = nitzoo * self.vol
self.zoono3 = 0.0
else: # ammonia off, so nitrogen excretion goes to nitrate
self.zoono3 = nitzoo * self.vol
self.zootam = 0.0
self.zoopo4 = po4zoo * self.vol
self.zoophy = -zeat * self.vol
self.zooorn = zorn * self.vol
self.zooorp = zorp * self.vol
self.zooorc = zorc * self.vol
self.grozoo = zgro * self.vol
self.dthzoo = -zdth * self.vol
self.totzoo = self.grozoo + self.dthzoo
# update phytoplankton state variable to account for zooplankton predation
self.phyto = self.phyto - zeat
# convert phytoplankton expressed as mg biomass/l to chlorophyll a expressed as ug/l
self.phycla = self.phyto * self.cvbcl
self.totphy = self.snkphy + self.zoophy + self.dthphy + self.grophy
#-----------------------------------------------------------
# benthic algae growth & respiration
#-----------------------------------------------------------
self.limbal = zeros(self.numbal, dtype=np.int32)
if self.BALFG > 0:
bgro = zeros(self.numbal)
bdth = zeros(self.numbal)
if self.BALFG == 1: # simulate benthic algae
(po4,no3,tam,dox,self.orn,self.orp,self.orc,bod,self.benal[0],self.limbal[0],self.baco2,self.balcla[0],
dobalg,bodbal,tambal,no3bal,po4bal,bgro[0],bdth[0],ornbal,orpbal,orcbal) \
= self.balrx(self.ballit,tw,self.talgrl,self.talgrh,self.talgrm,self.malgr,self.cmmp, \
self.cmmnp,NUTRX.TAMFG,self.AMRFG,self.NSFG,self.cmmn,self.cmmlt,self.delt60, \
self.cflit,self.alr20,self.cvbpn,self.PHFG,self.DECFG,self.cvbpc,self.paldh, \
self.naldh,self.aldl,self.aldh,NUTRX.anaer,self.oxald,self.cfbalg,self.cfbalr, \
self.alnpr,self.cvbo,self.refr,self.cvnrbo,self.cvpb,self.mbal,depcor, \
self.cvbcl,self.co2,self.nmingr,self.pmingr,self.cmingr,self.lmingr,self.nminc, \
po4,no3,tam,dox,self.orn,self.orp,self.orc,bod,self.benal[0])
elif self.BALFG == 2: # simulate enhanced benthic algae equations from dssamt (!)
# then perform reactions, balrx2 only called here
(po4,no3,tam,dox,self.orn,self.orp,self.orc,bod,self.benal,self.limbal,self.baco2,self.balcla,
dobalg,bodbal,tambal,no3bal,po4bal,bgro,bdth,ornbal,orpbal,orcbal) \
= self.balrx2 (self.ballit,tw,NUTRX.TAMFG,self.NSFG,self.delt60,self.cvbpn,self.PHFG,self.DECFG, \
self.cvbpc,self.alnpr,self.cvbo,self.refr,self.cvnrbo,self.cvpb,depcor, \
self.cvbcl,co2,self.numbal,self.mbalgr,self.cmmpb,self.cmmnb, \
self.balr20,self.tcbalg,self.balvel,self.cmmv,self.BFIXFG,self.cslit,self.cmmd1, \
self.cmmd2,self.tcbalr,self.frrif,self.cremvl,self.cmmbi,binv,self.tcgraz, \
self.cslof1,self.cslof2,self.minbal,self.fravl,self.BNPFG,self.campr,self.nmingr, \
self.pmingr,self.cmingr,self.lmingr,self.nminc,self.nmaxfx,self.grores, \
po4,no3,tam,dox,self.orn,self.orp,self.orc,bod,self.benal)
#compute associated fluxes
self.baldox = dobalg * self.vol
self.balbod = bodbal * self.vol
self.baltam = tambal * self.vol
self.balno3 = no3bal * self.vol
self.balpo4 = po4bal * self.vol
self.balorn = ornbal * self.vol
self.balorp = orpbal * self.vol
self.balorc = orcbal * self.vol
self.grobal = zeros(self.numbal)
self.dthbal = zeros(self.numbal)
for i in range(self.numbal):
self.grobal[i] = bgro[i]
self.dthbal[i] = -bdth[i]
else: # not enough water in reach/res to warrant simulation of quality processes
self.phyorn = 0.0
self.balorn = 0.0
self.zooorn = 0.0
self.phyorp = 0.0
self.balorp = 0.0
self.zooorp = 0.0
self.phyorc = 0.0
self.balorc = 0.0
self.zooorc = 0.0
self.pyco2 = 0.0
self.baco2 = 0.0
self.zoco2 = 0.0
self.phydox = 0.0
self.zoodox = 0.0
self.baldox = 0.0
self.phybod = 0.0
self.zoobod = 0.0
self.balbod = 0.0
self.phytam = 0.0
self.zootam = 0.0
self.baltam = 0.0
self.phyno3 = 0.0
self.zoono3 = 0.0
self.balno3 = 0.0
self.phypo4 = 0.0
self.zoopo4 = 0.0
self.balpo4 = 0.0
if self.PHYFG == 1: # water scarcity limits phytoplankton growth
self.limphy = 1 #'WAT'
self.phycla = self.phyto * self.cvbcl
self.grophy = 0.0
self.dthphy = 0.0
self.zoophy = 0.0
self.totphy = self.snkphy
if self.BALFG > 0: # water scarcity limits benthic algae growth
limc = 1 #'WAT'
self.limbal = zeros(self.numbal, dtype=np.int32)
self.balcla = zeros(self.numbal)
self.grobal = zeros(self.numbal)
self.dthbal = zeros(self.numbal)
for i in range(self.numbal):
self.balcla[i] = self.benal[i] * self.cvbcl
self.limbal[i] = limc
if self.ZOOFG == 1: # water scarcity limits zooplankton growth
self.grozoo= 0.0
self.dthzoo= 0.0
self.totzoo= 0.0
#-----------------------------------------------------------
# store final benthic sums and fluxes
#-----------------------------------------------------------
if self.BALFG > 0:
self.tbenal = zeros(3)
self.grotba = 0.0
self.dthtba = 0.0
for i in range(self.numbal):
self.flxbal[1,i] = self.grobal[i]
self.flxbal[2,i] = self.dthbal[i]
self.flxbal[3,i] = self.grobal[i] + self.dthbal[i]
self.tbenal[1] += self.benal[i]
self.grotba += self.grobal[i]
self.dthtba += self.dthbal[i]
self.tbenal[2] = self.tbenal[1] * self.cvbcl
self.tottba = self.grotba + self.dthtba
#-----------------------------------------------------------
# compute final process fluxes for oxygen, nutrients and organics
#-----------------------------------------------------------
self.totdox = OXRX.readox + OXRX.boddox + OXRX.bendox + NUTRX.nitdox + self.phydox + self.zoodox + self.baldox
self.totbod = OXRX.decbod + OXRX.bnrbod + OXRX.snkbod + NUTRX.denbod + self.phybod + self.zoobod + self.balbod
self.totno3 = NUTRX.nitno3 + NUTRX.denno3 + NUTRX.bodno3 + self.phyno3 + self.zoono3 + self.balno3
self.tottam = NUTRX.nittam + NUTRX.volnh3 + NUTRX.bnrtam + NUTRX.bodtam + self.phytam + self.zootam + self.baltam
self.totpo4 = NUTRX.bnrpo4 + NUTRX.bodpo4 + self.phypo4 + self.zoopo4 + self.balpo4
self.totorn = self.snkorn + self.phyorn + self.zooorn + self.balorn
self.totorp = self.snkorp + self.phyorp + self.zooorp + self.balorp
self.totorc = self.snkorc + self.phyorc + self.zooorc + self.balorc
#-----------------------------------------------------------
# compute summaries of total organics, total n and p, and potbod
#-----------------------------------------------------------
# concentrations:
if self.vol > 0.0:
for i in range(1, 4):
self.lsnh4[i] = NUTRX.rsnh4[i] / self.vol
self.lspo4[i] = NUTRX.rspo4[i] / self.vol
(self.torn, self.torp, self.torc, self.potbod, self.tn, self.tp) \
= self.pksums(NUTRX,self.phyto,self.zoo,self.orn,self.orp,self.orc,
no3,tam,no2,self.lsnh4,po4,self.lspo4,bod)
else:
self.torn = -1.0e30
self.torp = -1.0e30
self.torc = -1.0e30
self.potbod = -1.0e30
self.tn = -1.0e30
self.tp = -1.0e30
(self.itorn, self.itorp, self.itorc, dumval, self.itotn, self.itotp) \
= self.pksums(NUTRX,self.iphyto,self.izoo,self.iorn,self.iorp,self.iorc,
NUTRX.ino3,NUTRX.itam,NUTRX.ino2,NUTRX.isnh4,NUTRX.ipo4,NUTRX.ispo4,OXRX.ibod)
# total outflows:
(self.rotorn, self.rotorp, self.rotorc, dumval, self.rototn, self.rototp) \
= self.pksums(NUTRX,self.rophyt,self.rozoo,self.roorn,self.roorp,self.roorc,
NUTRX.rono3,NUTRX.rotam,NUTRX.rono2,NUTRX.rosnh4,NUTRX.ropo4,NUTRX.rospo4,OXRX.robod)
# outflows by exit:
self.otorn = zeros(nexits); self.otorp = zeros(nexits); self.otorc = zeros(nexits)
self.ototn = zeros(nexits); self.ototp = zeros(nexits)
if nexits > 1:
for i in range(nexits):
(self.otorn[i], self.otorp[i], self.otorc[i], dumval, self.ototn[i], self.ototp[i]) \
= self.pksums(NUTRX,self.ophyt[i],self.ozoo[i],self.oorn[i],self.oorp[i],self.oorc[i],
NUTRX.ono3[i],NUTRX.otam[i],NUTRX.ono2[i],NUTRX.osnh4[i],NUTRX.opo4[i],NUTRX.ospo4[i],OXRX.obod[i])
#-----------------------------------------------------------
# update DO/BOD and nutrient states (for OXRX/NUTRX):
#-----------------------------------------------------------
OXRX.dox = dox
OXRX.bod = bod
NUTRX.po4 = po4
NUTRX.no3 = no3
NUTRX.no2 = no2
NUTRX.tam = tam
# redistribute TAM after algal influence:
(NUTRX.nh3,NUTRX.nh4) = NUTRX.ammion(tw, phval, tam)
self.svol = self.vol # svol is volume at start of time step, update for next time thru
return OXRX, NUTRX
@staticmethod
def advplk(iplank,vols,srovol,vol,erovol,sovol,eovol,nexits,oref,mxstay,seed,delts,plank):
''' advect plankton'''
# calculate concentration of plankton not subject to advection during interval
oflo = (srovol + erovol) / delts
if oref > 0.0 and oflo / oref <= 100.0:
stay = (mxstay - seed) * (2.0**(-oflo / oref)) + seed
else:
stay = seed
if plank > stay:
# convert stay to units of mass; this mass will be converted
# back to units of concentration based on the volume of the
# reach/res at the end of the interval
mstay = stay * vols
# determine concentration of plankton subject to advection;
# this value is passed into subroutine advect
plnkad = plank - stay
# advect plankton
(plnkad, roplk, oplk) = advect(iplank,plnkad,nexits,vols,vol,srovol,erovol,sovol,eovol)
# determine final concentration of plankton in reach/res after advection
plank = plnkad + mstay / vol if vol > 0.0 else plnkad
else: # no plankton leaves the reach/res
roplk = 0.0
oplk = zeros(nexits)
mstay = plank * vols
plank = (mstay + iplank) / vol if vol > 0.0 else -1.0e30
return plank, roplk, oplk
@staticmethod
def algro(light,po4,no3,tw,talgrl,talgrh,talgrm,malgr, cmmp,cmmnp,
TAMFG,AMRFG,tam,NSFG,cmmn,cmmlt,alr20,cflit,delt60,
nmingr,pmingr,lmingr):
''' calculate unit growth and respiration rates for algae
population; both are expressed in units of per interval'''
lim = -999
if light > lmingr: # sufficient light to support growth
if po4 > pmingr and no3 > nmingr: # sufficient nutrients to support growth
if talgrh > tw > talgrl: # water temperature allows growth
if tw < talgrm: # calculate temperature correction fraction
tcmalg = (tw - talgrl) / (talgrm - talgrl)
else:
# no temperature correction to maximum unit growth rate
# is necessary; water temperature is in the optimum
# range for phytoplankton growth
tcmalg = 1.0
# perform temperature correction to maximum unit growth
# rate; units of malgrt are per interval
malgrt = malgr * tcmalg
# calculate maximum phosphorus limited unit growth rate
grop = malgrt * po4 * no3 / ((po4 + cmmp) * (no3 + cmmnp))
# calculate the maximum nitrogen limited unit growth rate
if TAMFG: # consider influence of tam on growth rate
if AMRFG: # calculate tam retardation to nitrogen limited growth rate
malgn = malgrt - 0.757 * tam + 0.051 * no3
# check that calculated unit growth rate does not
# exceed maximum allowable growth rate
if malgn > malgrt:
malgn = malgrt
else:
# check that calculated unit growth rate is not
# less than .001 of the maximum unit growth rate;
# if it is, set the unit growth rate equal to .001
# of the maximum unit growth rate
lolim = 0.001 * malgrt
if malgn < lolim:
malgn = lolim
else: # ammonia retardation is not considered
malgn = malgrt
if NSFG: # include tam in nitrogen pool for calculation of nitrogen limited growth rate
mmn = no3 + tam
else: # tam is not included in nitrogen pool for calculation of nitrogen limited growth
mmn = no3
else: # tam is not simulated