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NUTRX_Class.py
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import numpy as np
from numpy import zeros, array
from math import log
import numba as nb
from numba.experimental import jitclass
from HSP2.ADCALC import advect
from HSP2.RQUTIL import sink, decbal, benth
from HSP2.OXRX_Class import OXRX_Class
from HSP2.utilities import make_numba_dict, initm
spec = [
('adnh4', nb.float64[:]),
('ADNHFG', nb.int32),
('adnhpm', nb.float64[:]),
('adpo4', nb.float64[:]),
('ADPOFG', nb.int32),
('adpopm', nb.float64[:]),
('AFACT', nb.float64),
('AMVFG', nb.int32),
('anaer', nb.float64),
('benpo4', nb.float64),
('BENRFG', nb.int32),
('bentam', nb.float64),
('bnh4', nb.float64[:]),
('bnrpo4', nb.float64),
('bnrpo4', nb.float64),
('bnrtam', nb.float64),
('bnrtam', nb.float64),
('bodno3', nb.float64),
('bodpo4', nb.float64),
('bodtam', nb.float64),
('bpcntc', nb.float64),
('bpo4', nb.float64[:]),
('brpo4', nb.float64[:]),
('brtam', nb.float64[:]),
('conv', nb.float64),
('cvbn', nb.float64),
('cvbo', nb.float64),
('cvbp', nb.float64),
('cvbpc', nb.float64),
('cvbpn', nb.float64),
('cvoc', nb.float64),
('cvon', nb.float64),
('cvop', nb.float64),
('decco2', nb.float64),
('decnit', nb.float64),
('decpo4', nb.float64),
('delt60', nb.float64),
('delts', nb.float64),
('denbod', nb.float64),
('DENFG', nb.int32),
('denno3', nb.float64),
('denoxt', nb.float64),
('dnust', nb.float64[:]),
('dnust2', nb.float64[:]),
('dsnh4', nb.float64[:]),
('dspo4', nb.float64[:]),
('errors', nb.int64[:]),
('expnvg', nb.float64),
('expnvl', nb.float64),
('ino2', nb.float64),
('ino3', nb.float64),
('ipo4', nb.float64),
('isnh4', nb.float64[:]),
('ispo4', nb.float64[:]),
('itam', nb.float64),
('kno220', nb.float64),
('kno320', nb.float64),
('ktam20', nb.float64),
('nexits', nb.int32),
('nh3', nb.float64),
('nh3vlt', nb.float64),
('nh4', nb.float64),
('nitdox', nb.float64),
('nitno2', nb.float64),
('nitno3', nb.float64),
('nittam', nb.float64),
('no2', nb.float64),
('NO2FG', nb.int32),
('no3', nb.float64),
('nucf1', nb.float64[:]),
('nucf2', nb.float64[:,:]),
('nucf3', nb.float64[:,:]),
('nucf4', nb.float64[:]),
('nucf5', nb.float64[:]),
('nucf6', nb.float64[:]),
('nucf7', nb.float64[:]),
('nucf8', nb.float64[:,:]),
('nuecnt', nb.float64[:]),
('nust', nb.float64[:,:]),
('ono2', nb.float64[:]),
('ono3', nb.float64[:]),
('opo4', nb.float64[:]),
('osnh4', nb.float64[:,:]),
('ospo4', nb.float64[:,:]),
('otam', nb.float64[:]),
('PHFLAG', nb.int32),
('phval', nb.float64),
('phvalm', nb.float64),
('PLKFG', nb.int32),
('po4', nb.float64),
('PO4FG', nb.int32),
('rnh3', nb.float64),
('rnh4', nb.float64),
('rno2', nb.float64),
('rno3', nb.float64),
('rono2', nb.float64),
('rono3', nb.float64),
('ropo4', nb.float64),
('rosnh4', nb.float64[:]),
('rospo4', nb.float64[:]),
('rotam', nb.float64),
('rpo4', nb.float64),
('rrno2', nb.float64),
('rrno3', nb.float64),
('rrpo4', nb.float64),
('rrtam', nb.float64),
('rsed', nb.float64[:]),
('RSED1', nb.float64[:]),
('RSED2', nb.float64[:]),
('RSED3', nb.float64[:]),
('RSED4', nb.float64[:]),
('RSED5', nb.float64[:]),
('RSED6', nb.float64[:]),
('RSED7', nb.float64[:]),
('rsnh4', nb.float64[:]),
('rspo4', nb.float64[:]),
('rtam', nb.float64),
('SEDFG', nb.int32),
('simlen', nb.int32),
('snh4', nb.float64[:]),
('spo4', nb.float64[:]),
('svol', nb.float64),
('tam', nb.float64),
('TAMFG', nb.int32),
('tcden', nb.float64),
('tcnit', nb.float64),
('tnucf1', nb.float64[:]),
('tnucf2', nb.float64[:,:]),
('tnuif', nb.float64[:]),
('totno3', nb.float64),
('totpo4', nb.float64),
('tottam', nb.float64),
('uunits', nb.int32),
('vol', nb.float64),
('volnh3', nb.float64)
]
@jitclass(spec)
class NUTRX_Class:
#-------------------------------------------------------------------
# class initialization:
#-------------------------------------------------------------------
def __init__(self, siminfo, nexits, vol, ui_rq, ui, ts, OXRX):
''' Initialize instance variables for nutrient simulation '''
self.errors = zeros(int(ui['errlen']), dtype=np.int64)
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
# table-type nut-flags
self.TAMFG = int(ui['NH3FG'])
self.NO2FG = int(ui['NO2FG'])
self.PO4FG = int(ui['PO4FG'])
self.AMVFG = int(ui['AMVFG'])
self.DENFG = int(ui['DENFG'])
self.ADNHFG = int(ui['ADNHFG'])
self.ADPOFG = int(ui['ADPOFG'])
self.PHFLAG = int(ui['PHFLAG'])
self.PLKFG = int(ui_rq['PLKFG'])
self.SEDFG = int(ui_rq['SEDFG'])
self.BENRFG = int(ui_rq['BENRFG'])
# error handling:
if self.TAMFG == 0 and (self.AMVFG == 1 or self.ADNHFG == 1):
self.errors[0] += 1
# ERRMSG: tam is not being simulated and nh3 volat. or
# nh4 adsorption is being simulated
if (self.PO4FG == 0 and self.ADPOFG == 1):
self.errors[1] += 1
# ERRMSG: po4 is not being simulated, and
# po4 adsorption is being simulated
if (self.ADNHFG == 1 or self.ADPOFG == 1) and self.SEDFG == 0:
self.errors[2] += 1
# ERRMSG: sediment associated nh4 and/or po4 is being simulated,but sediment is not being simulated in section sedtrn
# conversion factors - table-type conv-val1
self.cvbo = ui['CVBO']
self.cvbpc = ui['CVBPC']
self.cvbpn = ui['CVBPN']
self.bpcntc = ui['BPCNTC']
# calculate derived values
self.cvbp = (31.0 * self.bpcntc) / (1200.0 * self.cvbpc)
self.cvbn = 14.0 * self.cvbpn * self.cvbp / 31.0
self.cvoc = self.bpcntc / (100.0 * self.cvbo)
self.cvon = self.cvbn / self.cvbo
self.cvop = self.cvbp / self.cvbo
# benthic release parameters - table-type nut-benparm
self.anaer = ui['ANAER']
self.brtam = zeros(2)
self.brpo4 = zeros(2)
if self.BENRFG == 1 or self.PLKFG == 1: # benthal release parms - table-type nut-benparm
self.brtam[0] = ui['BRNIT1'] * delt60 # convert units from 1/hr to 1/ivl
self.brtam[1] = ui['BRNIT2'] * delt60 # convert units from 1/hr to 1/ivl
self.brpo4[0] = ui['BRPO41'] * delt60 # convert units from 1/hr to 1/ivl
self.brpo4[1] = ui['BRPO42'] * delt60 # convert units from 1/hr to 1/ivl
self.bnrtam = 0.0
self.bnrpo4 = 0.0
# nitrification parameters - table-type nut-nitdenit
self.ktam20 = ui['KTAM20'] * delt60 # convert units from 1/hr to 1/ivl
self.kno220 = ui['KNO220'] * delt60 # convert units from 1/hr to 1/ivl
self.tcnit = ui['TCNIT']
self.kno320 = ui['KNO320'] * delt60 # convert units from 1/hr to 1/ivl
self.tcden = ui['TCDEN']
self.denoxt = ui['DENOXT']
if self.TAMFG == 1 and self.AMVFG == 1: # ammonia volatilization parameters table nut-nh3volat
self.expnvg = ui['EXPNVG']
self.expnvl = ui['EXPNVL']
if self.TAMFG == 1 and self.PHFLAG == 3: # monthly ph values table mon-phval, not in RCHRES.SEQ
self.phvalm = ui['PHVALM']
#self.nupm3 = zeros(7)
self.rsnh4 = zeros(13)
self.rspo4 = zeros(13)
# sediment mass storages:
self.RSED1 = zeros(self.simlen); self.RSED2 = zeros(self.simlen)
self.RSED3 = zeros(self.simlen); self.RSED4 = zeros(self.simlen)
self.RSED5 = zeros(self.simlen); self.RSED6 = zeros(self.simlen)
if 'RSED1' in ts: self.RSED1 = ts['RSED1']
if 'RSED2' in ts: self.RSED2 = ts['RSED2']
if 'RSED3' in ts: self.RSED3 = ts['RSED3']
if 'RSED4' in ts: self.RSED4 = ts['RSED4']
if 'RSED5' in ts: self.RSED5 = ts['RSED5']
if 'RSED6' in ts: self.RSED6 = ts['RSED6']
if 'RSED7' in ts: self.RSED7 = ts['RSED7']
self.rsed = zeros(8)
cf = 3.121e-8 if self.uunits == 1 else 1.00e-6
if self.SEDFG:
self.rsed[1] = ui_rq['SSED1'] * self.vol
self.rsed[2] = ui_rq['SSED2'] * self.vol
self.rsed[3] = ui_rq['SSED3'] * self.vol
self.rsed[4] = self.rsed[1] + self.rsed[2] + self.rsed[3]
self.rsed[5] = self.RSED5[0] / cf
self.rsed[6] = self.RSED6[0] / cf
self.rsed[7] = self.RSED7[0] / cf
# bed sediment concentrations of nh4 and po4 - table nut-bedconc, not in RCHRES.SEQ
# initialize constant bed concentrations (NH4, PO4)
# (convert concentrations from mg/kg to internal units of mg/mg)
self.bnh4 = zeros(4); self.bpo4 = zeros(4)
for i in range(1, 4):
key = 'BNH4' + str(i)
if key in ui: self.bnh4[i] = ui[key] / 1.0e6
key = 'BPO4' + str(i)
if key in ui: self.bpo4[i] = ui[key] / 1.0e6
self.adnhpm = zeros(4); self.adpopm = zeros(4)
if (self.TAMFG == 1 and self.ADNHFG == 1) or (self.PO4FG == 1 and self.ADPOFG == 1):
#self.nupm3[:] = ui['NUPM3'] / 1.0E6 # convert concentrations from mg/kg to internal units of mg/mg
# initialize adsorbed nutrient mass storages in bed
self.rsnh4[8] = 0.0
self.rspo4[8] = 0.0
for i in range(5, 8):
self.rsnh4[i] = self.bnh4[i-4] * self.rsed[i]
self.rspo4[i] = self.bpo4[i-4] * self.rsed[i]
self.rsnh4[8] += self.rsnh4[i]
self.rspo4[8] += self.rspo4[i]
# adsorption parameters - table-type nut-adsparm
for i in range(1, 4):
self.adnhpm[i] = ui['ADNHPM' + str(i)] / 1.0e6
self.adpopm[i] = ui['ADPOPM' + str(i)] / 1.0e6
# initial conditions - table-type nut-dinit
self.dnust = zeros(7); self.dnust2 = zeros(7)
self.dnust[1] = ui['NO3']; self.dnust2[1] = self.dnust[1] * self.vol
self.dnust[2] = ui['TAM']; self.dnust2[2] = self.dnust[2] * self.vol
self.dnust[3] = ui['NO2']; self.dnust2[3] = self.dnust[3] * self.vol
self.dnust[4] = ui['PO4']; self.dnust2[4] = self.dnust[4] * self.vol
self.phval = 0.0
if self.TAMFG == 1: # do the tam-associated initial values (nh4 nh3 phval)
self.phval = ui['PHVAL']
# assume nh4 and nh3 are 0.99 x tam and 0.01 x tam respectively
self.dnust[5] = 0.99 * self.dnust[2]
self.dnust2[5] = self.dnust[5] * self.vol
self.dnust[6] = 0.01 * self.dnust[2]
self.dnust2[6] = self.dnust[6] * self.vol
self.snh4 = zeros(4)
self.spo4 = zeros(4)
if (self.TAMFG == 1 and self.ADNHFG == 1) or (self.PO4FG == 1 and self.ADPOFG == 1):
# suspended sediment concentrations of nh4 and po4 - table nut-adsinit
# (input concentrations are mg/kg - these are converted to mg/mg for
# internal computations)
for i in range(1, 4):
self.snh4[i] = ui['SNH4' + str(i)] / 1.0e6 # suspended nh4 (sand, silt, clay)
self.spo4[i] = ui['SPO4' + str(i)] / 1.0e6 # suspended po4 (sand, silt, clay)
# initialize adsorbed nutrient mass storages in suspension
self.rsnh4[4] = 0.0
self.rspo4[4] = 0.0
for i in range(1, 4):
self.rsnh4[i] = self.snh4[i] * self.rsed[i]
self.rspo4[i] = self.spo4[i] * self.rsed[i]
self.rsnh4[4] += self.rsnh4[i]
self.rspo4[4] += self.rspo4[i]
# initialize totals on sand, silt, clay, and grand total
self.rsnh4[9] = self.rsnh4[1] + self.rsnh4[5]
self.rsnh4[10] = self.rsnh4[2] + self.rsnh4[6]
self.rsnh4[11] = self.rsnh4[3] + self.rsnh4[7]
self.rsnh4[12] = self.rsnh4[4] + self.rsnh4[8]
self.rspo4[9] = self.rspo4[1] + self.rspo4[5]
self.rspo4[10] = self.rspo4[2] + self.rspo4[6]
self.rspo4[11] = self.rspo4[3] + self.rspo4[7]
self.rspo4[12] = self.rspo4[4] + self.rspo4[8]
# initialize total storages of nutrients in reach
self.nust = zeros((5,2))
self.nust[1,1] = self.dnust2[1]
self.nust[2,1] = self.dnust2[2]
if self.ADNHFG == 1:
self.nust[2,1] += self.rsnh4[4]
self.nust[3,1] = self.dnust2[3]
self.nust[4,1] = self.dnust2[4]
if self.ADPOFG == 1:
self.nust[4,1] += self.rspo4[4]
# initialize nutrient flux if nutrient is not simulated
self.otam = zeros(nexits); self.ono2 = zeros(nexits); self.opo4 = zeros(nexits)
self.rosnh4 = zeros(5); self.rospo4 = zeros(5)
self.dspo4 = zeros(5); self.dsnh4 = zeros(5)
self.adpo4 = zeros(5); self.adnh4 = zeros(5)
self.ospo4 = zeros((nexits, 5)); self.osnh4 = zeros((nexits, 5))
self.nucf1 = zeros(5)
self.nucf4 = zeros(8)
self.nucf5 = zeros(9)
self.nucf6 = zeros(2)
self.nucf7 = zeros(7)
self.nucf2 = zeros((5,3))
self.nucf3 = zeros((5,3))
self.nucf8 = zeros((5,3))
self.tnucf1 = zeros(5)
self.tnucf2 = zeros((nexits,5))
self.tnuif = zeros(5)
# initialize outflow variables:
self.rono3 = 0.0; self.ono3 = zeros(nexits)
self.rotam = 0.0; self.otam = zeros(nexits)
self.rono2 = 0.0; self.ono2 = zeros(nexits)
self.ropo4 = 0.0; self.opo4 = zeros(nexits)
# initialize process variables:
self.decnit = 0.0; self.decpo4 = 0.0; self.decco2 = 0.0
self.nitdox = 0.0; self.denbod = 0.0; self.nittam = 0.0
self.bnrtam = 0.0; self.volnh3 = 0.0; self.bodtam = 0.0
self.nitno2 = 0.0; self.nitno3 = 0.0; self.denno3 = 0.0
self.bodno3 = 0.0
self.bnrpo4 = self.bodpo4 = 0.0
self.nh3vlt = 0.0
self.nuecnt = zeros(4)
# initialize nutrient states:
self.no3 = ui['NO3']
self.tam = ui['TAM']
self.no2 = ui['NO2']
self.po4 = ui['PO4']
self.nh3 = 0.01 * self.tam
self.nh4 = 0.99 * self.tam
# initialize total nutrient masses:
self.update_mass()
return
def simulate(self, loop, tw, wind, phval, OXRX, ino3, itam, ino2, ipo4, isnh4, ispo4,
scrfac, avdepe, depcor, sed_depscr, sed_rosed, sed_osed,
nuadep_no3, nuadep_nh3, nuadep_po4, advectData):
''' Determine primary inorganic nitrogen and phosphorus balances'''
# hydraulics:
(nexits, vols, vol, srovol, erovol, sovol, eovol) = advectData
self.vol = vol
# inflows: convert from [mass/ivld] to [conc.*vol/ivld]
self.ino3 = ino3 / self.conv
self.itam = itam / self.conv
self.ino2 = ino2 / self.conv
self.ipo4 = ipo4 / self.conv
self.isnh4 = isnh4 / self.conv
self.ispo4 = ispo4 / self.conv
# advect nitrate
self.tnuif[1] = self.ino3
inno3 = self.ino3 + nuadep_no3
self.no3, self.rono3, self.ono3 = \
advect(inno3, self.no3, nexits, self.svol, self.vol, srovol, erovol, sovol, eovol)
self.tnucf1[1] = self.rono3
if self.nexits > 1:
self.tnucf2[:,1] = self.ono3[:] # nexits
# advect total ammonia:
if self.TAMFG == 1:
intam = self.itam + nuadep_nh3
self.tam, self.rotam, self.otam = \
advect(intam, self.tam, nexits, self.svol, self.vol, srovol, erovol, sovol, eovol)
self.tnucf1[2] = self.rotam
if self.nexits > 1:
self.tnucf2[:,2] = self.otam[:]
# advect nitrite:
if self.NO2FG == 1:
self.tnuif[3] = self.ino2
self.no2, self.rono2, self.ono2 = \
advect(self.ino2, self.no2, nexits, self.svol, self.vol, srovol, erovol, sovol, eovol)
self.tnucf1[3] = self.rono2
if self.nexits > 1:
self.tnucf2[:,3] = self.ono2[:] # nexits
# advect dissolved PO4:
if self.PO4FG == 1:
inpo4 = self.ipo4 + nuadep_po4
self.po4, self.ropo4, self.opo4 = advect(inpo4,self.po4, nexits, self.svol, self.vol, srovol, erovol, sovol, eovol)
# sediment variables (require unit conversion):
self.rsed = zeros(8)
rosed = zeros(4)
osed = zeros((self.nexits,4))
depscr = zeros(4)
cf = 3.121e-8 if self.uunits == 1 else 1.00e-6
if self.SEDFG:
self.rsed[1] = self.RSED1[loop] / cf
self.rsed[2] = self.RSED2[loop] / cf
self.rsed[3] = self.RSED3[loop] / cf
self.rsed[4] = self.RSED4[loop] / cf
self.rsed[5] = self.RSED5[loop] / cf
self.rsed[6] = self.RSED6[loop] / cf
self.rsed[7] = self.RSED7[loop] / cf
for j in range(1, 4):
rosed[j] = sed_rosed[j] / cf
depscr[j] = sed_depscr[j] / cf
for i in range(nexits):
osed[i,j] = sed_osed[i,j] / cf
# advect adsorbed PO4:
if self.PO4FG == 1 and self.ADPOFG == 1:
# zero the accumulators
self.ispo4[4] = 0.0
self.dspo4[4] = 0.0
self.rospo4[4] = 0.0
if self.nexits > 1:
self.ospo4[:,4] = 0.0 # nexits
# repeat for each sediment fraction (LTI)
for j in range(1, 4): # get data on sediment-associated phosphate
osed_ = osed[:,j] # all exits for sed class "j"
ospo4_ = zeros(nexits)
(self.spo4[j], self.dspo4[j], self.rospo4[j], ospo4_) \
= self.advnut(self.ispo4[j],self.rsed[j],self.rsed[j+4],depscr[j],rosed[j],osed_,self.nexits,
self.rspo4[j],self.rspo4[j + 4],self.bpo4[j])
self.ospo4[:,j] = ospo4_
self.ispo4[4] += self.ispo4[j]
self.dspo4[4] += self.dspo4[j]
self.rospo4[4] += self.rospo4[j]
if self.nexits > 1:
self.ospo4[:,4] += self.ospo4[:,j] # nexits
self.tnuif[4] = self.ipo4 + self.ispo4[4]
self.tnucf1[4] = self.ropo4 + self.rospo4[4]
if self.nexits > 1:
self.tnucf2[:,4] = self.opo4[:]+ self.ospo4[:,4] # nexits
else: # no adsorbed fraction
self.tnuif[4] = self.ipo4
self.tnucf1[4] = self.ropo4
if self.nexits > 1:
self.tnucf2[:,4] = self.opo4[:]
# advect adsorbed ammonium
if self.TAMFG == 1 and self.ADNHFG == 1: # advect adsorbed ammonium
# zero the accumulators
self.isnh4[4] = 0.0;
self.dsnh4[4] = 0.0
self.rosnh4[4] = 0.0
if self.nexits > 1:
self.osnh4[:,4] = 0.0 # nexits
# repeat for each sediment fraction
for j in range(1, 4):
osed_ = osed[:,j] # all exits for sed class "j"
osnh4_ = zeros(nexits)
(self.snh4[j],self.dsnh4[j],self.rosnh4[j],osnh4_) \
= self.advnut(self.isnh4[j],self.rsed[j],self.rsed[j + 3],depscr[j],rosed[j],osed_,self.nexits,
self.rsnh4[j],self.rsnh4[j + 4],self.bnh4[j])
self.osnh4[:,j] = osnh4_
self.isnh4[4] += self.isnh4[j]
self.dsnh4[4] += self.dsnh4[j]
self.rosnh4[4] += self.rosnh4[j]
if self.nexits > 1:
self.osnh4[:,4] += self.osnh4[:,j] # nexits
self.tnuif[2] = self.itam + self.isnh4[4]
self.tnucf1[2] = self.rotam + self.rosnh4[4]
if self.nexits > 1:
self.tnucf2[:,2] = self.otam[:] + self.osnh4[:,4] # nexits
else: # no adsorbed fraction
self.tnuif[2] = self.itam
self.tnucf1[2] = self.rotam
if self.nexits > 1:
self.tnucf2[:,2] = self.otam[:] # nexits
# calculate ammonia ionization in water column
if self.TAMFG == 1:
# get ph values
# assign last computed value from RQUAL (i.e., via time series, monthly inputs, or constant):
if (phval >= 0.0):
self.phval = phval
# compute ammonia ionization
(self.nh3, self.nh4) = self.ammion(tw, self.phval, self.tam)
if avdepe > 0.17:
if self.BENRFG == 1:
# simulate benthal release of inorganic nitrogen and
# ortho-phosphorus; and compute associated fluxes
if self.TAMFG == 1:
(self.tam, self.bentam) = benth(OXRX.dox,self.anaer,self.brtam,scrfac,depcor,self.tam)
self.bnrtam = self.bentam * self.vol
if self.PO4FG == 1:
self.po4, self.benpo4 = benth(OXRX.dox,self.anaer,self.brpo4,scrfac,depcor, self.po4)
self.bnrpo4 = self.benpo4 * self.vol
if self.TAMFG == 1:
if self.AMVFG == 1: # compute ammonia volatilization
twkelv = tw + 273.16 # convert water temperature to degrees kelvin
avdepm = avdepe * 0.3048 # convert depth to meters
(self.tam, self.nh3vlt) = self.nh3vol(self.expnvg,self.expnvl,OXRX.korea,wind,self.delt60,self.delts,avdepm,twkelv,tw,self.phval,self.tam)
self.volnh3 = -self.nh3vlt * self.vol
else:
self.volnh3 = 0.0
# calculate amount of nitrification; nitrification does not
# take place if the do concentration is less than 2.0 mg/l
(self.tam,self.no2,self.no3,OXRX.dox,dodemd,tamnit,no2ntc,no3nit) = \
self.nitrif(self.ktam20,self.tcnit,tw,self.NO2FG,self.kno220,self.tam,self.no2,self.no3,OXRX.dox)
# compute nitrification fluxes
self.nitdox = -dodemd * self.vol
self.nittam = -tamnit * self.vol
self.nitno2 = no2ntc * self.vol
self.nitno3 = no3nit * self.vol
if self.DENFG == 1: # consider denitrification processes, and compute associated fluxes
no3de = 0.0
(self.no3, no3de) = self.denit(self.kno320, self.tcden, tw, OXRX.dox, self.denoxt, self.no3)
self.denno3 = -no3de * self.vol
# calculate amount of inorganic constituents released by bod decay in reach water
self.decnit = OXRX.bodox * self.cvon
self.decpo4 = OXRX.bodox * self.cvop
self.decco2 = OXRX.bodox * self.cvoc
# update state variables of inorganic constituents which
# are end products of bod decay; and compute associated fluxes
(self.tam, self.no3, self.po4) = decbal(self.TAMFG, self.PO4FG, self.decnit, self.decpo4,
self.tam, self.no3, self.po4)
if self.TAMFG == 1:
self.bodtam = self.decnit * self.vol
else:
self.bodno3 = self.decnit * self.vol
if self.PO4FG == 1:
self.bodpo4 = self.decpo4 * self.vol
if self.PO4FG == 1 and self.SEDFG == 1 and self.ADPOFG == 1: # compute adsorption/desorption of phosphate
dumxxx = 0.0
(self.po4, self.spo4, dumxxx, self.adpo4) \
= self.addsnu(self.vol, self.rsed, self.adpopm, self.po4, self.spo4, dumxxx, self.adpo4)
if self.TAMFG == 1 and self.SEDFG == 1 and self.ADNHFG == 1: # compute adsorption/desorption of ammonium
# first compute ammonia ionization
(self.nh3, self.nh4) = self.ammion(tw, self.phval, self.tam)
(self.nh4, self.snh4, self.tam, self.adnh4) \
= self.addsnu(self.vol, self.rsed, self.adnhpm, self.nh4, self.snh4, self.tam, self.adnh4)
# then re-compute ammonia ionization
(self.nh3, self.nh4) = self.ammion(tw, self.phval, self.tam)
else:
# too little water is in reach to warrant simulation of quality processes
self.decnit = 0.0; self.decpo4 = 0.0; self.decco2 = 0.0
self.nitdox = 0.0; self.denbod = 0.0; self.nittam = 0.0
self.bnrtam = 0.0; self.volnh3 = 0.0; self.bodtam = 0.0
self.nitno2 = 0.0; self.nitno3 = 0.0; self.denno3 = 0.0
self.bodno3 = 0.0
self.bnrpo4 = self.bodpo4 = 0.0
self.adnh4[1:5] = 0.0
self.adpo4[1:5] = 0.0
#self.totdox = self.readox + self.boddox + self.bendox + self.nitdox
#self.totbod = self.decbod + self.bnrbod + self.snkbod + self.denbod
self.totno3 = self.nitno3 + self.denno3 + self.bodno3
self.tottam = self.nittam + self.volnh3 + self.bnrtam + self.bodtam
self.totpo4 = self.bnrpo4 + self.bodpo4
if self.PO4FG == 1 and self.SEDFG == 1 and self.ADPOFG == 1: # find total quantity of phosphate on various forms of sediment
totpm1 = 0.0; totpm2 = 0.0; totpm3 = 0.0
for j in range(1, 4):
self.rspo4[j] = self.spo4[j] * self.rsed[j] # compute mass of phosphate adsorbed to each suspended fraction
self.rspo4[j + 4] = self.bpo4[j] * self.rsed[j + 3] # compute mass of phosphate adsorbed to each bed fraction
self.rspo4[j + 8] = self.rspo4[j] + self.rspo4[j + 4] # compute total mass of phosphate on each sediment fraction
totpm1 += self.rspo4[j]
totpm2 += self.rspo4[j + 4]
totpm3 += self.rspo4[j + 8]
self.rspo4[4] = totpm1 # compute total suspended phosphate
self.rspo4[8] = totpm2 # compute total bed phosphate
self.rspo4[12] = totpm3 # compute total sediment-associated phosphate
# calculate total amount of ammonium on various forms of sediment
if self.TAMFG == 1 and self.SEDFG == 1 and self.ADNHFG == 1:
totnm1 = 0.0; totnm2 = 0.0; totnm3 = 0.0
for j in range(1, 4):
self.rsnh4[j] = self.snh4[j] * self.rsed[j] # compute mass of ammonium adsorbed to each suspended fraction
self.rsnh4[j + 4] = self.bnh4[j] * self.rsed[j + 3] # compute mass of ammonium adsorbed to each bed fraction
self.rsnh4[j + 8] = self.rsnh4[j] + self.rsnh4[j + 4] # compute total mass of ammonium on each sediment fraction
totnm1 += self.rsnh4[j]
totnm2 += self.rsnh4[j + 4]
totnm3 += self.rsnh4[j + 8]
self.rsnh4[4] = totnm1 # compute total suspended ammonium
self.rsnh4[8] = totnm2 # compute total bed ammonium
self.rsnh4[12] = totnm3 # compute total sediment-associated ammonium
self.svol = self.vol # svol is volume at start of time step, update for next time thru
return OXRX
def update_mass(self):
# calculate total resident mass of nutrient species
self.rno3 = self.no3 * self.vol
self.rtam = self.tam * self.vol
self.rno2 = self.no2 * self.vol
self.rpo4 = self.po4 * self.vol
self.rnh4 = self.nh4 * self.vol
self.rnh3 = self.nh3 * self.vol
self.rrno3 = self.no3 * self.vol
self.rrtam = self.tam * self.vol
if self.ADNHFG == 1:
self.rrtam += self.rsnh4[4] # add adsorbed suspended nh4 to dissolved
self.rrno2 = self.no2 * self.vol
self.rrpo4 = self.po4 * self.vol
if self.ADPOFG == 1:
self.rrpo4 += self.rspo4[4] # add adsorbed suspended po4 to dissolved
return
#--------------------------------------------------------------
# static methods
#--------------------------------------------------------------
@staticmethod
def addsnu(vol, rsed, adpm, dnut, snut, dnutxx, adnut):
''' simulate exchange of nutrient (phosphate or ammonium) between the
dissolved state and adsorption on suspended sediment- 3 adsorption
sites are considered: 1- suspended sand 2- susp. silt
3- susp. clay
assumes instantaneous linear equilibrium'''
if vol > 0.0: # adsorption/desorption can take place
# establish nutrient equilibrium between reach water and suspended sediment; first find the new dissolved nutrient conc. in reach water
dnutin = dnut
num = vol * dnut
denom = vol
for j in range(1, 4):
if rsed[j] > 0.0: # accumulate terms for numerator and denominator in dnut equation
num += snut[j] * rsed[j]
denom += adpm[j] * rsed[j]
dnut = num / denom # calculate new dissolved concentration-units are mg/l
dnutxx= dnutxx - (dnutin - dnut) # also calculate new tam conc if doing nh4 adsorption
# calculate new conc on each sed class and the corresponding adsorption/desorption flux
adnut[4] = 0.0
for j in range(1, 4):
if rsed[j] > 0.0: # this sediment class is present-calculate data pertaining to it
temp = dnut * adpm[j] # new concentration
# quantity of material transferred
adnut[j]= (temp - snut[j])*rsed[j]
snut[j] = temp
# accumulate total adsorption/desorption flux above bed
adnut[4] += adnut[j]
else: # this sediment class is absent
adnut[j] = 0.0
# snut[j] is unchanged-"undefined"
else: # no water, no adsorption/desorption
adnut[1:5] = 0.0
# snut(1 thru 3) and dnut should already have been set to undefined values
return dnut, snut, dnutxx, adnut
def advnut(self,isnut,rsed,bsed,depscr,rosed,osed,nexits,rsnuts,rbnuts,bnut):
''' simulate the advective processes, including deposition and scour for the
inorganic nutrient adsorbed to one sediment size fraction'''
if depscr < 0.0: # there was sediment scour during the interval
# compute flux of nutrient mass into water column with scoured sediment fraction
dsnut = bnut * depscr
# calculate concentration in suspension-under these conditions, denominator should never be zero
snut = (isnut + rsnuts - dsnut) / (rsed + rosed)
rosnut = rosed * snut
else: # there was deposition or no scour/deposition during the interval
denom = rsed + depscr + rosed
if denom == 0.0: # there was no sediment in suspension during the interval
snut = -1.0e30
rosnut = 0.0
dsnut = 0.0
# fix sed-nut problem caused by very small sediment loads that are stored in
# wdm file as zero (due to wdm attribute tolr > 0.0) when adsorbed nut load
# is not zero; changed comparison from 0.0 to 1.0e-3; this should not cause
# any mass balance errors since the condition is not likely to exist over a
# long period and will be insignificant compared to
# the total mass over a printout period; note that 1.0e-3 mg*ft3/l is 0.028 mg
# (a very, very small mass)
if abs(isnut) > 1.0e-3 or abs(rsnuts) > 1.0e-3:
self.errors[3] += 1
# errmsg: error-under these conditions these values should be zero
else: # there was some suspended sediment during the interval
# calculate conc on suspended sed
snut = (isnut + rsnuts) / denom
rosnut= rosed * snut
dsnut = depscr * snut
if rsed == 0.0:
# rchres ended up without any suspended sediment-revise
# value for snut, but values obtained for rosnut, and dsnut are still ok
snut = -1.0e30
# calculate conditions on the bed
if bsed == 0.0:
# no bed sediments at end of interval
if abs(dsnut) > 0.0 or abs(rbnuts) > 0.0:
self.errors[4] += 1
# errmsg: error-under this condition these values should be zero
osnut = zeros(nexits)
if nexits > 1:
# compute outflow through each individual exit
if rosed == 0.0: # all zero
osnut[:] = 0.0
else:
osnut[:] = rosnut * osed[:] / rosed
return snut, dsnut, rosnut, osnut
@staticmethod
def ammion(tw, ph, tam):
''' simulate ionization of ammonia to ammonium using empirical relationships developed by loehr, 1973'''
if tam >= 0.0: # tam is defined, compute fractions
# adjust very low or high values of water temperature to fit limits of dat used to develop empirical relationship
if tw < 5.0: twx = 5.0
elif tw > 35.0: twx = 35.0
else: twx = tw
if ph < 4.0: phx = 4.0
elif ph > 10.0: phx = 10.0
else: phx = ph
# compute ratio of ionization constant values for aqueous ammonia and water at current water temperatue
ratio = (-3.39753 * log(0.02409 * twx)) * 1.0e9
# compute fraction of total ammonia that is un-ionized
frac = 10.0**(phx) / (10.0**phx + ratio)
# update nh3 and nh4 state variables to account for ionization
nh3 = frac * tam
nh4 = tam - nh3
else: # tam conc undefined
nh3 = -1.0e30
nh4 = -1.0e30
return nh3, nh4
@staticmethod
def denit(kno320, tcden, tw, dox, denoxt, no3):
''' calculate amount of denitrification; denitrification does not take place
if the do concentration is above user-specified threshold do value (denoxt)'''
denno3 = 0.0
if dox <= denoxt: # calculate amount of no3 denitirified to nitrogen gas
denno3 = 0.0
if no3 > 0.001:
denno3 = kno320 * (tcden**(tw - 20.0)) * no3
no3 = no3 - denno3
if no3 < 0.001: # adjust amount of no3 denitrified so that no3 state variable is not a negative number; set no3 to a value of .001 mg/l
denno3 = denno3 + no3 - 0.001
no3 = 0.001
else:
pass # denitrification does not occur
return no3, denno3
def hcintp (self, phval, tw):
''' calculate henry's constant for ammonia based on ph and water temperature'''
xtw = array([4.44, 15.56, 26.67, 37.78])
xhplus = array([1.0, 10.0, 100.0, 1000.0, 10000.0])
yhenc = array([[0.000266, 0.000754, 0.00198, 0.00486],
[0.00266, 0.00753, 0.0197, 0.0480],
[0.0263, 0.0734, 0.186, 0.428],
[0.238, 0.586, 1.20, 2.05],
[1.2, 1.94, 2.65, 3.31]]) # dimensions: fortran 4,5
yhenc = np.transpose(yhenc)
# adjust very low or very high values of water temperature to fit limits of henry's contant data range
if tw < 4.44: # use low temperature range values for henry's constant (4.4 degrees c or 40 degrees f)
twx = 4.44
elif tw > 37.78: # use high temperature range values for henry's constant (37.78 degrees c or 100 degrees f)
twx = 37.78
else: # use unmodified water temperature value in interpolation
twx = tw
# convert ph value to a modified version of hydrogen ion concentration
# because our interpolation routine cant seem to work with small numbers
hplus = 10.0**(phval) * 1.0e-6
# adjust very low or very high values of hydrogen ion concentration to fit limits of henry's constant data range
if hplus > 10000.0: # use low hydrogen ion concentration range values for henry's constant
hplus = 10000.0
elif hplus < 1.0: # use high hydrogen ion concentration range values for henry's constant
hplus = 1.0
# perform two-dimensional interpolation of henry's constant values to estimate henry's
# constant for water temperature and ph conditions in water column (based on p. 97 of numerical recipes)
i4 = 4
i5 = 5
yhtmp = zeros(5)
ytwtmp = zeros(4)
for i in range(4): # do 10 i= 1, 4
for j in range(5): # do 20 j= 1, 5
yhtmp[j] = yhenc[i,j] # copy row into temporary storage
# 20 continue
# perform linear interpolation within row of values
ytwtmp[i] = self.intrp1(xhplus, yhtmp, i5, hplus)
# 10 continue
# do final interpolation in remaining dimension
hcmf = self.intrp1(xtw, ytwtmp, i4, twx)
# convert henry's constant from molar fraction form to units of atm.m3/mole: assume
# 1) dilute air and water solutions
# 2) ideal gas law
# 3) stp i.e., 1 atm total pressure
# 4) 1 gram water = 1 cm3
# xa(air) 1
# --------- * -----------------------------------------
# xa(water) (1.e+6 m3/g water)/(18.01 g/mole water)
hcnh3 = hcmf * (18.01 * 1.e-6)
return hcnh3
@staticmethod
def intrp1(xarr0, yarr0, len_, xval):
''' perform one-dimensional interpolation of henry's constant values for ammonia (based on p. 82 of numerical recipes)'''
c = zeros(11); d = zeros(11)
# modify array indexing (1-based):
cnt = len(xarr0) + 1
xarr = zeros(cnt)
yarr = zeros(cnt)
xarr[1:cnt] = xarr0[0:cnt-1]
yarr[1:cnt] = yarr0[0:cnt-1]
# interpolate:
ns = 1
dif = abs(xval-xarr[1])
# find the index ns of the closest array entry
for i in range(1, len_+1): # do 10 i= 1, len
dift = abs(xval - xarr[i])
if dift < dif:
ns = i
dif = dift
# initialize correction array values
c[i] = yarr[i]
d[i] = yarr[i]
# select intial approximation of yval
yval = yarr[ns]
ns = ns - 1
# loop over the current values in correction value arrays (c & d) to update them
for j in range(1, len_): # do 30 j = 1, len -1
for i in range (1, len_ - j + 1): # do 20 i = 1, len - j
ho = xarr[i] - xval
hp = xarr[i + j] - xval
w = c[i + 1] - d[i]
den = ho - hp
den = w / den
# update correction array values
d[i] = hp * den
c[i] = ho * den