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GQUAL.py
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''' Copyright (c) 2020 by RESPEC, INC.
Authors: Robert Heaphy, Ph.D. and Paul Duda
License: LGPL2
'''
from numpy import array, zeros, int64
from numba import njit
from math import exp
from HSP2.utilities import initm, make_numba_dict, hoursval, dayval
from HSP2.ADCALC import advect, oxrea
ERRMSGS =('GQUAL: one or more gquals are sediment-associated, but section sedtrn not active', #ERRMSG0
'GQUAL: simulation of photolysis requires aux1fg to be on to calculate average depth', #ERRMSG1
'GQUAL: simulation of volatilization in a free flowing stream requires aux3fg on', #ERRMSG2
'GQUAL: simulation of volatilization in a lake requires aux1fg on to calculate average depth', #ERRMSG3
'GQUAL: in advqal, the value of denom is zero, and ISQAL and RSQALS should also be zero', #ERRMSG4
'GQUAL: in advqal, the value of bsed is zero, and DSQAL and RBQALS should also be zero', #ERRMSG5
'GQUAL: the value of tempfg is 1, but timeseries TW is not available as input', #ERRMSG6
'GQUAL: the value of phflag is 1, but timeseries PHVAL is not available as input', #ERRMSG7
'GQUAL: the value of roxfg is 1, but timeseries ROC is not available as input', #ERRMSG8
'GQUAL: the value of cldfg is 1, but timeseries CLOUD is not available as input', #ERRMSG9
'GQUAL: the value of sdfg is 1, but timeseries SSED4 is not available as input', #ERRMSG10
'GQUAL: the value of phytfg is 1, but timeseries PHYTO is not available as input') #ERRMSG11
def gqual(io_manager, siminfo, uci, ts):
''' Simulate the behavior of a generalized quality constituent'''
errors = zeros(len(ERRMSGS)).astype(int64)
delt60 = siminfo['delt'] / 60 # delt60 - simulation time interval in hours
simlen = siminfo['steps']
delts = siminfo['delt'] * 60
uunits = siminfo['units']
AFACT = 43560.0
if uunits == 2:
# si units conversion
AFACT = 1000000.0
advectData = uci['advectData']
(nexits, vol, VOL, SROVOL, EROVOL, SOVOL, EOVOL) = advectData
svol = vol * AFACT
ts['VOL'] = VOL
ts['SROVOL'] = SROVOL
ts['EROVOL'] = EROVOL
for i in range(nexits):
ts['SOVOL' + str(i + 1)] = SOVOL[:, i]
ts['EOVOL' + str(i + 1)] = EOVOL[:, i]
ui = make_numba_dict(uci)
ui['simlen'] = siminfo['steps']
ui['uunits'] = siminfo['units']
ui['svol'] = svol
ui['vol'] = vol
ui['delt60'] = delt60
ui['delts'] = delts
ui['errlen'] = len(ERRMSGS)
# table-type gq-gendata
ngqual = 1
tempfg = 2
phflag = 2
roxfg = 2
cldfg = 2
sdfg = 2
phytfg = 2
# ui = uci['PARAMETERS']
if 'NGQUAL' in ui:
ngqual = int(ui['NGQUAL'])
tempfg = ui['TEMPFG']
phflag = ui['PHFLAG']
roxfg = ui['ROXFG']
cldfg = ui['CLDFG']
sdfg = ui['SDFG']
phytfg = ui['PHYTFG']
ui['ngqual'] = ngqual
ts['HRFG'] = hour24Flag(siminfo).astype(float)
ui_base = ui # save base ui dict before adding qual specific parms
for index in range(1, ngqual+1):
ui = ui_base
ui['index'] = index
# update UI values for this constituent here!
ui_parms = uci['GQUAL' + str(index)]
if 'GQADFG' + str((index * 2) - 1) in ui_parms:
# get atmos dep timeseries
gqadfgf = ui_parms['GQADFG' + str((index * 2) - 1)]
if gqadfgf > 0:
ts['GQADFX'] = initm(siminfo, uci, gqadfgf, 'GQUAL' + str(index) + '_MONTHLY/GQADFX', 0.0)
elif gqadfgf == -1:
ts['GQADFX'] = ts['GQADFX' + str(index) + ' 1']
gqadfgc = ui_parms['GQADFG' + str(index * 2)]
if gqadfgc > 0:
ts['GQADCN'] = initm(siminfo, uci, gqadfgc, 'GQUAL' + str(index) + '_MONTHLY/GQADCN', 0.0)
elif gqadfgc == -1:
ts['GQADCN'] = ts['GQADCN' + str(index) + ' 1']
if 'GQADFX' in ts:
ts['GQADFX'] *= delt60 / (24.0 * AFACT)
if 'GQADFX' not in ts:
ts['GQADFX'] = zeros(simlen)
if 'GQADCN' not in ts:
ts['GQADCN'] = zeros(simlen)
# table-type gq-flg2
gqpm2 = zeros(8)
gqpm2[7] = 2
if 'GQPM21' in ui_parms:
gqpm2[1] = ui_parms['GQPM21']
gqpm2[2] = ui_parms['GQPM22']
gqpm2[3] = ui_parms['GQPM23']
gqpm2[4] = ui_parms['GQPM24']
gqpm2[5] = ui_parms['GQPM25']
gqpm2[6] = ui_parms['GQPM26']
gqpm2[7] = ui_parms['GQPM27']
biop = 0.0
qalfg5 = ui_parms['QALFG5']
if qalfg5 == 1: # qual undergoes biodegradation
# BIOPM(1,I) # table-type gq-biopm
biop = ui_parms['BIO']
ts['BIO'] = zeros(simlen)
ts['BIO'].fill(biop)
# specifies source of biomass data using GQPM2(7,I)
if gqpm2[7] == 1 or gqpm2[7] == 3:
# BIOM = # from ts, monthly, constant
ts['BIO'] = initm(siminfo, uci, ui_parms['GQPM27'], 'GQUAL' + str(index) + '_MONTHLY/BIO',
ui_parms['BIO'])
# table-type gq-values
if tempfg == 2 and "TWAT" in ui_parms:
twat = ui_parms["TWAT"]
else:
twat = 60.0
if phflag == 2 and "PHVAL" in ui_parms:
phval = ui_parms["PHVAL"]
else:
phval = 7.0
if roxfg == 2 and "ROC" in ui_parms:
roc = ui_parms["ROC"]
else:
roc = 0.0
if cldfg == 2 and "CLD" in ui_parms:
cld = ui_parms["CLD"]
else:
cld = 0.0
if sdfg == 2 and "SDCNC" in ui_parms:
sdcnc = ui_parms["SDCNC"]
else:
sdcnc = 0.0
if phytfg == 2 and "PHY" in ui_parms:
phy = ui_parms["PHY"]
else:
phy = 0.0
# for the following, if the flag value is 1 the timeseries should already be available as input
if tempfg == 2 or tempfg == 3:
ts['TW_GQ'] = initm(siminfo, uci, tempfg, 'GQUAL' + str(index) + '_MONTHLY/WATEMP', twat)
if phflag == 2 or phflag == 3:
ts['PHVAL_GQ'] = initm(siminfo, uci, phflag, 'GQUAL' + str(index) + '_MONTHLY/PHVAL', phval)
if roxfg == 2 or roxfg == 3:
ts['ROC_GQ'] = initm(siminfo, uci, roxfg, 'GQUAL' + str(index) + '_MONTHLY/ROXYGEN', roc)
if cldfg == 2 or cldfg == 3:
ts['CLOUD_GQ'] = initm(siminfo, uci, cldfg, 'GQUAL' + str(index) + '_MONTHLY/CLOUD', cld)
if sdfg == 2 or sdfg == 3:
ts['SDCNC_GQ'] = initm(siminfo, uci, sdfg, 'GQUAL' + str(index) + '_MONTHLY/SEDCONC', sdcnc)
if phytfg == 2 or phytfg == 3:
ts['PHYTO_GQ'] = initm(siminfo, uci, phytfg, 'GQUAL' + str(index) + '_MONTHLY/PHYTO', phy)
# if any of these flags are 1 and the timeseries does not exist, that's a problem -- trigger message
ts['DAYVAL'] = dayval(siminfo, [4, 4, 1, 1, 1, 2, 2, 2, 3, 3, 3, 4])
qalfg3 = ui_parms['QALFG3']
if qalfg3 == 1: # qual undergoes photolysis
# PHOTPM(1,I) # table-type gq-photpm
if 'EXTENDEDS_PHOTPM' in uci:
ttable = uci['EXTENDEDS_PHOTPM']
for i in range(1,21):
ui['photpm' + str(i)] = ttable['PHOTPM' + str(i-1)]
# table-type gq-alpha
if 'EXTENDEDS_ALPH' in uci:
ttable = uci['EXTENDEDS_ALPH']
for i in range(1,19):
ui['alph' + str(i)] = ttable['ALPH' + str(i-1)]
# table-type gq-gamma
if 'EXTENDEDS_GAMM' in uci:
ttable = uci['EXTENDEDS_GAMM']
for i in range(1,19):
ui['gamm' + str(i)] = ttable['GAMM' + str(i-1)]
# table-type gq-delta
if 'EXTENDEDS_DEL' in uci:
ttable = uci['EXTENDEDS_DEL']
for i in range(1,19):
ui['delta' + str(i)] = ttable['DEL' + str(i-1)]
# table-type gq-cldfact
if 'EXTENDEDS_KCLD' in uci:
ttable = uci['EXTENDEDS_KCLD']
for i in range(1,19):
ui['kcld' + str(i)] = ttable['KCLD' + str(i-1)]
# add contents of ui_parms to ui
for key, value in ui_parms.items():
if type(value) in {int, float}:
ui[key] = float(value)
# ui_combined = {**ui, **ui_parms}
############################################################################
errors = _gqual_(ui, ts) # run GQUAL simulation code
############################################################################
if nexits > 1:
u = uci['SAVE']
name = 'GQUAL' + str(index) # arbitrary identification
key1 = name + '_ODQAL'
for i in range(nexits):
u[f'{key1}{i + 1}'] = u['ODQAL']
del u['ODQAL']
key1 = name + '_OSQAL1'
for i in range(nexits):
u[f'{key1}{i + 1}'] = u['OSQAL']
key1 = name + '_OSQAL2'
for i in range(nexits):
u[f'{key1}{i + 1}'] = u['OSQAL']
key1 = name + '_OSQAL3'
for i in range(nexits):
u[f'{key1}{i + 1}'] = u['OSQAL']
del u['OSQAL']
key1 = name + '_TOSQAL'
for i in range(nexits):
u[f'{key1}{i + 1}'] = u['TOSQAL']
del u['TOSQAL']
return errors, ERRMSGS
#@njit(cache=True)
def _gqual_(ui, ts):
''' Simulate the behavior of a generalized quality constituent'''
errors = zeros(int(ui['errlen'])).astype(int64)
simlen = int(ui['simlen'])
nexits = int(ui['NEXITS'])
uunits = int(ui['uunits'])
delt60 = ui['delt60']
delts = ui['delts']
index = int(ui['index'])
ngqual = int(ui['ngqual'])
ddqal = zeros((8, ngqual + 1))
AFACT = 43560.0
if uunits == 2:
# si units conversion
AFACT = 1000000.0
tempfg = 2
phflag = 2
roxfg = 2
cldfg = 2
sdfg = 2
phytfg = 2
if 'TEMPFG' in ui:
tempfg = int(ui['TEMPFG'])
phflag = int(ui['PHFLAG'])
roxfg = int(ui['ROXFG'])
cldfg = int(ui['CLDFG'])
sdfg = int(ui['SDFG'])
phytfg = int(ui['PHYTFG'])
lat = int(ui['LAT'])
lkfg = int(ui['LKFG'])
len_ = 0.0
delth= 0.0
if 'LEN' in ui:
len_ = ui["LEN"] * 5280.0 # mi to feet
delth = ui["DELTH"]
if uunits == 2:
len_ = ui['LEN'] * 1000.0 # length of reach, in meters
HRFG = ts['HRFG'].astype(int64)
# table-type gq-qaldata
# qualid = ui['GQID']
dqal = ui['DQAL']
# concid = ui['CONCID']
conv = ui['CONV']
# qtyid = ui['QTYID']
vol = ui['vol']
svol = ui['svol']
rdqal = dqal * vol
cinv = 1.0 / conv # get reciprocal of unit conversion factor
# process flags for this constituent
# table-type gq-qalfg
qalfg = zeros(8)
qalfg[1] = ui['QALFG1']
qalfg[2] = ui['QALFG2']
qalfg[3] = ui['QALFG3']
qalfg[4] = ui['QALFG4']
qalfg[5] = ui['QALFG5']
qalfg[6] = ui['QALFG6']
qalfg[7] = ui['QALFG7']
# table-type gq-flg2
gqpm2 = zeros(8)
gqpm2[7] = 2
if 'GQPM21' in ui:
gqpm2[1] = ui['GQPM21']
gqpm2[2] = ui['GQPM22']
gqpm2[3] = ui['GQPM23']
gqpm2[4] = ui['GQPM24']
gqpm2[5] = ui['GQPM25']
gqpm2[6] = ui['GQPM26']
gqpm2[7] = ui['GQPM27']
# process parameters for this constituent
ka = 0.0
kb = 0.0
kn = 0.0
thhyd = 0.0
kox = 0.0
thox = 0.0
if qalfg[1] == 1: # qual undergoes hydrolysis
# HYDPM(1,I) # table-type gq-hydpm
ka = ui['KA'] * delts # convert rates from /sec to /ivl
kb = ui['KB'] * delts
kn = ui['KN'] * delts
thhyd = ui['THHYD']
if qalfg[2] == 1: # qual undergoes oxidation by free radical processes
# ROXPM(1,I) # table-type gq-roxpm
kox = ui['KOX'] * delts # convert rates from /sec to /ivl
thox = ui['THOX']
photpm = zeros(21)
if qalfg[3] == 1: # qual undergoes photolysis
# PHOTPM(1,I) # table-type gq-photpm
if 'photpm1' in ui:
for i in range(1,21):
photpm[i] = ui['photpm' + str(i)]
cfgas = 0.0
if qalfg[4] == 1: # qual undergoes volatilization
cfgas = ui['CFGAS'] # table-type gq-cfgas
biocon = 0.0
thbio = 0.0
biop = 0.0
if qalfg[5] == 1: # qual undergoes biodegradation
# BIOPM(1,I) # table-type gq-biopm
biocon = ui['BIOCON'] * delt60 / 24.0 # convert rate from /day to /ivl
thbio = ui['THBIO']
biop = ui['BIO']
fstdec = 0.0
thfst = 0.0
if qalfg[6] == 1: # qual undergoes "general" decay
# GENPM(1,I)) # table-type gq-gendecay
fstdec = ui['FSTDEC'] * delt60 / 24.0 # convert rate from /day to /ivl
thfst = ui['THFST']
adpm1 = zeros(7)
adpm2 = zeros(7)
adpm3 = zeros(7)
rsed = zeros(7)
sqal = zeros(7)
if qalfg[7] == 1: # constituent is sediment-associated
# get all required additional input
# ADDCPM # table-type gq-seddecay
# convert rates from /day to /ivl
addcpm1 = ui['ADDCP1'] * delt60 / 24.0 # convert rate from /day to /ivl
addcpm2 = ui['ADDCP2']
addcpm3 = ui['ADDCP3'] * delt60 / 24.0 # convert rate from /day to /ivl
addcpm4 = ui['ADDCP4']
# table-type gq-kd
adpm1[1] = ui['ADPM11']
adpm1[2] = ui['ADPM21']
adpm1[3] = ui['ADPM31']
adpm1[4] = ui['ADPM41']
adpm1[5] = ui['ADPM51']
adpm1[6] = ui['ADPM61']
# gq-adrate
adpm2[1] = ui['ADPM12'] * delt60 / 24.0 # convert rate from /day to /ivl
adpm2[2] = ui['ADPM22'] * delt60 / 24.0 # convert rate from /day to /ivl
adpm2[3] = ui['ADPM32'] * delt60 / 24.0 # convert rate from /day to /ivl
adpm2[4] = ui['ADPM42'] * delt60 / 24.0 # convert rate from /day to /ivl
adpm2[5] = ui['ADPM52'] * delt60 / 24.0 # convert rate from /day to /ivl
adpm2[6] = ui['ADPM62'] * delt60 / 24.0 # convert rate from /day to /ivl
# table-type gq-adtheta
if 'ADPM13' in ui:
adpm3[1] = ui['ADPM13']
adpm3[2] = ui['ADPM23']
adpm3[3] = ui['ADPM33']
adpm3[4] = ui['ADPM43']
adpm3[5] = ui['ADPM53']
adpm3[6] = ui['ADPM63']
else:
adpm3[1] = 1.07
adpm3[2] = 1.07
adpm3[3] = 1.07
adpm3[4] = 1.07
adpm3[5] = 1.07
adpm3[6] = 1.07
# table-type gq-sedconc
sqal[1] = ui['SQAL1']
sqal[2] = ui['SQAL2']
sqal[3] = ui['SQAL3']
sqal[4] = ui['SQAL4']
sqal[5] = ui['SQAL5']
sqal[6] = ui['SQAL6']
# find the total quantity of material on various forms of sediment
RSED1 = ts['RSED1'] # sediment storages - suspended sand
RSED2 = ts['RSED2'] # sediment storages - suspended silt
RSED3 = ts['RSED3'] # sediment storages - suspended clay
RSED4 = ts['RSED4'] # sediment storages - bed sand
RSED5 = ts['RSED5'] # sediment storages - bed silt
RSED6 = ts['RSED6'] # sediment storages - bed clay
rsed1 = RSED1[0]
rsed2 = RSED2[0]
rsed3 = RSED3[0]
if 'SSED1' in ui:
rsed1 = ui['SSED1']
rsed2 = ui['SSED2']
rsed3 = ui['SSED3']
if uunits == 1:
rsed[1] = RSED1[0] / 3.121E-08
rsed[2] = RSED2[0] / 3.121E-08
rsed[3] = RSED3[0] / 3.121E-08
rsed[4] = RSED4[0] / 3.121E-08
rsed[5] = RSED5[0] / 3.121E-08
rsed[6] = RSED6[0] / 3.121E-08
else:
rsed[1] = RSED1[0] / 1E-06 # 2.83E-08
rsed[2] = RSED2[0] / 1E-06
rsed[3] = RSED3[0] / 1E-06
rsed[4] = RSED4[0] / 1E-06
rsed[5] = RSED5[0] / 1E-06
rsed[6] = RSED6[0] / 1E-06
rsqal1 = sqal[1] * rsed1 * svol
rsqal2 = sqal[2] * rsed2 * svol
rsqal3 = sqal[3] * rsed3 * svol
rsqal4 = rsqal1 + rsqal2 + rsqal3
rsqal5 = sqal[4] * rsed[4]
rsqal6 = sqal[5] * rsed[5]
rsqal7 = sqal[6] * rsed[6]
rsqal8 = rsqal5 + rsqal6 + rsqal7
rsqal9 = rsqal1 + rsqal5
rsqal10 = rsqal2 + rsqal6
rsqal11 = rsqal3 + rsqal7
rsqal12 = rsqal9 + rsqal10 + rsqal11
else:
# qual not sediment-associated
rsqal1 = 0.0
rsqal2 = 0.0
rsqal3 = 0.0
rsqal4 = 0.0
rsqal5 = 0.0
rsqal6 = 0.0
rsqal7 = 0.0
rsqal8 = 0.0
rsqal9 = 0.0
rsqal10 = 0.0
rsqal11 = 0.0
rsqal12 = 0.0
# find total quantity of qual in the rchres
rrqal = rdqal + rsqal12
gqst1 = rrqal
# find values for global flags
# gqalfg indicates whether any qual undergoes each of the decay processes or is sediment-associated
# qalgfg indicates whether a qual undergoes any of the 6 decay processes
qalgfg = 0
if qalfg[1] > 0 or qalfg[2] > 0 or qalfg[3] > 0 or qalfg[4] > 0 or qalfg[5] > 0 or qalfg[6] > 0:
qalgfg = 1
# gdaufg indicates whether any constituent is a "daughter" compound through each of the 6 possible decay processes
gdaufg = 0
if gqpm2[1] > 0 or gqpm2[2] > 0 or gqpm2[3] > 0 or gqpm2[4] > 0 or gqpm2[5] > 0 or gqpm2[6] > 0:
gdaufg = 1
# daugfg indicates whether or not a given qual is a daughter compound
daugfg = 0
if gqpm2[1] > 0 or gqpm2[2] > 0 or gqpm2[3] > 0 or gqpm2[4] > 0 or gqpm2[5] > 0 or gqpm2[6] > 0:
daugfg = 1
# get initial value for all inputs which can be constant,
# vary monthly, or be a time series-some might be over-ridden by
# monthly values or time series
alph = zeros(19)
gamm = zeros(19)
delta = zeros(19)
kcld = zeros(19)
fact1 = 0.0
light = 1
if qalfg[3] == 1:
# table-type gq-alpha
if 'alph1' in ui:
for i in range(1, 19):
alph[i] = ui['alph' + str(i)]
# table-type gq-gamma
if 'gamm1' in ui:
for i in range(1, 19):
gamm[i] = ui['gamm' + str(i)]
# table-type gq-delta
if 'delta1' in ui:
for i in range(1, 19):
delta[i] = ui['delta' + str(i)]
# table-type gq-cldfact
if 'kcld1' in ui:
for i in range(1, 19):
kcld[i] = ui['kcld' + str(i)]
cfsaex = 1.0
if 'CFSAEX' in ui:
cfsaex = ui['CFSAEX']
# fact1 is a pre-calculated value used in photolysis simulation
fact1 = cfsaex * delt60 / 24.0
# decide which set of light data to use
light = (abs(int(lat)) + 5) // 10
if light == 0: # no table for equation, so use 10 deg table
light = 1
lset_month = ts['DAYVAL']
reamfg = 0
cforea = 0.0
tcginv = 0.0
reak = 0.0
reakt = 0.0
expred = 0.0
exprev = 0.0
if qalfg[4] == 1:
# one or more constituents undergoes volatilization process- input required to compute reaeration coefficient
# flags - table-type ox-flags
reamfg = 2
if 'REAMFG' in ui:
reamfg = ui["REAMFG"]
dopfg = 0
if 'DOPFG' in ui:
dopfg = ui["DOPFG"]
htfg = int(ui['HTFG'])
if htfg == 0:
elev = ui["ELEV"]
cfpres = ((288.0 - 0.001981 * elev) / 288.0) ** 5.256
lkfg = int(ui['LKFG'])
if lkfg == 1:
# table-type ox-cforea
cforea = 1.0
if 'CFOREA' in ui:
cforea = ui["CFOREA"]
if 'CFOREA' in ui:
cforea = ui["CFOREA"]
else:
if reamfg == 1:
# tsivoglou method - table-type ox-tsivoglou
reakt = ui["REAKT"]
tcginv = ui["TCGINV"]
elif reamfg == 2:
# owen/churchill/o'connor-dobbins # table-type ox-tcginv
tcginv = 1.047
if "TCGINV" in ui:
tcginv = ui["TCGINV"]
elif reamfg == 3:
# user formula - table-type ox-reaparm
tcginv = ui["TCGINV"]
reak = ui["REAK"]
expred = ui["EXPRED"]
exprev = ui["EXPREV"]
# process tables specifying relationship between "parent" and "daughter" compounds
# table-type gq-daughter
c = zeros((8,7))
if 'C21' in ui:
c[2,1] = ui["C21"]
c[3,1] = ui["C31"]
c[4,1] = ui["C41"]
c[5,1] = ui["C51"]
c[6,1] = ui["C61"]
c[7,1] = ui["C71"]
c[3,2] = ui["C32"]
c[4,2] = ui["C42"]
c[5,2] = ui["C52"]
c[6,2] = ui["C62"]
c[7,2] = ui["C72"]
c[4,3] = ui["C43"]
c[5,3] = ui["C53"]
c[6,3] = ui["C63"]
c[7,3] = ui["C73"]
c[5,4] = ui["C54"]
c[6,4] = ui["C64"]
c[7,4] = ui["C74"]
c[6,5] = ui["C65"]
c[7,5] = ui["C75"]
c[7,6] = ui["C76"]
if qalfg[7] == 1: # one or more quals are sediment-associated
sedfg = int(ui['SEDFG'])
if sedfg == 0: # section sedtrn not active
#ERRMSG
errors[0] += 1 # ERRMSG0: one or more gquals are sediment-associated, but section sedtrn not active
hydrfg = int(ui['HYDRFG'])
aux1fg = int(ui['AUX1FG'])
aux2fg = int(ui['AUX2FG'])
if hydrfg == 1: # check that required options in section hydr have been selected
if qalfg[3] == 1 and aux1fg == 0:
errors[1] += 1 # ERRMSG1: simulation of photolysis requires aux1fg to be on to calculate average depth
if qalfg[4] == 1:
lkfg = int(ui['LKFG'])
if lkfg == 0:
if aux2fg == 0:
errors[2] += 1 # ERRMSG2: simulation of volatilization in a free flowing stream requires aux3fg on
else:
if aux1fg == 0:
errors[3] += 1 # ERRMSG3: simulation of volatilization in a lake requires aux1fg on to calculate average depth
##################### end PGQUAL
if tempfg == 1:
if 'TW' not in ts:
errors[6] += 1 # ERRMSG6: timeseries not available
ts['TW_GQ'] = zeros(simlen)
else:
ts['TW_GQ'] = ts['TW']
if phflag == 1:
if 'PHVAL' not in ts:
errors[7] += 1 # ERRMSG7: timeseries not available
ts['PHVAL_GQ'] = zeros(simlen)
else:
ts['PHVAL_GQ'] = ts['PHVAL']
if roxfg == 1:
if 'ROC' not in ts:
errors[8] += 1 # ERRMSG8: timeseries not available
ts['ROC_GQ'] = zeros(simlen)
else:
ts['ROC_GQ'] = ts['ROC']
if cldfg == 1:
if 'CLOUD' not in ts:
errors[9] += 1 # ERRMSG9: timeseries not available
ts['CLOUD_GQ'] = zeros(simlen)
else:
ts['CLOUD_GQ'] = ts['CLOUD']
if sdfg == 1:
if 'SSED4' not in ts:
errors[10] += 1 # ERRMSG10: timeseries not available
ts['SDCNC_GQ'] = zeros(simlen)
else:
ts['SDCNC_GQ'] = ts['SSED4']
if phytfg == 1:
if 'PHYTO' not in ts:
errors[11] += 1 # ERRMSG11: timeseries not available
ts['PHYTO_GQ'] = zeros(simlen)
else:
ts['PHYTO_GQ'] = ts['PHYTO']
# get input timeseries
TW = ts['TW_GQ']
PHVAL = ts['PHVAL_GQ']
ROC = ts['ROC_GQ']
CLD = ts['CLOUD_GQ']
SDCNC = ts['SDCNC_GQ']
PHYTO = ts['PHYTO_GQ']
AVDEP = ts['AVDEP']
WIND = ts['WIND'] * 1609.0 # miles to meters
AVVEL = ts['AVVEL']
PREC = ts['PREC']
SAREA = ts['SAREA']
GQADFX = ts['GQADFX']
GQADCN = ts['GQADCN']
if 'BIO' not in ts:
ts['BIO'] = zeros(simlen)
BIO = ts['BIO']
VOL = ts['VOL']
SROVOL = ts['SROVOL']
EROVOL = ts['EROVOL']
SOVOL = zeros((simlen, nexits))
EOVOL = zeros((simlen, nexits))
for i in range(nexits):
SOVOL[:, i] = ts['SOVOL' + str(i + 1)]
EOVOL[:, i] = ts['EOVOL' + str(i + 1)]
# get incoming flow of constituent or zeros;
if ('GQUAL' + str(index) + '_IDQAL') not in ts:
ts['GQUAL' + str(index) + '_IDQAL'] = zeros(simlen)
IDQAL = ts['GQUAL' + str(index) + '_IDQAL']
if ('GQUAL' + str(index) + '_ISQAL1') not in ts:
ts['GQUAL' + str(index) + '_ISQAL1'] = zeros(simlen)
ISQAL1 = ts['GQUAL' + str(index) + '_ISQAL1']
if ('GQUAL' + str(index) + '_ISQAL2') not in ts:
ts['GQUAL' + str(index) + '_ISQAL2'] = zeros(simlen)
ISQAL2 = ts['GQUAL' + str(index) + '_ISQAL2']
if ('GQUAL' + str(index) + '_ISQAL3') not in ts:
ts['GQUAL' + str(index) + '_ISQAL3'] = zeros(simlen)
ISQAL3 = ts['GQUAL' + str(index) + '_ISQAL3']
if qalfg[7] == 1: # this constituent is associated with sediment
DEPSCR1 = ts['DEPSCR1']
DEPSCR2 = ts['DEPSCR2']
DEPSCR3 = ts['DEPSCR3']
ROSED1 = ts['ROSED1']
ROSED2 = ts['ROSED2']
ROSED3 = ts['ROSED3']
OSED1 = zeros((simlen, nexits))
OSED2 = zeros((simlen, nexits))
OSED3 = zeros((simlen, nexits))
for timeindex in range(simlen):
if nexits > 1:
for xindex in range(nexits):
OSED1[timeindex, xindex] = ts['OSED1' + str(xindex + 1)][timeindex]
OSED2[timeindex, xindex] = ts['OSED2' + str(xindex + 1)][timeindex]
OSED3[timeindex, xindex] = ts['OSED3' + str(xindex + 1)][timeindex]
else:
OSED1[timeindex, 0] = ts['ROSED1'][timeindex]
OSED2[timeindex, 0] = ts['ROSED2'][timeindex]
OSED3[timeindex, 0] = ts['ROSED3'][timeindex]
# this number is used to adjust reaction rates for temperature
# TW20 = TW - 20.0
name = 'GQUAL' + str(index) # arbitrary identification
# preallocate output arrays (always needed)
ADQAL1 = ts[name + '_ADQAL1'] = zeros(simlen)
ADQAL2 = ts[name + '_ADQAL2'] = zeros(simlen)
ADQAL3 = ts[name + '_ADQAL3'] = zeros(simlen)
ADQAL4 = ts[name + '_ADQAL4'] = zeros(simlen)
ADQAL5 = ts[name + '_ADQAL5'] = zeros(simlen)
ADQAL6 = ts[name + '_ADQAL6'] = zeros(simlen)
ADQAL7 = ts[name + '_ADQAL7'] = zeros(simlen)
DDQAL1 = ts[name + '_DDQAL1'] = zeros(simlen)
DDQAL2 = ts[name + '_DDQAL2'] = zeros(simlen)
DDQAL3 = ts[name + '_DDQAL3'] = zeros(simlen)
DDQAL4 = ts[name + '_DDQAL4'] = zeros(simlen)
DDQAL5 = ts[name + '_DDQAL5'] = zeros(simlen)
DDQAL6 = ts[name + '_DDQAL6'] = zeros(simlen)
DDQAL7 = ts[name + '_DDQAL7'] = zeros(simlen)
DQAL = ts[name + '_DQAL'] = zeros(simlen)
DSQAL1 = ts[name + '_DSQAL1'] = zeros(simlen)
DSQAL2 = ts[name + '_DSQAL2'] = zeros(simlen)
DSQAL3 = ts[name + '_DSQAL3'] = zeros(simlen)
DSQAL4 = ts[name + '_DSQAL4'] = zeros(simlen)
GQADDR = ts[name + '_GQADDR'] = zeros(simlen)
GQADEP = ts[name + '_GQADEP'] = zeros(simlen)
GQADWT = ts[name + '_GQADWT'] = zeros(simlen)
ISQAL4 = ts[name + '_ISQAL4'] = zeros(simlen)
PDQAL = ts[name + '_PDQAL'] = zeros(simlen)
RDQAL = ts[name + '_RDQAL'] = zeros(simlen)
RODQAL = ts[name + '_RODQAL'] = zeros(simlen)
ROSQAL1= ts[name + '_ROSQAL1'] = zeros(simlen)
ROSQAL2= ts[name + '_ROSQAL2'] = zeros(simlen)
ROSQAL3= ts[name + '_ROSQAL3'] = zeros(simlen)
ROSQAL4= ts[name + '_ROSQAL4'] = zeros(simlen)
RRQAL = ts[name + '_RRQAL'] = zeros(simlen)
RSQAL1 = ts[name + '_RSQAL1'] = zeros(simlen)
RSQAL2 = ts[name + '_RSQAL2'] = zeros(simlen)
RSQAL3 = ts[name + '_RSQAL3'] = zeros(simlen)
RSQAL4 = ts[name + '_RSQAL4'] = zeros(simlen)
RSQAL5 = ts[name + '_RSQAL5'] = zeros(simlen)
RSQAL6 = ts[name + '_RSQAL6'] = zeros(simlen)
RSQAL7 = ts[name + '_RSQAL7'] = zeros(simlen)
RSQAL8 = ts[name + '_RSQAL8'] = zeros(simlen)
RSQAL9 = ts[name + '_RSQAL9'] = zeros(simlen)
RSQAL10= ts[name + '_RSQAL10'] = zeros(simlen)
RSQAL11= ts[name + '_RSQAL11'] = zeros(simlen)
RSQAL12= ts[name + '_RSQAL12'] = zeros(simlen)
SQAL1 = ts[name + '_SQAL1'] = zeros(simlen)
SQAL2 = ts[name + '_SQAL2'] = zeros(simlen)
SQAL3 = ts[name + '_SQAL3'] = zeros(simlen)
SQAL4 = ts[name + '_SQAL4'] = zeros(simlen)
SQAL5 = ts[name + '_SQAL5'] = zeros(simlen)
SQAL6 = ts[name + '_SQAL6'] = zeros(simlen)
SQDEC1 = ts[name + '_SQDEC1'] = zeros(simlen)
SQDEC2 = ts[name + '_SQDEC2'] = zeros(simlen)
SQDEC3 = ts[name + '_SQDEC3'] = zeros(simlen)
SQDEC4 = ts[name + '_SQDEC4'] = zeros(simlen)
SQDEC5 = ts[name + '_SQDEC5'] = zeros(simlen)
SQDEC6 = ts[name + '_SQDEC6'] = zeros(simlen)
SQDEC7 = ts[name + '_SQDEC7'] = zeros(simlen)
TIQAL = ts[name + '_TIQAL'] = zeros(simlen)
TROQAL = ts[name + '_TROQAL'] = zeros(simlen)
TOQAL = zeros((simlen, nexits))
ODQAL = zeros((simlen, nexits))
OSQAL1 = zeros((simlen, nexits))
OSQAL2 = zeros((simlen, nexits))
OSQAL3 = zeros((simlen, nexits))
TOSQAL = zeros((simlen, nexits))
for loop in range(simlen):
# within time loop
# tw20 may be required for bed decay of qual even if tw is undefined (due to vol=0.0)
tw = TW[loop]
if uunits == 1:
tw = (tw - 32.0) * 0.5555 # 5.0 / 9.0
tw20 = tw - 20.0 # TW20[loop]
if tw <= -10.0:
tw20 = 0.0
# correct unrealistically high values of tw calculated in htrch
if tw >= 50.0:
tw20 = 30.0
phval = PHVAL[loop]
roc = ROC[loop]
cld = CLD[loop]
sdcnc = SDCNC[loop]
phy = PHYTO[loop]
prec = PREC[loop]
sarea= SAREA[loop]
vol = VOL[loop] * AFACT
toqal = TOQAL[loop]
tosqal = TOSQAL[loop]
# initialize sediment-related variables:
if qalfg[7] == 1: # constituent is sediment-associated
osed1 = zeros(nexits)
osed2 = zeros(nexits)
osed3 = zeros(nexits)
# define conversion factor:
cf = 1.0
if uunits == 1:
cf = 3.121e-8
else:
cf = 1.0e-6
depscr1 = DEPSCR1[loop] / cf
depscr2 = DEPSCR2[loop] / cf
depscr3 = DEPSCR3[loop] / cf
rosed1 = ROSED1[loop] / cf
rosed2 = ROSED2[loop] / cf
rosed3 = ROSED3[loop] / cf
for i in range(nexits):
osed1[i] = OSED1[loop, i] / cf
osed2[i] = OSED2[loop, i] / cf
osed3[i] = OSED3[loop, i] / cf
rsed = zeros(7)
rsed[1] = RSED1[loop] / cf
rsed[2] = RSED2[loop] / cf
rsed[3] = RSED3[loop] / cf
rsed[4] = RSED4[loop] / cf
rsed[5] = RSED5[loop] / cf
rsed[6] = RSED6[loop] / cf
isqal1 = ISQAL1[loop]
isqal2 = ISQAL2[loop]
isqal3 = ISQAL3[loop]
if uunits == 2: # uci is in metric units
avdepm = AVDEP[loop]
avdepe = AVDEP[loop] * 3.28
avvele = AVVEL[loop] * 3.28
else: # uci is in english units
avdepm = AVDEP[loop] * 0.3048
avdepe = AVDEP[loop]
avvele = AVVEL[loop]
fact2 = zeros(19)
if qalfg[3] > 0:
# one or more constituents undergoes photolysis decay
if avdepe > 0.17:
# depth of water in rchres is greater than two inches -
# consider photolysis; this criteria will also be applied to other decay processes
lset = lset_month[loop]
# southern hemisphere is 2 seasons out of phase
if lat < 0:
lset += 2
if lset > 4:
lset -= 4
for l in range(1, 19):
# evaluate the light extinction exponent- 2.76*klamda*d
kl = alph[l] + gamm[l] * sdcnc + delta[l] * phy
expnt= 2.76 * kl * avdepm * 100.0
# evaluate the cloud factor
cldl= (10.0 - cld * kcld[l]) / 10.0
if expnt <= -20.0:
expnt = -20.
if expnt >= 20.0:
expnt = 20.
# evaluate the precalculated factors fact2
# lit is data from the seq file
# fact2[l] = cldl * lit[l,lset] * (1.0 - exp(-expnt)) / expnt
fact2[l] = cldl * light_factor(l,lset,light) * (1.0 - exp(-expnt)) / expnt
else:
# depth of water in rchres is less than two inches -photolysis is not considered
pass
korea = 0.0
if qalfg[4] > 0:
# prepare to simulate volatilization by finding the oxygen reaeration coefficient
wind = 0.0
if lkfg == 1:
wind = WIND[loop]
if avdepe > 0.17: # rchres depth is sufficient to consider volatilization
# compute oxygen reaeration rate-korea
korea = oxrea(lkfg, wind, cforea, avvele, avdepe, tcginv, reamfg, reak, reakt, expred, exprev,
len_, delth, tw, delts, delt60, uunits)
# KOREA = OXREA(LKFG,WIND,CFOREA,AVVELE,AVDEPE,TCGINV,REAMFG,REAK,REAKT,EXPRED,EXPREV,LEN, DELTH,TWAT,DELTS,DELT60,UUNITS,KOREA)
else:
# rchres depth is not sufficient to consider volatilization
pass
# get data on inflow of dissolved material
gqadfx = GQADFX[loop]
gqadcn = GQADCN[loop]
gqaddr = sarea * conv * gqadfx # dry deposition;
gqadwt = prec * sarea * gqadcn # wet deposition;
gqadep = gqaddr + gqadwt # total atmospheric deposition
idqal = IDQAL[loop] * conv
indqal = idqal + gqaddr + gqadwt
# simulate advection of dissolved material
srovol = SROVOL[loop]
erovol = EROVOL[loop]
sovol = SOVOL[loop, :]
eovol = EOVOL[loop, :]
dqal, rodqal, odqal = advect(indqal, dqal, nexits, svol, vol, srovol, erovol, sovol, eovol)
bio = biop
if qalfg[5] > 0:
# get biomass input, if required (for degradation)
bio = BIO[loop]
if avdepe > 0.17: # simulate decay of dissolved material
hr = HRFG[loop]
ddqal[:,index] = ddecay(qalfg, tw20, ka, kb, kn, thhyd, phval,kox,thox, roc, fact2, fact1, photpm, korea, cfgas,
biocon, thbio, bio, fstdec, thfst, vol, dqal, hr, delt60)
# ddqal[1,index] = DDECAY(QALFG(1,I),TW20,HYDPM(1,I),PHVAL,ROXPM(1,I),ROC,FACT2(1),FACT1,PHOTPM(1,I),KOREA,CFGAS(I),
# BIOPM(1,I),BIO(I),GENPM(1,I),VOLSP,DQAL(I),HR,DELT60,DDQAL(1,I))
pdqal = 0.0
for k in range(1, 7):
if gqpm2[k] == 1: # this compound is a "daughter"-compute the contribution to it from its "parent(s)"
itobe = index - 1
for j in range(1,itobe):
pdqal = pdqal + ddqal[k,j]*c[j,k]
# update the concentration to account for decay and for input
# from decay of "parents"- units are conc/l
if vol > 0:
dqal = dqal + (pdqal - ddqal[7,index])/vol
else:
# rchres depth is less than two inches - dissolved decay is not considered
for l in range(1, 8):
ddqal[l,index] = 0.0
# 320 CONTINUE
pdqal = 0.0
adqal = zeros(8)
dsqal1 = 0.0
dsqal2 = 0.0
dsqal3 = 0.0
dsqal4 = 0.0
osqal1 = zeros(nexits)
osqal2 = zeros(nexits)
osqal3 = zeros(nexits)
osqal4 = zeros(nexits)
rosqal1 = 0.0
rosqal2 = 0.0
rosqal3 = 0.0
sqdec1 = 0.0
sqdec2 = 0.0
sqdec3 = 0.0
sqdec4 = 0.0
sqdec5 = 0.0
sqdec6 = 0.0
sqdec7 = 0.0
# zero the accumulators