def initialise(self, componentName=None):
"""
As in a fairy tale, if the emse software is introduced
"""
self.component = Phreeqc()
self.solver = self.component # To evolve to solver
self.componentName = "phreeqc" # We only have phreeqc as solver. Thoughreact 1.5 isn't validated
if self.componentName == "phreeqc":
#self.dB = self.component.fileRecognition(self.dB)
self.component.setDataBase(self.dB)
pass
self.component.setChemicalState(self.chemicalState)
if self.activityLaw:
self.component.setActivityLaw(self.activityLaw)
pass
if self.kineticLaws:
self.component.setKineticLaws(self.kineticLaws)
pass
if self.outputs:
self.component.setExpectedOutputs(self.outputs)
pass
if self.speciesBaseAddenda:
self.component.setSpeciesBaseAddenda(self.speciesBaseAddenda)
pass
if self.timeStep:
self.component.setTimeStep(self.timeStep)
pass
if isinstance(self.simulationTime, Time):
self.component.setSimulationTime(self.simulationTime)
if self.timeStep and self.simulationTime:
self.component.batch == True
return None
def initialise(self, componentName= None):
"""
As in a fairy tale, if the emse software is introduced
"""
self.component = Phreeqc()
self.solver = self.component # to evolve to solver
self.componentName = "phreeqc"
self.component.setDataBase(self.dB)
self.component.setChemicalState(self.chemicalState)
if self.activityLaw:
self.component.setActivityLaw(self.activityLaw)
pass
if self.kineticLaws:
self.component.setKineticLaws(self.kineticLaws)
pass
if self.outputs:
self.component.setExpectedOutputs(self.outputs)
pass
if self.speciesBaseAddenda:
self.component.setSpeciesBaseAddenda(self.speciesBaseAddenda)
pass
if self.timeStep:
self.component.setTimeStep(self.timeStep)
pass
if isinstance(self.simulationTime,Time):
self.component.setSimulationTime(self.simulationTime)
if self.timeStep and self.simulationTime:
self.component.batch == True
return None
class Chemical(object):
"""
Module of Chemistry
"""
def __init__(self):
"""
Init
Examples :
chem = Chemical()
"""
self.activityLaw = None
self.dB = None
self.chemicalState = None
self.comment = ""
self.kineticLaws = None
self.name = None
self.speciesBaseAddenda = None
self.outputs = None
self.timeStep = None
self.simulationTime = None
self.trace = 0
return None
def setComment(self, comment):
self.comment = comment
def setData(self, problem):
"""
Within that method we access through the problem to chemical data
That method is used in the python script.
"""
if not isinstance(problem, ChemicalProblem):
raise Exception(" the problem should be a chemical problem ")
self.activityLaw = problem.getActivityLaw()
self.dB = problem.getDB()
self.chemicalState = problem.getChemicalState()
self.kineticLaws = problem.getKineticLaws()
self.name = problem.getName()
self.outputs = problem.getOutputs()
self.speciesBaseAddenda = problem.getSpeciesBaseAddenda()
self.timeStep = problem.getTimeStep()
self.simulationTime = problem.simulationTime
return None
def setVerbose(self, trace):
self.component.setVerbose(trace)
def initialise(self, componentName=None):
"""
As in a fairy tale, if the emse software is introduced
"""
self.component = Phreeqc()
self.solver = self.component # To evolve to solver
self.componentName = "phreeqc" # We only have phreeqc as solver. Thoughreact 1.5 isn't validated
if self.componentName == "phreeqc":
#self.dB = self.component.fileRecognition(self.dB)
self.component.setDataBase(self.dB)
pass
self.component.setChemicalState(self.chemicalState)
if self.activityLaw:
self.component.setActivityLaw(self.activityLaw)
pass
if self.kineticLaws:
self.component.setKineticLaws(self.kineticLaws)
pass
if self.outputs:
self.component.setExpectedOutputs(self.outputs)
pass
if self.speciesBaseAddenda:
self.component.setSpeciesBaseAddenda(self.speciesBaseAddenda)
pass
if self.timeStep:
self.component.setTimeStep(self.timeStep)
pass
if isinstance(self.simulationTime, Time):
self.component.setSimulationTime(self.simulationTime)
if self.timeStep and self.simulationTime:
self.component.batch == True
return None
def setParameter(self, out):
"""
Set specific component parameters
Input :
parameter_name (string)
parameter_value ()
"""
if self.component:
self.component.setParameter(out)
else:
raise Exception(
"You have to execute setComponent before setParameter")
return None
def setComponent(self, name):
self.initialise()
def setComponentTimeParameters(self):
"""
Set specific time component parameters
Input :
"""
if self.component:
if isinstance(self.timeStep, Time) and isinstance(
self.simulationTime, Time):
self.component.setTimeParameters(self.timeStep,
self.simulationTime)
else:
raise Warning(
"check the definition of the time parameters of the chemicalproblem instance."
)
else:
raise Exception(
"You have to execute setComponent before setTimeParameters")
return None
def run(self):
"""
Used to simulate a chemical equilibrium once that one
has been defined within the problem
module = Chemical()
problem = ChemicalProblem(name = "soda",\
dB = "phreeqc.dat",\
speciesBaseAddenda = speciesAddenda,\
chemicalState = sodaChemicalState)
module.setData(problem)
module.initialise()
module.setParameter("soda.out")
module.run()
The evolution of a batch over time can also be modelled. Then time steps and the simulation time have
to be introduced.
"""
if self.component:
#raw_input(" call to run within py: chemicalmodule")
self.component.run()
#raw_input("end of call to run within py: chemicalmodule")
else:
raise Exception("You have to execute setComponent before run")
return
def launch(self):
self.run()
def end(self):
"""
To Stop phreeqc
"""
if self.component:
self.component.end()
return None
def getOutput(self, outputName=None, outputFormat=None):
"""
To get a specific output
Input :
outputName (string) : it can be the name of a specified
ExpectedOutput or 'state'. If 'state' specified, it returns a *
list of data.
Ouput :
()
pH = module.getOutput('pH')
"""
if (outputName == None):
outputName = 'state'
pass
if self.component:
if (outputName == 'state'):
if outputFormat == None:
return self.component.getOutputState()
else:
return self.component.getOutputState({})
elif (outputName == 'componentsConcentration'):
self.component.getPrimarySpeciesNames()
return self.component.getMobileConcentration()
else:
return self.component.getOutput(outputName)
pass
else:
raise Exception(
"Prior to this call, the simulation has to be setup accordingly"
)
return
def outputStateSaving(self):
"""
Permits to retrieve from Phreeqc information on the current state
It furnishes a unique list containing in order of appearance:
aqueous primary species number
aqueous secondary species number
sorbed species number
minerals number
ph
pe
water activity
ionicstrength
temperature
electrical_balance
total_h
total_o
and a list of tuples representing the aqueous and mineral states
"""
state = self.getOutput()
self.equilibriumState = state
#print type(state)
if self.component.outFile == None:
outFile = open("phreeqCFile.out", 'w')
else:
outFile = open(self.component.outFile, 'w')
outFile.write("%20s\n\n\n" % str(self.comment))
outFile.write("number of aqueous primary species %20s\n" %
str(state[0]))
outFile.write("number of aqueous secondary species %20s\n" %
str(state[1]))
outFile.write("number of minerals %20s\n" %
str(state[3]))
outFile.write("number of sorbed species %20s\n" %
str(state[2]))
outFile.write("\npH %20s\n" %
str(state[4]))
outFile.write("pe %20s\n" %
str(state[5]))
outFile.write("water activity %20s\n" %
str(state[6]))
outFile.write("ionicstrength %20s\n" %
str(state[7]))
outFile.write("temperature %20s\n" %
str(state[8]))
outFile.write("electrical_balance %20s\n" %
str(state[9]))
outFile.write("total H %20s\n" %
str(state[10]))
outFile.write("total O %20s\n" %
str(state[11]))
outFile.write("density of water (kg/m3) %20s\n" %
str(state[12]))
ind = 0
anf = 13
print " self.component.defaultPhreeqcVersion: ", self.component.version
#raw_input()
if (self.component.version == 3):
outFile.write("volume (L) %20s\n" %
str(state[14]))
outFile.write("totalCO2 (mol/kg) %20s\n" %
str(state[13]))
outFile.flush()
anf = 15
end = anf + int(state[0])
#print " type",state[11],type(state[10])
#print " state: ", state
#raw_input()
outFile.write("\n\n primary species: mol/l\n\n")
#print " state anf end: ", state[anf:end]
#raw_input()
for i in state[anf:end]:
print i[0], i[1], type(i[0]), type(i[1])
outFile.write("%20s %s\n" % (str(i[0]), str(i[1])))
pass
anf = end
end = anf + int(state[1])
outFile.write("\n\n secondary species: mol/l\n\n")
for i in state[anf:end]:
outFile.write("%20s %s\n" % (str(i[0]), str(i[1])))
pass
anf = end
end = anf + int(state[2])
outFile.write("\n\n sorbed species: moles\n\n")
for i in state[anf:end]:
outFile.write("%20s %s\n" % (str(i[0]), str(i[1])))
pass
anf = end
outFile.write(
"\n\n SI( target saturation index): SI < 0 undersaturation, 0: equilibrium and supersaturation otherwise\n\n"
)
outFile.write("\n\n")
outFile.write(
"\n\n mineral species: SI moles\n\n"
)
for i in state[anf:]:
outFile.write("%30s %15.8e %15.8e\n\n" %
(str(i[0]), float(str(i[2])), float(str(i[1]))))
pass
def printOutputState(self):
"""
Print chemical state speciation
Examples
chem_uo2.printOutputState()
"""
if self.component:
self.component.printOutputState()
else:
raise Exception("You have to execute setPrimary before getOutput")
return
class Chemical:
"""
Module of Chemistry
"""
def __init__(self):
"""
Init
Examples :
chem = Chemical()
"""
self.activityLaw = None
self.dB = None
self.chemicalState = None
self.comment = ""
self.kineticLaws = None
self.name = None
self.speciesBaseAddenda = None
self.outputs= None
self.timeStep= None
self.simulationTime = None
self.trace= 0
return None
def setComment(self, comment):
self.comment = comment
def setData(self, problem):
"""
Within that method we access through the problem to chemical data
That method is used in the python script.
"""
if not isinstance(problem, ChemicalProblem):
raise Exception(" the problem should be a chemical problem ")
self.activityLaw = problem.getActivityLaw()
self.dB = problem.getDB()
self.chemicalState = problem.getChemicalState()
self.kineticLaws = problem.getKineticLaws()
self.name = problem.getName()
self.outputs = problem.getOutputs()
self.speciesBaseAddenda = problem.getSpeciesBaseAddenda()
self.timeStep = problem.getTimeStep()
self.simulationTime = problem.simulationTime
return None
def setVerbose(self, trace):
self.component.setVerbose(trace)
def initialise(self, componentName= None):
"""
As in a fairy tale, if the emse software is introduced
"""
self.component = Phreeqc()
self.solver = self.component # to evolve to solver
self.componentName = "phreeqc"
self.component.setDataBase(self.dB)
self.component.setChemicalState(self.chemicalState)
if self.activityLaw:
self.component.setActivityLaw(self.activityLaw)
pass
if self.kineticLaws:
self.component.setKineticLaws(self.kineticLaws)
pass
if self.outputs:
self.component.setExpectedOutputs(self.outputs)
pass
if self.speciesBaseAddenda:
self.component.setSpeciesBaseAddenda(self.speciesBaseAddenda)
pass
if self.timeStep:
self.component.setTimeStep(self.timeStep)
pass
if isinstance(self.simulationTime,Time):
self.component.setSimulationTime(self.simulationTime)
if self.timeStep and self.simulationTime:
self.component.batch == True
return None
def setParameter(self, out):
"""
Set specific component parameters
Input :
parameter_name (string)
parameter_value ()
"""
if self.component:
self.component.setParameter(out)
else:
raise Exception("You have to execute setComponent before setParameter")
return None
def setComponent(self,name):
self.initialise()
def setComponentTimeParameters(self):
"""
Set specific time component parameters
Input :
"""
if self.component:
if isinstance(self.timeStep,Time) and isinstance(self.simulationTime,Time):
self.component.setTimeParameters(self.timeStep, self.simulationTime)
else:
raise Warning("check the definition of the time parameters of the chemicalproblem instance.")
else:
raise Exception("You have to execute setComponent before setTimeParameters")
return None
def run(self):
"""
Used to simulate a chemical equilibrium once that one
has been defined within the problem
module = Chemical()
problem = ChemicalProblem(name = "soda",\
dB = "phreeqc.dat",\
speciesBaseAddenda = speciesAddenda,\
chemicalState = sodaChemicalState)
module.setData(problem)
module.initialise()
module.setParameter("soda.out")
module.run()
The evolution of a batch over time can also be modelled. Then time steps and the simulation time have
to be introduced.
"""
if self.component:
self.component.run()
else:
raise Exception("You have to execute setComponent before run")
return
def launch(self):
self.run()
def end(self):
"""
To Stop phreeqc
"""
if self.component:
self.component.end()
return None
def getOutput(self, outputName=None, outputFormat = None):
"""
To get a specific output
Input :
outputName (string) : it can be the name of a specified
ExpectedOutput or 'state'. If 'state' specified, it returns a *
list of data.
Ouput :
()
pH = module.getOutput('pH')
"""
if (outputName==None):
outputName='state'
if self.component:
if (outputName=='state'):
if outputFormat == None:
return self.component.getOutputState()
else:
return self.component.getOutputState({})
elif (outputName=='componentsConcentration'):
self.component.getPrimarySpeciesNames()
return self.component.getMobileConcentration()
else:
return self.component.getOutput(outputName)
pass
else:
raise Exception("You have to execute setPrimary before getOutput")
return
def outputStateSaving(self):
"""
Permits to retrieve from Phreeqc information on the current state
It furnishes a unique list containing in order of appearance:
aqueous primary species number
aqueous secondary species number
sorbed species number
minerals number
ph
pe
water activity
ionicstrength
temperature
electrical_balance
total_h
total_o
and a list of tuples representing the aqueous and mineral states
"""
state = self.getOutput()
#print type(state)
if self.component.outFile == None:
outFile = open("phreeqCFile.out", 'w')
else:
outFile = open(self.component.outFile, 'w')
outFile.write("%20s\n\n\n"%str(self.comment))
outFile.write("number of aqueous primary species %20s\n"%str(state[0]))
outFile.write("number of aqueous secondary species %20s\n"%str(state[1]))
outFile.write("number of minerals %20s\n"%str(state[3]))
outFile.write("number of sorbed species %20s\n"%str(state[2]))
outFile.write("\npH %20s\n"%str(state[4]))
outFile.write("pe %20s\n"%str(state[5]))
outFile.write("water activity %20s\n"%str(state[6]))
outFile.write("ionicstrength %20s\n"%str(state[7]))
outFile.write("temperature %20s\n"%str(state[8]))
outFile.write("electrical_balance %20s\n"%str(state[9]))
outFile.write("total H %20s\n"%str(state[10]))
outFile.write("total O %20s\n"%str(state[11]))
outFile.write("density of water %20s\n"%str(state[12]))
#print " type",state[11],type(state[10])
ind = 0
anf = 13
end = anf + int(state[0])
#print state
outFile.write("\n\n primary species: mol/l\n\n")
for i in state[anf:end]:
outFile.write("%20s %s\n"%(str(i[0]),str(i[1])))
anf = end
end = anf + int(state[1])
outFile.write("\n\n secondary species: mol/l\n\n")
for i in state[anf:end]:
outFile.write("%20s %s\n"%(str(i[0]),str(i[1])))
anf = end
end = anf + int(state[2])
outFile.write("\n\n sorbed species: moles\n\n")
for i in state[anf:end]:
outFile.write("%20s %s\n"%(str(i[0]),str(i[1])))
anf = end
outFile.write("\n\n SI( target saturation index): SI < 0 undersaturation, 0: equilibrium and supersaturation otherwise\n\n")
outFile.write("\n\n")
outFile.write("\n\n mineral species: SI moles\n\n")
for i in state[anf:]:
outFile.write("%30s %15.8e %15.8e\n\n"%(str(i[0]),float(str(i[2])),float(str(i[1]))))
def printOutputState(self):
"""
Print chemical state speciation
Examples
chem_uo2.printOutputState()
"""
if self.component:
self.component.printOutputState()
else:
raise Exception("You have to execute setPrimary before getOutput")
return
from __future__ import division
from phreeqc import Phreeqc
from species import molarMassStringEval
from species import *
import numpy as np
import os
chemistrySolver = Phreeqc()
#
databaseFile = os.getenv("PHREEQCDAT") + "/phreeqc.dat"
molarMassDico = chemistrySolver.getMolarMassList(databaseFile, typ={})
#
caCl2SSp = AqueousSecondarySpecies(symbol = "CaCl2",\
formationReaction = [("Ca++",1),("2Cl-",1)],\
logK25 = -0.64,\
logK = [1.56212e+03, 2.55796e-01, -8.58012e+04, -5.69819e+02, 5.22119e+06],\
name = "CaCl2",)
molarMassCaCl2 = caCl2SSp.getMolarMass(molarMassDico)
naClSSp = AqueousSecondarySpecies(symbol = "NaCl",\
formationReaction = [("1Cl-",1),("1Na+",1)],\
logK25 = -0.5,\
name = "NaCl",)
molarMassNaCl = naClSSp.getMolarMass(molarMassDico)
#
h2OSSp = AqueousSecondarySpecies(symbol = "H2O",\
formationReaction = [("H+",2),("0--",1)],\
logK25 = 0.0,\
name = "H2O",)
molarMassH2O = h2OSSp.getMolarMass(molarMassDico)
#
kClSSp = AqueousSecondarySpecies(symbol = "KCl",\
formationReaction = [("1Cl-",1),("1K+",1)],\