def _simulate(self,event):
if self.params.getParam(parameters.Mode_is_structured).getValue():
studyName = self.params.getParam(parameters.Title).getValue()
dataBase = self.params.getParam(parameters.CurrentDatabasePath).getValue()
darcy = self.params.getParam(parameters.DarcyVelocity_list).getValue()
if darcy != []:
darcyVelocity = str(darcy[0])+","+str(darcy[1])+","+str(darcy[2])
initialTime = self.params.getParam(parameters.Iterate_InitialTime).getValue()
finalTime = self.params.getParam(parameters.Iterate_SimulationTime).getValue()
simulationTime = "["+str(initialTime)+","+str(finalTime)+"]"
structuredCase = open (studyName+".py",'w')
structuredCase.write("from constant import epspH\n")
structuredCase.write("from datamodel import *\n")
structuredCase.write("import fields\n")
structuredCase.write("from listtools import normMaxListComparison, subtractLists\n")
structuredCase.write("from chemicaltransport import *\n")
structuredCase.write("from chemicaltransportmodule import *\n")
structuredCase.write("from mt3d import Mt3d # mt3d\n")
structuredCase.write("from cartesianmesh import * # Cartesian mesh\n")
structuredCase.write("from phreeqc import * # phreeqc\n")
structuredCase.write("\n")
structuredCase.write("import os\n")
structuredCase.write("Phreeqc_file = \""+studyName+".txt\" # bounded to Phreeqc\n")
structuredCase.write("ProblemName = \""+studyName+"\" # Phreeqc file \n")
structuredCase.write("mesh = CartesianMesh2D(\"global\",\"XY\")\n")
nx = self.params.getParam(parameters.MeshLineInINumberOfCells).getValue()
ny = self.params.getParam(parameters.MeshLineInJNumberOfCells).getValue()
structuredCase.write("nx = "+str(nx)+"\n")
structuredCase.write("ny = "+str(ny)+"\n")
#
# writing the mesh extension
#
structuredCase.write("#~~~~~~~~~~~~~~~~~~\n")
structuredCase.write("#~ Mesh extension ~\n")
structuredCase.write("#~~~~~~~~~~~~~~~~~~\n")
structuredCase.write("deltax = []\n")
xlist = self.params.getParam(parameters.Mesh_list_InI).getValue()
ind = 0
while xlist[ind][0] != 0:
structuredCase.write("dx = ["+str(xlist[ind][1])+"/"+str(xlist[ind][0])+"]*"+str(xlist[ind][0])+"\n")
structuredCase.write("deltax.extend(dx)\n")
ind+=1
structuredCase.write("deltay = []\n")
ylist = self.params.getParam(parameters.Mesh_list_InJ).getValue()
ind = 0
while ylist[ind][0] != 0:
structuredCase.write("dy = ["+str(ylist[ind][1])+"/"+str(ylist[ind][0])+"]*"+str(ylist[ind][0])+"\n")
structuredCase.write("deltay.extend(dy)\n")
ind+=1
structuredCase.write("mesh.setdAxis(\"X\",deltax)\n")
structuredCase.write("mesh.setdAxis(\"Y\",deltay)\n")
zone_list = self.params.getParam(parameters.Zones_list).getValue()
zone_Material_AqueousState_list = self.params.getParam(parameters.Zone_Material_AqueousState_list).getValue()
ind = 0
for zone in zone_list:
structuredCase.write(str(zone)+str(ind)+"Body = CartesianMesh2D(\""+str(zone)+"\", \"XY\")\n")
imin = zone_Material_AqueousState_list[ind][2]
imax = zone_Material_AqueousState_list[ind][3]
jmin = zone_Material_AqueousState_list[ind][4]
jmax = zone_Material_AqueousState_list[ind][5]
string = str(zone)+str(ind)
structuredCase.write(string+"Body.setZone(\""+str(zone)+"\",index_min = Index2D ("+str(imin)+","+str(jmin)+\
"), index_max = Index2D ("+str(imax)+","+str(jmax)+"))\n")
ind+=1
structuredCase.write("#~~~~~~~~~~~~~\n")
structuredCase.write("#~ Materials ~\n")
structuredCase.write("#~~~~~~~~~~~~~\n")
materials = self.params.getParamValue(parameters.CUSTOM_MATERIAL_DB).getMaterials()
for toto in materials.keys():
materialName = str(toto)+"Material"
longDisp = str(materials[toto]["LongitudinalDispersivity"])
transDisp = str(materials[toto]["TransverseDispersivity"])
structuredCase.write(materialName+" = Material (name = \""+str(toto)+"\",")
structuredCase.write("effectiveDiffusion = EffectiveDiffusion ("+str(materials[toto]["EffectiveDiffusion"])+",unit=\"m**2/s\"),\\")
structuredCase.write("\npermeability = Permeability(value = "+str(materials[toto]["KxPermeability"])+"),\\")
structuredCase.write("\nporosity = Porosity(value = "+str(materials[toto]["EffectivePorosity"])+"),\\")
structuredCase.write("\nkinematicDispersion = KinematicDispersion ("+longDisp+","+transDisp+"))\n")
# print materials
structuredCase.write("\n#~~~~~~~~~~~\n")
structuredCase.write("#~ Regions ~\n")
structuredCase.write("#~~~~~~~~~~~\n")
ind = 0
regionList = "["
for zone in zone_list:
if ind!=0: regionList+=","
materialName = str(zone_Material_AqueousState_list[ind][0])+"Material"
structuredCase.write(str(zone)+str(ind)+"Region = Region(support="+str(zone)+str(ind)+"Body, material= "+materialName+")\n")
regionList+=str(zone)+str(ind)+"Region"
ind+=1
regionList+="]"
#
#
_chemical(self.params,structuredCase)
#
#
#
#chemical_state_quartz = ChemicalState ("column", AqueousSolution_column, columnMineralPhase)
#
structuredCase.write("#~~~~~~~~~~~~~~~~~~~~\n")
structuredCase.write("# Initial condition ~\n")
structuredCase.write("#~~~~~~~~~~~~~~~~~~~~\n")
initialConditionList = self.params.getParam(parameters.InitialConditions_list).getValue()
print "initialConditionList: ",initialConditionList
boundaryConditionList = self.params.getParam(parameters.BoundaryConditions_list).getValue()
iCLS = "["
for iC in initialConditionList:
iCName = str(iC)+"IC"
iCLS+=iCName+","
iCParameters = zone_Material_AqueousState_list[zone_list.index(iC)]
materialName = str(iCParameters[0]) + "Material"
aqueousStateName = str(iCParameters[1])+"ChemicalState"
structuredCase.write(iCName+" = InitialCondition (body = "+str(iC)+str(zone_list.index(iC))+"Body, value = "+aqueousStateName+")\n")
iCLS = iCLS[0:len(iCLS)-1]
iCLS += "]"
structuredCase.write("#~~~~~~~~~~~~~~~~~~~~~\n")
structuredCase.write("# Boundary condition ~\n")
structuredCase.write("#~~~~~~~~~~~~~~~~~~~~~\n")
bCLS = "["
for iC in boundaryConditionList:
iCName = str(iC)+"BC"
bCLS+=iCName+","
iCParameters = zone_Material_AqueousState_list[zone_list.index(iC)]
materialName = str(iCParameters[0])+"Material"
aqueousStateName = str(iCParameters[1])+"ChemicalState"
structuredCase.write(iCName+" = BoundaryCondition (boundary = "+str(iC)+str(zone_list.index(iC))+"Body, btype=\"Dirichlet\", value = "+aqueousStateName+")\n")
#bIC = BoundaryCondition (boundary = b0Zone, btype='Dirichlet', value = sodaChemicalState)
bCLS = bCLS[0:len(bCLS)-1]
bCLS += "]"
structuredCase.write("#~~~~~~~~~~~~~~~~~~~\n")
structuredCase.write("# Expected outputs ~\n")
structuredCase.write("#~~~~~~~~~~~~~~~~~~~\n")
outputList = self.params.getParam(parameters.ExpectedOutputs_list).getValue()
# print "outputList",outputList
if outputList != []:
string = "expectedOutputs = ["
for out in outputList:
if str(out) == "pH":
string+="ExpectedOutput(\"pH\",format=\"table\",name=\"pH_output\"),\n"
else:
string+="ExpectedOutput(\"Concentration\",\""+out+"\",format=\"table\",name=\""+out+"Output\"),\n"
string = string[0:-2]+"]\n"
structuredCase.write(string)
else:
structuredCase.write("expectedOutputs = []\n")
structuredCase.write("#~~~~~~~~~\n")
structuredCase.write("# Module ~\n")
structuredCase.write("#~~~~~~~~~\n")
structuredCase.write("module = ChemicalTransportModule()\n")
structuredCase.write("problem = ChemicalTransportProblem(name = \""+\
str(studyName)+"\",\\")
structuredCase.write("\n regions = "+regionList+",\\\n")
structuredCase.write(" initialConditions = "+iCLS+",\\\n")
structuredCase.write(" boundaryConditions = "+bCLS+",\\\n")
structuredCase.write(" calculationTimes = "+simulationTime+",\\\n")
structuredCase.write(" sources = None,\\\n")
if darcy == []:
structuredCase.write(" darcyVelocity = None,\\\n")
else:
structuredCase.write(" darcyVelocity = Velocity(Vector(["+darcyVelocity+"])),\\\n")
#
# The database should be placed in the Phreeqc_dat directory
#
dataBase = os.path.split(dataBase)[-1]
structuredCase.write(" chemistryDB = \""+dataBase+"\",\\\n")
structuredCase.write(" speciesBaseAddenda = speciesAddenda,\\\n")
structuredCase.write(" kineticLaws = None,\\\n")
structuredCase.write(" activityLaw = None,\\\n")
structuredCase.write(" outputs = expectedOutputs)\n")
algorithm = self.params.getParam(parameters.Iterate_Algorithm).getValue()
structuredCase.write("module.setData (problem, trace = 0, mesh = mesh, algorithm=\""+algorithm+"\")\n")
structuredCase.write("\nmodule.setComponent(\"mt3d\",\"phreeqc\")\n")
scheme = self.params.getParam(parameters.Mt3d_advection).getValue()
structuredCase.write("module.setTransportParameters(\""+scheme+"\")\n")
preconditionner = self.params.getParam(parameters.Mt3d_ConjugateGradientPreconditioner).getValue()
epsPred = str(self.params.getParam(parameters.Mt3d_cclose).getValue())
structuredCase.write("module.setTransportParameters(\""+preconditionner+"\","+epsPred+")\n")
if str(algorithm) == "NI":
minStepSize = self.params.getParam(parameters.Iterate_InitialTimeStepSize).getValue()
maxStepSize = self.params.getParam(parameters.Iterate_InitialTimeStepSize).getValue()
else:
minStepSize = self.params.getParam(parameters.Iterate_MinTimeStep).getValue()
maxStepSize = self.params.getParam(parameters.Iterate_MaxTimeStep).getValue()
structuredCase.write("module.setCouplingParameter(initialTimeStep = "+\
str(self.params.getParam(parameters.Iterate_InitialTimeStepSize).getValue())+","+\
"\n minTimeStep = "+\
str(minStepSize)+","\
"\n maxTimeStep = "+\
str(maxStepSize)+","\
"\n couplingPrecision = "+\
str(self.params.getParam(parameters.Iterate_CouplingPrecision).getValue())+","\
"\n optimalIterationNumber = "+\
str(self.params.getParam(parameters.Iterate_PicardTargetNumber).getValue())+","\
"\n maxIterationNumber = "+\
str(self.params.getParam(parameters.Iterate_PicardMaxOfIterations).getValue())+","\
"\n decreaTimeStepCoef = "+\
str(self.params.getParam(parameters.Iterate_RelaxationMinFactor).getValue())+","\
"\n increaTimeStepCoef = "+\
str(self.params.getParam(parameters.Iterate_RelaxationMaxFactor).getValue())+")")
if self.params.getParam(parameters.PostprocessingContours_AqueousComponentsToPlot_list).getValue() != []:
structuredCase.write("\n#~~~~~~~~~~~\n")
structuredCase.write("# Contours ~\n")
structuredCase.write("#~~~~~~~~~~~\n")
string = "module.setVtkOutputsParameters(["
for species in self.params.getParam(parameters.PostprocessingContours_AqueousComponentsToPlot_list).getValue():
string += "\""+str(species)+"\","
string = string[0:len(string)-1]+"],"
string += "\""+str(self.params.getParam(parameters.PostprocessingContours_Parameters_list).getValue()[1])+"\","
string += str(self.params.getParam(parameters.PostprocessingContours_Parameters_list).getValue()[0])+")\n"
structuredCase.write(string)
# module.setVtkOutputsParameters(["Na"],"days",2)
structuredCase.write("\nmodule.run()\n")
if string!= "":
structuredCase.write("#~~~~~~~~~~~~~~~~~~\n")
structuredCase.write("# Post processing ~\n")
structuredCase.write("#~~~~~~~~~~~~~~~~~~\n")
string = self.params.getParam(parameters.PyOutputHandler).getValue()
structuredCase.write(string)
lenString = len(" End of the ")+len(studyName)+len(" case ~")
en = "~"*lenString
structuredCase.write("\nprint \""+en+"\"\n")
structuredCase.write("print \" End of the "+studyName+" case ~\"")
structuredCase.write("\nprint \""+en+"\"\n")
structuredCase.write("\nmodule.end()\n")
structuredCase.close()
#
# Running the generated file in a PyShell
#
from wx import py
import wx.py as py
#namespace = { 'wx' : wx,
# 'app' : wx.GetApp(),
# 'frame' : self,
# }
#DEFAULT_SHELL_WINDOW_SIZE = (640,480)
#self.shell = py.shell.ShellFrame(None, title = " interactive launch browser", locals=namespace)
#self.shell.SetSize( DEFAULT_SHELL_WINDOW_SIZE )
#self.shell.Show()
os.system("python "+studyName+".py")
#toto = Myne("Coupling browser",studyName+".py")
else: # case of an unstructured file. In that case, we should restructure that if/elif statement
print("noch zu machen")
return True
def _simulate(self,event):
# if not os.path.isdir("/home/david/Wrapper/Api/Geoi/src/geoi/Simulation"):
# os.mkdir("/home/david/Wrapper/Api/Geoi/src/geoi/Simulation")
# else :
# pass
nameFile = self.params.getParam(parameters.Title).getValue()
params=self.params
self.retpython = None
# directory = params.getParam(parameters.ResultDirectory).getValue()
# os.chdir(directory)
# print directory
pythonFile = os.getcwd()+"/"+nameFile+".py"
f1=open(pythonFile,"w")
#
# elmer imports
#
_elmerimport(f1)
f1.write("setProblemType(\"ChemicalTransport\")\n\n")
#
# elmer mesh import
#
f1.write("#~~~~~~~~~~~~~~~~~~~~~~\n")
f1.write("# Mesh definition\n")
f1.write("#~~~~~~~~~~~~~~~~~~~~~~\n")
#
_meshimport(self.params,f1)
#
zone_list = self.params.getParam(parameters.Zones_list).getValue()
i=0
for zone in zone_list:
f1.write(str(zone)+str(i)+"Body = mesh.getBody(\""+str(zone)+"\")\n")
f1.write(str(zone)+str(i)+"Body.getNodesNumber()\n")
i+=1
f1.write("numberOfVertices = mesh._getNumberOfVertices()\n")
#
# materials
#
f1.write("#~~~~~~~~~~~~~~~~~~~~~~\n")
f1.write("# Material\n")
f1.write("#~~~~~~~~~~~~~~~~~~~~~~\n")
#
_materials(self.params,f1)
#
# regions
#
f1.write("\n#~~~~~~~~~~~\n")
f1.write("#~ Regions ~\n")
f1.write("#~~~~~~~~~~~\n")
#
zone_Material_AqueousState_list, regionList = _regions(self.params,f1)
#
# chemistry
#
_chemical(self.params,f1)
#
#
#
#chemical_state_quartz = ChemicalState ("column", AqueousSolution_column, columnMineralPhase)
#
f1.write("#~~~~~~~~~~~~~~~~~~~~\n")
f1.write("# Initial condition ~\n")
f1.write("#~~~~~~~~~~~~~~~~~~~~\n")
initialConditionList = self.params.getParam(parameters.InitialConditions_list).getValue()
boundaryConditionList = self.params.getParam(parameters.BoundaryConditions_list).getValue()
iCLS = "["
for iC in initialConditionList:
iCName = str(iC)+"IC"
iCLS+=iCName+","
iCParameters = zone_Material_AqueousState_list[zone_list.index(iC)]
materialName = str(iCParameters[0]) + "Material"
aqueousStateName = str(iCParameters[1])+"ChemicalState"
f1.write(iCName+" = InitialCondition (body = "+str(iC)+str(zone_list.index(iC))+"Body, value = "+aqueousStateName+")\n")
if iCLS != "[": iCLS = iCLS[0:len(iCLS)-1]
iCLS += "]"
f1.write("#~~~~~~~~~~~~~~~~~~~~~\n")
f1.write("# Boundary condition ~\n")
f1.write("#~~~~~~~~~~~~~~~~~~~~~\n")
bCLS = "["
for iC in boundaryConditionList:
iCName = str(iC)+"BC"
bCLS+=iCName+","
iCParameters = zone_Material_AqueousState_list[zone_list.index(iC)]
materialName = str(iCParameters[0])+"Material"
aqueousStateName = str(iCParameters[1])+"ChemicalState"
f1.write(iCName+" = BoundaryCondition (boundary = "+str(iC)+str(zone_list.index(iC))+"Body, btype=\"Dirichlet\", value = "+aqueousStateName+")\n")
#bIC = BoundaryCondition (boundary = b0Zone, btype='Dirichlet', value = sodaChemicalState)
if bCLS != "[": bCLS = bCLS[0:len(bCLS)-1]
bCLS += "]"
#
# outputs
#
f1.write("#~~~~~~~~~~~~~~~~~~~\n")
f1.write("# Expected outputs ~\n")
f1.write("#~~~~~~~~~~~~~~~~~~~\n")
#
_outputs(self.params,f1)
#
# module
#
f1.write("#~~~~~~~~~\n")
f1.write("# Module ~\n")
f1.write("#~~~~~~~~~\n")
#
_problem(self.params,f1, regionList, iCLS, bCLS)
_chemicaltransportmodule(self.params,f1,"Elmer")
species = self.params.getParam(parameters.PostprocessingContours_AqueousComponentsToPlot_list).getValue()
frequency = self.params.getParam(parameters.PostprocessingContours_Parameters_list).getValue()
if len(species)>0 :
f1.write("module.setVtkOutputsParameters([")
for ind in range(len(species)-1) :
f1.write("\""+species[ind]+"\",")
f1.write("\""+species[len(species)-1]+"\"]," + "\"" + str(frequency[1]) + "\"," + frequency[0] + ")\n\n")
#
# algebraic resolution
#
_algebraicResolution(self.params,f1)
#
# running module
#
# f1.write("#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n")
# f1.write("module.run()\n")
# f1.write("#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n")
f1.write("#~~~~~~~~~~~~~~~~~~~~~~~~~~\n")
f1.write("# transient algorithm ~\n")
f1.write("#~~~~~~~~~~~~~~~~~~~~~~~~~~\n")
_moduleLooping(self.params,f1)
#
# post processing
#
f1.write("\n\n")
f1.write("#~~~~~~~~~~~~~~~~~~~~\n")
f1.write("# Post Processing ~\n")
f1.write("#~~~~~~~~~~~~~~~~~~~~\n")
_postProcessing(self.params,f1)
f1.flush()
f1.close()
while f1.closed == False:
pass
# wx.MessageDialog(self.parent, "Regarde le Terminal", "Warning", wx.OK | wx.ICON_WARNING).ShowModal()
# os.chdir(directory)
# try:
# retcode = subprocess.Popen("rm -f commandfile.eg", shell = True)
# if retcode < 0:
# print >>sys.stderr, "Child was terminated by signal", -retcode
# else:
# print >>sys.stderr, "Child returned", retcode
# except OSError, e:
# print >>sys.stderr, "Execution failed:", e
# try:
# retcode = subprocess.Popen("rm -rf " + nameFile , shell = True)
# if retcode < 0:
# print >>sys.stderr, "Child was terminated by signal", -retcode
# else:
# print >>sys.stderr, "Child returned", retcode
# except OSError, e:
# print >>sys.stderr, "Execution failed:", e
self.retpython = subprocess.Popen("python " +nameFile+".py", shell = True)
