def run_SHM(self, work, wind_dict):
if wind_dict["procnr"] > 1:
self._r.status("Running SHM parallel")
decomposeDict = ParsedParameterFile(
path.join(work.systemDir(), "decomposeParDict"))
decomposeDict["method"] = "ptscotch"
decomposeDict.writeFile()
self.mpirun(procnr=wind_dict['procnrSnappy'], argv=['snappyHexMesh',
'-overwrite', '-case', work.name],output_file=path.join(work.name, 'SHM.log'))
print 'running clearCase'
ClearCase(args=work.name+' --processors-remove')
else:
SHMrun = BasicRunner(argv=["snappyHexMesh",
'-overwrite','-case',work.name],
server=False,logname="SHM")
self._r.status("Running SHM uniprocessor")
SHMrun.start()
def runCasesFiles(names, cases, runArg, n):
start = os.getcwd()
for case in cases:
os.chdir(case)
# change customeRegexp
customRegexpName = "customRegexp.base"
with open(os.path.join(case, 'customRegexp.base'), 'w+') as fd:
fd.write(custom_reg_exp_contents)
title = "Residuals for %s" %case
customRegexpFile = ParsedParameterFile(customRegexpName)
customRegexpFile["myFigure"]["theTitle"] = ('"'+title+'"')
customRegexpFile.writeFile()
# delete the header lines - ParsedParameterFile requires them, but the customRegexp dosen't seem to work when their around...
lines = open(customRegexpName).readlines()
open('customRegexp', 'w').writelines(lines[12:])
print n
# if n>1 make sure case is decomposed into n processors
if n > 1:
print "decomposing %(case)s" % locals()
ClearCase(" --processors-remove %(case)s" % locals())
Decomposer('--silent %(case)s %(n)s' % locals())
#!/usr/bin/python from PyFoam.Applications.ClearCase import ClearCase ClearCase()
def run_decompose(self, work, wind_dict):
if wind_dict['procnr'] < 2:
self._r.status('skipped decompose')
return
ClearCase(args=work.name+' --processors-remove')
Decomposer(args=[work.name, wind_dict['procnr']])
def FOAM_model(xtr, y, ztr, Patient, Template):
errorCode = True ## True when simulation has succesfully run
## Specify simulation folder
Simulation = Patient + "/simulation"
## Clear case
ClearCase(args=["--clear-history", Simulation])
print("Complete cleaning the case done")
if not os.path.exists(Simulation): ## if simulation directory doesnt exist
## Clone template onto simulation folder
CloneCase(args=[Template, Simulation])
print("Copied generic case to patient specific folder")
## copy betavSolid and actual skin temperature data onto the gland 0 folder
shutil.copyfile(Template + "/0/gland/betavSolid",
Simulation + "/0/gland/betavSolid")
shutil.copyfile(Patient + "/actualSkinData",
Simulation + "/0/gland/actualSkinData")
## define different cell zones using topoSetDict
bmName = os.path.join(Simulation, 'system', "topoSetDict")
template = TemplateFile(bmName + ".template", expressionDelimiter="$")
template.writeToFile(bmName, {
'x': xtr,
'y': y,
'z': ztr,
'r': radius,
'gr': gr
})
print("Setting template file for topoSet done")
## Run topoSet
topoSetRun = BasicRunner(argv=["topoSet", "-case", Simulation],
silent=True,
server=False,
logname='log.topoSet')
topoSetRun.start()
if not topoSetRun.runOK():
error("There was a problem with topoSet")
print("topoSet done")
print(xtr, y, ztr)
## Split mesh regions based on toposet
splitMeshRegionsRun = BasicRunner(
argv=["splitMeshRegions -cellZones -overwrite", "-case", Simulation],
silent=True,
server=False,
logname='log.splitMeshRegions')
splitMeshRegionsRun.start()
if not splitMeshRegionsRun.runOK():
error("There was a problem with split mesh regions")
print("split mesh regions done")
## Run change dictionary for gland region
changeDictionaryGlandRun = BasicRunner(
argv=[" changeDictionary -region gland", "-case", Simulation],
silent=True,
server=False,
logname='log.changeDictionaryGland')
changeDictionaryGlandRun.start()
if not changeDictionaryGlandRun.runOK():
error("There was a problem with change dictionary for gland")
print("change dictionary gland done")
## Run change dictionary for tumor region
changeDictionaryTumorRun = BasicRunner(
argv=[" changeDictionary -region tumor", "-case", Simulation],
silent=True,
server=False,
logname='log.changeDictionaryTumor')
changeDictionaryTumorRun.start()
if not changeDictionaryTumorRun.runOK():
error("There was a problem with change dictionary for tumor")
print("change dictionary tumor done")
## Run setFields for gland region
setFieldsGlandRun = BasicRunner(
argv=["setFields -region gland", "-case", Simulation],
silent=True,
server=False,
logname='log.setFieldsGland')
setFieldsGlandRun.start()
if not setFieldsGlandRun.runOK():
error("There was a problem with setFields for gland")
print("set fields for gland done")
## define gland anisotropic thermal conductivity
bmName = os.path.join(Simulation, 'constant', 'gland',
"thermophysicalProperties")
template = TemplateFile(bmName + ".template", expressionDelimiter="$")
template.writeToFile(bmName, {'x': xtr, 'y': y, 'z': ztr})
print("Setting anisotropic thermal conductivity for gland done")
## define tumor anisotropic thermal conductivity
bmName = os.path.join(Simulation, 'constant', 'tumor',
"thermophysicalProperties")
template = TemplateFile(bmName + ".template", expressionDelimiter="$")
template.writeToFile(bmName, {'x': xtr, 'y': y, 'z': ztr})
print("Setting anisotropic thermal conductivity for tumor done")
## removing fvoptions if benign tumor
if state == 'benign':
if not os.path.exists(Simulation + "/constant/tumor/fvOptions"):
print("Removing heat sources for benign tumors done")
else:
os.remove(Simulation + "/constant/tumor/fvOptions")
print("Removing heat sources for benign tumors done")
## multi region simple foam with two heat sources specified for tumor region
print("Running")
theRun = BasicRunner(
argv=["chtMultiRegionSimpleFoam", "-case", Simulation],
silent=True,
server=False,
logname='log.solver')
#"-postProcess", "-func", "surfaces"
theRun.start()
errorCode = theRun.endSeen
if not theRun.runOK():
error("There was a problem while running the solver")
print("Solver run done")
## converting latest simulation step to VTK- gland
print("Converting gland region to VTK")
VTKGlandRun = BasicRunner(argv=[
"foamToVTK -fields '(T)' -latestTime -ascii -region gland", "-case",
Simulation
],
silent=True,
server=False,
logname='log.VTKGland')
VTKGlandRun.start()
if not VTKGlandRun.runOK():
error(
"There was a problem while converting the gland region to VTK for post-processing"
)
print("Conversion of Gland region to VTK done")
## converting latest simulation step to VTK- tumor
print("Converting tumor region to VTK")
VTKTumorRun = BasicRunner(argv=[
"foamToVTK -fields '(T)' -latestTime -ascii -region tumor", "-case",
Simulation
],
silent=True,
server=False,
logname='log.VTKTumor')
VTKTumorRun.start()
if not VTKTumorRun.runOK():
error(
"There was a problem while converting the tumor region to VTK for post-processing"
)
print("Conversion of Tumor region to VTK done")
## Moving VTK for post processing by rounding off to two decimal places
if ((y * 100) % 1) == 0:
y_str = str(round(y * 100) / 100) + '0'
else:
y_str = str(y)
shutil.move(Simulation + "/VTK", Patient + "/VTK" + "/VTK" + y_str)
return errorCode