def run_block_mesh(self, work):
blockRun = BasicRunner(argv=["blockMesh", '-case', work.name],
silent=True,
server=False,
logname="blockMesh")
self._r.status("Running blockMesh")
blockRun.start()
if not blockRun.runOK():
self._r.error("there was an error with blockMesh")
def execute(self,para,log):
argv=[self.utility,".",para['case']]+self.options.split()
print_(" Executing"," ".join(argv),end=" ")
sys.stdout.flush()
run=BasicRunner(argv,silent=True,lam=Command.parallel,logname="_".join(argv))
run.start()
if run.runOK():
print_()
else:
print_("---> there was a problem")
return run.runOK(),None
def execute(self,para,log):
if Command.parallel!=None:
print_(" Doing reconstruction")
argv=["reconstructPar",".",para['case']]
if self.onlyLatest:
argv.append("-latestTime")
run=BasicRunner(argv=argv,silent=True,logname="Reconstruction")
run.start()
Command.parallel.stop()
else:
print_(" No reconstruction done")
Command.parallel=None
return True,None
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 run(self):
cName = self.parser.casePath()
self.checkCase(cName)
sol = SolutionDirectory(cName, archive=None)
print_("Clearing out old timesteps ....")
sol.clearResults()
self.checkAndCommit(SolutionDirectory(cName, archive=None))
run = BasicRunner(argv=self.parser.getArgs(),
server=self.opts.server,
logname="PyFoamMeshUtility")
self.addLibFunctionTrigger(run, sol)
self.addToCaseLog(cName, "Starting")
run.start()
self.setData(run.data)
sol.reread(force=True)
self.addToCaseLog(cName, "Ending")
if sol.latestDir() != sol.initialDir():
for f in listdir(path.join(sol.latestDir(), "polyMesh")):
system("mv -f " + path.join(sol.latestDir(), "polyMesh", f) +
" " + sol.polyMeshDir())
print_("\nClearing out new timesteps ....")
sol.clearResults()
else:
print_("\n\n No new timestep. Utility propably failed")
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
base_case = "base"
templateCase = SolutionDirectory(base_case, archive=None, paraviewLink=False)
omegas = nm.linspace(0, 3, 13)
nus = nm.ones(omegas.shape) * 1e-6
for i, eps in enumerate(omegas):
case = templateCase.cloneCase("testCase{:02}".format(i))
epsilonBC = ParsedParameterFile(path.join(case.name, "0", "omega"))
epsilonBC["boundaryField"]["fixedWalltop_patch1"]["value"].setUniform(eps)
epsilonBC["boundaryField"]["fixedWallbot_patch1"]["value"].setUniform(eps)
epsilonBC.writeFile()
run = BasicRunner(argv=[solver, "-case", case.name], silent=False)
# run.start()
case = SolutionDirectory(case.name, archive=None, paraviewLink=False)
if float(max(case.times)) < .28:
case.clear()
case.clearResults()
trans = ParameterFile(
path.join(case.name, "constant/transportProperties"))
trans.readFile()
trans.replaceParameter("nu", "[0 2 -1 0 0 0 0] 1e-5")
trans.writeFile()
# trans.closeFile()
nus[i] = 1e-5
run = BasicRunner(argv=[solver, "-case", case.name], silent=False)
controlDict["functions"]["forcesCoeffs"]["liftDir"] = Vector(
-sin(radians(angle)), cos(radians(angle)), 0)
controlDict["functions"]["forcesCoeffs"]["dragDir"] = Vector(
cos(radians(angle)), sin(radians(angle)), 0)
controlDict["functions"]["forcesCoeffs"][
"magUInf"] = mach * speedOfSound
controlDict.writeFile()
#implement parallelization
print('Decomposing...')
Decomposer(args=['--progress', clone_name, num_procs])
CaseReport(args=['--decomposition', clone_name])
machine = LAMMachine(nr=num_procs)
#run simpleFoam
foamRun = BasicRunner(argv=[solver, "-case", clone_name],
logname="simpleFoam")
print("Running simpleFoam")
foamRun.start()
if not foamRun.runOK():
error("There was a problem with simpleFoam")
#get headers and last line of postprocessing file
with open(
path.join(clone_name, 'postProcessing', 'forcesCoeffs', '0',
'coefficient.dat'), "rb") as table:
last = table.readlines()[-1].decode()
print("last line of coefficients" + last)
splitLast = last.split()
print(splitLast)
Cd = float(splitLast[2])
Cl = float(splitLast[3])
orig=SolutionDirectory(case_prev_dir, archive=None, paraviewLink=False)
work=orig.cloneCase(case_i_dir)
# Modyfikacja w pliku "turbulenceProperties" wartości wybranych współczynników modelu turbulencji i ich sczytanie
turb_coeffs_values_updated = write_read_turbulence_coefficients(i, case_i_dir, turb_coeffs, turb_coeffs_values, delta_turb_coeffs)
turb_coeffs_values = turb_coeffs_values_updated
# Dekompozycja case'u na potrzeby obliczeń równoległych
print "\nDecomposing case"
Decomposer(args=["--progress", work.name, cpu_number])
CaseReport(args=["--decomposition", work.name])
machine=LAMMachine(nr=cpu_number)
# Obliczenia
print "Running calculations\n"
theRun=BasicRunner(argv=["simpleFoam", "-case", work.name], silent=True, lam=machine)
theRun.start()
print "Calculations finish\n"
# Rekonstrukcja case'u po zakończeniu obliczeń
print "Reconstructing case\n"
reconstruction=BasicRunner(argv=["reconstructPar", "-case", work.name], silent=True)
reconstruction.start()
# Lokalizacja punktu oderwania przepływu
cases_numbers_updated, detachment_point_coordinates_updated = dp.find_detachment_point(case_i_dir, i, cases_numbers, detachment_point_coordinates)
cases_numbers = cases_numbers_updated
detachment_point_coordinates = detachment_point_coordinates_updated
# Usunięcie zbędnych folderów i plików pozostałych po obliczeniach i działaniu skryptów
print "Removing debris\n"
'Rx_one_over': 1 / Rx,
'ns': ns
})
# writing ground shape (hill, or whatever you want - equation in function writeGroundShape.py)
# sample file is changed as well - for sampling h=10 meters above ground
import writeGroundShape
sampleName = path.join(work.systemDir(), "sampleDict.template")
writeGroundShape.main(bmName, H, L, sampleName, hSample)
# changing Y line limits
bmName = path.join(work.systemDir(), "sampleDict")
template = TemplateFile(bmName + ".template")
template.writeToFile(bmName, {'hillTopY': h, 'maxY': 500})
# running blockMesh
blockRun = BasicRunner(argv=["blockMesh", '-case', work.name],
silent=True,
server=False,
logname="blockMesh")
print "Running blockMesh"
blockRun.start()
if not blockRun.runOK(): error("there was an error with blockMesh")
#--------------------------------------------------------------------------------------
# changing inlet profile - - - - according to Martinez 2010
#--------------------------------------------------------------------------------------
# change inlet profile
Uref = Utop = us / k * math.log(Href / z0)
print "Htop = " + str(Htop) + ", Utop = " + str(Utop)
# calculating turbulentKE
TKE = us * us / math.sqrt(Cmu)
print "TKE = " + str(TKE)
# 1: changing ABLConditions
def prepareCase_2dHill(template0, targetDir, target0, hillName, AR, r, x, Ls, L, L1, H, x0, z0, us, yM, h, caseType):
# case definitions Martinez2DBump
ks = 19.58 * z0 # [m] Martinez 2011
k = 0.4
Cmu = 0.03 # Castro 96
Htop = Href = H # [m]
# yp/ks = 0.02 = x/ks
funky = 0
plotMartinez = 1
hSample = 10
fac = 10 # currecting calculation of number of cells and Rx factor to get a smooth transition
# from the inner refined cell and the outer less refined cells of the blockMesh Mesh
procnr = 4
caseStr = "_AR_" + str(AR) + "_z0_" + str(z0)
if caseType=="Crude":
caseStr = caseStr + "Crude"
target = os.path.join(targetDir, target0 + caseStr)
if not os.path.exists(template0):
print "there is no %r directory in the current directory %r" % (template0, os.getcwd())
raise SystemExit
orig = SolutionDirectory(template0,
archive=None,
paraviewLink=False)
#--------------------------------------------------------------------------------------
# clonning case
#--------------------------------------------------------------------------------------
if not os.path.exists(targetDir):
os.mkdir(targetDir)
work = orig.cloneCase(target)
#--------------------------------------------------------------------------------------
# creating mesh
#--------------------------------------------------------------------------------------
y0 = 2 * x * z0 # setting first cell according to Martinez 2011 p. 25
ny = int(round(math.log(H/y0*(r-1)+1)/math.log(r))) # number of cells in the y direction of the hill block
Ry = r**(ny-1.)
nx = int(L/x0-1)
rx = max(r,1.1)
ns = int(round(math.log((Ls-L)/x0*(rx-1)/rx**fac+1)/math.log(rx))) # number of cells in the x direction of the hill block
Rx = rx**(ns-1)
# changing blockMeshDict - from template file
bmName = path.join(work.constantDir(),"polyMesh/blockMeshDict")
if AR==1000: # if flat terrain
template = TemplateFile(bmName+"_flat_3cell.template")
else:
template = TemplateFile(bmName+"_3cell.template")
template.writeToFile(bmName,{'H':H,'ny':ny,'Ry':Ry,'nx':nx,'L':L,'L1':L1,'Ls':Ls,'Rx':Rx,'Rx_one_over':1/Rx,'ns':ns})
# writing ground shape (hill, or whatever you want - equation in function writeGroundShape.py)
# sample file is changed as well - for sampling h=10 meters above ground
sampleName = path.join(work.systemDir(),"sampleDict.template")
write2dShape(bmName,H,L,sampleName,hSample,hillName,AR)
# changing Y line limits
bmName = path.join(work.systemDir(),"sampleDict")
template = TemplateFile(bmName + ".template")
if AR==1000: # if flat terrain
template.writeToFile(bmName,{'hillTopY':0,'maxY':yM*2.5})
else:
template.writeToFile(bmName,{'hillTopY':h,'maxY':yM*2.5+h})
# running blockMesh
print "running blockMesh"
blockRun = BasicRunner(argv=["blockMesh",'-case',work.name],silent=True,server=False,logname="blockMesh")
blockRun.start()
if not blockRun.runOK():
error("there was an error with blockMesh")
#--------------------------------------------------------------------------------------
# changing inlet profile - - - - according to Martinez 2010
#--------------------------------------------------------------------------------------
# change inlet profile
Uref = Utop = us/k*math.log(Href/z0)
# calculating turbulentKE
TKE = us*us/math.sqrt(Cmu)
# 1: changing ABLConditions
bmName = path.join(work.initialDir(),"include/ABLConditions")
template = TemplateFile(bmName+".template")
template.writeToFile(bmName,{'us':us,'Uref':Uref,'Href':Href,'z0':z0})
# 2: changing initialConditions
bmName = path.join(work.initialDir(),"include/initialConditions")
template = TemplateFile(bmName+".template")
template.writeToFile(bmName,{'TKE':TKE})
if funky:
# 3: changing U (inserting variables into groovyBC for inlet profile)
bmName = path.join(work.initialDir(),"U")
template = TemplateFile(bmName + ".template")
template.writeToFile(bmName,{'us':us,'z0':z0,'K':k,'Utop':Utop})
# 4: changing k (inserting variables into groovyBC for inlet profile)
bmName = path.join(work.initialDir(),"k")
template = TemplateFile(bmName + ".template")
template.writeToFile(bmName,{'us':us,'z0':z0,'K':k,'Utop':Utop,'Cmu':Cmu})
# 5: changing epsilon (inserting variables into groovyBC for inlet profile)
bmName = path.join(work.initialDir(),"epsilon")
template = TemplateFile(bmName + ".template")
template.writeToFile(bmName,{'us':us,'z0':z0,'K':k,'Utop':Utop,'Cmu':Cmu})
# 6: changing initial and boundary conditions for new z0
# changing ks in nut, inside nutRoughWallFunction
nutFile = ParsedParameterFile(path.join(work.initialDir(),"nut"))
nutFile["boundaryField"]["ground"]["Ks"].setUniform(ks)
nutFile.writeFile()
# 7: changing convergence criterion for Crude runs
if caseType == "Crude":
fvSolutionFile = ParsedParameterFile(path.join(work.systemDir(),"fvSolution"))
fvSolutionFile["SIMPLE"]["residualControl"]["p"] = 1e-6
fvSolutionFile["SIMPLE"]["residualControl"]["U"] = 1e-6
fvSolutionFile.writeFile()
# mapping fields - From earlier result if exists
if caseType == "mapFields":
#finding the most converged run. assuming the "crude" run had the same dirName with "Crude" attached
setName = glob.glob(target + 'Crude/sets/*')
lastRun = range(len(setName))
for num in range(len(setName)):
lastRun[num] = int(setName[num][setName[num].rfind("/")+1:])
sourceTimeArg = str(max(lastRun))
mapRun = BasicRunner(argv=['mapFields -consistent -sourceTime ' + sourceTimeArg +
' -case ' + work.name + ' ' + target + "Crude"],silent=True,server=False,logname='mapLog')
mapRun.start()
# parallel rule
cells = nx * (ny+2*ns)
print "Mesh has " + str(cells) + " cells"
if cells>40000: parallel=1
else: parallel=0
if parallel:
#--------------------------------------------------------------------------------------
# decomposing
#--------------------------------------------------------------------------------------
# removing U.template from 0/ directory
subprocess.call("rm " + bmName + ".template ",shell=True)
arg = " -case " + work.name
decomposeRun = BasicRunner(argv=["decomposePar -force" + arg],silent=True,server=False,logname="decompose")
decomposeRun.start()
#clone base case
clone_name = '/%s/dTdz%0.3f_z%d' % (path.join(getcwd(),
copy_dir), temp, depth)
clone = dire.cloneCase(clone_name)
#read parameter file and change parameter
param_file = ParsedParameterFile(
path.join(clone_name, 'constant', 'parameterFile'))
param_file['dTdz'] = 'dTdz [0 -1 0 0 0 0 0] %0.3f' % temp
param_file['z0'] = 'z0 [0 1 0 0 0 0 0] %.1f' % depth
param_file.writeFile()
#set initial fields
run_initFields = BasicRunner(
argv=['setInitialFields', '-case', clone_name],
logname='setInitialFields')
run_initFields.start()
print('initial fields set')
#implement parallelization
print('Decomposing...')
Decomposer(args=['--progress', clone_name, num_procs])
CaseReport(args=['--decomposition', clone_name])
machine = LAMMachine(nr=num_procs)
#run solver
print('Running solver...')
print('PID: ' + str(getpid()))
run_solver = BasicRunner(argv=['trainingSolver', '-case', clone_name],
logname='trainingSolver',
subprocess.call(activator, shell=True)
activator = 'funkySetFields -case '+refCase+' -field Ct -expression "1e-3" -condition "(pow(pos().x-'+str(pancakesCenters[pancackes,0])+',2) + pow(pos().y-'+str(pancakesCenters[pancackes,1])+',2) < pow('+str(radius)+',2) )&&(pos().z>0) && (pos().z<=(1e-6+0))" -time "0"'
subprocess.call(activator, shell=True)
dire=SolutionDirectory(refCase)
sol=SolutionFile(dire.initialDir(),"Ct")
sol.replaceBoundary("inlet","0")
a= 'sh fixInlet.sh'
subprocess.call(a, shell=True)
# tobinary()
# parallel decomposition
if nproc > 1:
args = ["--method=scotch", "--clear", refCase, nproc]
Decomposer(args=args)
run = BasicRunner(
argv=[
solver,
"-case",
caseName],
silent=True,
noLog=False)
run.start()
runCmd = 'pyFoamRunner.py advDiffMicellesNoFlow -case '+caseName+' > /dev/null 2>&1 &'
# subprocess.call(runCmd, shell=True)
post = 'mpirun -np ' + str(nproc) + ' foamToEnsight -case '+refCase+' -parallel -name pancanke_noflow_radius='+str(radius)+'_loc='+str(pancackes)
subprocess.call(post, shell=True)
a = "rm 0/t* 0/*.backup"
subprocess.call(a, shell=True)
def buildCase(self, cName, args):
"""Builds the case
@param cName: The name of the case directory
@param args: The arguments (as a dictionary)"""
args = self.calculateVariables(args)
os.mkdir(cName)
for d in self.parameterTree().getElementsByTagName("directory"):
dName = path.join(cName, d.getAttribute("name"))
if not path.isdir(dName):
os.mkdir(dName)
sName = path.join(self.templatePath(), d.getAttribute("name"))
for f in d.getElementsByTagName("file"):
dFile = path.join(dName, f.getAttribute("name"))
shutil.copy(path.join(sName, f.getAttribute("name")), dFile)
if len(f.getElementsByTagName("parameter")) > 0:
pf = ParsedParameterFile(dFile)
for p in f.getElementsByTagName("parameter"):
pName = p.getAttribute("name")
pValue = self.expandVars(p.getAttribute("value"), args)
exec_("pf" + pName + "=" + pValue)
pf.writeFile()
prep = self.getSingleElement(self.doc, "meshpreparation")
util = prep.getElementsByTagName("utility")
copy = self.getSingleElement(prep, "copy", optional=True)
if len(util) > 0 and copy:
error("Copy and utilitiy mesh preparation specified")
elif len(util) > 0:
for u in util:
app = u.getAttribute("command")
arg = self.expandVars(u.getAttribute("arguments"), args)
argv = [app, "-case", cName] + arg.split()
if oldApp():
argv[1] = "."
run = BasicRunner(argv=argv,
silent=True,
logname="CaseBuilder.prepareMesh." + app)
run.start()
if not run.runOK():
error(app, "failed. Check the logs")
elif copy:
source = self.expandVars(copy.getAttribute("template"), args)
time = self.expandVars(copy.getAttribute("time"), args)
if time == "":
time = "constant"
shutil.copytree(path.join(source, time, "polyMesh"),
path.join(cName, "constant", "polyMesh"))
else:
error("Neither copy nor utilitiy mesh preparation specified")
dName = path.join(cName, self.initialDir())
if not path.isdir(dName):
os.mkdir(dName)
sName = path.join(self.templatePath(), self.initialDir())
for f in self.fieldTree().getElementsByTagName("field"):
dFile = path.join(dName, f.getAttribute("name"))
shutil.copy(path.join(sName, f.getAttribute("name")), dFile)
default = self.makeBC(self.getSingleElement(f, "defaultbc"), args)
CreateBoundaryPatches(args=[
"--fix-types", "--overwrite", "--clear", "--default=" +
default, dFile
])
bcDict = {}
bounds = self.boundaries()
for b in f.getElementsByTagName("bc"):
nm = b.getAttribute("name")
if nm not in bounds:
error("Boundary", nm, "not in list", bounds, "for field",
f.getAttribute("name"))
bcDict[nm] = b
for name, pattern in self.boundaryPatterns():
if name in bcDict:
default = self.makeBC(bcDict[name], args)
CreateBoundaryPatches(args=[
"--filter=" + pattern, "--overwrite", "--default=" +
default, dFile
])
ic = self.expandVars(
self.getSingleElement(f, "ic").getAttribute("value"), args)
pf = ParsedParameterFile(dFile)
pf["internalField"] = "uniform " + ic
pf.writeFile()
def prepare(self,
sol,
cName=None,
overrideParameters=None,
numberOfProcessors=None):
"""Do the actual preparing
:param numberOfProcessors: If set this overrides the value set in the
command line"""
if cName == None:
cName = sol.name
if self.opts.onlyVariables:
self.opts.verbose = True
vals = {}
vals, self.metaData = self.getDefaultValues(cName)
vals.update(
self.addDictValues(
"System", "Automatically defined values", {
"casePath":
'"' + path.abspath(cName) + '"',
"caseName":
'"' + path.basename(path.abspath(cName)) + '"',
"foamVersion":
foamVersion(),
"foamFork":
foamFork(),
"numberOfProcessors":
numberOfProcessors if numberOfProcessors != None else
self.opts.numberOfProcessors
}))
if len(self.opts.extensionAddition) > 0:
vals.update(
self.addDictValues(
"ExtensionAdditions",
"Additional extensions to be processed",
dict((e, True) for e in self.opts.extensionAddition)))
valsWithDefaults = set(vals.keys())
self.info("Looking for template values", cName)
for f in self.opts.valuesDicts:
self.info("Reading values from", f)
vals.update(
ParsedParameterFile(f, noHeader=True,
doMacroExpansion=True).getValueDict())
setValues = {}
for v in self.opts.values:
self.info("Updating values", v)
vals.update(eval(v))
setValues.update(eval(v))
if overrideParameters:
vals.update(overrideParameters)
unknownValues = set(vals.keys()) - valsWithDefaults
if len(unknownValues) > 0:
self.warning("Values for which no default was specified: " +
", ".join(unknownValues))
if self.opts.verbose and len(vals) > 0:
print_("\nUsed values\n")
nameLen = max(len("Name"), max(*[len(k) for k in vals.keys()]))
format = "%%%ds - %%s" % nameLen
print_(format % ("Name", "Value"))
print_("-" * 40)
for k, v in sorted(iteritems(vals)):
print_(format % (k, v))
print_("")
else:
self.info("\nNo values specified\n")
self.checkCorrectOptions(vals)
derivedScript = path.join(cName, self.opts.derivedParametersScript)
derivedAdded = None
derivedChanged = None
if path.exists(derivedScript):
self.info("Deriving variables in script", derivedScript)
scriptText = open(derivedScript).read()
glob = {}
oldVals = vals.copy()
exec_(scriptText, glob, vals)
derivedAdded = []
derivedChanged = []
for k, v in iteritems(vals):
if k not in oldVals:
derivedAdded.append(k)
elif vals[k] != oldVals[k]:
derivedChanged.append(k)
if len(derivedChanged) > 0 and (
not self.opts.allowDerivedChanges
and not configuration().getboolean("PrepareCase",
"AllowDerivedChanges")):
self.error(
self.opts.derivedParametersScript, "changed values of",
" ".join(derivedChanged),
"\nTo allow this set --allow-derived-changes or the configuration item 'AllowDerivedChanges'"
)
if len(derivedAdded) > 0:
self.info("Added values:", " ".join(derivedAdded))
if len(derivedChanged) > 0:
self.info("Changed values:", " ".join(derivedChanged))
if len(derivedAdded) == 0 and len(derivedChanged) == 0:
self.info("Nothing added or changed")
else:
self.info("No script", derivedScript, "for derived values")
if self.opts.onlyVariables:
return
self.__writeToStateFile(sol, "Starting")
if self.opts.doClear:
self.info("Clearing", cName)
self.__writeToStateFile(sol, "Clearing")
sol.clear(processor=True,
pyfoam=True,
vtk=True,
removeAnalyzed=True,
keepParallel=False,
clearHistory=False,
clearParameters=True,
additional=["postProcessing"])
self.__writeToStateFile(sol, "Done clearing")
if self.opts.writeParameters:
fName = path.join(cName, self.parameterOutFile)
self.info("Writing parameters to", fName)
with WriteParameterFile(fName, noHeader=True) as w:
w.content.update(vals, toString=True)
w["foamVersion"] = vals["foamVersion"]
w.writeFile()
if self.opts.writeReport:
fName = path.join(cName, self.parameterOutFile + ".rst")
self.info("Writing report to", fName)
with open(fName, "w") as w:
helper = RestructuredTextHelper(defaultHeading=1)
w.write(".. title:: " + self.__strip(vals["caseName"]) + "\n")
w.write(".. sectnum::\n")
w.write(".. header:: " + self.__strip(vals["caseName"]) + "\n")
w.write(".. header:: " + time.asctime() + "\n")
w.write(".. footer:: ###Page### / ###Total###\n\n")
w.write("Parameters set in case directory " +
helper.literal(self.__strip(vals["casePath"])) +
" at " + helper.emphasis(time.asctime()) + "\n\n")
w.write(".. contents::\n\n")
if len(self.opts.valuesDicts):
w.write(helper.heading("Parameter files"))
w.write("Parameters read from files\n\n")
w.write(
helper.enumerateList([
helper.literal(f) for f in self.opts.valuesDicts
]))
w.write("\n")
if len(setValues) > 0:
w.write(helper.heading("Overwritten parameters"))
w.write(
"These parameters were set from the command line\n\n")
w.write(helper.definitionList(setValues))
w.write("\n")
w.write(helper.heading("Parameters with defaults"))
w.write(self.makeReport(vals))
if len(unknownValues) > 0:
w.write(helper.heading("Unspecified parameters"))
w.write(
"If these parameters are actually used then specify them in "
+ helper.literal(self.defaultParameterFile) + "\n\n")
tab = helper.table(True)
for u in unknownValues:
tab.addRow(u)
tab.addItem("Value", vals[u])
w.write(str(tab))
if not derivedAdded is None:
w.write(helper.heading("Derived Variables"))
w.write("Script with derived Parameters" +
helper.literal(derivedScript) + "\n\n")
if len(derivedAdded) > 0:
w.write("These values were added:\n")
tab = helper.table(True)
for a in derivedAdded:
tab.addRow(a)
tab.addItem("Value", str(vals[a]))
w.write(str(tab))
if len(derivedChanged) > 0:
w.write("These values were changed:\n")
tab = helper.table(True)
for a in derivedChanged:
tab.addRow(a)
tab.addItem("Value", str(vals[a]))
tab.addItem("Old", str(oldVals[a]))
w.write(str(tab))
w.write("The code of the script:\n")
w.write(helper.code(scriptText))
self.addToCaseLog(cName)
for over in self.opts.overloadDirs:
self.info("Overloading files from", over)
self.__writeToStateFile(sol, "Overloading")
self.overloadDir(sol.name, over)
self.__writeToStateFile(sol, "Initial")
zeroOrig = path.join(sol.name, "0.org")
hasOrig = path.exists(zeroOrig)
cleanZero = True
if not hasOrig:
self.info("Not going to clean '0'")
self.opts.cleanDirectories.remove("0")
cleanZero = False
if self.opts.doCopy:
if hasOrig:
self.info("Found 0.org. Clearing 0")
zeroDir = path.join(sol.name, "0")
if path.exists(zeroDir):
rmtree(zeroDir)
else:
self.info("No 0-directory")
self.info("")
else:
cleanZero = False
if self.opts.doTemplates:
self.__writeToStateFile(sol, "Templates")
self.searchAndReplaceTemplates(
sol.name,
vals,
self.opts.templateExt,
ignoreDirectories=self.opts.ignoreDirectories)
self.info("")
backupZeroDir = None
if self.opts.doMeshCreate:
self.__writeToStateFile(sol, "Meshing")
if self.opts.meshCreateScript:
scriptName = path.join(sol.name, self.opts.meshCreateScript)
if not path.exists(scriptName):
self.error("Script", scriptName, "does not exist")
elif path.exists(path.join(sol.name, self.defaultMeshCreate)):
scriptName = path.join(sol.name, self.defaultMeshCreate)
else:
scriptName = None
if scriptName:
self.info("Executing", scriptName, "for mesh creation")
if self.opts.verbose:
echo = "Mesh: "
else:
echo = None
self.executeScript(scriptName, workdir=sol.name, echo=echo)
else:
self.info(
"No script for mesh creation found. Looking for 'blockMeshDict'"
)
if sol.blockMesh() != "":
self.info(sol.blockMesh(), "found. Executing 'blockMesh'")
bm = BasicRunner(argv=["blockMesh", "-case", sol.name])
bm.start()
if not bm.runOK():
self.error("Problem with blockMesh")
for r in sol.regions():
self.info("Checking region", r)
s = SolutionDirectory(sol.name,
region=r,
archive=None,
paraviewLink=False)
if s.blockMesh() != "":
self.info(s.blockMesh(),
"found. Executing 'blockMesh'")
bm = BasicRunner(argv=[
"blockMesh", "-case", sol.name, "-region", r
])
bm.start()
if not bm.runOK():
self.error("Problem with blockMesh")
self.info("")
if cleanZero and path.exists(zeroDir):
self.warning("Mesh creation recreated 0-directory")
if self.opts.keepZeroDirectoryFromMesh:
backupZeroDir = zeroDir + ".bakByPyFoam"
self.info("Backing up", zeroDir, "to", backupZeroDir)
move(zeroDir, backupZeroDir)
else:
self.info("Data in", zeroDir, "will be removed")
self.__writeToStateFile(sol, "Done Meshing")
if self.opts.doCopy:
self.__writeToStateFile(sol, "Copying")
self.copyOriginals(sol.name)
self.info("")
if backupZeroDir:
self.info("Copying backups from", backupZeroDir, "to", zeroDir)
self.overloadDir(zeroDir, backupZeroDir)
self.info("Removing backup", backupZeroDir)
rmtree(backupZeroDir)
if self.opts.doPostTemplates:
self.__writeToStateFile(sol, "Post-templates")
self.searchAndReplaceTemplates(
sol.name,
vals,
self.opts.postTemplateExt,
ignoreDirectories=self.opts.ignoreDirectories)
self.info("")
if self.opts.doCaseSetup:
self.__writeToStateFile(sol, "Case setup")
if self.opts.caseSetupScript:
scriptName = path.join(sol.name, self.opts.caseSetupScript)
if not path.exists(scriptName):
self.error("Script", scriptName, "does not exist")
elif path.exists(path.join(sol.name, self.defaultCaseSetup)):
scriptName = path.join(sol.name, self.defaultCaseSetup)
else:
scriptName = None
if scriptName:
self.info("Executing", scriptName, "for case setup")
if self.opts.verbose:
echo = "Case:"
else:
echo = None
self.executeScript(scriptName, workdir=sol.name, echo=echo)
elif path.exists(path.join(sol.name, "system", "setFieldsDict")):
self.info(
"So setup script found. But 'setFieldsDict'. Executing setFields"
)
sf = BasicRunner(argv=["setFields", "-case", sol.name])
sf.start()
if not sf.runOK():
self.error("Problem with setFields")
else:
self.info("No script for case-setup found. Nothing done")
self.info("")
self.__writeToStateFile(sol, "Done case setup")
if self.opts.doFinalTemplates:
self.__writeToStateFile(sol, "Final templates")
self.searchAndReplaceTemplates(
sol.name,
vals,
self.opts.finalTemplateExt,
ignoreDirectories=self.opts.ignoreDirectories)
if self.opts.doTemplateClean:
self.info("Clearing templates")
for d in self.opts.cleanDirectories:
for e in [
self.opts.templateExt, self.opts.postTemplateExt,
self.opts.finalTemplateExt
]:
self.cleanExtension(path.join(sol.name, d), e)
self.info("")
self.info("Case setup finished")
self.__writeToStateFile(sol, "Finished OK")
def prepare(self, sol, cName=None, overrideParameters=None):
if cName == None:
cName = sol.name
if self.opts.onlyVariables:
self.opts.verbose = True
vals = {}
vals["casePath"] = '"' + path.abspath(cName) + '"'
vals["caseName"] = '"' + path.basename(path.abspath(cName)) + '"'
vals["foamVersion"] = foamVersion()
vals["foamFork"] = foamFork()
if self.opts.verbose:
print_("Looking for template values", cName)
for f in self.opts.valuesDicts:
if self.opts.verbose:
print_("Reading values from", f)
vals.update(
ParsedParameterFile(f, noHeader=True,
doMacroExpansion=True).getValueDict())
for v in self.opts.values:
if self.opts.verbose:
print_("Updating values", v)
vals.update(eval(v))
if overrideParameters:
vals.update(overrideParameters)
if self.opts.verbose and len(vals) > 0:
print_("\nUsed values\n")
nameLen = max(len("Name"), max(*[len(k) for k in vals.keys()]))
format = "%%%ds - %%s" % nameLen
print_(format % ("Name", "Value"))
print_("-" * 40)
for k, v in sorted(iteritems(vals)):
print_(format % (k, v))
print_("")
elif self.opts.verbose:
print_("\nNo values specified\n")
if self.opts.onlyVariables:
return
if self.opts.doClear:
if self.opts.verbose:
print_("Clearing", cName)
sol.clear(processor=True,
pyfoam=True,
vtk=True,
removeAnalyzed=True,
keepParallel=False,
clearHistory=False,
clearParameters=True,
additional=["postProcessing"])
if self.opts.writeParameters:
fName = path.join(cName, self.parameterOutFile)
if self.opts.verbose:
print_("Writing parameters to", fName)
with WriteParameterFile(fName, noHeader=True) as w:
w.content.update(vals, toString=True)
w["foamVersion"] = vals["foamVersion"]
w.writeFile()
self.addToCaseLog(cName)
for over in self.opts.overloadDirs:
if self.opts.verbose:
print_("Overloading files from", over)
self.overloadDir(sol.name, over)
zeroOrig = path.join(sol.name, "0.org")
hasOrig = path.exists(zeroOrig)
if not hasOrig:
if self.opts.verbose:
print_("Not going to clean '0'")
self.opts.cleanDirectories.remove("0")
if self.opts.doCopy:
if hasOrig:
if self.opts.verbose:
print_("Found 0.org. Clearing 0")
zeroDir = path.join(sol.name, "0")
if path.exists(zeroDir):
rmtree(zeroDir)
elif self.opts.verbose:
print_("No 0-directory")
if self.opts.verbose:
print_("")
if self.opts.doTemplates:
self.searchAndReplaceTemplates(sol.name, vals,
self.opts.templateExt)
if self.opts.verbose:
print_("")
if self.opts.doMeshCreate:
if self.opts.meshCreateScript:
scriptName = path.join(sol.name, self.opts.meshCreateScript)
if not path.exists(scriptName):
self.error("Script", scriptName, "does not exist")
elif path.exists(path.join(sol.name, self.defaultMeshCreate)):
scriptName = path.join(sol.name, self.defaultMeshCreate)
else:
scriptName = None
if scriptName:
if self.opts.verbose:
print_("Executing", scriptName, "for mesh creation")
if self.opts.verbose:
echo = "Mesh: "
else:
echo = None
result = "".join(
execute([scriptName], workdir=sol.name, echo=echo))
open(scriptName + ".log", "w").write(result)
else:
if self.opts.verbose:
print_(
"No script for mesh creation found. Looking for 'blockMeshDict'"
)
if sol.blockMesh() != "":
if self.opts.verbose:
print_(sol.blockMesh(), "found. Executing 'blockMesh'")
bm = BasicRunner(argv=["blockMesh", "-case", sol.name])
bm.start()
if not bm.runOK():
self.error("Problem with blockMesh")
if self.opts.verbose:
print_("")
if self.opts.doCopy:
self.copyOriginals(sol.name)
if self.opts.verbose:
print_("")
if self.opts.doPostTemplates:
self.searchAndReplaceTemplates(sol.name, vals,
self.opts.postTemplateExt)
if self.opts.verbose:
print_("")
if self.opts.doCaseSetup:
if self.opts.caseSetupScript:
scriptName = path.join(sol.name, self.opts.caseSetupScript)
if not path.exists(scriptName):
self.error("Script", scriptName, "does not exist")
elif path.exists(path.join(sol.name, self.defaultCaseSetup)):
scriptName = path.join(sol.name, self.defaultCaseSetup)
else:
scriptName = None
if scriptName:
if self.opts.verbose:
print_("Executing", scriptName, "for case setup")
if self.opts.verbose:
echo = "Case:"
else:
echo = None
result = "".join(
execute([scriptName], workdir=sol.name, echo=echo))
open(scriptName + ".log", "w").write(result)
else:
if self.opts.verbose:
print_("No script for case-setup found. Nothing done")
if self.opts.verbose:
print_("")
if self.opts.doTemplateClean:
if self.opts.verbose:
print_("Clearing templates")
for d in self.opts.cleanDirectories:
for e in [self.opts.templateExt, self.opts.postTemplateExt]:
self.cleanExtension(path.join(sol.name, d), e)
if self.opts.verbose:
print_("")
if self.opts.verbose:
print_("Case setup finished")
'X3': x4,
'Y0': y1,
'Y1': y2,
'Y2': y3,
'Y3': y4,
'Z0': Href,
'n': int(n),
'm': int(m),
'q': int(q)
})
#--------------------------------------------------------------------------------------
# running blockMesh
#--------------------------------------------------------------------------------------
blockRun = BasicRunner(argv=["blockMesh", '-case', work.name],
silent=True,
server=False,
logname="blockMesh")
print "Running blockMesh"
blockRun.start()
if not blockRun.runOK(): print("there was an error with blockMesh")
#--------------------------------------------------------------------------------------
# changing ABLconditions
#--------------------------------------------------------------------------------------
# 1: changing ABLConditions
bmName = path.join(work.initialDir(), "include/ABLConditions")
template = TemplateFile(bmName + ".template")
template.writeToFile(
bmName, {
'us': us,
logger.info(' Start time: %s' % startTime)
logger.info(' End time: %s' % endTime)
logger.info(' pressureDiff: %s' % dp0)
logger.info(' U0_0: %s' % U0_0)
logger.info(' U0_Target: %s' % U0_Target)
run = 0
while run < 10:
# Run the model
logger.info(
'-------------------------------------------------------------')
logger.info(' Starting run of model.......RUN: %s' % run)
logger.info(' Starting time: %s' % datetime.datetime.now())
BasicRunner(argv=["pisoFoam", "-case ", dire.name],
silent=True).start()
logger.info(' Ending time: %s' % datetime.datetime.now())
time.sleep(1)
# Run the sample utility
logger.info(' Extracting the velocity profile')
sample_str = "sample -latestTime -case "
sample_str += case
os.system(sample_str)
time.sleep(5)
# Read the velocity
L1UfilePath = path.join(case, 'postProcessing/sets', str(endTime),
profile_name)
U0_1 = getU0(L1UfilePath, level)
logger.info(' The end velocity was: %s m/s, the target is: %s m/s' %
def run3dHillBase(template0, AR, z0, us, caseType):
# loading other parameters from dictionary file
inputDict = ParsedParameterFile("testZ0InfluenceDict")
h = inputDict["simParams"]["h"]
yM = inputDict["simParams"]["yM"]
# SHM parameters
cell = inputDict["SHMParams"]["cellSize"]["cell"]
Href = inputDict["SHMParams"]["domainSize"]["domZ"]
zz = inputDict["SHMParams"]["pointInDomain"]["zz"]
# case definitions Martinez2DBump
ks = 19.58 * z0 # [m] Martinez 2011
k = inputDict["kEpsParams"]["k"]
Cmu = inputDict["kEpsParams"]["Cmu"]
# yp/ks = 0.02 = x/ks
hSample = inputDict["sampleParams"]["hSample"]
procnr = multiprocessing.cpu_count()
caseStr = "_z0_" + str(z0)
target = "runs/" + template0 + caseStr
x0, y0, phi = inputDict["SHMParams"]["centerOfDomain"]["x0"], inputDict["SHMParams"]["centerOfDomain"]["x0"], \
inputDict["SHMParams"]["flowOrigin"]["deg"]*pi/180
H = h
a = h*AR
#--------------------------------------------------------------------------------------
# cloning case
#--------------------------------------------------------------------------------------
orig = SolutionDirectory(template0,
archive=None,
paraviewLink=False)
work = orig.cloneCase(target)
#--------------------------------------------------------------------------------------
# changing inlet profile - - - - according to Martinez 2010
#--------------------------------------------------------------------------------------
# change inlet profile
Uref = Utop = us/k*math.log(Href/z0)
# calculating turbulentKE
TKE = us*us/math.sqrt(Cmu)
# 1: changing ABLConditions
bmName = path.join(work.initialDir(),"include/ABLConditions")
template = TemplateFile(bmName+".template")
template.writeToFile(bmName,{'us':us,'Uref':Uref,'Href':Href,'z0':z0,'xDirection':sin(phi),'yDirection':cos(phi)})
# 2: changing initialConditions
bmName = path.join(work.initialDir(),"include/initialConditions")
template = TemplateFile(bmName+".template")
template.writeToFile(bmName,{'TKE':TKE})
# 3: changing initial and boundary conditions for new z0
# changing ks in nut, inside nutRoughWallFunction
nutFile = ParsedParameterFile(path.join(work.initialDir(),"nut"))
nutFile["boundaryField"]["ground"]["Ks"].setUniform(ks)
nutFile["boundaryField"]["terrain_.*"]["Ks"].setUniform(ks)
nutFile.writeFile()
#--------------------------------------------------------------------------------------
# changing sample file
#--------------------------------------------------------------------------------------
# 2: changing initialConditions
bmName = path.join(work.systemDir(),"sampleDict")
template = TemplateFile(bmName+".template")
if AR>100:# flat terrain
h=0
template.writeToFile(bmName,{'hillTopY':0,'sampleHeightAbovePlain':50,'sampleHeightAboveHill':50,'inletX':3500})
else:
template.writeToFile(bmName,{'hillTopY':h,'sampleHeightAbovePlain':50,'sampleHeightAboveHill':h+50,'inletX':h*AR*4*0.9})
# if SHM - create mesh
if caseType.find("SHM")>0:
phi = phi - pi/180 * 90 #--------------------------------------------------------------------------------------
# creating blockMeshDict
#--------------------------------------------------------------------------------------
l, d = a*inputDict["SHMParams"]["domainSize"]["fX"], a*inputDict["SHMParams"]["domainSize"]["fY"]
x1 = x0 - (l/2*sin(phi) + d/2*cos(phi))
y1 = y0 - (l/2*cos(phi) - d/2*sin(phi))
x2 = x0 - (l/2*sin(phi) - d/2*cos(phi))
y2 = y0 - (l/2*cos(phi) + d/2*sin(phi))
x3 = x0 + (l/2*sin(phi) + d/2*cos(phi))
y3 = y0 + (l/2*cos(phi) - d/2*sin(phi))
x4 = x0 + (l/2*sin(phi) - d/2*cos(phi))
y4 = y0 + (l/2*cos(phi) + d/2*sin(phi))
n = floor(d/(cell*inputDict["SHMParams"]["cellSize"]["cellYfactor"]))
m = floor(l/(cell*inputDict["SHMParams"]["cellSize"]["cellYfactor"]))
q = floor((Href+450)/cell) # -450 is the minimum of the blockMeshDict.template - since that is slightly lower then the lowest point on the planet
bmName = path.join(work.constantDir(),"polyMesh/blockMeshDict")
template = TemplateFile(bmName+".template")
template.writeToFile(bmName,{'X0':x1,'X1':x2,'X2':x3,'X3':x4,'Y0':y1,'Y1':y2,'Y2':y3,'Y3':y4,'Z0':Href,'n':int(n),'m':int(m),'q':int(q)})
#--------------------------------------------------------------------------------------
# running blockMesh
#--------------------------------------------------------------------------------------
blockRun = BasicRunner(argv=["blockMesh",'-case',work.name],silent=True,server=False,logname="blockMesh")
print "Running blockMesh"
blockRun.start()
if not blockRun.runOK(): error("there was an error with blockMesh")
#--------------------------------------------------------------------------------------
# running SHM
#--------------------------------------------------------------------------------------
print "calculating SHM parameters"
# calculating refinement box positions
l1, l2, h1, h2 = 2*a, 1.3*a, 4*H, 2*H # refinement rulls - Martinez 2011
refBox1_minx, refBox1_miny, refBox1_minz = x0 - l1*(sin(phi)+cos(phi)), y0 - l1*(cos(phi)-sin(phi)), 0 #enlarging to take acount of the rotation angle
refBox1_maxx, refBox1_maxy, refBox1_maxz = x0 + l1*(sin(phi)+cos(phi)), y0 + l1*(cos(phi)-sin(phi)), h1 #enlarging to take acount of the rotation angle
refBox2_minx, refBox2_miny, refBox2_minz = x0 - l2*(sin(phi)+cos(phi)), y0 - l2*(cos(phi)-sin(phi)), 0 #enlarging to take acount of the rotation angle
refBox2_maxx, refBox2_maxy, refBox2_maxz = x0 + l2*(sin(phi)+cos(phi)), y0 + l2*(cos(phi)-sin(phi)),h2 #enlarging to take acount of the rotation angle
# changing cnappyHexMeshDict - with parsedParameterFile
SHMDict = ParsedParameterFile(path.join(work.systemDir(),"snappyHexMeshDict"))
SHMDict["geometry"]["refinementBox1"]["min"] = "("+str(refBox1_minx)+" "+str(refBox1_miny)+" "+str(refBox1_minz)+")"
SHMDict["geometry"]["refinementBox1"]["max"] = "("+str(refBox1_maxx)+" "+str(refBox1_maxy)+" "+str(refBox1_maxz)+")"
SHMDict["geometry"]["refinementBox2"]["min"] = "("+str(refBox2_minx)+" "+str(refBox2_miny)+" "+str(refBox2_minz)+")"
SHMDict["geometry"]["refinementBox2"]["max"] = "("+str(refBox2_maxx)+" "+str(refBox2_maxy)+" "+str(refBox2_maxz)+")"
SHMDict["castellatedMeshControls"]["locationInMesh"] = "("+str(x0)+" "+str(y0)+" "+str(zz)+")"
levelRef = inputDict["SHMParams"]["cellSize"]["levelRef"]
SHMDict["castellatedMeshControls"]["refinementSurfaces"]["terrain"]["level"] = "("+str(levelRef)+" "+str(levelRef)+")"
r = inputDict["SHMParams"]["cellSize"]["r"]
SHMDict["addLayersControls"]["expansionRatio"] = r
fLayerRatio = inputDict["SHMParams"]["cellSize"]["fLayerRatio"]
SHMDict["addLayersControls"]["finalLayerThickness"] = fLayerRatio
# calculating finalLayerRatio for getting
zp_z0 = inputDict["SHMParams"]["cellSize"]["zp_z0"]
firstLayerSize = 2*zp_z0*z0
L = math.log(fLayerRatio/firstLayerSize*cell/2**levelRef)/math.log(r)+1
SHMDict["addLayersControls"]["layers"]["terrain_solid"]["nSurfaceLayers"] = int(round(L))
SHMDict.writeFile()
"""
# changing snappyHexMeshDict - with template file
snapName = path.join(work.systemDir(),"snappyHexMeshDict")
template = TemplateFile(snapName+".template")
template.writeToFile(snapName,{ 'refBox1_minx':refBox1_minx,'refBox1_miny':refBox1_miny,'refBox1_minz':refBox1_minz,
'refBox1_maxx':refBox1_maxx,'refBox1_maxy':refBox1_maxy,'refBox1_maxz':refBox1_maxz,
'refBox2_minx':refBox2_minx,'refBox2_miny':refBox2_miny,'refBox2_minz':refBox2_minz,
'refBox2_maxx':refBox2_maxx,'refBox2_maxy':refBox2_maxy,'refBox2_maxz':refBox2_maxz,
'locInMesh_x':x0,'locInMesh_y':y0,'locInMesh_z':zz})
"""
# TODO - add parallel runs!
SHMrun = BasicRunner(argv=["snappyHexMesh",'-overwrite','-case',work.name],server=False,logname="SHM")
print "Running SHM"
SHMrun.start()
# mapping fields - From earlier result if exists
if caseType.find("mapFields")>0: #TODO - fix mapping issue. mucho importante!
#copying results from other z0 converged runs
setName = glob.glob(target + 'Crude/sets/*')
lastRun = range(len(setName))
for num in range(len(setName)):
lastRun[num] = int(setName[num][setName[num].rfind("/")+1:])
sourceTimeArg = str(max(lastRun))
mapRun = BasicRunner(argv=['mapFields -consistent -sourceTime ' + sourceTimeArg +
' -case ' + work.name + ' ' + target + "Crude"],silent=True,server=False,logname='mapLog')
mapRun.start()
# parallel rule
#print "Mesh has " + str(cells) + " cells"
#if cells>100000: parallel=1
#else: parallel=0
parallel = 1
cluster = 1
if parallel:
#--------------------------------------------------------------------------------------
# decomposing
#--------------------------------------------------------------------------------------
# removing U.template from 0/ directory
subprocess.call("rm " + bmName + ".template ",shell=True)
arg = " -case " + work.name
decomposeRun = BasicRunner(argv=["decomposePar -force" + arg],silent=True,server=False,logname="decompose")
decomposeRun.start()
#--------------------------------------------------------------------------------------
# running
#--------------------------------------------------------------------------------------
machine = LAMMachine(nr=procnr)
# run case
PlotRunner(args=["--proc=%d"%procnr,"--progress","--no-continuity","--hardcopy", "--non-persist", "simpleFoam","-case",work.name])
#--------------------------------------------------------------------------------------
# reconstruct
#-------------------------------------------------------------------------
reconstructRun = BasicRunner(argv=["reconstructPar -latestTime" + arg],silent=True,server=False,logname="reconstructLog")
reconstructRun.start()
else:
#--------------------------------------------------------------------------------------
# running
#--------------------------------------------------------------------------------------
PlotRunner(args=["--progress","simpleFoam","-case",work.name])
# sample results
dirNameList = glob.glob(target + "*")
dirNameList.sort()
for dirName in dirNameList:
# sampling
arg = " -case " + dirName + "/"
sampleRun = BasicRunner(argv=["sample -latestTime" + arg],silent=True,server=False,logname="sampleLog")
sampleRun.start()
#finding the most converged run.
setName = glob.glob(dirName + '/sets/*')
lastRun = range(len(setName))
for num in range(len(setName)):
lastRun[num] = int(setName[num][setName[num].rfind("/")+1:])
m = max(lastRun)
p = lastRun.index(m)
data_y = genfromtxt(setName[p] + '/line_y_U.xy',delimiter=' ')
y, Ux_y, Uy_y = data_y[:,0], data_y[:,1], data_y[:,2]
if AR<100: # if terrain isn't flat
#TODO find the height of the hill - the exact one! because of truncation errors etc -
#just follow the line measurements and look for the first place above 0
h = min(data_y[:,0])
y = y-h # normalizing data to height of hill-top above ground
return y,Ux_y,Uy_y
pi = 3.1415926
ratio_max = 0
theta = 0
#Obtain Value of Theta from dummy theta file
with open("theta", "r") as f:
for line in f:
theta = float(line.split("e")[0]) * 10**(float(line.split("e")[1]))
#Calculate new velocity
Ux = U * np.cos(theta * pi / 180.)
Uy = U * np.sin(theta * pi / 180.)
#Replace the existing U boundary conditions
new_vel = "uniform (" + str(Ux) + " " + str(Uy) + " 0)"
vel["internalField"] = new_vel
vel.writeFile()
#Run the solver
BasicRunner(argv=["simpleFoam", "-case", "."]).start()
#Store the Cl/Cd ratio in a dummy file
cl = 0
cd = 0
count = 0
with open(pproc, "r") as p:
for i, line in enumerate(p):
if i > 9:
cl_i = abs(float(line.split()[3]))
cd_i = abs(float(line.split()[2]))
cl = cl_i
cd = cd_i
#count = count + 1
cl = float(cl)
cd = float(cd)
ratio = cl / cd
# from os import path
from PyFoam.Execution.BasicRunner import BasicRunner
from setupCases import pbe_grids
if __name__ == "__main__":
for c in ["pure_coal", "pure_br"]:
for N in pbe_grids:
block_mesh = BasicRunner(
argv=["blockMesh", "-case", "{0}{1}".format(c, N)],
silent=True)
block_mesh.start()
run = BasicRunner(
argv=["twoPhaseEulerFoam", "-case", "{0}{1}".format(c, N)],
silent=True)
run.start()
def reWriteBlockMeshDict(target, caseType):
# read dictionaries of target case - with 3 different z0 (assuming standard case, 0.1, 0.03 and 0.005
z0Str = target[target.find("z0") + 3:]
dict005Name = target.replace(z0Str, "0.005")
dict03Name = target.replace(z0Str, "0.03")
dict1Name = target.replace(z0Str, "0.1")
# - just for memory sake ... dict005 = ParsedBlockMeshDict(target.replace(z0Str,"0.005")+"/constant/polyMesh/blockMeshDict")
# - just for memory sake... dict03["blocks"][4][1] = dict005["blocks"][4][1]
# erase all previous mesh files
# for 0.03 case
curDir = os.getcwd()
os.chdir(dict03Name)
os.chdir('constant/polyMesh')
os.system("rm -rf *")
os.chdir(curDir)
# for 0.1 case
os.chdir(dict1Name)
os.chdir('constant/polyMesh')
os.system("rm -rf *")
os.chdir(curDir)
# copy the 0.005 blockMeshDict to the 0.03 and 0.1 cases
os.system("cp %s %s" % (dict005Name + "/constant/polyMesh/blockMeshDict",
dict03Name + "/constant/polyMesh/blockMeshDict"))
os.system("cp %s %s" % (dict005Name + "/constant/polyMesh/blockMeshDict",
dict1Name + "/constant/polyMesh/blockMeshDict"))
# running blockMesh on 0.03 case
blockRun = BasicRunner(argv=["blockMesh", '-case', dict03Name],
silent=True,
server=False,
logname="blockMesh")
blockRun.start()
if not blockRun.runOK(): print "there was an error with blockMesh"
# running blockMesh on 0.005 case
blockRun = BasicRunner(argv=["blockMesh", '-case', dict1Name],
silent=True,
server=False,
logname="blockMesh")
blockRun.start()
if not blockRun.runOK(): print "there was an error with blockMesh"
# mapping fields - From earlier result if exists
if caseType == "mapFields":
# copying 0 time files from Crude run - because mapFields won't start with a non similar p and points size
os.system('cp -r ' + dict03Name + 'Crude/0/* ' + dict03Name + '/0/')
os.system('cp -r ' + dict1Name + 'Crude/0/* ' + dict1Name + '/0/')
# finding the most converged run. assuming the "crude" run had the same dirName with "Crude" attached
# for z0 = 0.03
mapRun = BasicRunner(argv=[
'mapFields -consistent -sourceTime latestTime' + ' -case ' +
dict03Name + ' ' + dict03Name + "Crude"
],
silent=True,
server=False,
logname='mapLog')
mapRun.start()
# for z0 = 0.1
mapRun = BasicRunner(argv=[
'mapFields -consistent -sourceTime latestTime' + ' -case ' +
dict1Name + ' ' + dict1Name + "Crude"
],
silent=True,
server=False,
logname='mapLog')
mapRun.start()
#f.Q *= stdNoise ** 2
#ensemble = f.initialize(x=x, P=P)
# Generating lists for data collection and for plots
thetaList = []
ThetaListOne = []
ThetaListAll = []
ThetaListMeanT = []
ThetaListMeanT1Grid = []
ThetaListMeanT1Time = []
ThetaListMeanT1TimeForPlot = []
ThetaListMeanTAll = []
ThetaListMeanTAllForPlot = []
# Prediction using the OpenFoam -- RichardsFoam2
blockRun = BasicRunner(argv=["blockMesh"], silent=True, server=False)
print("Running blockMesh")
blockRun.start()
if not blockRun.runOK():
error("There was a problem with blockMesh")
print("Running RichardsFoam2")
for i in range(N): # N ensemble member
print('Ensemble number: ', i + 1)
ThetaListOne = []
for j in range(timeSpan):
print('At day: ', j + 1)
control["startTime"] = j * dt
control["endTime"] = (j + 1) * dt
control.writeFile()
state = ParsedParameterFile(str(control["startTime"]) + '/psi')
def run(self):
config = ConfigParser.ConfigParser()
files = self.parser.getArgs()
good = config.read(files)
# will work with 2.4
# if len(good)!=len(files):
# print_("Problem while trying to parse files",files)
# print_("Only ",good," could be parsed")
# sys.exit(-1)
benchName = config.get("General", "name")
if self.opts.nameAddition != None:
benchName += "_" + self.opts.nameAddition
if self.opts.foamVersion != None:
benchName += "_v" + self.opts.foamVersion
isParallel = config.getboolean("General", "parallel")
lam = None
if isParallel:
nrCpus = config.getint("General", "nProcs")
machineFile = config.get("General", "machines")
if not path.exists(machineFile):
self.error("Machine file ", machineFile,
"needed for parallel run")
lam = LAMMachine(machineFile, nr=nrCpus)
if lam.cpuNr() > nrCpus:
self.error("Wrong number of CPUs: ", lam.cpuNr())
print_("Running parallel on", lam.cpuNr(), "CPUs")
if config.has_option("General", "casesDirectory"):
casesDirectory = path.expanduser(
config.get("General", "casesDirectory"))
else:
casesDirectory = foamTutorials()
if not path.exists(casesDirectory):
self.error("Directory", casesDirectory,
"needed with the benchmark cases is missing")
else:
print_("Using cases from directory", casesDirectory)
benchCases = []
config.remove_section("General")
for sec in config.sections():
print_("Reading: ", sec)
skipIt = False
skipReason = ""
if config.has_option(sec, "skip"):
skipIt = config.getboolean(sec, "skip")
skipReason = "Switched off in file"
if self.opts.excases != None and not skipIt:
for p in self.opts.excases:
if fnmatch(sec, p):
skipIt = True
skipReason = "Switched off by pattern '" + p + "'"
if self.opts.cases != None:
for p in self.opts.cases:
if fnmatch(sec, p):
skipIt = False
skipReason = ""
if skipIt:
print_("Skipping case ..... Reason:" + skipReason)
continue
sol = config.get(sec, "solver")
cas = config.get(sec, "case")
pre = eval(config.get(sec, "prepare"))
preCon = []
if config.has_option(sec, "preControlDict"):
preCon = eval(config.get(sec, "preControlDict"))
con = eval(config.get(sec, "controlDict"))
bas = config.getfloat(sec, "baseline")
wei = config.getfloat(sec, "weight")
add = []
if config.has_option(sec, "additional"):
add = eval(config.get(sec, "additional"))
print_("Adding: ", add)
util = []
if config.has_option(sec, "utilities"):
util = eval(config.get(sec, "utilities"))
print_("Utilities: ", util)
nr = 99999
if config.has_option(sec, "nr"):
nr = eval(config.get(sec, "nr"))
sp = None
if config.has_option(sec, "blockSplit"):
sp = eval(config.get(sec, "blockSplit"))
toRm = []
if config.has_option(sec, "filesToRemove"):
toRm = eval(config.get(sec, "filesToRemove"))
setInit = []
if config.has_option(sec, "setInitial"):
setInit = eval(config.get(sec, "setInitial"))
parallelOK = False
if config.has_option(sec, "parallelOK"):
parallelOK = config.getboolean(sec, "parallelOK")
deMet = ["metis"]
if config.has_option(sec, "decomposition"):
deMet = config.get(sec, "decomposition").split()
if deMet[0] == "metis":
pass
elif deMet[0] == "simple":
if len(deMet) < 2:
deMet.append(0)
else:
deMet[1] = int(deMet[1])
else:
print_("Unimplemented decomposition method", deMet[0],
"switching to metis")
deMet = ["metis"]
if isParallel == False or parallelOK == True:
if path.exists(path.join(casesDirectory, sol, cas)):
benchCases.append(
(nr, sec, sol, cas, pre, con, preCon, bas, wei, add,
util, sp, toRm, setInit, deMet))
else:
print_("Skipping", sec, "because directory",
path.join(casesDirectory, sol, cas),
"could not be found")
else:
print_("Skipping", sec, "because not parallel")
benchCases.sort()
parallelString = ""
if isParallel:
parallelString = ".cpus=" + str(nrCpus)
resultFile = open(
"Benchmark." + benchName + "." + uname()[1] + parallelString +
".results", "w")
totalSpeedup = 0
minSpeedup = None
maxSpeedup = None
totalWeight = 0
runsOK = 0
currentEstimate = 1.
print_("\nStart Benching\n")
csv = CSVCollection("Benchmark." + benchName + "." + uname()[1] +
parallelString + ".csv")
# csvHeaders=["description","solver","case","caseDir","base",
# "benchmark","machine","arch","cpus","os","version",
# "wallclocktime","cputime","cputimeuser","cputimesystem","maxmemory","cpuusage","speedup"]
for nr, description, solver, case, prepare, control, preControl, base, weight, additional, utilities, split, toRemove, setInit, decomposition in benchCases:
# control.append( ("endTime",-2000) )
print_("Running Benchmark: ", description)
print_("Solver: ", solver)
print_("Case: ", case)
caseName = solver + "_" + case + "_" + benchName + "." + uname(
)[1] + ".case"
print_("Short name: ", caseName)
caseDir = caseName + ".runDir"
csv["description"] = description
csv["solver"] = solver
csv["case"] = case
csv["caseDir"] = caseDir
csv["base"] = base
csv["benchmark"] = benchName
csv["machine"] = uname()[1]
csv["arch"] = uname()[4]
if lam == None:
csv["cpus"] = 1
else:
csv["cpus"] = lam.cpuNr()
csv["os"] = uname()[0]
csv["version"] = uname()[2]
workDir = path.realpath(path.curdir)
orig = SolutionDirectory(path.join(casesDirectory, solver, case),
archive=None,
paraviewLink=False)
for a in additional + utilities:
orig.addToClone(a)
orig.cloneCase(path.join(workDir, caseDir))
if oldApp():
argv = [solver, workDir, caseDir]
else:
argv = [solver, "-case", path.join(workDir, caseDir)]
run = BasicRunner(silent=True,
argv=argv,
logname="BenchRunning",
lam=lam)
runDir = run.getSolutionDirectory()
controlFile = ParameterFile(runDir.controlDict())
for name, value in preControl:
print_("Setting parameter", name, "to", value,
"in controlDict")
controlFile.replaceParameter(name, value)
for rm in toRemove:
fn = path.join(caseDir, rm)
print_("Removing file", fn)
remove(fn)
for field, bc, val in setInit:
print_("Setting", field, "on", bc, "to", val)
SolutionFile(runDir.initialDir(),
field).replaceBoundary(bc, val)
oldDeltaT = controlFile.replaceParameter("deltaT", 0)
for u in utilities:
print_("Building utility ", u)
execute("wmake 2>&1 >%s %s" % (path.join(
caseDir, "BenchCompile." + u), path.join(caseDir, u)))
print_("Preparing the case: ")
if lam != None:
prepare = prepare + [("decomposePar", "")]
if decomposition[0] == "metis":
lam.writeMetis(
SolutionDirectory(path.join(workDir, caseDir)))
elif decomposition[0] == "simple":
lam.writeSimple(
SolutionDirectory(path.join(workDir, caseDir)),
decomposition[1])
if split:
print_("Splitting the mesh:", split)
bm = BlockMesh(runDir.blockMesh())
bm.refineMesh(split)
for pre, post in prepare:
print_("Doing ", pre, " ....")
post = post.replace("%case%", caseDir)
if oldApp():
args = string.split("%s %s %s %s" %
(pre, workDir, caseDir, post))
else:
args = string.split(
"%s -case %s %s" %
(pre, path.join(workDir, caseDir), post))
util = BasicRunner(silent=True,
argv=args,
logname="BenchPrepare_" + pre)
util.start()
controlFile.replaceParameter("deltaT", oldDeltaT)
# control.append(("endTime",-1000))
for name, value in control:
print_("Setting parameter", name, "to", value,
"in controlDict")
controlFile.replaceParameter(name, value)
print_("Starting at ", asctime(localtime(time())))
print_(
" Baseline is %f, estimated speedup %f -> estimated end at %s "
% (base, currentEstimate,
asctime(localtime(time() + base / currentEstimate))))
print_("Running the case ....")
run.start()
speedup = None
cpuUsage = 0
speedupOut = -1
try:
speedup = base / run.run.wallTime()
cpuUsage = 100. * run.run.cpuTime() / run.run.wallTime()
except ZeroDivisionError:
print_("Division by Zero: ", run.run.wallTime())
if not run.runOK():
print_("\nWARNING!!!!")
print_(
"Run had a problem, not using the results. Check the log\n"
)
speedup = None
if speedup != None:
speedupOut = speedup
totalSpeedup += speedup * weight
totalWeight += weight
runsOK += 1
if maxSpeedup == None:
maxSpeedup = speedup
elif speedup > maxSpeedup:
maxSpeedup = speedup
if minSpeedup == None:
minSpeedup = speedup
elif speedup < minSpeedup:
minSpeedup = speedup
print_("Wall clock: ", run.run.wallTime())
print_("Speedup: ", speedup, " (Baseline: ", base, ")")
print_("CPU Time: ", run.run.cpuTime())
print_("CPU Time User: "******"CPU Time System: ", run.run.cpuSystemTime())
print_("Memory: ", run.run.usedMemory())
print_("CPU Usage: %6.2f%%" % (cpuUsage))
csv["wallclocktime"] = run.run.wallTime()
csv["cputime"] = run.run.cpuTime()
csv["cputimeuser"] = run.run.cpuUserTime()
csv["cputimesystem"] = run.run.cpuSystemTime()
csv["maxmemory"] = run.run.usedMemory()
csv["cpuusage"] = cpuUsage
if speedup != None:
csv["speedup"] = speedup
else:
csv["speedup"] = "##"
csv.write()
resultFile.write(
"Case %s WallTime %g CPUTime %g UserTime %g SystemTime %g Memory %g MB Speedup %g\n"
% (caseName, run.run.wallTime(), run.run.cpuTime(),
run.run.cpuUserTime(), run.run.cpuSystemTime(),
run.run.usedMemory(), speedupOut))
resultFile.flush()
if speedup != None:
currentEstimate = totalSpeedup / totalWeight
if self.opts.removeCases:
print_("Clearing case", end=" ")
if speedup == None:
print_("not ... because it failed")
else:
print_("completely")
rmtree(caseDir, ignore_errors=True)
print_()
print_()
