def _configure(self):
"""
Setup members using inventory.
"""
Application._configure(self)
self.elasThick = self.inventory.elasThick
self.lockDepth = self.inventory.lockDepth
self.recurrenceTime = self.inventory.recurrenceTime
self.viscosity = self.inventory.viscosity
self.shearModulus = self.inventory.shearModulus
self.velocity = self.inventory.plateVelocity / 2.0
self.numberCycles = self.inventory.numberCycles
self.numberSteps = self.inventory.numberSteps
self.numberTerms = self.inventory.numberTerms
self.numberPoints = self.inventory.numberPoints
self.deltaX = self.inventory.deltaX
self.xEpsilon = self.inventory.xEpsilon
self.outputDisp = self.inventory.outputDisp
self.outputVel = self.inventory.outputVel
self.dispFilename = self.inventory.dispFilename
self.velFilename = self.inventory.velFilename
self.deltaT = self.recurrenceTime / self.numberSteps
self.tauFac = 0.5 * self.shearModulus / self.viscosity
self.tau0 = self.recurrenceTime * self.tauFac
return
def _configure(self):
Script._configure(self)
self.clerk = self.inventory.clerk
self.clerk.director = self
self.wwwuser = self.inventory.wwwuser
self.tables = self.inventory.tables
return
def _configure(self):
"""
Setup members using inventory.
"""
Application._configure(self)
# import pdb
# pdb.set_trace()
# File info.
self.vtkInputFile = self.inventory.vtkInputFile
self.vtkOutputFile = self.inventory.vtkOutputFile
# Index information
self.tensorIndex = self.inventory.tensorIndex
self.tensorComponentsOrder = self.inventory.tensorComponentsOrder
# Parameters
self.frictionAngle = self.inventory.frictionAngle.value
self.cohesion = self.inventory.cohesion.value
sinFric = math.sin(self.frictionAngle)
cosFric = math.cos(self.frictionAngle)
denomFriction = math.sqrt(3.0) * (3.0 - sinFric)
self.alphaYield = 2.0 * sinFric/denomFriction
self.beta = 6.0 * self.cohesion * cosFric/denomFriction
return
def _configure(self): """ Set members using inventory. """ Script._configure(self) self.data = self.inventory.data return
def _configure(self):
"""
Setup members using inventory.
"""
Application._configure(self)
return
def _configure(self):
"""
Setup members using inventory.
"""
Application._configure(self)
self.dataDim = self.inventory.dataDim
self.pointsFile = self.inventory.pointsFile
self.segsFile = self.inventory.segsFile
self.slipScale = self.inventory.slipScale
self.spaceDim = 3
self.pointsSpatialDB = self.inventory.pointsSpatialDB
self.upDir = self.inventory.upDir
self.normalDir = self.inventory.normalDir
self.dipSlip = self.inventory.dipSlip
self.dipCutoff = self.inventory.dipCutoff
self.xMinVal = self.inventory.xMin.value
self.xMaxVal = self.inventory.xMax.value
self.yMinVal = self.inventory.yMin.value
self.yMaxVal = self.inventory.yMax.value
self.zMinVal = self.inventory.zMin.value
self.zMaxVal = self.inventory.zMax.value
self.defaultValues = self.inventory.defaultValues
self.upVec = numpy.array([float(self.upDir[0]), float(self.upDir[1]),
float(self.upDir[2])], dtype=numpy.float64)
self.normalVec = numpy.array([float(self.normalDir[0]),
float(self.normalDir[1]),
float(self.normalDir[2])], dtype=numpy.float64)
self.dipCutoffProj = abs(math.sin(self.dipCutoff.value))
return
def _configure(self):
"""
Setup members using inventory.
"""
Application._configure(self)
# import pdb
# pdb.set_trace()
# File info.
self.vtkInputFile = self.inventory.vtkInputFile
self.vtkOutputFile = self.inventory.vtkOutputFile
# Index information
self.vtkTensorIndex = self.inventory.vtkTensorIndex
self.vtkTensorComponentsOrder = self.inventory.vtkTensorComponentsOrder
# Regional field
s1 = float(self.inventory.regionalSigma1[0])
s2 = float(self.inventory.regionalSigma1[0])
s3 = float(self.inventory.regionalSigma1[0])
sVec = numpy.array([s1, s2, s3], dtype=numpy.float64)
self.regionalSigma = numpy.diag(sVec)
self.regionalAxes = numpy.zeros((3,3), dtype=numpy.float64)
for i in range(3):
self.regionalAxes[0,i] = float(self.inventory.regionalSigma1[i+1])
self.regionalAxes[1,i] = float(self.inventory.regionalSigma2[i+1])
self.regionalAxes[2,i] = float(self.inventory.regionalSigma3[i+1])
return
def _configure(self): """ Setup members using inventory. """ Application._configure(self) self.cfgFile = self.inventory.cfgFile self.pylith = self.inventory.pylith self.petscOptions = self.inventory.petscOptions return
def _configure(self): """ Set members using inventory. """ Script._configure(self) self.data = self.inventory.data self.mesh = self.inventory.mesh self.quadrature = self.inventory.quadrature return
def _configure(self): """ Setup members based on inventory. """ Script._configure(self) self.geometry = self.inventory.geometry self.values = self.inventory.values self.iohandler = self.inventory.iohandler return
def _configure(self): """ Setup members using inventory. """ Application._configure(self) self.mesh = self.inventory.mesh self.groups = self.inventory.groups self.materials = self.inventory.materials return
def _configure(self): """ Setup members using inventory. """ Application._configure(self) self.polesInputFile = self.inventory.polesInputFile self.polesOutputFile = self.inventory.polesOutputFile self.geogToCart = self.inventory.geogToCart self.spaceDim = 3 return
def _configure(self):
Script._configure(self)
self.name = self.inventory.name
self.unitcell_path = self.inventory.unitcell
self.ecutoff = self.inventory.ecutoff
self.xcf = self.inventory.xcf
self.mpmesh = self.inventory.mpmesh
self.generateInputsOnly = self.inventory.generateInputsOnly
self.cmd = self.inventory.cmd
return
def _configure(self):
from mystic import strategy as detools
Script._configure(self)
mod = __import__(self.inventory.inputs)
self.mod = mod
if self.inventory.verbose:
logging.basicConfig(level=logging.DEBUG,
format='%(asctime)s %(levelname)s %(message)s',
datefmt='%a, %d %b %Y %H:%M:%S')
def _configure(self):
Script._configure(self)
for param in self.parameters:
exec "self.%s = self.inventory.%s" % (param, param)
continue
self.C_ms = numpy.array(eval(self.C_ms))
# it seems that it works better to make viewDirectory equal to outputDir
self.outputDir = self.viewDirectory
return
def _configure(self): """ Setup members using inventory. """ Application._configure(self) self.ucdFaceFile = self.inventory.ucdFaceFile self.faultIDNum = self.inventory.faultIDNum self.pointOutputFile = self.inventory.pointOutputFile self.nodeValuesList = self.inventory.nodeValuesList self.excludeZeroNormals = self.inventory.excludeZeroNormals return
def _configure(self): """ Set members using inventory. """ Script._configure(self) self.data = self.inventory.data self.mesh = self.inventory.mesh self.quadrature = self.inventory.quadrature self.material = self.inventory.material self.solution = self.inventory.solution return
def _configure(self): """ Setup members using inventory. """ Application._configure(self) self.psetFile = self.inventory.psetFile self.ucdFile = self.inventory.ucdFile self.pointOutputFile = self.inventory.pointOutputFile self.valuesList = self.inventory.valuesList self.outputIndex = self.inventory.outputIndex self.excludeZeroNormals = self.inventory.excludeZeroNormals return
def _configure(self):
"""
Setup members using inventory.
"""
Application._configure(self)
self.penaltyWeights = numpy.array(self.penaltyWeightVals, dtype=numpy.float64)
self.numPenaltyWeights = self.penaltyWeights.shape[0]
# Left-lateral and updip components from assumed rake.
self.llComp = math.cos(self.rake.value)
self.udComp = math.sin(self.rake.value)
return
def _configure(self):
"""
Setup members using inventory.
"""
Application._configure(self)
# Filenames
self.inFile = self.inventory.inFile
self.outRoot = self.inventory.outRoot
self.journalOut = self.inventory.journalOut
self.surfaceOut = self.inventory.surfaceOut
return
def _configure(self):
"""
Setup members using inventory.
"""
Application._configure(self)
self.srcCoordSys = self.inventory.srcCoordSys
self.destCoordSys = self.inventory.destCoordSys
self.dataDim = self.inventory.dataDim
self.bcType = self.inventory.bcType
self.pointsFile = self.inventory.pointsFile
self.pointsSpatialDB = self.inventory.pointsSpatialDB
self.bcScale = self.inventory.bcScale
self.upDir = self.inventory.upDir
self.normalDir = self.inventory.normalDir
self.eulerLat = self.inventory.eulerLat
self.eulerLon = self.inventory.eulerLon
self.eulerRot = self.inventory.eulerRot
self.spaceDim = self.srcCoordSys.spaceDim
self.dipSlip = self.inventory.dipSlip
self.dipCutoff = self.inventory.dipCutoff
self.xMinVal = self.inventory.xMin.value
self.xMaxVal = self.inventory.xMax.value
self.yMinVal = self.inventory.yMin.value
self.yMaxVal = self.inventory.yMax.value
self.zMinVal = self.inventory.zMin.value
self.zMaxVal = self.inventory.zMax.value
self.defaultValues = self.inventory.defaultValues
lat = self.eulerLat.value
lon = self.eulerLon.value
rot = self.eulerRot.value
clat = math.cos(lat)
slat = math.sin(lat)
clon = math.cos(lon)
slon = math.sin(lon)
# Note that the Euler pole already includes the earth radius term.
self.eulerPole[0] = self.earthRad * rot * clat * clon
self.eulerPole[1] = self.earthRad * rot * clat * slon
self.eulerPole[2] = self.earthRad * rot * slat
self.upVec = numpy.array([float(self.upDir[0]), float(self.upDir[1]),
float(self.upDir[2])], dtype=numpy.float64)
self.normalVec = numpy.array([float(self.normalDir[0]),
float(self.normalDir[1]),
float(self.normalDir[2])], dtype=numpy.float64)
self.dipCutoffProj = abs(math.sin(self.dipCutoff.value))
return
def _configure(self):
base._configure(self)
self.id = self.inventory.id
self.type = self.inventory.type
self.debug = self.inventory.debug
self.idd = self.inventory.idd
self.clerk = self.inventory.clerk
self.clerk.director = self
self.dds = self.inventory.dds
self.dds.director = self
self.csaccessor = self.inventory.csaccessor
return
def _configure(self):
"""
Setup members using inventory.
"""
Application._configure(self)
self.faults = self.inventory.faults
self.filenamePattern = self.inventory.filenamePattern
self.snapshots = map(float, self.inventory.snapshots)
self.snapshotUnits = self.inventory.snapshotUnits
self.dbProps = self.inventory.dbProps
self.cs = self.inventory.cs
self.filenameOut = self.inventory.filenameOut
self.typos = self.inventory.typos
return
def _configure(self):
"""
Setup members using inventory.
"""
Application._configure(self)
# Filenames
self.inFile = self.inventory.inFile
self.outFile = self.inventory.outFile
# Parameters
self.intervalSize = self.inventory.intervalSize
self.minCheck = self.inventory.minCheck
self.maxCheck = self.inventory.maxCheck
return
def _configure(self):
"""
Setup members using inventory.
"""
Application._configure(self)
import os
import re
# Set up info for input files
totalInputPath = os.path.normpath(os.path.join(os.getcwd(),
self.inventory.vtkInputRoot))
self.vtkInputDir = os.path.dirname(totalInputPath)
baseInputName = os.path.basename(totalInputPath)
baseInputNameLen = len(baseInputName)
if baseInputName.endswith(".vtk"):
baseInputNameStripped = baseInputName[0:baseInputNameLen-4]
else:
baseInputNameStripped = baseInputName
testFind = re.search('_t[0-9]*$', baseInputNameStripped)
if testFind != None:
timeInd = baseInputNameStripped.rfind(testFind.group(0))
self.vtkInputRoot = baseInputNameStripped[0:timeInd]
else:
self.vtkInputRoot = baseInputNameStripped
# Set up info for output files
totalOutputPath = os.path.normpath(os.path.join(
os.getcwd(), self.inventory.vtkOutputRoot))
self.vtkOutputDir = os.path.dirname(totalOutputPath)
baseOutputName = os.path.basename(totalOutputPath)
baseOutputNameLen = len(baseOutputName)
if baseOutputName.endswith(".vtk"):
baseOutputNameStripped = baseOutputName[0:baseOutputNameLen-4]
else:
baseOutputNameStripped = baseOutputName
testFind = re.search('_t[0-9]*$', baseOutputNameStripped)
if testFind != None:
timeInd = baseOutputNameStripped.rfind(testFind.group(0))
self.vtkOutputRoot = baseOutputNameStripped[0:timeInd]
else:
self.vtkOutputRoot = baseOutputNameStripped
self.scaleFactor = self.inventory.scaleFactor
return
def _configure(self):
"""
Setup members using inventory.
"""
Application._configure(self)
# Filenames
self.faultInfoFile = self.inventory.faultInfoFile
self.faultResultsFile = self.inventory.faultResultsFile
self.faultOutputFile = self.inventory.faultOutputFile
# Parameters
self.frictionCoeff = self.inventory.frictionCoeff
self.stressScaleFactor = self.inventory.stressScaleFactor
self.slipScaleFactor = self.inventory.slipScaleFactor
self.shearDirection = self.inventory.shearDirection
return
def _configure(self):
"""
Set members using inventory.
"""
Script._configure(self)
if self.inventory.reader.name == "dummy":
self.reader = None
else:
self.reader = self.inventory.reader
if self.inventory.converter.name == "dummy":
self.converter = None
else:
self.converter = self.inventory.converter
if self.inventory.writer.name == "dummy":
self.writer = self.reader
else:
self.writer = self.inventory.writer
return
def _configure(self):
from mystic import strategy as detools
Script._configure(self)
mod = __import__(self.inventory.costfunc)
self.mod = mod
self.scale = self.inventory.scale
self.probability = self.inventory.probability
try:
self.probability = self.mod.probability
except:
pass
try:
self.scale = self.mod.scale
except:
pass
self.strategy = getattr(detools, self.inventory.strategy)
if self.inventory.verbose:
logging.basicConfig(level=logging.DEBUG,
format='%(asctime)s %(levelname)s %(message)s',
datefmt='%a, %d %b %Y %H:%M:%S')
def _configure(self):
from mystic import strategy as detools
Script._configure(self)
mod = __import__(self.inventory.costfunc)
self.mod = mod
self.scale = self.inventory.scale
self.probability = self.inventory.probability
try:
self.probability = self.mod.probability
except:
pass
try:
self.scale = self.mod.scale
except:
pass
self.strategy = getattr(detools,self.inventory.strategy)
if self.inventory.verbose:
logging.basicConfig(level=logging.DEBUG,
format='%(asctime)s %(levelname)s %(message)s',
datefmt='%a, %d %b %Y %H:%M:%S')
def _configure(self):
"""
Setup members using inventory.
"""
Application._configure(self)
self.elasThick = self.inventory.elasThick.value
self.lockDepth = self.inventory.lockDepth.value
self.recurrenceTime = self.inventory.recurrenceTime.value
self.viscosity = self.inventory.viscosity.value
self.shearModulus = self.inventory.shearModulus.value
self.velocity = self.inventory.plateVelocity.value/2.0
self.numberCycles = self.inventory.numberCycles
self.numberSteps = self.inventory.numberSteps
self.numberTerms = self.inventory.numberTerms
self.numberPoints = self.inventory.numberPoints
self.deltaX = self.inventory.deltaX.value
self.xEpsilon = self.inventory.xEpsilon.value
self.outputDisplVTK = self.inventory.outputDisplVTK
self.outputDisplCSV = self.inventory.outputDisplCSV
self.outputVelVTK = self.inventory.outputVelVTK
self.outputVelCSV = self.inventory.outputVelCSV
self.displVTKBaseName = self.inventory.displVTKBaseName
self.displCSVFileName = self.inventory.displCSVFileName
self.velVTKBaseName = self.inventory.velVTKBaseName
self.velCSVFileName = self.inventory.velCSVFileName
self.displScaleFactor = self.inventory.displScaleFactor
self.velScaleFactor = self.inventory.velScaleFactor
self.coordScaleFactor = self.inventory.coordScaleFactor
self.coordUnits = self.inventory.coordUnits
self.timeUnits = self.inventory.timeUnits.value
self.timeStampWidth = self.inventory.timeStampWidth
self.title = self.inventory.title
self.deltaT = self.recurrenceTime/self.numberSteps
self.tauFac = 0.5*self.shearModulus/self.viscosity
self.tau0 = self.recurrenceTime * self.tauFac
return
def _configure(self):
"""
Setup members using inventory.
"""
Application._configure(self)
# Filenames
self.inputDem = self.inventory.inputDem
self.vtkOutputFile = self.inventory.vtkOutputFile
self.masterJournal = self.inventory.masterJournal
self.uLinePrefix = self.inventory.uLinePrefix
self.uLineJournal = self.inventory.uLineJournal
self.vLinePrefix = self.inventory.vLinePrefix
self.vLineJournal = self.inventory.vLineJournal
self.acisFilename = self.inventory.acisFilename
# Parameters
self.xMin = self.inventory.xMin
self.xMax = self.inventory.xMax
self.yMin = self.inventory.yMin
self.yMax = self.inventory.yMax
self.skipInterval = self.inventory.skipInterval
return
def _configure(self):
"""
Setup members using inventory.
"""
Application._configure(self)
# Filenames
self.inputDem = self.inventory.inputDem
self.vtkOutputFile = self.inventory.vtkOutputFile
self.masterJournal = self.inventory.masterJournal
self.uLinePrefix = self.inventory.uLinePrefix
self.uLineJournal = self.inventory.uLineJournal
self.vLinePrefix = self.inventory.vLinePrefix
self.vLineJournal = self.inventory.vLineJournal
self.acisFilename = self.inventory.acisFilename
# Parameters
self.xMin = self.inventory.xMin
self.xMax = self.inventory.xMax
self.yMin = self.inventory.yMin
self.yMax = self.inventory.yMax
self.skipInterval = self.inventory.skipInterval
return
def _configure(self):
Script._configure(self)
self.client = self.inventory.client
return
def _configure(self):
Script._configure(self)
self.stream = self.inventory.stream
return
def _configure(self):
Script._configure(self)
self.friend = self.inventory.name
return
def _configure(self):
Base._configure(self)
self.friend = self.inventory.name
return
def _configure(self):
"""
Setup members using inventory.
"""
Application._configure(self)
import pdb
pdb.set_trace()
# Set up info for input files
totalInputPath = os.path.normpath(
os.path.join(os.getcwd(), self.inventory.vtkInputRoot))
self.vtkInputDir = os.path.dirname(totalInputPath)
baseInputName = os.path.basename(totalInputPath)
baseInputNameLen = len(baseInputName)
if baseInputName.endswith(".vtk"):
baseInputNameStripped = baseInputName[0:baseInputNameLen-4]
else:
baseInputNameStripped = baseInputName
testFind = re.search('_t[0-9]*$', baseInputNameStripped)
if testFind != None:
timeInd = baseInputNameStripped.rfind(testFind.group(0))
self.vtkInputRoot = baseInputNameStripped[0:timeInd]
else:
self.vtkInputRoot = baseInputNameStripped
# Solution mode info
self.stressRefMode = self.inventory.stressRefMode
self.orientationMode = self.inventory.orientationMode
self.initialStateIndex = self.inventory.initialStateIndex
self.constantStateValues = self.inventory.constantStateValues
self.isotropicPoroelastic = self.inventory.isotropicPoroelastic
# Index information
self.vtkStressIndex = self.inventory.vtkStressIndex
self.vtkStressComponentsOrder = self.inventory.vtkStressComponentsOrder
# Parameters
self.frictionCoeff = self.inventory.frictionCoeff
self.skemptonCoeff = self.inventory.skemptonCoeff
self.cffPlaneNormal = numpy.array([float(self.inventory.cffPlaneNormal[0]),
float(self.inventory.cffPlaneNormal[1]),
float(self.inventory.cffPlaneNormal[2]),
dtype=numpy.float64)
# Set up info for output files
totalOutputPath = os.path.normpath(os.path.join(
os.getcwd(), self.inventory.vtkOutputRoot))
self.vtkOutputDir = os.path.dirname(totalOutputPath)
baseOutputName = os.path.basename(totalOutputPath)
baseOutputNameLen = len(baseOutputName)
if baseOutputName.endswith(".vtk"):
baseOutputNameStripped = baseOutputName[0:baseOutputNameLen-4]
else:
baseOutputNameStripped = baseOutputName
testFind = re.search('_t[0-9]*$', baseOutputNameStripped)
if testFind != None:
timeInd = baseOutputNameStripped.rfind(testFind.group(0))
self.vtkOutputRoot = baseOutputNameStripped[0:timeInd]
else:
self.vtkOutputRoot = baseOutputNameStripped
return
def _getFileInfo(self):
"""
Find input files and set up filenames for input and output.
"""
# Create list of input files and associated times
fileString = self.vtkInputRoot + "_t[0-9]*.vtk"
searchString = os.path.join(self.vtkInputDir, fileString)
self.vtkInputList = glob.glob(searchString)
self.numVtkInputFiles = len(self.vtkInputList)
index1 = self.vtkInputList[0].rfind("_t")
index2 = self.vtkInputList[0].rfind(".vtk")
self.timeStampWidth = index2 - index1 - 2
for vtkFile in self.vtkInputList:
timeString = vtkFile[index1+2:index2]
self.vtkInputTimes.append(float(timeString))
# Determine time index from which to start processing
if self.stressRefMode == "constant_state":
self.startIndex = 0
elif self.stressRefMode == "previous_state":
self.startIndex = 1
else:
self.startIndex = self.initialStateIndex + 1
# Raise exception if there aren't enough files to process
numFilesToProcess = self.numVtkInputFiles - self.startIndex - 1
if numFilesToProcess < 1:
try:
raise TooFewFilesError(numFilesToProcess)
except TooFewFilesError, e:
print 'Not enough files found for search string: ', searchString
print 'Number of files found: ', e.value
# Create output directory if it doesn't exist
if not os.path.isdir(self.vtkOutputDir):
os.mkdir(self.vtkOutputDir)
return
def _cffLoop(self):
"""
Function to loop over input files, compute Cff relative to reference state,
and write the results to output files.
"""
# Define function to use, depending on whether we are computing CFF on a
# predefined plane or an optimally-oriented plane.
if self.orientationMode == "optimally_oriented":
cffFunct = self._cffOop
else:
cffFunct = self._cffPredefined
# Define reference stresses unless differences are computed between each
# time step.
if self.stressRefMode == "constant_state":
testFile = os.path.join(self.vtkInputDir, self.vtkInputList[0]))
testStress = self._readStress(testFile)
refStress = numpy.tile(self.constantStateValues,
(self.numStressPoints, 1))
def _configure(self):
Script._configure(self)
self.toolkit = self.inventory.toolkit
self.maingml = self.inventory.maingml
return
def _configure(self):
Script._configure(self)
self.out = self.inventory.out
self.filename = self.inventory.name
return
def _configure(self):
Script._configure(self)
self._delay = self.inventory.delay
self._doClient = self.inventory.client
self._doServer = self.inventory.server
return
def _configure(self):
Script._configure(self)
self.db = self.inventory.db
return
def _configure(self):
Script._configure(self)
self.modeller = self.inventory.modeller
return
def _configure(self):
Script._configure(self)
self.launcher = self.inventory.launcher
return
def _configure(self):
Script._configure(self)
return
def _configure(self):
base._configure(self)
self.clerk = self.inventory.clerk
self.clerk.director = self
return
def _configure(self):
Script._configure(self)
self.friend = self.inventory.name
self.greeter1 = self.inventory.greeter1
self.greeter2 = self.inventory.greeter2
return
