def __init__(self, name="simpledbqueryapp"):
"""
Constructor.
"""
Script.__init__(self, name)
# Database information
self.numLocs = None
self.spaceDim = None
self.numVals = None
self.dataDim = None
self.dbCoords = None
self.dbData = None
self.names = None
self.units = None
# Query information
self.numPts = None
self.coords = None
self.dist2 = None
self.area = None
self.areaDir = None
self.volume = None
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 __init__(self, name="slip_invert"):
Application.__init__(self, name)
self.dataCoords = None
self.dataVals = None
self.dataCov = None
self.dataNames = []
self.numDataPoints = 0
self.numDesignRows = 0
self.numFaultVerts = 0
self.numFaultCells = 0
self.faultVertCoords = None
self.faultCells = None
self.numImpulses = 0
self.impulseInds = None
self.impulseCoords = None
self.summaryHead = 'Penalty-weight\tData-residual\t' + \
'Weighted-data-residual\tPenalty-residual\t' + \
'Weighted-penalty-residual\tTotal-residual\t' + \
'Total-weighted-residual'
self.numSummaryCols = 7
self.design = None
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):
"""
Setup members using inventory.
"""
Application._configure(self)
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 __init__(self, name="quadratureapp"):
"""
Constructor.
"""
Script.__init__(self, name)
# Mesh information
self.spaceDim = None
self.cellDim = None
self.numVertices = None
self.numCells = None
self.vertices = None
self.cells = None
# Reference cell information
self.numBasis = None
self.numQuadPts = None
self.verticesRef = None
self.quadPtsRef = None
self.quadWts = None
self.basis = None
self.basisDerivRef = None
self.basisDeriv = None
# Computed quadrature information
self.quadPts = None
self.jacobian = None
self.jacobianDet = None
self.jacobianInv = None
return
def _configure(self): """ Set members using inventory. """ Script._configure(self) self.data = self.inventory.data return
def _configure(self):
"""
Get the inventory items
"""
Script._configure(self)
self.model = self.inventory.model
return
def _configure(self):
"""
Setup members using inventory.
"""
Application._configure(self)
return
def __init__(self, name=None):
Script.__init__(self, name)
DynamicComponentHarness.__init__(self)
self.client = ''
return
def __init__(self, name="quadratureapp"):
"""
Constructor.
"""
Script.__init__(self, name)
# Mesh information
self.spaceDim = None
self.cellDim = None
self.numVertices = None
self.numCells = None
self.vertices = None
self.cells = None
# Reference cell information
self.numBasis = None
self.numQuadPts = None
self.verticesRef = None
self.quadPtsRef = None
self.quadWts = None
self.basis = None
self.basisDerivRef = None
self.basisDeriv = None
# Computed quadrature information
self.quadPts = None
self.jacobian = None
self.jacobianDet = None
self.jacobianInv = None
return
def __init__(self, name="slip_invert"):
Application.__init__(self, name)
self.dataCoords = None
self.dataVals = None
self.dataCov = None
self.dataNames = []
self.numDataPoints = 0
self.numDesignRows = 0
self.numFaultVerts = 0
self.numFaultCells = 0
self.faultVertCoords = None
self.faultCells = None
self.numImpulses = 0
self.impulseInds = None
self.impulseCoords = None
self.summaryHead = 'Penalty-weight\tData-residual\t' + \
'Weighted-data-residual\tPenalty-residual\t' + \
'Weighted-penalty-residual\tTotal-residual\t' + \
'Total-weighted-residual'
self.numSummaryCols = 7
self.design = None
return
def _configure(self):
Script._configure(self)
self.stream = self.inventory.stream
self.content = self.inventory.content
self.debug = self.inventory.debug
return
def __init__(self, name="unittestapp", petsc_options=[("malloc_dump", "true")]):
"""
Constructor.
"""
Script.__init__(self, name)
self.petscOptions = petsc_options
return
def _init(self):
Script._init(self)
import pyre.db
self.db = pyre.db.connect(self.inventory.db)
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)
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.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):
Script._configure(self)
self.clerk = self.inventory.clerk
self.clerk.director = self
self.wwwuser = self.inventory.wwwuser
self.tables = self.inventory.tables
return
def __init__(self, name=None):
Script.__init__(self, name)
DynamicComponentHarness.__init__(self)
self.client = ""
return
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):
"""
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):
"""
Set members using inventory.
"""
Script._configure(self)
self.data = self.inventory.data
return
def __init__(self, name="simpledbqueryapp"):
"""
Constructor.
"""
Script.__init__(self, name)
# Database information
self.numLocs = None
self.spaceDim = None
self.numVals = None
self.dataDim = None
self.dbCoords = None
self.dbData = None
self.names = None
self.units = None
# Query information
self.numPts = None
self.coords = None
self.dist2 = None
self.area = None
self.areaDir = None
self.volume = None
return
def __init__(self, name=None):
if name is None:
name = 'sample'
Script.__init__(self, name)
ComponentHarness.__init__(self)
return
def __init__(self, name=None):
if name is None:
name = 'sample'
Script.__init__(self, name)
ComponentHarness.__init__(self)
return
def __init__(self):
Script.__init__(self, 'derunapp')
self.scale = ''
self.probability = ''
self.mod = ''
self.strategy = ''
self.solution = None
return
def _init(self):
Script._init(self)
import pyre.db
self.db = pyre.db.connect(self.inventory.db,
self.inventory.dbwrapper)
return
def __init__(self, name="transform"): Application.__init__(self, name) self.numPoints = 0 self.numSegs = 0 self.segInfo = None self.pointsUTM = [] self.normals = [] return
def _init(self):
Script._init(self)
if not self._showHelpOnly:
unitcell = self._readUnitCell(self.unitcell_path)
from crystal.UnitCell import positive_volume_unitcell
unitcell = positive_volume_unitcell(unitcell)
self.unitcell = unitcell
return
def __init__(self):
Script.__init__(self, 'derunapp')
self.scale = ''
self.probability = ''
self.mod = ''
self.strategy = ''
self.solution = None
return
def __init__(self, name="transform"):
Application.__init__(self, name)
self.numPoints = 0
self.numSegs = 0
self.segInfo = None
self.pointsUTM = []
self.normals = []
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):
"""
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 __init__(self, name):
Script.__init__(self, name)
self.stream = None
self.content = "html"
# debugging mode
self.debug = False
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 __init__(self,
name="unittestapp",
petsc_options=[("malloc_dump", "true")]):
"""
Constructor.
"""
Script.__init__(self, name)
self.petscOptions = petsc_options
return
def __init__(self, name, asCGI=None):
Script.__init__(self, name)
self.stream = None
if asCGI is None:
asCGI = True
self.asCGIScript(asCGI)
return
def _init(self):
Script._init(self)
import pyre.db
dbname = self.inventory.db
dbengine = self.inventory.dbengine
self.db = pyre.db.connect(dbname, wrapper=dbengine)
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 __init__(self, name, asCGI=None):
Script.__init__(self, name)
self.stream = None
if asCGI is None:
asCGI = True
self.asCGIScript(asCGI)
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):
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 __init__(self, name="euler"): Application.__init__(self, name) self.numPoints = 0 self.pointsUTM = [] self.normals = [] self.eulerPole = numpy.array([0.0, 0.0, 0.0], dtype=numpy.float64) # Note that we use a mean radius since we are doing rotations on a # spherical Earth. self.earthRad = 6372795.477598 return
def _configure(self):
Application._configure(self)
self.modeler = self.inventory.modeler
self.contours = self.inventory.contours
self.extender = self.inventory.extender
self.slabTopFilename = self.inventory.slabTopFilename
self.slabBotFilename = self.inventory.slabBotFilename
self.splayFilename = self.inventory.splayFilename
self.slabThickness = self.inventory.slabThickness
self.slabNormalDir = self.inventory.slabNormalDir
def __init__(self, name="euler"): Application.__init__(self, name) self.numPoints = 0 self.pointsUTM = [] self.normals = [] self.eulerPole = numpy.array([0.0, 0.0, 0.0], dtype=numpy.float64) # Note that we use a mean radius since we are doing rotations on a # spherical Earth. self.earthRad = 6372795.477598 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):
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 __init__(self):
Script.__init__(self, "fmc")
self.out = None
self.thermo = ""
self.mechanism = ""
self.read = ""
self.write = ""
self.pickler = None
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 __init__(self, name="generate_slowslip"):
Application.__init__(self, name)
self.lon = None
self.lat = None
self.z = None
self.grid = None
self.faultSlip = None
return
def __init__(self, name):
Script.__init__(self, name)
self._connection = None
self._marshaller = None
import journal
journal.info("pyre.ipc.connection").activate()
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):
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): """ 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 __init__(self, name="memoryusage"):
"""
Constructor.
"""
Application.__init__(self, name)
self.memory = {'mesh': 0,
'stratification': 0,
'groups': 0}
self.mesh = None
self.groups = None
self.materials = None
return
