def setUp(self):
"""
Setup mesh and associated field.
"""
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
from pylith.meshio.MeshIOAscii import MeshIOAscii
importer = MeshIOAscii()
importer.inventory.filename = "data/tri3.mesh"
importer.inventory.coordsys = cs
importer._configure()
self.mesh = importer.read(debug=False, interpolate=False)
from pylith.topology.SolutionFields import SolutionFields
fields = SolutionFields(self.mesh)
fields.add("disp t+dt", "displacement")
fields.solutionName("disp t+dt")
solution = fields.solution()
solution.newSection(solution.VERTICES_FIELD, self.mesh.dimension())
solution.allocate()
solution.zero()
self.fields = fields
self.jacobian = Jacobian(solution)
return
def setUp(self):
from pylith.meshio.MeshIOAscii import MeshIOAscii
iohandler = MeshIOAscii()
filename = "data/twohex8.txt"
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
from spatialdata.geocoords.CSCart import CSCart
iohandler.inventory.filename = filename
iohandler.inventory.coordsys = CSCart()
iohandler._configure()
mesh = iohandler.read(debug=False, interpolate=False)
from pylith.topology.SolutionFields import SolutionFields
fields = SolutionFields(mesh)
name = "disp(t)"
fields.add(name, "displacement")
fields.solutionName(name)
field = fields.get(name)
field.subfieldAdd("displacement", mesh.dimension(), field.VECTOR)
field.subfieldsSetup()
field.newSection(field.VERTICES_FIELD, mesh.dimension())
field.allocate()
self.mesh = mesh
self.fields = fields
self.normalizer = normalizer
return
def setUp(self):
"""
Setup mesh and associated field.
"""
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
from pylith.meshio.MeshIOAscii import MeshIOAscii
importer = MeshIOAscii()
importer.inventory.filename = "data/tri3.mesh"
importer.inventory.coordsys = cs
importer._configure()
self.mesh = importer.read(debug=False, interpolate=False)
from pylith.topology.SolutionFields import SolutionFields
fields = SolutionFields(self.mesh)
fields.add("disp t+dt", "displacement")
fields.solutionName("disp t+dt")
solution = fields.solution()
solution.newSection(solution.VERTICES_FIELD, self.mesh.dimension())
solution.allocate()
solution.zero()
self.fields = fields
self.jacobian = Jacobian(solution)
return
def setUp(self):
from pylith.meshio.MeshIOAscii import MeshIOAscii
iohandler = MeshIOAscii()
filename = "data/twohex8.txt"
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
from spatialdata.geocoords.CSCart import CSCart
iohandler.inventory.filename = filename
iohandler.inventory.coordsys = CSCart()
iohandler._configure()
mesh = iohandler.read(debug=False, interpolate=False)
from pylith.topology.SolutionFields import SolutionFields
fields = SolutionFields(mesh)
name = "disp(t)"
fields.add(name, "displacement")
fields.solutionName(name)
field = fields.get(name)
field.subfieldAdd("displacement", mesh.dimension(), field.VECTOR)
field.subfieldsSetup()
field.newSection(field.VERTICES_FIELD, mesh.dimension())
field.allocate()
self.mesh = mesh
self.fields = fields
self.normalizer = normalizer
return
def setUp(self):
"""
Setup mesh and associated field.
"""
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
from pylith.meshio.MeshIOAscii import MeshIOAscii
importer = MeshIOAscii()
importer.inventory.filename = "data/tri3.mesh"
importer.inventory.coordsys = cs
importer._configure()
self.mesh = importer.read(debug=False, interpolate=False)
self.fields = SolutionFields(self.mesh)
return
def setUp(self):
"""
Setup mesh and associated field.
"""
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
from pylith.meshio.MeshIOAscii import MeshIOAscii
importer = MeshIOAscii()
importer.inventory.filename = "data/tri3.mesh"
importer.inventory.coordsys = cs
importer._configure()
self.mesh = importer.read(debug=False, interpolate=False)
self.fields = SolutionFields(self.mesh)
return
class TestSolutionFields(unittest.TestCase):
"""
Unit testing of SolutionFields object.
"""
def setUp(self):
"""
Setup mesh and associated field.
"""
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
from pylith.meshio.MeshIOAscii import MeshIOAscii
importer = MeshIOAscii()
importer.inventory.filename = "data/tri3.mesh"
importer.inventory.coordsys = cs
importer._configure()
self.mesh = importer.read(debug=False, interpolate=False)
self.fields = SolutionFields(self.mesh)
return
def test_constructor(self):
"""
Test constructor.
"""
return
def test_solutionName(self):
"""
Test mesh().
"""
fields = self.fields
fields.add("field A", "A");
fields.add("field B", "B");
fields.add("field C", "C");
fields.solutionName("field B")
return
def test_solution(self):
"""
Test solution().
"""
fields = self.fields
fields.add("field A", "A");
fields.add("field B", "B");
fields.add("field C", "C");
fields.solutionName("field B")
solution = self.fields.solution()
return
def test_fieldAdd(self):
"""
Test fieldAdd().
"""
fields = self.fields
fields.add("field A", "A");
fields.add("field B", "B");
helper_fieldAdd(fields)
fieldA = fields.get("field A")
fieldB = fields.get("field B")
fieldA.allocate()
fieldB.allocate()
fieldA.copy(fieldB)
return
def _initialize(self):
"""
Initialize fault.
"""
dt = 2.4
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
# Setup mesh
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
from pylith.meshio.MeshIOAscii import MeshIOAscii
importer = MeshIOAscii()
importer.inventory.filename = "data/tri3.mesh"
importer.inventory.coordsys = cs
importer._configure()
mesh = importer.read(debug=False, interpolate=False)
# Setup quadrature
from pylith.feassemble.FIATSimplex import FIATSimplex
cell = FIATSimplex()
cell.inventory.dimension = 1
cell.inventory.degree = 1
cell.inventory.order = 1
cell._configure()
from pylith.feassemble.Quadrature import Quadrature
quadrature = Quadrature()
quadrature.inventory.cell = cell
quadrature._configure()
# Setup earthquake source
from spatialdata.spatialdb.SimpleDB import SimpleDB
from spatialdata.spatialdb.SimpleIOAscii import SimpleIOAscii
ioFinalSlip = SimpleIOAscii()
ioFinalSlip.inventory.filename = "data/tri3_finalslip.spatialdb"
ioFinalSlip._configure()
dbFinalSlip = SimpleDB()
dbFinalSlip.inventory.iohandler = ioFinalSlip
dbFinalSlip.inventory.label = "final slip"
dbFinalSlip._configure()
ioSlipTime = SimpleIOAscii()
ioSlipTime.inventory.filename = "data/tri3_sliptime.spatialdb"
ioSlipTime._configure()
dbSlipTime = SimpleDB()
dbSlipTime.inventory.iohandler = ioSlipTime
dbSlipTime.inventory.label = "slip time"
dbSlipTime._configure()
from pylith.faults.StepSlipFn import StepSlipFn
slipfn = StepSlipFn()
slipfn.inventory.dbSlip = dbFinalSlip
slipfn.inventory.dbSlipTime = dbSlipTime
slipfn._configure()
# Setup fault
fault = FaultCohesiveKin()
fault.inventory.output.inventory.writer._configure()
fault.inventory.output._configure()
fault.inventory.matId = 10
fault.inventory.faultLabel = "fault"
fault.inventory.upDir = [0, 0, 1]
fault.inventory.faultQuadrature = quadrature
fault._configure()
eqsrc = fault.eqsrcs.components()[0]
eqsrc.inventory.originTime = 1.23*second
eqsrc.inventory.slipfn = slipfn
eqsrc._configure()
nvertices = fault.numVerticesNoMesh(mesh)
firstFaultVertex = 0
firstLagrangeVertex = nvertices
firstFaultCell = 2*nvertices
fault.adjustTopology(mesh, firstFaultVertex, firstLagrangeVertex,
firstFaultCell)
fault.preinitialize(mesh)
fault.timeStep(dt)
fault.verifyConfiguration()
from pyre.units.time import s
fault.initialize(totalTime=0.0*s, numTimeSteps=1, normalizer=normalizer)
# Setup fields
from pylith.topology.SolutionFields import SolutionFields
fields = SolutionFields(mesh)
fields.add("residual", "residual")
fields.add("dispIncr(t->t+dt)", "displacement_increment")
fields.add("disp(t)", "displacement")
fields.solutionName("dispIncr(t->t+dt)")
residual = fields.get("residual")
residual.subfieldAdd("displacement", cs.spaceDim(), residual.VECTOR)
residual.subfieldAdd("lagrange_multiplier", cs.spaceDim(), residual.VECTOR)
residual.subfieldsSetup()
residual.setupSolnChart()
residual.setupSolnDof(cs.spaceDim())
fault.setupSolnDof(residual)
residual.allocate()
residual.zero()
fields.copyLayout("residual")
return (mesh, fault, fields)
class Formulation(PetscComponent, ModuleFormulation):
"""
Python abstract base class for formulations of solving equations.
In general, we use some explicit or implicit formulation of the PDEs
to create a linear form, [A]{u}={b} that we can solve.
Factory: pde_formulation.
"""
# INVENTORY //////////////////////////////////////////////////////////
class Inventory(PetscComponent.Inventory):
"""
Python object for managing Formulation facilities and properties.
"""
## @class Inventory
## Python object for managing Formulation facilities and properties.
##
## \b Properties
## @li \b matrix_type Type of PETSc sparse matrix.
## @li \b split_fields Split solution fields into displacements and Lagrange constraints.
## @li \b use_custom_constraint_pc Use custom preconditioner for Lagrange constraints.
## @li \b view_jacobian Flag to output Jacobian matrix when it is reformed.
##
## \b Facilities
## @li \b time_step Time step size manager.
## @li \b solver Algebraic solver.
## @li \b output Output manager associated with solution.
## @li \b jacobian_viewer Writer for Jacobian sparse matrix.
import pyre.inventory
matrixType = pyre.inventory.str("matrix_type", default="unknown")
matrixType.meta['tip'] = "Type of PETSc sparse matrix."
useSplitFields = pyre.inventory.bool("split_fields", default=False)
useSplitFields.meta['tip'] = "Split solution fields into displacements "\
"and Lagrange multipliers for separate preconditioning."
useCustomConstraintPC = pyre.inventory.bool("use_custom_constraint_pc",
default=False)
useCustomConstraintPC.meta['tip'] = "Use custom preconditioner for " \
"Lagrange constraints."
viewJacobian = pyre.inventory.bool("view_jacobian", default=False)
viewJacobian.meta['tip'] = "Write Jacobian matrix to binary file."
from TimeStepUniform import TimeStepUniform
timeStep = pyre.inventory.facility("time_step", family="time_step",
factory=TimeStepUniform)
timeStep.meta['tip'] = "Time step size manager."
from SolverLinear import SolverLinear
solver = pyre.inventory.facility("solver", family="solver",
factory=SolverLinear)
solver.meta['tip'] = "Algebraic solver."
from pylith.meshio.SingleOutput import SingleOutput
output = pyre.inventory.facilityArray("output",
itemFactory=outputFactory,
factory=SingleOutput)
output.meta['tip'] = "Output managers associated with solution."
from pylith.topology.JacobianViewer import JacobianViewer
jacobianViewer = pyre.inventory.facility("jacobian_viewer",
family="jacobian_viewer",
factory=JacobianViewer)
jacobianViewer.meta['tip'] = "Writer for Jacobian sparse matrix."
from pylith.perf.MemoryLogger import MemoryLogger
perfLogger = pyre.inventory.facility("perf_logger", family="perf_logger",
factory=MemoryLogger)
perfLogger.meta['tip'] = "Performance and memory logging."
# PUBLIC METHODS /////////////////////////////////////////////////////
def __init__(self, name="formulation"):
"""
Constructor.
"""
PetscComponent.__init__(self, name, facility="formulation")
# ModuleFormulation constructor called in base clase
self.integrators = None
self.constraints = None
self.jacobian = None
self.fields = None
return
def preinitialize(self, mesh, materials, boundaryConditions,
interfaceConditions, gravityField):
"""
Create integrator for each element family.
"""
self._setupLogging()
logEvent = "%spreinit" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent)
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
self.timeStep.preinitialize()
import weakref
self.mesh = weakref.ref(mesh)
self.integrators = []
self.constraints = []
self.gravityField = gravityField
self.solver.preinitialize()
self._setupMaterials(materials)
self._setupBC(boundaryConditions)
self._setupInterfaces(interfaceConditions)
if 0 == comm.rank:
self._info.log("Pre-initializing output.")
for output in self.output.components():
output.preinitialize()
self._eventLogger.eventEnd(logEvent)
return
def verifyConfiguration(self):
"""
Verify compatibility of configuration.
"""
logEvent = "%sverify" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent)
self.timeStep.verifyConfiguration()
for integrator in self.integrators:
integrator.verifyConfiguration()
for constraint in self.constraints:
constraint.verifyConfiguration()
for output in self.output.components():
output.verifyConfiguration(self.mesh())
self._eventLogger.eventEnd(logEvent)
return
def initialize(self, dimension, normalizer):
"""
Initialize formulation.
"""
raise NotImplementedError("Please implement 'initialize' in derived class.")
def getStartTime(self):
"""
Get start time for simulation.
"""
return self.timeStep.startTimeN
def getTotalTime(self):
"""
Get total time for simulation.
"""
return self.timeStep.totalTimeN # Nondimensionalized total time
def getTimeStep(self):
"""
Get stable time step for advancing forward in time.
"""
logEvent = "%stimestep" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent)
dt = self.timeStep.timeStep(self.mesh(), self.integrators)
self._eventLogger.eventEnd(logEvent)
return dt
def prestep(self, t, dt):
"""
Hook for doing stuff before advancing time step.
"""
logEvent = "%sprestep" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent)
self._eventLogger.eventEnd(logEvent)
return
def step(self, t, dt):
"""
Advance to next time step.
"""
logEvent = "%sstep" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent)
self._eventLogger.eventEnd(logEvent)
return
def poststep(self, t, dt):
"""
Hook for doing stuff after advancing time step.
"""
logEvent = "%spoststep" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent)
for integrator in self.integrators:
integrator.poststep(t, dt, self.fields)
for constraint in self.constraints:
constraint.poststep(t, dt, self.fields)
self._eventLogger.eventEnd(logEvent)
return
def finalize(self):
"""
Cleanup after time stepping.
"""
logEvent = "%sfinalize" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent)
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Formulation finalize.")
self._debug.log(resourceUsageString())
for integrator in self.integrators:
integrator.finalize()
for constraint in self.constraints:
constraint.finalize()
for output in self.output.components():
output.close()
output.finalize()
self._debug.log(resourceUsageString())
self._modelMemoryUse()
self._eventLogger.eventEnd(logEvent)
return
# PRIVATE METHODS ////////////////////////////////////////////////////
def _configure(self):
"""
Set members based using inventory.
"""
PetscComponent._configure(self)
self.matrixType = self.inventory.matrixType
self.timeStep = self.inventory.timeStep
self.solver = self.inventory.solver
self.output = self.inventory.output
self.viewJacobian = self.inventory.viewJacobian
self.jacobianViewer = self.inventory.jacobianViewer
self.perfLogger = self.inventory.perfLogger
import journal
self._debug = journal.debug(self.name)
if self.inventory.useCustomConstraintPC and \
not self.inventory.useSplitFields:
print "WARNING: Request to use custom preconditioner for Lagrange " \
"constraints without splitting fields. " \
"Setting split fields flag to 'True'."
self.inventory.useSplitFields = True
ModuleFormulation.splitFields(self, self.inventory.useSplitFields)
ModuleFormulation.useCustomConstraintPC(self, self.inventory.useCustomConstraintPC)
return
def _setJacobianMatrixType(self):
"""
Determine appropriate PETSc matrix type for Jacobian matrix.
"""
# Mapping from symmetric matrix type to nonsymmetric matrix type
matrixMap = {'sbaij': 'baij',
'seqsbaij': 'seqbaij',
'mpisbaij': 'mpibaij',
'unknown': 'aij'}
isJacobianSymmetric = True
for integrator in self.integrators:
if not integrator.isJacobianSymmetric():
isJacobianSymmetric = False
if not isJacobianSymmetric:
if self.matrixType in matrixMap.keys():
print "WARNING: Jacobian matrix will not be symmetric.\n" \
" Switching matrix type from '%s' to '%s'." % \
(self.matrixType, matrixMap[self.matrixType])
self.matrixType = matrixMap[self.matrixType]
self.blockMatrixOkay = True
if self.matrixType == "unknown" and self.solver.useCUDA:
self.matrixType = "aijcusp"
for constraint in self.constraints:
numDimConstrained = constraint.numDimConstrained()
if numDimConstrained > 0 and self.mesh().dimension() != numDimConstrained:
self.blockMatrixOkay = False
return
def _setupMaterials(self, materials):
"""
Setup materials as integrators.
"""
from pylith.feassemble.Integrator import implementsIntegrator
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Pre-initializing materials.")
self._debug.log(resourceUsageString())
for material in materials.components():
integrator = self.elasticityIntegrator()
if not implementsIntegrator(integrator):
raise TypeError, \
"Could not use '%s' as an integrator for material '%s'. " \
"Functionality missing." % (integrator.name, material.label())
integrator.preinitialize(self.mesh(), material)
self.integrators.append(integrator)
self._debug.log(resourceUsageString())
if 0 == comm.rank:
self._info.log("Added elasticity integrator for material '%s'." % material.label())
return
def _setupBC(self, boundaryConditions):
"""
Setup boundary conditions as integrators or constraints.
"""
from pylith.feassemble.Integrator import implementsIntegrator
from pylith.feassemble.Constraint import implementsConstraint
from pylith.bc.PointForce import PointForce
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Pre-initializing boundary conditions.")
self._debug.log(resourceUsageString())
for bc in boundaryConditions.components():
bc.preinitialize(self.mesh())
foundType = False
if implementsIntegrator(bc):
foundType = True
self.integrators.append(bc)
if 0 == comm.rank:
self._info.log("Added boundary condition '%s' as an integrator." % \
bc.label())
if implementsConstraint(bc):
foundType = True
self.constraints.append(bc)
if 0 == comm.rank:
self._info.log("Added boundary condition '%s' as a constraint." % \
bc.label())
if not foundType:
raise TypeError, \
"Could not determine whether boundary condition '%s' is an " \
"integrator or a constraint." % bc.name
self._debug.log(resourceUsageString())
return
def _setupInterfaces(self, interfaceConditions):
"""
Setup interfaces as integrators or constraints.
"""
from pylith.feassemble.Integrator import implementsIntegrator
from pylith.feassemble.Constraint import implementsConstraint
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Pre-initializing interior interfaces.")
for ic in interfaceConditions.components():
ic.preinitialize(self.mesh())
foundType = False
if implementsIntegrator(ic):
foundType = True
self.integrators.append(ic)
if 0 == comm.rank:
self._info.log("Added interface condition '%s' as an integrator." % \
ic.label())
if implementsConstraint(ic):
foundType = True
self.constraints.append(ic)
if 0 == comm.rank:
self._info.log("Added interface condition '%s' as a constraint." % \
ic.label())
if not foundType:
raise TypeError, \
"Could not determine whether interface condition '%s' is an " \
"integrator or a constraint." % ic.name
self._debug.log(resourceUsageString())
return
def _initialize(self, dimension, normalizer):
"""
Create integrators for each element family.
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
self.timeStep.initialize(normalizer)
numTimeSteps = self.timeStep.numTimeSteps()
totalTime = self.timeStep.totalTime
from pylith.topology.SolutionFields import SolutionFields
self.fields = SolutionFields(self.mesh())
self._debug.log(resourceUsageString())
if 0 == comm.rank:
self._info.log("Initializing integrators.")
for integrator in self.integrators:
if not self.gravityField is None:
integrator.gravityField(self.gravityField)
integrator.initialize(totalTime, numTimeSteps, normalizer)
ModuleFormulation.integrators(self, self.integrators)
self._debug.log(resourceUsageString())
if 0 == comm.rank:
self._info.log("Initializing constraints.")
for constraint in self.constraints:
constraint.initialize(totalTime, numTimeSteps, normalizer)
self._debug.log(resourceUsageString())
if 0 == comm.rank:
self._info.log("Setting up solution output.")
for output in self.output.components():
output.initialize(self.mesh(), normalizer)
output.writeInfo()
output.open(totalTime, numTimeSteps)
self._debug.log(resourceUsageString())
# Setup fields
if 0 == comm.rank:
self._info.log("Creating solution field.")
#from pylith.utils.petsc import MemoryLogger
#memoryLogger = MemoryLogger.singleton()
#memoryLogger.setDebug(0)
#memoryLogger.stagePush("Problem")
self.fields.add("dispIncr(t->t+dt)", "displacement_increment")
self.fields.add("disp(t)", "displacement")
self.fields.add("residual", "residual")
self.fields.solutionName("dispIncr(t->t+dt)")
lengthScale = normalizer.lengthScale()
pressureScale = normalizer.pressureScale()
solution = self.fields.get("dispIncr(t->t+dt)")
solution.subfieldAdd("displacement", dimension, solution.VECTOR, lengthScale.value)
solution.subfieldAdd("lagrange_multiplier", dimension, solution.VECTOR, pressureScale.value)
solution.subfieldsSetup()
solution.setupSolnChart()
solution.setupSolnDof(dimension)
# Loop over integrators to adjust DOF layout
for integrator in self.integrators:
integrator.setupSolnDof(solution)
solution.vectorFieldType(solution.VECTOR)
solution.scale(lengthScale.value)
for constraint in self.constraints:
constraint.setConstraintSizes(solution)
solution.allocate()
solution.zeroAll()
for constraint in self.constraints:
constraint.setConstraints(solution)
for integrator in self.integrators:
integrator.checkConstraints(solution)
#memoryLogger.stagePop()
# This also creates a global order.
solution.createScatter(solution.mesh())
#memoryLogger.stagePush("Problem")
dispT = self.fields.get("disp(t)")
dispT.vectorFieldType(dispT.VECTOR)
dispT.scale(lengthScale.value)
residual = self.fields.get("residual")
residual.vectorFieldType(residual.VECTOR)
residual.scale(lengthScale.value)
#memoryLogger.stagePop()
#memoryLogger.setDebug(0)
self._debug.log(resourceUsageString())
return
def _reformJacobian(self, t, dt):
"""
Reform Jacobian matrix for operator.
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
self._debug.log(resourceUsageString())
if 0 == comm.rank:
self._info.log("Integrating Jacobian operator.")
self._eventLogger.stagePush("Reform Jacobian")
self.updateSettings(self.jacobian, self.fields, t, dt)
self.reformJacobian()
self._eventLogger.stagePop()
if self.viewJacobian:
from pylith.mpi.Communicator import Communicator
comm = Communicator(self.mesh().comm())
self.jacobianViewer.view(self.jacobian, t, comm)
self._debug.log(resourceUsageString())
return
def _collectNeedNewJacobian(self, flagLocal):
"""
Aggregate needNewJacobian results across processors.
"""
if flagLocal:
countLocal = 1
else:
countLocal = 0
import pylith.mpi.mpi as mpi
comm = self.mesh().comm()
countAll = mpi.allreduce_scalar_int(countLocal, mpi.mpi_max(), comm.handle)
return countAll > 0
def _reformResidual(self, t, dt):
"""
Reform residual vector for operator.
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Integrating residual term in operator.")
self._eventLogger.stagePush("Reform Residual")
self.updateSettings(self.jacobian, self.fields, t, dt)
self.reformResidual()
self._eventLogger.stagePop()
self._debug.log(resourceUsageString())
return
def _writeData(self, t):
"""
Write data for time t.
"""
logEvent = "%swrite" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent)
for integrator in self.integrators:
integrator.writeData(t, self.fields)
for constraint in self.constraints:
constraint.writeData(t, self.fields)
self._eventLogger.eventEnd(logEvent)
return
def _setupLogging(self):
"""
Setup event logging.
"""
if not "_loggingPrefix" in dir(self):
self._loggingPrefix = ""
from pylith.utils.EventLogger import EventLogger
logger = EventLogger()
logger.className("PDE Formulation")
logger.initialize()
events = ["preinit",
"verify",
"init",
"timestep",
"prestep",
"step",
"poststep",
"write",
"finalize"]
for event in events:
logger.registerEvent("%s%s" % (self._loggingPrefix, event))
stages = ["Reform Jacobian",
"Reform Residual",
"Solve"]
for stage in stages:
logger.registerStage(stage)
self._eventLogger = logger
return
def _modelMemoryUse(self):
"""
Model memory allocation.
"""
self.perfLogger.logFields('Problem', self.fields)
self.perfLogger.logJacobian('Jacobian', 'dummy')
self.perfLogger.logGlobalOrder('GlobalOrder', 'VectorOrder',
self.fields.get('residual'))
for integrator in self.integrators:
self.perfLogger.logQuadrature('Quadrature', integrator.quadrature())
return
def _cleanup(self):
"""
Deallocate PETSc and local data structures.
"""
if not self.jacobian is None:
self.jacobian.cleanup()
if not self.fields is None:
self.fields.cleanup()
if not self.integrators is None:
for integrator in self.integrators:
integrator.cleanup()
return
def _initialize(self):
"""
Initialize fault.
"""
dt = 2.4
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
# Setup mesh
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
from pylith.meshio.MeshIOAscii import MeshIOAscii
importer = MeshIOAscii()
importer.inventory.filename = "data/tri3.mesh"
importer.inventory.coordsys = cs
importer._configure()
mesh = importer.read(debug=False, interpolate=False)
# Setup quadrature
from pylith.feassemble.FIATSimplex import FIATSimplex
cell = FIATSimplex()
cell.inventory.dimension = 1
cell.inventory.degree = 1
cell.inventory.order = 1
cell._configure()
from pylith.feassemble.Quadrature import Quadrature
quadrature = Quadrature()
quadrature.inventory.cell = cell
quadrature._configure()
# Setup rupture info
from spatialdata.spatialdb.SimpleDB import SimpleDB
from spatialdata.spatialdb.SimpleIOAscii import SimpleIOAscii
ioTractions = SimpleIOAscii()
ioTractions.inventory.filename = "data/tri3_initialtractions.spatialdb"
ioTractions._configure()
dbTractions = SimpleDB()
dbTractions.inventory.iohandler = ioTractions
dbTractions.inventory.label = "initial tractions"
dbTractions._configure()
from pylith.faults.TractPerturbation import TractPerturbation
tract = TractPerturbation()
tract.inventory.dbInitial = dbTractions
tract._configure()
ioFriction = SimpleIOAscii()
ioFriction.inventory.filename = "data/tri3_staticfriction.spatialdb"
ioFriction._configure()
dbFriction = SimpleDB()
dbFriction.inventory.iohandler = ioFriction
dbFriction.inventory.label = "friction"
dbFriction._configure()
from pylith.friction.StaticFriction import StaticFriction
friction = StaticFriction()
friction.inventory.label = "Static friction"
friction.inventory.dbProperties = dbFriction
friction._configure()
# Setup fault
fault = FaultCohesiveDyn()
fault.inventory.output.inventory.writer._configure()
fault.inventory.output._configure()
fault.inventory.matId = 10
fault.inventory.faultLabel = "fault"
fault.inventory.upDir = [0, 0, 1]
fault.inventory.faultQuadrature = quadrature
fault.inventory.tract = tract
fault.inventory.friction = friction
fault._configure()
nvertices = fault.numVerticesNoMesh(mesh)
firstFaultVertex = 0
firstLagrangeVertex = nvertices
firstFaultCell = 2*nvertices
fault.adjustTopology(mesh, firstFaultVertex, firstLagrangeVertex,
firstFaultCell)
from pylith.topology.topology import MeshOps_nondimensionalize
MeshOps_nondimensionalize(mesh, normalizer)
fault.preinitialize(mesh)
fault.timeStep(dt)
fault.verifyConfiguration()
from pyre.units.time import s
fault.initialize(totalTime=0.0*s, numTimeSteps=1, normalizer=normalizer)
# Setup fields
from pylith.topology.SolutionFields import SolutionFields
fields = SolutionFields(mesh)
fields.add("residual", "residual")
fields.add("dispIncr(t->t+dt)", "displacement_increment")
fields.add("disp(t)", "displacement")
fields.add("velocity(t)", "velocity")
fields.solutionName("dispIncr(t->t+dt)")
residual = fields.get("residual")
residual.subfieldAdd("displacement", cs.spaceDim(), residual.VECTOR)
residual.subfieldAdd("lagrange_multiplier", cs.spaceDim(), residual.VECTOR)
residual.subfieldsSetup()
residual.setupSolnChart()
residual.setupSolnDof(cs.spaceDim())
fault.setupSolnDof(residual)
residual.allocate()
residual.zero()
fields.copyLayout("residual")
return (mesh, fault, fields)
def _initialize(self, dimension, normalizer):
"""
Create integrators for each element family.
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
self.timeStep.initialize(normalizer)
numTimeSteps = self.timeStep.numTimeSteps()
totalTime = self.timeStep.totalTime
from pylith.topology.SolutionFields import SolutionFields
self.fields = SolutionFields(self.mesh())
self._debug.log(resourceUsageString())
if 0 == comm.rank:
self._info.log("Initializing integrators.")
for integrator in self.integrators:
if not self.gravityField is None:
integrator.gravityField(self.gravityField)
integrator.initialize(totalTime, numTimeSteps, normalizer)
ModuleFormulation.integrators(self, self.integrators)
self._debug.log(resourceUsageString())
if 0 == comm.rank:
self._info.log("Initializing constraints.")
for constraint in self.constraints:
constraint.initialize(totalTime, numTimeSteps, normalizer)
self._debug.log(resourceUsageString())
if 0 == comm.rank:
self._info.log("Setting up solution output.")
for output in self.output.components():
output.initialize(self.mesh(), normalizer)
output.writeInfo()
output.open(totalTime, numTimeSteps)
self._debug.log(resourceUsageString())
# Setup fields
if 0 == comm.rank:
self._info.log("Creating solution field.")
#from pylith.utils.petsc import MemoryLogger
#memoryLogger = MemoryLogger.singleton()
#memoryLogger.setDebug(0)
#memoryLogger.stagePush("Problem")
self.fields.add("dispIncr(t->t+dt)", "displacement_increment")
self.fields.add("disp(t)", "displacement")
self.fields.add("residual", "residual")
self.fields.solutionName("dispIncr(t->t+dt)")
lengthScale = normalizer.lengthScale()
pressureScale = normalizer.pressureScale()
solution = self.fields.get("dispIncr(t->t+dt)")
solution.subfieldAdd("displacement", dimension, solution.VECTOR, lengthScale.value)
solution.subfieldAdd("lagrange_multiplier", dimension, solution.VECTOR, pressureScale.value)
solution.subfieldsSetup()
solution.setupSolnChart()
solution.setupSolnDof(dimension)
# Loop over integrators to adjust DOF layout
for integrator in self.integrators:
integrator.setupSolnDof(solution)
solution.vectorFieldType(solution.VECTOR)
solution.scale(lengthScale.value)
for constraint in self.constraints:
constraint.setConstraintSizes(solution)
solution.allocate()
solution.zeroAll()
for constraint in self.constraints:
constraint.setConstraints(solution)
for integrator in self.integrators:
integrator.checkConstraints(solution)
#memoryLogger.stagePop()
# This also creates a global order.
solution.createScatter(solution.mesh())
#memoryLogger.stagePush("Problem")
dispT = self.fields.get("disp(t)")
dispT.vectorFieldType(dispT.VECTOR)
dispT.scale(lengthScale.value)
residual = self.fields.get("residual")
residual.vectorFieldType(residual.VECTOR)
residual.scale(lengthScale.value)
#memoryLogger.stagePop()
#memoryLogger.setDebug(0)
self._debug.log(resourceUsageString())
return
def _initialize(self, mesh, integrator):
"""
Initialize integrator.
"""
dt = 2.3
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
from pyre.units.time import s
integrator.initialize(totalTime=0.0*s, numTimeSteps=1,
normalizer=normalizer)
integrator.timeStep(dt)
# Setup fields
from pylith.topology.SolutionFields import SolutionFields
fields = SolutionFields(mesh)
fields.add("residual", "residual")
fields.add("disp(t+dt)", "displacement")
fields.add("disp(t)", "displacement")
fields.add("disp(t-dt)", "displacement")
fields.add("velocity(t)", "velocity")
fields.add("acceleration(t)", "acceleration")
fields.solutionName("disp(t+dt)")
residual = fields.get("residual")
residual.newSection(residual.VERTICES_FIELD, mesh.coordsys().spaceDim())
residual.allocate()
fields.copyLayout("residual")
residual.zero()
return fields
def _initialize(self):
"""
Initialize fault.
"""
dt = 2.4
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
# Setup mesh
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
from pylith.meshio.MeshIOAscii import MeshIOAscii
importer = MeshIOAscii()
importer.inventory.filename = "data/tri3.mesh"
importer.inventory.coordsys = cs
importer._configure()
mesh = importer.read(debug=False, interpolate=False)
# Setup quadrature
from pylith.feassemble.FIATSimplex import FIATSimplex
cell = FIATSimplex()
cell.inventory.dimension = 1
cell.inventory.degree = 1
cell.inventory.order = 1
cell._configure()
from pylith.feassemble.Quadrature import Quadrature
quadrature = Quadrature()
quadrature.inventory.cell = cell
quadrature._configure()
# Setup impulses
from spatialdata.spatialdb.SimpleDB import SimpleDB
from spatialdata.spatialdb.SimpleIOAscii import SimpleIOAscii
ioImpulseAmp = SimpleIOAscii()
ioImpulseAmp.inventory.filename = "data/tri3_impulses.spatialdb"
ioImpulseAmp._configure()
dbImpulseAmp = SimpleDB()
dbImpulseAmp.inventory.iohandler = ioImpulseAmp
dbImpulseAmp.inventory.label = "impulse amplitude"
dbImpulseAmp._configure()
# Setup fault
fault = FaultCohesiveImpulses()
fault.inventory.output.inventory.writer._configure()
fault.inventory.output._configure()
fault.inventory.matId = 10
fault.inventory.faultLabel = "fault"
fault.inventory.upDir = [0, 0, 1]
fault.inventory.faultQuadrature = quadrature
fault.inventory.dbImpulseAmp = dbImpulseAmp
fault._configure()
nvertices = fault.numVerticesNoMesh(mesh)
firstFaultVertex = 0
firstLagrangeVertex = nvertices
firstFaultCell = 2*nvertices
fault.adjustTopology(mesh, firstFaultVertex, firstLagrangeVertex,
firstFaultCell)
fault.preinitialize(mesh)
fault.timeStep(dt)
fault.verifyConfiguration()
from pyre.units.time import s
fault.initialize(totalTime=0.0*s, numTimeSteps=1, normalizer=normalizer)
# Setup fields
from pylith.topology.SolutionFields import SolutionFields
fields = SolutionFields(mesh)
fields.add("residual", "residual")
fields.add("dispIncr(t->t+dt)", "displacement_increment")
fields.add("disp(t)", "displacement")
fields.solutionName("dispIncr(t->t+dt)")
residual = fields.get("residual")
residual.subfieldAdd("displacement", cs.spaceDim(), residual.VECTOR)
residual.subfieldAdd("lagrange_multiplier", cs.spaceDim(), residual.VECTOR)
residual.subfieldsSetup()
residual.setupSolnChart()
residual.setupSolnDof(cs.spaceDim())
fault.setupSolnDof(residual)
residual.allocate()
residual.zero()
fields.copyLayout("residual")
return (mesh, fault, fields)
def _initialize(self, mesh, integrator):
"""
Initialize integrator.
"""
dt = 2.3
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
from pyre.units.time import s
integrator.initialize(totalTime=0.0 * s,
numTimeSteps=1,
normalizer=normalizer)
integrator.timeStep(dt)
# Setup fields
from pylith.topology.SolutionFields import SolutionFields
fields = SolutionFields(mesh)
fields.add("residual", "residual")
fields.add("disp(t)", "displacement")
fields.add("dispIncr(t->t+dt)", "displacement_increment")
fields.solutionName("dispIncr(t->t+dt)")
residual = fields.get("residual")
spaceDim = mesh.coordsys().spaceDim()
lengthScale = normalizer.lengthScale()
residual.subfieldAdd("displacement", spaceDim, residual.VECTOR,
lengthScale.value)
residual.subfieldAdd("lagrange_multiplier", spaceDim, residual.VECTOR)
residual.subfieldsSetup()
residual.setupSolnChart()
residual.setupSolnDof(spaceDim)
residual.allocate()
residual.zeroAll()
fields.copyLayout("residual")
return fields
class Formulation(PetscComponent, ModuleFormulation):
"""
Python abstract base class for formulations of solving equations.
In general, we use some explicit or implicit formulation of the PDEs
to create a linear form, [A]{u}={b} that we can solve.
Factory: pde_formulation.
"""
# INVENTORY //////////////////////////////////////////////////////////
class Inventory(PetscComponent.Inventory):
"""
Python object for managing Formulation facilities and properties.
"""
## @class Inventory
## Python object for managing Formulation facilities and properties.
##
## \b Properties
## @li \b matrix_type Type of PETSc sparse matrix.
## @li \b split_fields Split solution fields into displacements and Lagrange constraints.
## @li \b use_custom_constraint_pc Use custom preconditioner for Lagrange constraints.
## @li \b view_jacobian Flag to output Jacobian matrix when it is reformed.
##
## \b Facilities
## @li \b time_step Time step size manager.
## @li \b solver Algebraic solver.
## @li \b output Output manager associated with solution.
## @li \b jacobian_viewer Writer for Jacobian sparse matrix.
import pyre.inventory
matrixType = pyre.inventory.str("matrix_type", default="unknown")
matrixType.meta['tip'] = "Type of PETSc sparse matrix."
useSplitFields = pyre.inventory.bool("split_fields", default=False)
useSplitFields.meta['tip'] = "Split solution fields into displacements "\
"and Lagrange multipliers for separate preconditioning."
useCustomConstraintPC = pyre.inventory.bool("use_custom_constraint_pc",
default=False)
useCustomConstraintPC.meta['tip'] = "Use custom preconditioner for " \
"Lagrange constraints."
viewJacobian = pyre.inventory.bool("view_jacobian", default=False)
viewJacobian.meta['tip'] = "Write Jacobian matrix to binary file."
from TimeStepUniform import TimeStepUniform
timeStep = pyre.inventory.facility("time_step", family="time_step",
factory=TimeStepUniform)
timeStep.meta['tip'] = "Time step size manager."
from SolverLinear import SolverLinear
solver = pyre.inventory.facility("solver", family="solver",
factory=SolverLinear)
solver.meta['tip'] = "Algebraic solver."
from pylith.meshio.SingleOutput import SingleOutput
output = pyre.inventory.facilityArray("output",
itemFactory=outputFactory,
factory=SingleOutput)
output.meta['tip'] = "Output managers associated with solution."
from pylith.topology.JacobianViewer import JacobianViewer
jacobianViewer = pyre.inventory.facility("jacobian_viewer",
family="jacobian_viewer",
factory=JacobianViewer)
jacobianViewer.meta['tip'] = "Writer for Jacobian sparse matrix."
from pylith.perf.MemoryLogger import MemoryLogger
perfLogger = pyre.inventory.facility("perf_logger", family="perf_logger",
factory=MemoryLogger)
perfLogger.meta['tip'] = "Performance and memory logging."
# PUBLIC METHODS /////////////////////////////////////////////////////
def __init__(self, name="formulation"):
"""
Constructor.
"""
PetscComponent.__init__(self, name, facility="formulation")
# ModuleFormulation constructor called in base clase
self.integrators = None
self.constraints = None
self.jacobian = None
self.fields = None
return
def preinitialize(self, mesh, materials, boundaryConditions,
interfaceConditions, gravityField):
"""
Create integrator for each element family.
"""
self._setupLogging()
logEvent = "%spreinit" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent)
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
self.timeStep.preinitialize()
import weakref
self.mesh = weakref.ref(mesh)
self.integrators = []
self.constraints = []
self.gravityField = gravityField
self.solver.preinitialize()
self._setupMaterials(materials)
self._setupBC(boundaryConditions)
self._setupInterfaces(interfaceConditions)
if 0 == comm.rank:
self._info.log("Pre-initializing output.")
for output in self.output.components():
output.preinitialize()
self._eventLogger.eventEnd(logEvent)
return
def verifyConfiguration(self):
"""
Verify compatibility of configuration.
"""
logEvent = "%sverify" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent)
self.timeStep.verifyConfiguration()
for integrator in self.integrators:
integrator.verifyConfiguration()
for constraint in self.constraints:
constraint.verifyConfiguration()
for output in self.output.components():
output.verifyConfiguration(self.mesh())
self._eventLogger.eventEnd(logEvent)
return
def initialize(self, dimension, normalizer):
"""
Initialize formulation.
"""
raise NotImplementedError("Please implement 'initialize' in derived class.")
def getStartTime(self):
"""
Get start time for simulation.
"""
return self.timeStep.startTimeN
def getTotalTime(self):
"""
Get total time for simulation.
"""
return self.timeStep.totalTimeN # Nondimensionalized total time
def getTimeStep(self):
"""
Get stable time step for advancing forward in time.
"""
logEvent = "%stimestep" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent)
dt = self.timeStep.timeStep(self.mesh(), self.integrators)
self._eventLogger.eventEnd(logEvent)
return dt
def prestep(self, t, dt):
"""
Hook for doing stuff before advancing time step.
"""
logEvent = "%sprestep" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent)
self._eventLogger.eventEnd(logEvent)
return
def step(self, t, dt):
"""
Advance to next time step.
"""
logEvent = "%sstep" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent)
self._eventLogger.eventEnd(logEvent)
return
def poststep(self, t, dt):
"""
Hook for doing stuff after advancing time step.
"""
logEvent = "%spoststep" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent)
for integrator in self.integrators:
integrator.poststep(t, dt, self.fields)
for constraint in self.constraints:
constraint.poststep(t, dt, self.fields)
self._eventLogger.eventEnd(logEvent)
return
def finalize(self):
"""
Cleanup after time stepping.
"""
logEvent = "%sfinalize" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent)
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Formulation finalize.")
self._debug.log(resourceUsageString())
for integrator in self.integrators:
integrator.finalize()
for constraint in self.constraints:
constraint.finalize()
for output in self.output.components():
output.close()
output.finalize()
self._debug.log(resourceUsageString())
self._modelMemoryUse()
self._eventLogger.eventEnd(logEvent)
return
# PRIVATE METHODS ////////////////////////////////////////////////////
def _configure(self):
"""
Set members based using inventory.
"""
PetscComponent._configure(self)
self.matrixType = self.inventory.matrixType
self.timeStep = self.inventory.timeStep
self.solver = self.inventory.solver
self.output = self.inventory.output
self.viewJacobian = self.inventory.viewJacobian
self.jacobianViewer = self.inventory.jacobianViewer
self.perfLogger = self.inventory.perfLogger
import journal
self._debug = journal.debug(self.name)
if self.inventory.useCustomConstraintPC and \
not self.inventory.useSplitFields:
print "WARNING: Request to use custom preconditioner for Lagrange " \
"constraints without splitting fields. " \
"Setting split fields flag to 'True'."
self.inventory.useSplitFields = True
ModuleFormulation.splitFields(self, self.inventory.useSplitFields)
ModuleFormulation.useCustomConstraintPC(self, self.inventory.useCustomConstraintPC)
return
def _setJacobianMatrixType(self):
"""
Determine appropriate PETSc matrix type for Jacobian matrix.
"""
# Mapping from symmetric matrix type to nonsymmetric matrix type
matrixMap = {'sbaij': 'baij',
'seqsbaij': 'seqbaij',
'mpisbaij': 'mpibaij',
'unknown': 'aij'}
isJacobianSymmetric = True
for integrator in self.integrators:
if not integrator.isJacobianSymmetric():
isJacobianSymmetric = False
if not isJacobianSymmetric:
if self.matrixType in matrixMap.keys():
print "WARNING: Jacobian matrix will not be symmetric.\n" \
" Switching matrix type from '%s' to '%s'." % \
(self.matrixType, matrixMap[self.matrixType])
self.matrixType = matrixMap[self.matrixType]
self.blockMatrixOkay = True
if self.matrixType == "unknown" and self.solver.useCUDA:
self.matrixType = "aijcusp"
for constraint in self.constraints:
numDimConstrained = constraint.numDimConstrained()
if numDimConstrained > 0 and self.mesh().dimension() != numDimConstrained:
self.blockMatrixOkay = False
return
def _setupMaterials(self, materials):
"""
Setup materials as integrators.
"""
from pylith.feassemble.Integrator import implementsIntegrator
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Pre-initializing materials.")
self._debug.log(resourceUsageString())
for material in materials.components():
integrator = self.elasticityIntegrator()
if not implementsIntegrator(integrator):
raise TypeError, \
"Could not use '%s' as an integrator for material '%s'. " \
"Functionality missing." % (integrator.name, material.label())
integrator.preinitialize(self.mesh(), material)
self.integrators.append(integrator)
self._debug.log(resourceUsageString())
if 0 == comm.rank:
self._info.log("Added elasticity integrator for material '%s'." % material.label())
return
def _setupBC(self, boundaryConditions):
"""
Setup boundary conditions as integrators or constraints.
"""
from pylith.feassemble.Integrator import implementsIntegrator
from pylith.feassemble.Constraint import implementsConstraint
from pylith.bc.PointForce import PointForce
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Pre-initializing boundary conditions.")
self._debug.log(resourceUsageString())
for bc in boundaryConditions.components():
bc.preinitialize(self.mesh())
foundType = False
if implementsIntegrator(bc):
foundType = True
self.integrators.append(bc)
if 0 == comm.rank:
self._info.log("Added boundary condition '%s' as an integrator." % \
bc.label())
if implementsConstraint(bc):
foundType = True
self.constraints.append(bc)
if 0 == comm.rank:
self._info.log("Added boundary condition '%s' as a constraint." % \
bc.label())
if not foundType:
raise TypeError, \
"Could not determine whether boundary condition '%s' is an " \
"integrator or a constraint." % bc.name
self._debug.log(resourceUsageString())
return
def _setupInterfaces(self, interfaceConditions):
"""
Setup interfaces as integrators or constraints.
"""
from pylith.feassemble.Integrator import implementsIntegrator
from pylith.feassemble.Constraint import implementsConstraint
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Pre-initializing interior interfaces.")
for ic in interfaceConditions.components():
ic.preinitialize(self.mesh())
foundType = False
if implementsIntegrator(ic):
foundType = True
self.integrators.append(ic)
if 0 == comm.rank:
self._info.log("Added interface condition '%s' as an integrator." % \
ic.label())
if implementsConstraint(ic):
foundType = True
self.constraints.append(ic)
if 0 == comm.rank:
self._info.log("Added interface condition '%s' as a constraint." % \
ic.label())
if not foundType:
raise TypeError, \
"Could not determine whether interface condition '%s' is an " \
"integrator or a constraint." % ic.name
self._debug.log(resourceUsageString())
return
def _initialize(self, dimension, normalizer):
"""
Create integrators for each element family.
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
self.timeStep.initialize(normalizer)
numTimeSteps = self.timeStep.numTimeSteps()
totalTime = self.timeStep.totalTime
from pylith.topology.SolutionFields import SolutionFields
self.fields = SolutionFields(self.mesh())
self._debug.log(resourceUsageString())
if 0 == comm.rank:
self._info.log("Initializing integrators.")
for integrator in self.integrators:
if not self.gravityField is None:
integrator.gravityField(self.gravityField)
integrator.initialize(totalTime, numTimeSteps, normalizer)
ModuleFormulation.integrators(self, self.integrators)
self._debug.log(resourceUsageString())
if 0 == comm.rank:
self._info.log("Initializing constraints.")
for constraint in self.constraints:
constraint.initialize(totalTime, numTimeSteps, normalizer)
self._debug.log(resourceUsageString())
if 0 == comm.rank:
self._info.log("Setting up solution output.")
for output in self.output.components():
output.initialize(self.mesh(), normalizer)
output.writeInfo()
output.open(totalTime, numTimeSteps)
self._debug.log(resourceUsageString())
# Setup fields
if 0 == comm.rank:
self._info.log("Creating solution field.")
#from pylith.utils.petsc import MemoryLogger
#memoryLogger = MemoryLogger.singleton()
#memoryLogger.setDebug(0)
#memoryLogger.stagePush("Problem")
self.fields.add("dispIncr(t->t+dt)", "displacement_increment")
self.fields.add("disp(t)", "displacement")
self.fields.add("residual", "residual")
self.fields.solutionName("dispIncr(t->t+dt)")
lengthScale = normalizer.lengthScale()
pressureScale = normalizer.pressureScale()
solution = self.fields.get("dispIncr(t->t+dt)")
solution.subfieldAdd("displacement", dimension, solution.VECTOR, lengthScale.value)
solution.subfieldAdd("lagrange_multiplier", dimension, solution.VECTOR, pressureScale.value)
solution.subfieldsSetup()
solution.setupSolnChart()
solution.setupSolnDof(dimension)
# Loop over integrators to adjust DOF layout
for integrator in self.integrators:
integrator.setupSolnDof(solution)
solution.vectorFieldType(solution.VECTOR)
solution.scale(lengthScale.value)
for constraint in self.constraints:
constraint.setConstraintSizes(solution)
solution.allocate()
solution.zeroAll()
for constraint in self.constraints:
constraint.setConstraints(solution)
for integrator in self.integrators:
integrator.checkConstraints(solution)
#memoryLogger.stagePop()
# This also creates a global order.
solution.createScatter(solution.mesh())
#memoryLogger.stagePush("Problem")
dispT = self.fields.get("disp(t)")
dispT.vectorFieldType(dispT.VECTOR)
dispT.scale(lengthScale.value)
residual = self.fields.get("residual")
residual.vectorFieldType(residual.VECTOR)
residual.scale(lengthScale.value)
#memoryLogger.stagePop()
#memoryLogger.setDebug(0)
self._debug.log(resourceUsageString())
return
def _reformJacobian(self, t, dt):
"""
Reform Jacobian matrix for operator.
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
self._debug.log(resourceUsageString())
if 0 == comm.rank:
self._info.log("Integrating Jacobian operator.")
self._eventLogger.stagePush("Reform Jacobian")
self.updateSettings(self.jacobian, self.fields, t, dt)
self.reformJacobian()
self._eventLogger.stagePop()
if self.viewJacobian:
from pylith.mpi.Communicator import Communicator
comm = Communicator(self.mesh().comm())
self.jacobianViewer.view(self.jacobian, t, comm)
self._debug.log(resourceUsageString())
return
def _reformResidual(self, t, dt):
"""
Reform residual vector for operator.
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Integrating residual term in operator.")
self._eventLogger.stagePush("Reform Residual")
self.updateSettings(self.jacobian, self.fields, t, dt)
self.reformResidual()
self._eventLogger.stagePop()
self._debug.log(resourceUsageString())
return
def _writeData(self, t):
"""
Write data for time t.
"""
logEvent = "%swrite" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent)
for integrator in self.integrators:
integrator.writeData(t, self.fields)
for constraint in self.constraints:
constraint.writeData(t, self.fields)
self._eventLogger.eventEnd(logEvent)
return
def _setupLogging(self):
"""
Setup event logging.
"""
if not "_loggingPrefix" in dir(self):
self._loggingPrefix = ""
from pylith.utils.EventLogger import EventLogger
logger = EventLogger()
logger.className("PDE Formulation")
logger.initialize()
events = ["preinit",
"verify",
"init",
"timestep",
"prestep",
"step",
"poststep",
"write",
"finalize"]
for event in events:
logger.registerEvent("%s%s" % (self._loggingPrefix, event))
stages = ["Reform Jacobian",
"Reform Residual",
"Solve"]
for stage in stages:
logger.registerStage(stage)
self._eventLogger = logger
return
def _modelMemoryUse(self):
"""
Model memory allocation.
"""
self.perfLogger.logFields('Problem', self.fields)
self.perfLogger.logJacobian('Jacobian', 'dummy')
self.perfLogger.logGlobalOrder('GlobalOrder', 'VectorOrder',
self.fields.get('residual'))
for integrator in self.integrators:
self.perfLogger.logQuadrature('Quadrature', integrator.quadrature())
return
def _cleanup(self):
"""
Deallocate PETSc and local data structures.
"""
if not self.jacobian is None:
self.jacobian.cleanup()
if not self.fields is None:
self.fields.cleanup()
if not self.integrators is None:
for integrator in self.integrators:
integrator.cleanup()
return
def _initialize(self):
"""
Initialize AbsorbingDampers boundary condition.
"""
from spatialdata.spatialdb.SimpleDB import SimpleDB
db = SimpleDB()
db.inventory.label = "TestAbsorbingDampers tri3"
db.inventory.iohandler.inventory.filename = \
"data/elasticplanestrain.spatialdb"
db.inventory.iohandler._configure()
db._configure()
from pylith.feassemble.FIATSimplex import FIATSimplex
cell = FIATSimplex()
cell.inventory.dimension = 1
cell.inventory.degree = 1
cell.inventory.order = 1
cell._configure()
from pylith.feassemble.Quadrature import Quadrature
quadrature = Quadrature()
quadrature.inventory.cell = cell
quadrature._configure()
from pylith.bc.AbsorbingDampers import AbsorbingDampers
bc = AbsorbingDampers()
bc.inventory.quadrature = quadrature
bc.inventory.db = db
bc.inventory.id = 0
bc.inventory.label = "bc"
bc._configure()
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
from pylith.meshio.MeshIOAscii import MeshIOAscii
importer = MeshIOAscii()
importer.inventory.filename = "data/tri3.mesh"
importer.inventory.coordsys = cs
importer._configure()
mesh = importer.read(debug=False, interpolate=False)
bc.preinitialize(mesh)
bc.initialize(totalTime=0.0, numTimeSteps=1, normalizer=normalizer)
bc.timeStep(0.01)
# Setup fields
from pylith.topology.SolutionFields import SolutionFields
fields = SolutionFields(mesh)
fields.add("residual", "residual")
fields.add("dispIncr(t->t+dt)", "displacement")
fields.add("disp(t)", "displacement")
fields.add("disp(t-dt)", "displacement")
fields.add("velocity(t)", "velocity")
fields.solutionName("dispIncr(t->t+dt)")
residual = fields.get("residual")
residual.newSection(residual.VERTICES_FIELD, cs.spaceDim())
residual.allocate()
residual.zero()
fields.copyLayout("residual")
return (mesh, bc, fields)
def _initialize(self):
"""
Initialize fault.
"""
dt = 2.4
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
# Setup mesh
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
from pylith.meshio.MeshIOAscii import MeshIOAscii
importer = MeshIOAscii()
importer.inventory.filename = "data/tri3.mesh"
importer.inventory.coordsys = cs
importer._configure()
mesh = importer.read(debug=False, interpolate=False)
# Setup quadrature
from pylith.feassemble.FIATSimplex import FIATSimplex
cell = FIATSimplex()
cell.inventory.dimension = 1
cell.inventory.degree = 1
cell.inventory.order = 1
cell._configure()
from pylith.feassemble.Quadrature import Quadrature
quadrature = Quadrature()
quadrature.inventory.cell = cell
quadrature._configure()
# Setup impulses
from spatialdata.spatialdb.SimpleDB import SimpleDB
from spatialdata.spatialdb.SimpleIOAscii import SimpleIOAscii
ioImpulseAmp = SimpleIOAscii()
ioImpulseAmp.inventory.filename = "data/tri3_impulses.spatialdb"
ioImpulseAmp._configure()
dbImpulseAmp = SimpleDB()
dbImpulseAmp.inventory.iohandler = ioImpulseAmp
dbImpulseAmp.inventory.label = "impulse amplitude"
dbImpulseAmp._configure()
# Setup fault
fault = FaultCohesiveImpulses()
fault.inventory.output.inventory.writer._configure()
fault.inventory.output._configure()
fault.inventory.matId = 10
fault.inventory.faultLabel = "fault"
fault.inventory.upDir = [0, 0, 1]
fault.inventory.faultQuadrature = quadrature
fault.inventory.dbImpulseAmp = dbImpulseAmp
fault._configure()
nvertices = fault.numVerticesNoMesh(mesh)
firstFaultVertex = 0
firstLagrangeVertex = nvertices
firstFaultCell = 2*nvertices
fault.adjustTopology(mesh, firstFaultVertex, firstLagrangeVertex,
firstFaultCell)
fault.preinitialize(mesh)
fault.timeStep(dt)
fault.verifyConfiguration()
from pyre.units.time import s
fault.initialize(totalTime=0.0*s, numTimeSteps=1, normalizer=normalizer)
# Setup fields
from pylith.topology.SolutionFields import SolutionFields
fields = SolutionFields(mesh)
fields.add("residual", "residual")
fields.add("dispIncr(t->t+dt)", "displacement_increment")
fields.add("disp(t)", "displacement")
fields.solutionName("dispIncr(t->t+dt)")
residual = fields.get("residual")
residual.newSection(residual.VERTICES_FIELD, cs.spaceDim())
residual.allocate()
residual.zero()
fields.copyLayout("residual")
return (mesh, fault, fields)
def _initialize(self):
"""
Initialize AbsorbingDampers boundary condition.
"""
from spatialdata.spatialdb.SimpleDB import SimpleDB
db = SimpleDB()
db.inventory.label = "TestAbsorbingDampers tri3"
db.inventory.iohandler.inventory.filename = \
"data/elasticplanestrain.spatialdb"
db.inventory.iohandler._configure()
db._configure()
from pylith.feassemble.FIATSimplex import FIATSimplex
cell = FIATSimplex()
cell.inventory.dimension = 1
cell.inventory.degree = 1
cell.inventory.order = 1
cell._configure()
from pylith.feassemble.Quadrature import Quadrature
quadrature = Quadrature()
quadrature.inventory.cell = cell
quadrature._configure()
from pylith.bc.AbsorbingDampers import AbsorbingDampers
bc = AbsorbingDampers()
bc.inventory.quadrature = quadrature
bc.inventory.db = db
bc.inventory.id = 0
bc.inventory.label = "bc"
bc._configure()
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
from pylith.meshio.MeshIOAscii import MeshIOAscii
importer = MeshIOAscii()
importer.inventory.filename = "data/tri3.mesh"
importer.inventory.coordsys = cs
importer._configure()
mesh = importer.read(debug=False, interpolate=False)
bc.preinitialize(mesh)
bc.initialize(totalTime=0.0, numTimeSteps=1, normalizer=normalizer)
bc.timeStep(0.01)
# Setup fields
from pylith.topology.SolutionFields import SolutionFields
fields = SolutionFields(mesh)
fields.add("residual", "residual")
fields.add("dispIncr(t->t+dt)", "displacement")
fields.add("disp(t)", "displacement")
fields.add("disp(t-dt)", "displacement")
fields.add("velocity(t)", "velocity")
fields.solutionName("dispIncr(t->t+dt)")
residual = fields.get("residual")
residual.newSection(residual.VERTICES_FIELD, cs.spaceDim())
residual.allocate()
residual.zero()
fields.copyLayout("residual")
return (mesh, bc, fields)
def _initialize(self, dimension, normalizer):
"""
Create integrators for each element family.
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
self.timeStep.initialize(normalizer)
numTimeSteps = self.timeStep.numTimeSteps()
totalTime = self.timeStep.totalTime
from pylith.topology.SolutionFields import SolutionFields
self.fields = SolutionFields(self.mesh())
self._debug.log(resourceUsageString())
if 0 == comm.rank:
self._info.log("Initializing integrators.")
for integrator in self.integrators:
if not self.gravityField is None:
integrator.gravityField(self.gravityField)
integrator.initialize(totalTime, numTimeSteps, normalizer)
ModuleFormulation.integrators(self, self.integrators)
self._debug.log(resourceUsageString())
if 0 == comm.rank:
self._info.log("Initializing constraints.")
for constraint in self.constraints:
constraint.initialize(totalTime, numTimeSteps, normalizer)
self._debug.log(resourceUsageString())
if 0 == comm.rank:
self._info.log("Setting up solution output.")
for output in self.output.components():
output.initialize(self.mesh(), normalizer)
output.writeInfo()
output.open(totalTime, numTimeSteps)
self._debug.log(resourceUsageString())
# Setup fields
if 0 == comm.rank:
self._info.log("Creating solution field.")
#from pylith.utils.petsc import MemoryLogger
#memoryLogger = MemoryLogger.singleton()
#memoryLogger.setDebug(0)
#memoryLogger.stagePush("Problem")
self.fields.add("dispIncr(t->t+dt)", "displacement_increment")
self.fields.add("disp(t)", "displacement")
self.fields.add("residual", "residual")
self.fields.solutionName("dispIncr(t->t+dt)")
lengthScale = normalizer.lengthScale()
pressureScale = normalizer.pressureScale()
solution = self.fields.get("dispIncr(t->t+dt)")
solution.subfieldAdd("displacement", dimension, solution.VECTOR, lengthScale.value)
solution.subfieldAdd("lagrange_multiplier", dimension, solution.VECTOR, pressureScale.value)
solution.subfieldsSetup()
solution.setupSolnChart()
solution.setupSolnDof(dimension)
# Loop over integrators to adjust DOF layout
for integrator in self.integrators:
integrator.setupSolnDof(solution)
solution.vectorFieldType(solution.VECTOR)
solution.scale(lengthScale.value)
for constraint in self.constraints:
constraint.setConstraintSizes(solution)
solution.allocate()
solution.zeroAll()
for constraint in self.constraints:
constraint.setConstraints(solution)
for integrator in self.integrators:
integrator.checkConstraints(solution)
#memoryLogger.stagePop()
# This also creates a global order.
solution.createScatter(solution.mesh())
#memoryLogger.stagePush("Problem")
dispT = self.fields.get("disp(t)")
dispT.vectorFieldType(dispT.VECTOR)
dispT.scale(lengthScale.value)
residual = self.fields.get("residual")
residual.vectorFieldType(residual.VECTOR)
residual.scale(lengthScale.value)
#memoryLogger.stagePop()
#memoryLogger.setDebug(0)
self._debug.log(resourceUsageString())
return
def _initialize(self, mesh, integrator):
"""
Initialize integrator.
"""
dt = 2.3
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
from pyre.units.time import s
integrator.initialize(totalTime=0.0*s, numTimeSteps=1,
normalizer=normalizer)
integrator.timeStep(dt)
# Setup fields
from pylith.topology.SolutionFields import SolutionFields
fields = SolutionFields(mesh)
fields.add("residual", "residual")
fields.add("disp(t)", "displacement")
fields.add("dispIncr(t->t+dt)", "displacement_increment")
fields.solutionName("dispIncr(t->t+dt)")
residual = fields.get("residual")
spaceDim = mesh.coordsys().spaceDim()
lengthScale = normalizer.lengthScale()
residual.subfieldAdd("displacement", spaceDim, residual.VECTOR, lengthScale.value);
residual.subfieldAdd("lagrange_multiplier", spaceDim, residual.VECTOR);
residual.subfieldsSetup();
residual.setupSolnChart();
residual.setupSolnDof(spaceDim);
residual.allocate();
residual.zeroAll();
fields.copyLayout("residual")
return fields
class TestSolutionFields(unittest.TestCase):
"""
Unit testing of SolutionFields object.
"""
def setUp(self):
"""
Setup mesh and associated field.
"""
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
from pylith.meshio.MeshIOAscii import MeshIOAscii
importer = MeshIOAscii()
importer.inventory.filename = "data/tri3.mesh"
importer.inventory.coordsys = cs
importer._configure()
self.mesh = importer.read(debug=False, interpolate=False)
self.fields = SolutionFields(self.mesh)
return
def test_constructor(self):
"""
Test constructor.
"""
return
def test_solutionName(self):
"""
Test mesh().
"""
fields = self.fields
fields.add("field A", "A");
fields.add("field B", "B");
fields.add("field C", "C");
fields.solutionName("field B")
return
def test_solution(self):
"""
Test solution().
"""
fields = self.fields
fields.add("field A", "A");
fields.add("field B", "B");
fields.add("field C", "C");
fields.solutionName("field B")
solution = self.fields.solution()
return
def test_fieldAdd(self):
"""
Test fieldAdd().
"""
fields = self.fields
fields.add("field A", "A");
fields.add("field B", "B");
helper_fieldAdd(fields)
fieldA = fields.get("field A")
fieldB = fields.get("field B")
fieldA.allocate()
fieldB.allocate()
fieldA.copy(fieldB)
return