def read(self, debug, interpolate):
"""
Read finite-element mesh and store in Sieve mesh object.
@returns PETSc mesh object containing finite-element mesh
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Reading finite-element mesh")
# Set flags
self.debug(debug)
self.interpolate(interpolate)
# Initialize coordinate system
if self.coordsys is None:
raise ValueError, "Coordinate system for mesh is unknown."
from pylith.mpi.Communicator import petsc_comm_world
from pylith.topology.Mesh import Mesh
mesh = Mesh(dim=self.coordsys.spaceDim(), comm=petsc_comm_world())
mesh.coordsys(self.coordsys)
# Read mesh
ModuleMeshIO.read(self, mesh)
return mesh
def poststep(self, t, dt):
"""
Hook for doing stuff after advancing time step.
"""
logEvent = "%spoststep" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent)
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
# The velocity and acceleration at time t depends on the
# displacement at time t+dt, we want to output BEFORE updating the
# displacement fields so that the displacement, velocity, and
# acceleration files are all at time t.
if 0 == comm.rank:
self._info.log("Writing solution fields.")
for output in self.output.components():
output.writeData(t, self.fields)
self._writeData(t)
# Update displacement field from time t to time t+dt.
dispIncr = self.fields.get("dispIncr(t->t+dt)")
dispT = self.fields.get("disp(t)")
dispTmdt = self.fields.get("disp(t-dt)")
dispTmdt.copy(dispT)
dispT.add(dispIncr)
dispIncr.zeroAll()
# Complete post-step processing.
Formulation.poststep(self, t, dt)
self._eventLogger.eventEnd(logEvent)
return
def read(self, debug, interpolate):
"""
Read finite-element mesh and store in Sieve mesh object.
@returns PETSc mesh object containing finite-element mesh
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Reading finite-element mesh")
# Set flags
self.debug(debug)
self.interpolate(interpolate)
# Initialize coordinate system
if self.coordsys is None:
raise ValueError, "Coordinate system for mesh is unknown."
from pylith.mpi.Communicator import petsc_comm_world
from pylith.topology.Mesh import Mesh
mesh = Mesh(dim=self.coordsys.spaceDim(), comm=petsc_comm_world())
mesh.coordsys(self.coordsys)
# Read mesh
ModuleMeshIO.read(self, mesh)
return mesh
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 poststep(self, t, dt):
"""
Hook for doing stuff after advancing time step.
"""
logEvent = "%spoststep" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent)
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
# The velocity and acceleration at time t depends on the
# displacement at time t+dt, we want to output BEFORE updating the
# displacement fields so that the displacement, velocity, and
# acceleration files are all at time t.
if 0 == comm.rank:
self._info.log("Writing solution fields.")
for output in self.output.components():
output.writeData(t, self.fields)
self._writeData(t)
# Update displacement field from time t to time t+dt.
dispIncr = self.fields.get("dispIncr(t->t+dt)")
dispT = self.fields.get("disp(t)")
dispTmdt = self.fields.get("disp(t-dt)")
dispTmdt.copy(dispT)
dispT.add(dispIncr)
dispIncr.zeroAll()
# Complete post-step processing.
Formulation.poststep(self, t, dt)
self._eventLogger.eventEnd(logEvent)
return
def preinitialize(self, mesh):
"""
Do pre-initialization setup.
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Pre-initializing fault '%s'." % self.label())
FaultCohesive.preinitialize(self, mesh)
Integrator.preinitialize(self, mesh)
ModuleFaultCohesiveKin.quadrature(self, self.faultQuadrature)
for eqsrc in self.eqsrcs.components():
eqsrc.preinitialize()
ModuleFaultCohesiveKin.eqsrcs(self, self.eqsrcs.inventory.facilityNames(),
self.eqsrcs.components())
for name in self.eqsrcs.inventory.facilityNames():
self.availableFields['vertex']['info'] += ["final_slip_%s" % name]
self.availableFields['vertex']['info'] += ["slip_time_%s" % name]
if mesh.dimension() == 2:
self.availableFields['vertex']['info'] += ["strike_dir"]
elif mesh.dimension() == 3:
self.availableFields['vertex']['info'] += ["strike_dir",
"dip_dir"]
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 preinitialize(self, mesh):
"""
Do pre-initialization setup.
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Pre-initializing fault '%s'." % self.label())
FaultCohesive.preinitialize(self, mesh)
Integrator.preinitialize(self, mesh)
ModuleFaultCohesiveDyn.quadrature(self, self.faultQuadrature)
if mesh.dimension() == 2:
self.availableFields['vertex']['info'] += ["strike_dir"]
elif mesh.dimension() == 3:
self.availableFields['vertex']['info'] += ["strike_dir", "dip_dir"]
if not isinstance(self.tract, NullComponent):
self.tract.preinitialize(mesh)
self.availableFields['vertex'][
'info'] += self.tract.availableFields['vertex']['info']
self.availableFields['vertex']['info'] += \
self.friction.availableFields['vertex']['info']
self.availableFields['vertex']['data'] += \
self.friction.availableFields['vertex']['data']
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 _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 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
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 preinitialize(self, problem, mesh):
"""Do minimal initialization of solution.
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Performing minimal initialization of solution.")
from pylith.topology.Field import Field
self.field = Field(mesh)
self.field.setLabel("solution")
spaceDim = mesh.getCoordSys().getSpaceDim()
for subfield in self.subfields.components():
subfield.initialize(problem.normalizer, spaceDim)
if 0 == comm.rank:
self._debug.log(
"Adding subfield '%s' as '%s' with components %s to solution."
% (subfield.fieldName, subfield.userAlias,
subfield.componentNames))
descriptor = subfield.getTraitDescriptor("quadrature_order")
if hasattr(descriptor.locator,
"source") and descriptor.locator.source == "default":
quadOrder = problem.defaults.quadOrder
else:
quadOrder = subfield.quadOrder
self.field.subfieldAdd(
subfield.fieldName, subfield.userAlias,
subfield.vectorFieldType, subfield.componentNames,
subfield.scale.value, subfield.basisOrder, quadOrder,
subfield.dimension, subfield.cellBasis,
subfield.isBasisContinuous, subfield.feSpace)
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
def preinitialize(self, mesh):
"""
Setup integrators for each element family (material/quadrature,
bc/quadrature, etc.).
"""
self._setupLogging()
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Pre-initializing problem.")
import weakref
self.mesh = weakref.ref(mesh)
self.formulation.preinitialize(mesh, self.materials, self.bc,
self.interfaces, self.gravityField)
# Find fault for impulses
found = False
for fault in self.interfaces.components():
if self.faultId == fault.id():
self.source = fault
found = True
break
if not found:
raise ValueError("Could not find fault interface with id '%d' for "
"Green's function impulses." % self.faultId)
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 step(self, t, dt):
"""
Advance to next time step.
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
dispIncr = self.fields.get("dispIncr(t->t+dt)")
self._reformResidual(t+dt, dt)
if 0 == comm.rank:
self._info.log("Solving equations.")
self._eventLogger.stagePush("Solve")
residual = self.fields.get("residual")
#self.jacobian.view() # TEMPORARY
self.solver.solve(dispIncr, self.jacobian, residual)
#dispIncr.view("DISP INCR") # TEMPORARY
# DEBUGGING Verify solution makes residual 0
#self._reformResidual(t+dt, dt)
#residual.view("RESIDUAL")
self._eventLogger.stagePop()
return
def poststep(self, t, dt):
"""
Hook for doing stuff after advancing time step.
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
# Update displacement field from time t to time t+dt.
dispIncr = self.fields.get("dispIncr(t->t+dt)")
disp = self.fields.get("disp(t)")
disp.add(dispIncr)
dispIncr.zeroAll()
# Complete post-step processing, then write data.
Formulation.poststep(self, t, dt)
# Write data. Velocity at time t will be based upon displacement
# at time t-dt and t.
if 0 == comm.rank:
self._info.log("Writing solution fields.")
for output in self.output.components():
output.writeData(t+dt, self.fields)
self._writeData(t+dt)
return
def preinitialize(self, mesh):
"""
Do pre-initialization setup.
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Pre-initializing fault '%s'." % self.label())
FaultCohesive.preinitialize(self, mesh)
Integrator.preinitialize(self, mesh)
ModuleFaultCohesiveDyn.quadrature(self, self.faultQuadrature)
if mesh.dimension() == 2:
self.availableFields['vertex']['info'] += ["strike_dir"]
elif mesh.dimension() == 3:
self.availableFields['vertex']['info'] += ["strike_dir",
"dip_dir"]
if not isinstance(self.tract, NullComponent):
self.tract.preinitialize(mesh)
self.availableFields['vertex']['info'] += self.tract.availableFields['vertex']['info']
self.availableFields['vertex']['info'] += \
self.friction.availableFields['vertex']['info']
self.availableFields['vertex']['data'] += \
self.friction.availableFields['vertex']['data']
return
def run(self, app):
"""
Compute Green's functions associated with fault slip.
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Computing Green's functions.")
self.checkpointTimer.toplevel = app # Set handle for saving state
# Limit material behavior to linear regime
for material in self.materials.components():
material.useElasticBehavior(True)
nimpulses = self.source.numImpulses()
if nimpulses > 0:
self.progressMonitor.open()
ipulse = 0;
dt = 1.0
while ipulse < nimpulses:
self.progressMonitor.update(ipulse, 0, nimpulses)
self._eventLogger.stagePush("Prestep")
if 0 == comm.rank:
self._info.log("Main loop, impulse %d of %d." % (ipulse+1, nimpulses))
# Implicit time stepping computes solution at t+dt, so set
# t=ipulse-dt, so that t+dt corresponds to the impulse
t = float(ipulse)-dt
# Checkpoint if necessary
self.checkpointTimer.update(t)
if 0 == comm.rank:
self._info.log("Preparing impulse %d of %d." % \
(ipulse+1, nimpulses))
self.formulation.prestep(t, dt)
self._eventLogger.stagePop()
if 0 == comm.rank:
self._info.log("Computing response to impulse %d of %d." %
(ipulse+1, nimpulses))
self._eventLogger.stagePush("Step")
self.formulation.step(t, dt)
self._eventLogger.stagePop()
if 0 == comm.rank:
self._info.log("Finishing impulse %d of %d." % \
(ipulse+1, nimpulses))
self._eventLogger.stagePush("Poststep")
self.formulation.poststep(t, dt)
self._eventLogger.stagePop()
# Update time/impulse
ipulse += 1
self.progressMonitor.close()
return
def preinitialize(self, mesh):
"""
Setup integrators for each element family (material/quadrature,
bc/quadrature, etc.).
"""
self._setupLogging()
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Pre-initializing problem.")
import weakref
self.mesh = weakref.ref(mesh)
self.formulation.preinitialize(mesh, self.materials, self.bc, self.interfaces, self.gravityField)
# Find fault for impulses
found = False
for fault in self.interfaces.components():
if self.faultId == fault.id():
self.source = fault
found = True
break
if not found:
raise ValueError("Could not find fault interface with id '%d' for "
"Green's function impulses." % self.faultId)
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 main(self, *args, **kwds):
"""
Run the application.
"""
if self.pdbOn:
import pdb
pdb.set_trace()
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Running on %d process(es)." % comm.size)
from pylith.utils.profiling import resourceUsageString
self._debug.log(resourceUsageString())
self._setupLogging()
# Create mesh (adjust to account for interfaces (faults) if necessary)
self._eventLogger.stagePush("Meshing")
interfaces = None
if "interfaces" in dir(self.problem):
interfaces = self.problem.interfaces.components()
mesh = self.mesher.create(self.problem.normalizer, interfaces)
del interfaces
del self.mesher
self._debug.log(resourceUsageString())
self._eventLogger.stagePop()
# Setup problem, verify configuration, and then initialize
self._eventLogger.stagePush("Setup")
self.problem.preinitialize(mesh)
self._debug.log(resourceUsageString())
self.problem.verifyConfiguration()
self.problem.initialize()
self._debug.log(resourceUsageString())
self._eventLogger.stagePop()
# If initializing only, stop before running problem
if self.initializeOnly:
return
# Run problem
self.problem.run(self)
self._debug.log(resourceUsageString())
# Cleanup
self._eventLogger.stagePush("Finalize")
self.problem.finalize()
self._eventLogger.stagePop()
self.perfLogger.logMesh('Mesh', mesh)
self.compilePerformanceLog()
if self.perfLogger.verbose:
self.perfLogger.show()
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 preinitialize(self, mesh):
"""
Do pre-initialization setup.
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Pre-initializing fault '%s'." % self.label())
FaultCohesive.preinitialize(self, mesh)
Integrator.preinitialize(self, mesh)
ModuleFaultCohesiveKin.quadrature(self, self.faultQuadrature)
for eqsrc in self.eqsrcs.components():
eqsrc.preinitialize()
ModuleFaultCohesiveKin.eqsrcs(self,
self.eqsrcs.inventory.facilityNames(),
self.eqsrcs.components())
for name in self.eqsrcs.inventory.facilityNames():
self.availableFields['vertex']['info'] += ["final_slip_%s" % name]
self.availableFields['vertex']['info'] += ["slip_time_%s" % name]
if mesh.dimension() == 2:
self.availableFields['vertex']['info'] += ["strike_dir"]
elif mesh.dimension() == 3:
self.availableFields['vertex']['info'] += ["strike_dir", "dip_dir"]
return
def main(self, *args, **kwds):
"""Run the application.
"""
if self.pdbOn:
import pdb
pdb.set_trace()
# Dump parameters and version information
self.parameters.preinitialize()
self.parameters.write(self)
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Running on %d process(es)." % comm.size)
from pylith.utils.profiling import resourceUsageString
self._debug.log(resourceUsageString())
self._setupLogging()
# Create mesh (adjust to account for interfaces (faults) if necessary)
self._eventLogger.stagePush("Meshing")
interfaces = None
if "interfaces" in dir(self.problem):
interfaces = self.problem.interfaces.components()
self.mesher.preinitialize(self.problem)
mesh = self.mesher.create(self.problem, interfaces)
del interfaces
self.mesher = None
self._debug.log(resourceUsageString())
self._eventLogger.stagePop()
# Setup problem, verify configuration, and then initialize
self._eventLogger.stagePush("Setup")
self.problem.preinitialize(mesh)
self._debug.log(resourceUsageString())
self.problem.verifyConfiguration()
self.problem.initialize()
self._debug.log(resourceUsageString())
self._eventLogger.stagePop()
# If initializing only, stop before running problem
if self.initializeOnly:
return
# Run problem
self.problem.run(self)
self._debug.log(resourceUsageString())
# Cleanup
self._eventLogger.stagePush("Finalize")
self.problem.finalize()
self._eventLogger.stagePop()
return
def initialize(self, dimension, normalizer):
"""
Initialize problem for implicit time integration.
"""
logEvent = "%sinit" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent)
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
self._initialize(dimension, normalizer)
#from pylith.utils.petsc import MemoryLogger
#memoryLogger = MemoryLogger.singleton()
#memoryLogger.setDebug(0)
#memoryLogger.stagePush("Problem")
# Allocate other fields, reusing layout from dispIncr
if 0 == comm.rank:
self._info.log("Creating other fields.")
self.fields.add("velocity(t)", "velocity")
self.fields.copyLayout("dispIncr(t->t+dt)")
# Setup fields and set to zero
dispT = self.fields.get("disp(t)")
dispT.zeroAll()
residual = self.fields.get("residual")
residual.zeroAll()
residual.createScatter(residual.mesh())
lengthScale = normalizer.lengthScale()
timeScale = normalizer.timeScale()
velocityScale = lengthScale / timeScale
velocityT = self.fields.get("velocity(t)")
velocityT.scale(velocityScale.value)
velocityT.zeroAll()
self._debug.log(resourceUsageString())
#memoryLogger.stagePop()
# Allocates memory for nonzero pattern and Jacobian
if 0 == comm.rank:
self._info.log("Creating Jacobian matrix.")
self._setJacobianMatrixType()
from pylith.topology.Jacobian import Jacobian
self.jacobian = Jacobian(self.fields.solution(),
self.matrixType, self.blockMatrixOkay)
self.jacobian.zero() # TEMPORARY, to get correct memory usage
self._debug.log(resourceUsageString())
#memoryLogger.stagePush("Problem")
if 0 == comm.rank:
self._info.log("Initializing solver.")
self.solver.initialize(self.fields, self.jacobian, self)
self._debug.log(resourceUsageString())
#memoryLogger.stagePop()
#memoryLogger.setDebug(0)
return
def finalize(self):
"""Cleanup after running problem.
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Finalizing problem.")
return
def resourceUsageString():
"""Get CPU time and memory usage as a string.
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
(cputime, memory) = resourceUsage()
return "[%d] CPU time: %s, Memory usage: %.2f MB" % \
(comm.rank, cputime, memory)
def resourceUsageString():
"""
Get CPU time and memory usage as a string.
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
(cputime, memory) = resourceUsage()
return "[%d] CPU time: %s, Memory usage: %.2f MB" % \
(comm.rank, cputime, memory)
def preinitialize(self, problem):
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Performing minimal initialization of poroelasticity rheology '%s'." %
self.aliases[-1])
self._createModuleObj()
return
def initialize(self):
"""Initialize integrators and constraints.
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Initializing {} problem.".format(self.formulation))
ModuleProblem.initialize(self)
return
def write(self, mesh):
"""Write finite-element mesh.stored in Sieve mesh object.
@param mesh PETSc mesh object containing finite-element mesh
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Writing finite-element mesh")
ModuleMeshIO.write(self, mesh)
return
def run(self, app):
"""Solve time dependent problem.
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Solving problem.")
ModuleTimeDependent.solve(self)
return
def write(self, mesh):
"""
Write finite-element mesh.stored in Sieve mesh object.
@param mesh PETSc mesh object containing finite-element mesh
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Writing finite-element mesh")
ModuleMeshIO.write(self, mesh)
return
def verifyConfiguration(self):
"""Verify compatibility of configuration.
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Verifying compatibility of problem configuration.")
ModuleProblem.verifyConfiguration(self)
self._printInfo()
return
def initialize(self):
"""
Setup integrators for each element family (material/quadrature,
bc/quadrature, etc.).
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Initializing problem.")
self.checkpointTimer.initialize(self.normalizer)
self.formulation.initialize(self.dimension, self.normalizer)
return
def initialize(self):
"""
Setup integrators for each element family (material/quadrature,
bc/quadrature, etc.).
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Initializing problem.")
self.checkpointTimer.initialize(self.normalizer)
self.formulation.initialize(self.dimension, self.normalizer)
return
def mkpath(self, filename):
"""Create path for output file.
"""
self._info.log("Creating path for output file '{}'".format(filename))
relpath = os.path.dirname(filename)
if relpath and not os.path.exists(relpath):
# Only create directory on proc 0
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if not comm.rank:
os.makedirs(relpath)
return
def _createPath(self, filename):
"""Create path for filename if it doesn't exist.
"""
import os
relpath = os.path.dirname(filename)
if len(relpath) > 0 and not os.path.exists(relpath):
# Only create directory on proc 0
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
os.makedirs(relpath)
return
def _createPath(self, filename):
"""Create path for filename if it doesn't exist.
"""
import os
relpath = os.path.dirname(filename)
if len(relpath) > 0 and not os.path.exists(relpath):
# Only create directory on proc 0
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
os.makedirs(relpath)
return
def close(self):
"""
Close writer.
"""
ModuleDataWriterHDF5Ext.close(self)
# Only write Xdmf file on proc 0
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if not comm.rank:
from Xdmf import Xdmf
xdmf = Xdmf()
xdmf.write(ModuleDataWriterHDF5Ext.hdf5Filename(self), verbose=False)
return
def close(self):
"""
Close writer.
"""
ModuleDataWriterHDF5.close(self)
# Only write Xdmf file on proc 0
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if not comm.rank:
from Xdmf import Xdmf
xdmf = Xdmf()
xdmf.write(ModuleDataWriterHDF5.hdf5Filename(self), verbose=False)
return
def verifyConfiguration(self):
"""
Verify compatibility of configuration.
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Verifying compatibility of problem configuration.")
if self.dimension != self.mesh().dimension():
raise ValueError, \
"Spatial dimension of problem is '%d' but mesh contains cells " \
"for spatial dimension '%d'." % \
(self.dimension, self.mesh().dimension())
if self.dimension != self.mesh().coordsys().spaceDim():
raise ValueError, \
"Spatial dimension of problem is '%d' but mesh coordinate system " \
"is for spatial dimension '%d'." % \
(self.dimension, self.mesh().coordsys().spaceDim())
# Check to make sure ids of materials and interfaces are unique
materialIds = {}
for material in self.materials.components():
if material.quadrature.spaceDim() != self.dimension:
raise ValueError, \
"Spatial dimension of problem is '%d' but quadrature " \
"for material '%s' is for spatial dimension '%d'." % \
(self.dimension, material.label(), material.quadrature.spaceDim())
if material.id() in materialIds.keys():
raise ValueError, \
"ID values for materials '%s' and '%s' are both '%d'. " \
"Material id values must be unique." % \
(material.label(), materialIds[material.id()], material.id())
materialIds[material.id()] = material.label()
for interface in self.interfaces.components():
if interface.id() in materialIds.keys():
raise ValueError, \
"ID values for material '%s' and interface '%s' are both '%d'. " \
"Material and interface id values must be unique." % \
(materialIds[interface.id()], interface.label(), interface.id())
materialIds[interface.id()] = interface.label()
# Check to make sure material-id for each cell matches the id of a material
import numpy
idValues = numpy.array(materialIds.keys(), dtype=numpy.int32)
self.mesh().checkMaterialIds(idValues)
return
def verifyConfiguration(self):
"""
Verify compatibility of configuration.
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Verifying compatibility of problem configuration.")
if self.dimension != self.mesh().dimension():
raise ValueError, \
"Spatial dimension of problem is '%d' but mesh contains cells " \
"for spatial dimension '%d'." % \
(self.dimension, self.mesh().dimension())
if self.dimension != self.mesh().coordsys().spaceDim():
raise ValueError, \
"Spatial dimension of problem is '%d' but mesh coordinate system " \
"is for spatial dimension '%d'." % \
(self.dimension, self.mesh().coordsys().spaceDim())
# Check to make sure ids of materials and interfaces are unique
materialIds = {}
for material in self.materials.components():
if material.quadrature.spaceDim() != self.dimension:
raise ValueError, \
"Spatial dimension of problem is '%d' but quadrature " \
"for material '%s' is for spatial dimension '%d'." % \
(self.dimension, material.label(), material.quadrature.spaceDim())
if material.id() in materialIds.keys():
raise ValueError, \
"ID values for materials '%s' and '%s' are both '%d'. " \
"Material id values must be unique." % \
(material.label(), materialIds[material.id()], material.id())
materialIds[material.id()] = material.label()
for interface in self.interfaces.components():
if interface.id() in materialIds.keys():
raise ValueError, \
"ID values for material '%s' and interface '%s' are both '%d'. " \
"Material and interface id values must be unique." % \
(materialIds[interface.id()], interface.label(), interface.id())
materialIds[interface.id()] = interface.label()
# Check to make sure material-id for each cell matches the id of a material
import numpy
idValues = numpy.array(materialIds.keys(), dtype=numpy.int32)
self.mesh().checkMaterialIds(idValues)
return
def writeData(self, t, fields):
"""
Hook for writing data at time t.
"""
logEvent = "%swrite" % 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("Writing material data.")
self.output.writeData(t, fields)
self._eventLogger.eventEnd(logEvent)
return
def preinitialize(self, mesh):
"""
Setup integrators for each element family (material/quadrature,
bc/quadrature, etc.).
"""
self._setupLogging()
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Pre-initializing problem.")
import weakref
self.mesh = weakref.ref(mesh)
self.formulation.preinitialize(mesh, self.materials, self.bc, self.interfaces, self.gravityField)
return
def writeData(self, t, fields):
"""
Hook for writing data at time t.
"""
logEvent = "%swrite" % 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("Writing material data.")
self.output.writeData(t, fields)
self._eventLogger.eventEnd(logEvent)
return
def initialize(self, normalizer, filename):
"""
Initialize writer.
"""
import os
relpath = os.path.dirname(filename)
if len(relpath) > 0 and not os.path.exists(relpath):
# Only create directory on proc 0
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if not comm.rank:
os.makedirs(relpath)
return
def preinitialize(self, mesh):
"""
Setup integrators for each element family (material/quadrature,
bc/quadrature, etc.).
"""
self._setupLogging()
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Pre-initializing problem.")
import weakref
self.mesh = weakref.ref(mesh)
self.formulation.preinitialize(mesh, self.materials, self.bc, self.interfaces, self.gravityField)
return
def preinitialize(self, spaceDim):
"""
Setup quadrature object.
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Initializing reference cell.")
cell = self.cell
cell.initialize(spaceDim)
if 0 == comm.rank:
self._info.log("Initializing C++ quadrature.")
self._initialize(cell)
self.refGeometry(cell.geometry)
return
def preinitialize(self, spaceDim):
"""
Setup quadrature object.
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Initializing reference cell.")
cell = self.cell
cell.initialize(spaceDim)
if 0 == comm.rank:
self._info.log("Initializing C++ quadrature.")
self._initialize(cell)
self.refGeometry(cell.geometry)
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 preinitialize(self, problem):
"""Do pre-initialization setup.
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
if 0 == comm.rank:
self._info.log("Pre-initializing fault '%s'." % self.label)
FaultCohesive.preinitialize(self, problem)
for eqsrc in self.eqRuptures.components():
eqsrc.preinitialize()
ModuleFaultCohesiveKin.setEqRuptures(
self, self.eqRuptures.inventory.facilityNames(),
self.eqRuptures.components())
return
def step(self, t, dt):
"""
Advance to next time step.
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
self._reformResidual(t, dt)
if 0 == comm.rank:
self._info.log("Solving equations.")
residual = self.fields.get("residual")
dispIncr = self.fields.get("dispIncr(t->t+dt)")
self.solver.solve(dispIncr, self.jacobian, residual)
return
def initialize(self, totalTime, numTimeSteps, normalizer):
"""
Initialize material properties.
"""
logEvent = "%sinit" % 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("Initializing integrator for material '%s'." % \
self.materialObj.label())
Integrator.initialize(self, totalTime, numTimeSteps, normalizer)
self.materialObj.normalizer(normalizer)
self._eventLogger.eventEnd(logEvent)
return
def step(self, t, dt):
"""
Advance to next time step.
"""
from pylith.mpi.Communicator import mpi_comm_world
comm = mpi_comm_world()
self._reformResidual(t, dt)
if 0 == comm.rank:
self._info.log("Solving equations.")
residual = self.fields.get("residual")
dispIncr = self.fields.get("dispIncr(t->t+dt)")
self.solver.solve(dispIncr, self.jacobian, residual)
return
def initialize(self, totalTime, numTimeSteps, normalizer):
"""
Initialize cohesive elements.
"""
logEvent = "%sinit" % 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("Initializing fault '%s'." % self.label())
Integrator.initialize(self, totalTime, numTimeSteps, normalizer)
FaultCohesive.initialize(self, totalTime, numTimeSteps, normalizer)
self._eventLogger.eventEnd(logEvent)
return
def initialize(self, totalTime, numTimeSteps, normalizer):
"""
Initialize PointForce boundary condition.
"""
logEvent = "%sinit" % 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("Initializing point forces '%s'." % self.label())
Integrator.initialize(self, totalTime, numTimeSteps, normalizer)
BoundaryCondition.initialize(self, totalTime, numTimeSteps, normalizer)
self._eventLogger.eventEnd(logEvent)
return
