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 _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 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 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 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 _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 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 create(self, normalizer, faults=None):
"""
Hook for creating mesh.
"""
from pylith.utils.profiling import resourceUsageString
from pylith.mpi.Communicator import petsc_comm_world
comm = petsc_comm_world()
self._setupLogging()
logEvent = "%screate" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent)
# Read mesh
mesh = self.reader.read(self.debug, self.interpolate)
if self.debug:
mesh.view()
# Reorder mesh
if self.reorderMesh:
logEvent2 = "%sreorder" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent2)
self._debug.log(resourceUsageString())
if 0 == comm.rank:
self._info.log("Reordering cells and vertices.")
from pylith.topology.ReverseCuthillMcKee import ReverseCuthillMcKee
ordering = ReverseCuthillMcKee()
ordering.reorder(mesh)
self._eventLogger.eventEnd(logEvent2)
# Adjust topology
self._debug.log(resourceUsageString())
if 0 == comm.rank:
self._info.log("Adjusting topology.")
self._adjustTopology(mesh, faults)
# Distribute mesh
if comm.size > 1:
if 0 == comm.rank:
self._info.log("Distributing mesh.")
mesh = self.distributor.distribute(mesh, normalizer)
if self.debug:
mesh.view()
mesh.memLoggingStage = "DistributedMesh"
# Refine mesh (if necessary)
newMesh = self.refiner.refine(mesh)
if not newMesh == mesh:
mesh.cleanup()
newMesh.memLoggingStage = "RefinedMesh"
# Can't reorder mesh again, because we do not have routine to
# unmix normal and hybrid cells.
# Nondimensionalize mesh (coordinates of vertices).
from pylith.topology.topology import MeshOps_nondimensionalize
MeshOps_nondimensionalize(newMesh, normalizer)
self._eventLogger.eventEnd(logEvent)
return newMesh
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 create(self, normalizer, faults=None):
"""
Hook for creating mesh.
"""
from pylith.utils.profiling import resourceUsageString
from pylith.mpi.Communicator import petsc_comm_world
comm = petsc_comm_world()
self._setupLogging()
logEvent = "%screate" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent)
# Read mesh
mesh = self.reader.read(self.debug, self.interpolate)
if self.debug:
mesh.view()
# Reorder mesh
if self.reorderMesh:
logEvent2 = "%sreorder" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent2)
self._debug.log(resourceUsageString())
if 0 == comm.rank:
self._info.log("Reordering cells and vertices.")
from pylith.topology.ReverseCuthillMcKee import ReverseCuthillMcKee
ordering = ReverseCuthillMcKee()
ordering.reorder(mesh)
self._eventLogger.eventEnd(logEvent2)
# Adjust topology
self._debug.log(resourceUsageString())
if 0 == comm.rank:
self._info.log("Adjusting topology.")
self._adjustTopology(mesh, faults)
# Distribute mesh
if comm.size > 1:
if 0 == comm.rank:
self._info.log("Distributing mesh.")
mesh = self.distributor.distribute(mesh, normalizer)
if self.debug:
mesh.view()
mesh.memLoggingStage = "DistributedMesh"
# Refine mesh (if necessary)
newMesh = self.refiner.refine(mesh)
if not newMesh == mesh:
mesh.cleanup()
newMesh.memLoggingStage = "RefinedMesh"
# Can't reorder mesh again, because we do not have routine to
# unmix normal and hybrid cells.
# Nondimensionalize mesh (coordinates of vertices).
from pylith.topology.topology import MeshOps_nondimensionalize
MeshOps_nondimensionalize(newMesh, normalizer)
self._eventLogger.eventEnd(logEvent)
return newMesh
def initialize(self, dimension, normalizer):
"""
Initialize problem for implicit time integration.
"""
logEvent = "%sinit" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent)
comm = self.mesh().comm()
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 _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 _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 main(self, *args, **kwds):
"""
Run the application.
"""
from pylith.utils.profiling import resourceUsageString
self.petsc.initialize()
self._debug.log(resourceUsageString())
# Create mesh (adjust to account for interfaces (faults) if necessary)
interfaces = None
mesh = self.mesher.create(interfaces)
self._debug.log(resourceUsageString())
self.petsc.finalize()
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)
ModuleExplicit.reformJacobianLumped(self)
self._eventLogger.stagePop()
if self.viewJacobian:
self.jacobian.view("Jacobian")
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)
ModuleExplicit.reformJacobianLumped(self)
self._eventLogger.stagePop()
if self.viewJacobian:
self.jacobian.view("Jacobian")
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 _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 _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 _showStatus(self, stage):
import sys
from pylith.utils.profiling import resourceUsageString
from pylith.mpi.Communicator import petsc_comm_world
comm = petsc_comm_world()
if comm.rank == 0:
print "\n----------------------------------------------------------------------"
print "STAGE: %s" % stage
print "----------------------------------------------------------------------"
for irank in xrange(comm.size):
comm.barrier()
if comm.rank == irank:
print "\nPROCESSOR %d" % comm.rank
print "\nStatus from ps: %s\n" % resourceUsageString()
self.logger.show()
sys.stdout.flush()
comm.barrier()
return
def create(self, normalizer, faults=None):
"""Hook for creating mesh.
"""
from pylith.utils.profiling import resourceUsageString
self._setupLogging()
logEvent = "%screate" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent)
mesh = self.reader.read(self.debug, self.interpolate)
if self.debug:
mesh.view()
self._debug.log(resourceUsageString())
# refine mesh (if necessary)
mesh = self.refiner.refine(mesh)
# Nondimensionalize mesh (coordinates of vertices).
from pylith.topology.topology import MeshOps_nondimensionalize
MeshOps_nondimensionalize(mesh, normalizer)
self._eventLogger.eventEnd(logEvent)
return mesh
def create(self, normalizer, faults=None):
"""
Hook for creating mesh.
"""
from pylith.utils.profiling import resourceUsageString
self._setupLogging()
logEvent = "%screate" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent)
mesh = self.reader.read(self.debug, self.interpolate)
if self.debug:
mesh.view("Finite-element mesh.")
self._debug.log(resourceUsageString())
# refine mesh (if necessary)
mesh = self.refiner.refine(mesh)
# Nondimensionalize mesh (coordinates of vertices).
from pylith.topology.topology import MeshOps_nondimensionalize
MeshOps_nondimensionalize(mesh, normalizer)
self._eventLogger.eventEnd(logEvent)
return mesh
def initialize(self, dimension, normalizer):
"""
Initialize problem for explicit 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("disp(t-dt)", "displacement")
self.fields.add("velocity(t)", "velocity")
self.fields.add("acceleration(t)", "acceleration")
self.fields.copyLayout("dispIncr(t->t+dt)")
self._debug.log(resourceUsageString())
# Setup fields and set to zero
dispTmdt = self.fields.get("disp(t-dt)")
dispTmdt.zeroAll()
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()
accelerationScale = velocityScale / timeScale
accelerationT = self.fields.get("acceleration(t)")
accelerationT.scale(accelerationScale.value)
accelerationT.zeroAll()
self._debug.log(resourceUsageString())
#memoryLogger.stagePop()
if 0 == comm.rank:
self._info.log("Creating lumped Jacobian matrix.")
from pylith.topology.Field import Field
jacobian = Field(self.mesh())
jacobian.newSection(jacobian.VERTICES_FIELD, dimension)
jacobian.allocate()
jacobian.label("jacobian")
jacobian.vectorFieldType(jacobian.VECTOR)
self.jacobian = jacobian
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)
self._eventLogger.eventEnd(logEvent)
return
def initialize(self, dimension, normalizer):
"""
Initialize problem for explicit 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("disp(t-dt)", "displacement")
self.fields.add("velocity(t)", "velocity")
self.fields.add("acceleration(t)", "acceleration")
self.fields.copyLayout("dispIncr(t->t+dt)")
self._debug.log(resourceUsageString())
# Setup fields and set to zero
dispTmdt = self.fields.get("disp(t-dt)")
dispTmdt.zeroAll()
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()
accelerationScale = velocityScale / timeScale
accelerationT = self.fields.get("acceleration(t)")
accelerationT.scale(accelerationScale.value)
accelerationT.zeroAll()
self._debug.log(resourceUsageString())
#memoryLogger.stagePop()
if 0 == comm.rank:
self._info.log("Creating lumped Jacobian matrix.")
from pylith.topology.Field import Field
jacobian = Field(self.mesh())
jacobian.label("jacobian")
# Setup section manually. Cloning the solution field includes
# constraints which messes up the solve for constrained DOF.
pressureScale = normalizer.pressureScale()
jacobian.subfieldAdd("displacement", dimension, jacobian.VECTOR, lengthScale.value)
jacobian.subfieldAdd("lagrange_multiplier", dimension, jacobian.VECTOR, pressureScale.value)
jacobian.subfieldsSetup()
jacobian.setupSolnChart()
jacobian.setupSolnDof(dimension)
# Loop over integrators to adjust DOF layout
for integrator in self.integrators:
integrator.setupSolnDof(jacobian)
jacobian.vectorFieldType(jacobian.VECTOR)
jacobian.allocate()
jacobian.zeroAll()
self.jacobian = jacobian
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)
self._eventLogger.eventEnd(logEvent)
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 test_resourceUsageString(self):
usage = resourceUsageString()
self.assertFalse(usage is None)
def initialize(self, dimension, normalizer):
"""
Initialize problem for explicit 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("disp(t-dt)", "displacement")
self.fields.add("velocity(t)", "velocity")
self.fields.add("acceleration(t)", "acceleration")
self.fields.copyLayout("dispIncr(t->t+dt)")
self._debug.log(resourceUsageString())
# Setup fields and set to zero
dispTmdt = self.fields.get("disp(t-dt)")
dispTmdt.zeroAll()
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()
accelerationScale = velocityScale / timeScale
accelerationT = self.fields.get("acceleration(t)")
accelerationT.scale(accelerationScale.value)
accelerationT.zeroAll()
self._debug.log(resourceUsageString())
#memoryLogger.stagePop()
if 0 == comm.rank:
self._info.log("Creating lumped Jacobian matrix.")
from pylith.topology.Field import Field
jacobian = Field(self.mesh())
jacobian.label("jacobian")
# Setup section manually. Cloning the solution field includes
# constraints which messes up the solve for constrained DOF.
pressureScale = normalizer.pressureScale()
jacobian.subfieldAdd("displacement", dimension, jacobian.VECTOR,
lengthScale.value)
jacobian.subfieldAdd("lagrange_multiplier", dimension, jacobian.VECTOR,
pressureScale.value)
jacobian.subfieldsSetup()
jacobian.setupSolnChart()
jacobian.setupSolnDof(dimension)
# Loop over integrators to adjust DOF layout
for integrator in self.integrators:
integrator.setupSolnDof(jacobian)
jacobian.vectorFieldType(jacobian.VECTOR)
jacobian.allocate()
jacobian.zeroAll()
self.jacobian = jacobian
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)
self._eventLogger.eventEnd(logEvent)
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
