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 test_dimension(self): """ Test debug(). """ mesh = Mesh() self.assertEqual(0, mesh.dimension()) return
def test_dimension(self):
"""
Test debug().
"""
mesh = Mesh()
self.assertEqual(0, mesh.dimension())
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 test_coordsys(self):
"""
Test coordsys().
"""
mesh = self._getMesh()
submesh = Mesh(mesh=mesh, label="bc")
self.assertEqual(2, submesh.coordsys().spaceDim())
return
def test_constructorA(self): """ Test constructor. """ mesh = Mesh() self.assertEqual(0, mesh.dimension()) self.assertEqual(False, mesh.debug()) return
def test_coordsys(self): """ Test coordsys(). """ mesh = self._getMesh() submesh = Mesh(mesh=mesh, label="bc") self.assertEqual(2, submesh.coordsys().spaceDim()) return
def test_constructorA(self):
"""
Test constructor.
"""
mesh = Mesh()
self.assertEqual(0, mesh.dimension())
self.assertEqual(False, mesh.debug())
return
def test_constructorB(self): """ Test constructor. """ mesh = self._getMesh() submesh = Mesh(mesh=mesh, label="bc") self.assertEqual(1, submesh.dimension()) self.assertEqual(False, mesh.debug()) return
def test_dimension(self):
"""
Test debug().
"""
mesh = self._getMesh()
submesh = Mesh(mesh=mesh, label="bc")
self.assertEqual(1, submesh.dimension())
return
def test_constructorB(self):
"""
Test constructor.
"""
dim = 2
mesh = Mesh(dim=dim)
self.assertEqual(dim, mesh.dimension())
self.assertEqual(False, mesh.debug())
return
def test_dimension(self):
"""
Test debug().
"""
mesh = self._getMesh()
submesh = Mesh(mesh=mesh, label="bc")
self.assertEqual(1, submesh.dimension())
return
def test_constructorB(self): """ Test constructor. """ dim = 2 mesh = Mesh(dim=dim) self.assertEqual(dim, mesh.dimension()) self.assertEqual(False, mesh.debug()) return
def test_constructorB(self):
"""
Test constructor.
"""
mesh = self._getMesh()
submesh = Mesh(mesh=mesh, label="bc")
self.assertEqual(1, submesh.dimension())
self.assertEqual(False, mesh.debug())
return
def test_comm(self):
"""
Test comm().
"""
from pylith.mpi.Communicator import petsc_comm_self
mesh = Mesh(dim=3, comm=petsc_comm_self())
comm = mesh.comm()
self.assertEqual(0, comm.rank)
self.assertEqual(1, comm.size)
return
def test_constructorC(self):
"""
Test constructor.
"""
dim = 2
from pylith.mpi.Communicator import mpi_comm_self
mesh = Mesh(dim=dim, comm=mpi_comm_self())
self.assertEqual(dim, mesh.dimension())
self.assertEqual(False, mesh.debug())
return
def test_comm(self): """ Test comm(). """ from pylith.mpi.Communicator import petsc_comm_self mesh = Mesh(dim=3, comm=petsc_comm_self()) comm = mesh.comm() self.assertEqual(0, comm.rank) self.assertEqual(1, comm.size) return
def test_constructorC(self): """ Test constructor. """ dim = 2 from pylith.mpi.Communicator import mpi_comm_self mesh = Mesh(dim=dim, comm=mpi_comm_self()) self.assertEqual(dim, mesh.dimension()) self.assertEqual(False, mesh.debug()) return
def test_debug(self):
"""
Test debug().
"""
mesh = Mesh()
self.assertEqual(False, mesh.debug())
mesh.debug(True)
self.assertEqual(True, mesh.debug())
return
def test_comm(self):
"""
Test comm().
"""
mesh = self._getMesh()
submesh = Mesh(mesh=mesh, label="bc")
comm = submesh.comm()
self.assertEqual(0, comm.rank)
self.assertEqual(1, comm.size)
return
def test_comm(self):
"""
Test comm().
"""
mesh = self._getMesh()
submesh = Mesh(mesh=mesh, label="bc")
comm = submesh.comm()
self.assertEqual(0, comm.rank)
self.assertEqual(1, comm.size)
return
def test_debug(self):
"""
Test debug().
"""
mesh = self._getMesh()
submesh = Mesh(mesh=mesh, label="bc")
self.assertEqual(False, submesh.debug())
submesh.debug(True)
self.assertEqual(True, submesh.debug())
return
def test_coordsys(self):
"""
Test coordsys().
"""
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
mesh = Mesh()
mesh.coordsys(cs)
self.assertEqual(cs.spaceDim(), mesh.coordsys().spaceDim())
return
def test_coordsys(self):
"""
Test coordsys().
"""
from spatialdata.geocoords.CSCart import CSCart
cs = CSCart()
cs.inventory.spaceDim = 2
cs._configure()
mesh = Mesh()
mesh.coordsys(cs)
self.assertEqual(cs.spaceDim(), mesh.coordsys().spaceDim())
return
def test_timeStep(self):
"""
Test timeStep().
"""
tstep = self.tstep
integrators = [Integrator(4.0), Integrator(8.0)]
from pylith.topology.Mesh import Mesh
mesh = Mesh()
self.assertEqual(1.0, tstep.timeStep(mesh, integrators))
tstep.dtN = 0.5
self.assertEqual(0.5, tstep.timeStep(mesh, integrators))
caught = False
try:
tstep.dtN = 10.0
tstep.timeStep(mesh, integrators)
except RuntimeError:
caught = True
self.failUnless(caught)
return
def distribute(self, mesh, normalizer):
"""
Distribute a Mesh
"""
self._setupLogging()
logEvent = "%sdistribute" % self._loggingPrefix
self._eventLogger.eventBegin(logEvent)
from pylith.topology.Mesh import Mesh
newMesh = Mesh(mesh.dimension())
if self.partitioner == "metis":
partitionerName = "parmetis"
else:
partitionerName = self.partitioner
ModuleDistributor.distribute(newMesh, mesh, partitionerName)
#from pylith.utils.petsc import MemoryLogger
#memoryLogger = MemoryLogger.singleton()
#memoryLogger.stagePush(mesh.memLoggingStage)
mesh.cleanup()
#memoryLogger.stagePop()
if self.writePartition:
self.dataWriter.initialize(normalizer)
ModuleDistributor.write(self.dataWriter, newMesh)
self._eventLogger.eventEnd(logEvent)
return newMesh
def testStableTimeStepImplicit(self):
"""
Test stableTimeStepImplicit().
"""
from pylith.topology.Mesh import Mesh
mesh = Mesh()
dt = self.material.stableTimeStepImplicit(mesh)
from pylith.utils.utils import maxdouble
self.assertAlmostEqual(1.0, dt / maxdouble())
def test_timeStep(self):
"""
Test timeStep().
"""
tstep = self.tstep
tstep.adaptSkip = 2
integrators = [Integrator(2.0), Integrator(0.5)]
from pylith.topology.Mesh import Mesh
mesh = Mesh()
# Set time step
dt = 0.5 / 2.0
self.assertEqual(dt, tstep.timeStep(mesh, integrators))
# Increase stable time step, but time step should not change (skipped)
integrators[1].dt = 0.8
self.assertEqual(dt, tstep.timeStep(mesh, integrators))
# Reduce time step even if though should have skipped
integrators[1].dt = 0.2
dt = 0.2 / 2.0
self.assertEqual(dt, tstep.timeStep(mesh, integrators))
# Skip adjusting time step
integrators[1].dt = 0.8
self.assertEqual(dt, tstep.timeStep(mesh, integrators))
# Skip adjusting time step
self.assertEqual(dt, tstep.timeStep(mesh, integrators))
# Adjust time step and stability factor
tstep.stabilityFactor = 3.0
dt = 0.8 / 3.0
self.assertEqual(dt, tstep.timeStep(mesh, integrators))
# Skip adjusting time step
integrators[1].dt = 2.0
self.assertEqual(dt, tstep.timeStep(mesh, integrators))
# Skip adjusting time step
self.assertEqual(dt, tstep.timeStep(mesh, integrators))
# Adjust time step with value bigger than max
dt = 0.5
self.assertEqual(dt, tstep.timeStep(mesh, integrators))
return
def test_debug(self):
"""
Test debug().
"""
mesh = Mesh()
self.assertEqual(False, mesh.debug())
mesh.debug(True)
self.assertEqual(True, mesh.debug())
return
def test_currentStep(self):
"""
Test currentStep().
"""
tstep = self.tstep
integrators = [Integrator(4.0), Integrator(8.0)]
from pylith.topology.Mesh import Mesh
from pylith.mpi.Communicator import petsc_comm_world
mesh = Mesh()
#mesh.setComm(petsc_comm_world())
tstep.timeStep(mesh, integrators)
stepE = 1.0 / 0.5 # Nondimensionalize
self.assertEqual(stepE, tstep.currentStep())
return
def test_debug(self):
"""
Test debug().
"""
mesh = self._getMesh()
submesh = Mesh(mesh=mesh, label="bc")
self.assertEqual(False, submesh.debug())
submesh.debug(True)
self.assertEqual(True, submesh.debug())
return
def test_currentStep(self):
"""
Test currentStep().
"""
tstep = self.tstep
tstep.maxDtN = 10.0
tstep.dtN = tstep.maxDtN
self.assertEqual(10.0, tstep.currentStep())
integrators = [Integrator(3.0), Integrator(2.4)]
from pylith.topology.Mesh import Mesh
mesh = Mesh()
dt = 2.4 / 2.0
tstep.timeStep(mesh, integrators)
self.assertEqual(dt, tstep.currentStep())
return
def test_timeStep(self):
"""
Test timeStep().
"""
tstep = self.tstep
step1 = 1.0 / 0.5 # nondimensionalize
step2 = 2.0 / 0.5 # nondimensionalize
step3 = 3.0 / 0.5 # nondimensionalize
integrators = [Integrator(40.0), Integrator(80.0)]
from pylith.topology.Mesh import Mesh
mesh = Mesh()
self.assertEqual(step1, tstep.timeStep(mesh, integrators))
self.assertEqual(step2, tstep.timeStep(mesh, integrators))
self.assertEqual(step3, tstep.timeStep(mesh, integrators))
self.assertEqual(step3, tstep.timeStep(mesh, integrators))
self.assertEqual(step3, tstep.timeStep(mesh, integrators))
tstep.index = 0
tstep.loopSteps = True
self.assertEqual(step1, tstep.timeStep(mesh, integrators))
self.assertEqual(step2, tstep.timeStep(mesh, integrators))
self.assertEqual(step3, tstep.timeStep(mesh, integrators))
self.assertEqual(step1, tstep.timeStep(mesh, integrators))
self.assertEqual(step2, tstep.timeStep(mesh, integrators))
integrators = [Integrator(0.01), Integrator(8.0)]
caught = False
try:
tstep.timeStep(mesh, integrators)
except RuntimeError:
caught = True
self.failUnless(caught)
return
def __init__(self):
"""
Constructor.
"""
self.availableFields = \
{'vertex': \
{'info': ["vertex info"],
'data': ["vertex data 1",
"vertex data 2"]},
'cell': \
{'info': ["cell info"],
'data': ["cell data"]}}
filename = "data/twohex8.txt"
from pylith.meshio.MeshIOAscii import MeshIOAscii
iohandler = MeshIOAscii()
iohandler.inventory.filename = filename
from spatialdata.geocoords.CSCart import CSCart
iohandler.inventory.coordsys = CSCart()
iohandler._configure()
from spatialdata.units.Nondimensional import Nondimensional
normalizer = Nondimensional()
normalizer._configure()
mesh = iohandler.read(debug=False, interpolate=False)
from pylith.topology.Mesh import Mesh
submesh = Mesh(mesh=mesh, label="4")
from pylith.topology.Fields import Fields
fields = Fields(submesh)
self.mesh = mesh
self.submesh = submesh
self.fields = fields
return
def test_constructor(self):
mesh = Mesh()
field = Field(mesh)
self.assertTrue(not field is None)
def test_constructor(self):
mesh = Mesh()
self.assertTrue(not mesh is None)