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 test_integrateJacobian(self):
"""
Test integrateJacobian().
WARNING: This is not a rigorous test of integrateJacobian()
because we neither set the input fields or verify the results.
"""
(mesh, integrator) = self._preinitialize()
fields = self._initialize(mesh, integrator)
from pylith.topology.Field import Field
jacobian = Field(mesh)
spaceDim = mesh.coordsys().spaceDim()
jacobian.subfieldAdd("displacement", spaceDim, jacobian.VECTOR);
jacobian.subfieldAdd("lagrange_multiplier", spaceDim, jacobian.VECTOR);
jacobian.subfieldsSetup();
jacobian.setupSolnChart();
jacobian.setupSolnDof(spaceDim);
jacobian.allocate();
jacobian.zeroAll();
t = 7.3
self.assertEqual(True, integrator.needNewJacobian())
integrator.integrateJacobian(jacobian, t, fields)
self.assertEqual(False, integrator.needNewJacobian())
# No test of result.
return
def test_cloneSectionField(self):
"""
Test newSection(field).
"""
fieldB = Field(self.mesh)
fieldB.cloneSection(self.field)
# No test of result
return
def test_copy(self):
"""
Test newSection(field).
"""
fieldB = Field(self.mesh)
fieldB.allocate()
fieldB.copy(self.field)
# No test of result
return
def test_operatorAdd(self):
"""
Test add().
"""
fieldB = Field(self.mesh)
fieldB.allocate()
self.field.add(fieldB)
# No test of result
return
def _initialize(self):
"""
Initialize DirichletBoundary boundary condition.
"""
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)
from spatialdata.spatialdb.SimpleDB import SimpleDB
db = SimpleDB()
db.inventory.label = "TestDirichletBoundary tri3"
db.inventory.iohandler.inventory.filename = "data/tri3_disp.spatialdb"
db.inventory.iohandler._configure()
db._configure()
from spatialdata.spatialdb.SimpleDB import SimpleDB
dbRate = SimpleDB()
dbRate.inventory.label = "TestDirichletBoundary tri3"
dbRate.inventory.iohandler.inventory.filename = "data/tri3_vel.spatialdb"
dbRate.inventory.iohandler._configure()
dbRate._configure()
from pylith.bc.DirichletBoundary import DirichletBoundary
bc = DirichletBoundary()
bc.inventory.output._configure()
bc.inventory.output.writer._configure()
bc.inventory.label = "bc"
bc.inventory.bcDOF = [1]
bc.inventory.dbInitial = db
bc.inventory.dbRate = dbRate
bc._configure()
bc.preinitialize(mesh)
bc.initialize(totalTime=0.0, numTimeSteps=1, normalizer=normalizer)
# Setup field
from pylith.topology.Field import Field
field = Field(mesh)
field.newSection(field.VERTICES_FIELD, cs.spaceDim())
return (mesh, bc, field)
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.field = Field(self.mesh)
self.field.allocate()
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 test_constructor(self):
mesh = Mesh()
field = Field(mesh)
self.assertTrue(not field is None)
