def _create_penalty_objects(self):
# using this function se we don't need to add anything extra to the stokeSLE struct
velocityField = self._velocityField
pressureField = self._pressureField
stokesSLE = self._stokesSLE
# create junk force vectors -- we provide no assembly terms for these so they are 0 vectors.
self._vmfvector = sle.AssembledVector(velocityField,
stokesSLE._eqNums[velocityField])
self._junkfvector = sle.AssembledVector(
pressureField, stokesSLE._eqNums[pressureField])
# and matrices
self._vmmatrix = sle.AssembledMatrix(stokesSLE._velocitySol,
stokesSLE._velocitySol,
rhs=self._vmfvector)
self._mmatrix = sle.AssembledMatrix(stokesSLE._pressureSol,
stokesSLE._pressureSol,
rhs=self._junkfvector)
# create assembly terms
self._pressMassMatTerm = sle.MatrixAssemblyTerm_NA__NB__Fn(
integrationSwarm=uw.swarm.GaussIntegrationSwarm(
velocityField.mesh),
fn=1.0,
assembledObject=self._mmatrix,
mesh=velocityField._mesh)
# attach terms to live solver struct
self._cself.vmForceVec = self._vmfvector._cself
self._cself.vmStiffMat = self._vmmatrix._cself
self._cself.jForceVec = self._junkfvector._cself
self._cself.mStiffMat = self._mmatrix._cself
def _create_penalty_objects(self):
# using this function se we don't need to add anything extra to the stokeSLE struct
velocityField = self._velocityField
pressureField = self._pressureField
stokesSLE = self._stokesSLE
# create junk force vectors -- we provide no assembly terms for these so they are 0 vectors.
self._vmfvector = sle.AssembledVector(velocityField)
self._junkfvector = sle.AssembledVector(pressureField)
# and matrices
self._vmmatrix = sle.AssembledMatrix(velocityField,
velocityField,
rhs=self._vmfvector)
self._mmatrix = sle.AssembledMatrix(pressureField,
pressureField,
rhs=self._junkfvector)
# create assembly terms
self._velocMassMatTerm = sle.VelocityMassMatrixTerm(
integrationSwarm=stokesSLE._gaussSwarm,
assembledObject=self._vmmatrix)
self._pressMassMatTerm = sle.PressureMassMatrixTerm(
integrationSwarm=stokesSLE._gaussSwarm,
assembledObject=self._mmatrix,
mesh=velocityField._mesh)
# attach terms to live solver struct
self._cself.vmForceVec = self._vmfvector._cself
self._cself.vmStiffMat = self._vmmatrix._cself
self._cself.jForceVec = self._junkfvector._cself
self._cself.mStiffMat = self._mmatrix._cself
def __init__(self,
pressureField,
fn_diffusivity,
fn_bodyforce=None,
voronoi_swarm=None,
conditions=[],
velocityField=None,
swarmVarVelocity=None,
_removeBCs=True,
**kwargs):
if not isinstance(pressureField, uw.mesh.MeshVariable):
raise TypeError(
"Provided 'pressureField' must be of 'MeshVariable' class.")
self._pressureField = pressureField
try:
_fn_diffusivity = uw.function.Function.convert(fn_diffusivity)
except Exception as e:
raise uw._prepend_message_to_exception(
e,
"Exception encountered. Note that provided 'fn_diffusivity' must be of or convertible to 'Function' class.\nEncountered exception message:\n"
)
if not fn_bodyforce:
if pressureField.mesh.dim == 2:
fn_bodyforce = (0., 0.)
else:
fn_bodyforce = (0., 0., 0.)
try:
_fn_bodyforce = uw.function.Function.convert(fn_bodyforce)
except Exception as e:
raise uw._prepend_message_to_exception(
e,
"Exception encountered. Note that provided 'fn_bodyforce' must be of or convertible to 'Function' class.\nEncountered exception message:\n"
)
if voronoi_swarm and not isinstance(voronoi_swarm, uw.swarm.Swarm):
raise TypeError("Provided 'swarm' must be of 'Swarm' class.")
self._swarm = voronoi_swarm
if len(numpy.unique(voronoi_swarm.owningCell.data[:])) != len(
voronoi_swarm.owningCell.data[:]):
import warnings
warnings.warn(
"It is not advised to fill any cell with more than one particle, as the Q1 shape function cannot capture material interfaces. Use at your own risk."
)
if velocityField and not isinstance(velocityField,
uw.mesh.MeshVariable):
raise TypeError(
"Provided 'velocityField' must be of 'MeshVariable' class.")
self._velocityField = velocityField
if swarmVarVelocity and not isinstance(swarmVarVelocity,
uw.swarm.SwarmVariable):
raise TypeError(
"Provided 'swarmVarVelocity' must be of 'SwarmVariable' class."
)
self._swarmVarVelocity = swarmVarVelocity
if voronoi_swarm and pressureField.mesh.elementType == 'Q2':
import warnings
warnings.warn(
"Voronoi integration may yield unsatisfactory results for Q2 element types. Q2 element types can also result in spurious velocity calculations."
)
if not isinstance(_removeBCs, bool):
raise TypeError("Provided '_removeBCs' must be of type bool.")
self._removeBCs = _removeBCs
# error check dcs 'dirichlet conditions' and ncs 'neumann cond.' FeMesh_IndexSets
nbc = None
mesh = pressureField.mesh
if not isinstance(conditions, (list, tuple)):
conditionslist = []
conditionslist.append(conditions)
conditions = conditionslist
for cond in conditions:
if not isinstance(cond, uw.conditions.SystemCondition):
raise TypeError(
"Provided 'conditions' must be a list 'SystemCondition' objects."
)
# set the bcs on here
if type(cond) == uw.conditions.DirichletCondition:
if cond.variable == pressureField:
libUnderworld.StgFEM.FeVariable_SetBC(
pressureField._cself, cond._cself)
elif type(cond) == uw.conditions.NeumannCondition:
nbc = cond
else:
raise RuntimeError("Can't decide on input condition")
# build the equation numbering for the temperature field discretisation
tEqNums = self._tEqNums = sle.EqNumber(pressureField,
removeBCs=self._removeBCs)
# create solutions vector
self._solutionVector = sle.SolutionVector(pressureField, tEqNums)
libUnderworld.StgFEM.SolutionVector_LoadCurrentFeVariableValuesOntoVector(
self._solutionVector._cself)
# create force vectors
self._fvector = sle.AssembledVector(pressureField, tEqNums)
# and matrices
self._kmatrix = sle.AssembledMatrix(self._solutionVector,
self._solutionVector,
rhs=self._fvector)
# we will use voronoi if that has been requested by the user, else use
# gauss integration.
if self._swarm:
intswarm = self._swarm._voronoi_swarm
# need to ensure voronoi is populated now, as assembly terms will call
# initial test functions which may require a valid voronoi swarm
self._swarm._voronoi_swarm.repopulate()
else:
intswarm = uw.swarm.GaussIntegrationSwarm(mesh)
self._kMatTerm = sle.MatrixAssemblyTerm_NA_i__NB_i__Fn(
integrationSwarm=intswarm,
assembledObject=self._kmatrix,
fn=_fn_diffusivity)
self._forceVecTerm = sle.VectorAssemblyTerm_NA_i__Fn_i(
integrationSwarm=intswarm,
assembledObject=self._fvector,
fn=fn_bodyforce * fn_diffusivity)
# search for neumann conditions
for cond in conditions:
if isinstance(cond, uw.conditions.NeumannCondition):
#NOTE many NeumannConditions can be used but the _sufaceFluxTerm only records the last
### -VE flux because of Energy_SLE_Solver ###
negativeCond = uw.conditions.NeumannCondition(
fn_flux=-1.0 * cond.fn_flux,
variable=cond.variable,
indexSetsPerDof=cond.indexSet)
self._surfaceFluxTerm = sle.VectorSurfaceAssemblyTerm_NA__Fn__ni(
assembledObject=self._fvector,
surfaceGaussPoints=2,
nbc=negativeCond)
super(SteadyStateDarcyFlow, self).__init__(**kwargs)
def __init__(self,
phiField,
phiDotField,
velocityField,
fn_diffusivity,
fn_sourceTerm=None,
conditions=[],
**kwargs):
self._diffusivity = fn_diffusivity
self._source = fn_sourceTerm
if not isinstance(phiField, uw.mesh.MeshVariable):
raise TypeError(
"Provided 'phiField' must be of 'MeshVariable' class.")
if phiField.data.shape[1] != 1:
raise TypeError("Provided 'phiField' must be a scalar")
self._phiField = phiField
if not isinstance(phiDotField, (uw.mesh.MeshVariable, type(None))):
raise TypeError(
"Provided 'phiDotField' must be 'None' or of 'MeshVariable' class."
)
if self._phiField.data.shape != phiDotField.data.shape:
raise TypeError(
"Provided 'phiDotField' is not the same shape as the provided 'phiField'"
)
self._phiDotField = phiDotField
# check compatibility of phiField and velocityField
if velocityField.data.shape[1] != self._phiField.mesh.dim:
raise TypeError(
"Provided 'velocityField' must be the same dimensionality as the phiField's mesh"
)
self._velocityField = velocityField
if not isinstance(conditions, (list, tuple)):
conditionslist = []
conditionslist.append(conditions)
conditions = conditionslist
# check input 'conditions' list is valid
nbc = None
for cond in conditions:
if not isinstance(cond, uw.conditions.SystemCondition):
raise TypeError(
"Provided 'conditions' must be a list 'SystemCondition' objects."
)
# set the bcs on here
if type(cond) == uw.conditions.NeumannCondition:
if nbc != None:
# check only one nbc condition is given in 'conditions' list
RuntimeError(
"Provided 'conditions' can only accept one NeumannConditions condition object."
)
elif type(cond) == uw.conditions.DirichletCondition:
if cond.variable == self._phiField:
libUnderworld.StgFEM.FeVariable_SetBC(
self._phiField._cself, cond._cself)
libUnderworld.StgFEM.FeVariable_SetBC(
self._phiDotField._cself, cond._cself)
else:
raise RuntimeError("Input condition type not recognised.")
self._conditions = conditions
# force removal of BCs as SUPG cannot handle leaving them in
self._eqNumPhi = sle.EqNumber(phiField, removeBCs=True)
self._eqNumPhiDot = sle.EqNumber(phiDotField, removeBCs=True)
self._phiSolution = sle.SolutionVector(phiField, self._eqNumPhi)
self._phiDotSolution = sle.SolutionVector(phiDotField,
self._eqNumPhiDot)
# create force vectors
self._residualVector = sle.AssembledVector(phiField, self._eqNumPhi)
self._massVector = sle.AssembledVector(phiField, self._eqNumPhi)
# create swarm
self._gaussSwarm = uw.swarm.GaussIntegrationSwarm(self._phiField.mesh)
super(AdvectionDiffusion, self).__init__(**kwargs)
self._cself.phiVector = self._phiSolution._cself
self._cself.phiDotVector = self._phiDotSolution._cself
def __init__(self,
temperatureField,
fn_diffusivity,
fn_heating=0.,
voronoi_swarm=None,
conditions=[],
_removeBCs=True,
**kwargs):
if not isinstance(temperatureField, uw.mesh.MeshVariable):
raise TypeError(
"Provided 'temperatureField' must be of 'MeshVariable' class.")
self._temperatureField = temperatureField
try:
_fn_diffusivity = uw.function.Function.convert(fn_diffusivity)
except Exception as e:
raise uw._prepend_message_to_exception(
e,
"Exception encountered. Note that provided 'fn_diffusivity' must be of or convertible to 'Function' class.\nEncountered exception message:\n"
)
try:
_fn_heating = uw.function.Function.convert(fn_heating)
except Exception as e:
raise uw._prepend_message_to_exception(
e,
"Exception encountered. Note that provided 'fn_heating' must be of or convertible to 'Function' class.\nEncountered exception message:\n"
)
if voronoi_swarm and not isinstance(voronoi_swarm, uw.swarm.Swarm):
raise TypeError("Provided 'swarm' must be of 'Swarm' class.")
self._swarm = voronoi_swarm
if voronoi_swarm and temperatureField.mesh.elementType == 'Q2':
import warnings
warnings.warn(
"Voronoi integration may yield unsatisfactory results for Q2 element types."
)
if not isinstance(_removeBCs, bool):
raise TypeError("Provided '_removeBCs' must be of type bool.")
self._removeBCs = _removeBCs
# error check dcs 'dirichlet conditions' and ncs 'neumann cond.' FeMesh_IndexSets
nbc = None
mesh = temperatureField.mesh
if not isinstance(conditions, (list, tuple)):
conditionslist = []
conditionslist.append(conditions)
conditions = conditionslist
for cond in conditions:
if not isinstance(cond, uw.conditions.SystemCondition):
raise TypeError(
"Provided 'conditions' must be a list 'SystemCondition' objects."
)
# set the bcs on here
if type(cond) == uw.conditions.DirichletCondition:
if cond.variable == temperatureField:
libUnderworld.StgFEM.FeVariable_SetBC(
temperatureField._cself, cond._cself)
elif type(cond) == uw.conditions.NeumannCondition:
nbc = cond
else:
raise RuntimeError("Can't decide on input condition")
# build the equation numbering for the temperature field discretisation
tEqNums = self._tEqNums = sle.EqNumber(temperatureField,
removeBCs=self._removeBCs)
# create solutions vector
self._solutionVector = sle.SolutionVector(temperatureField, tEqNums)
libUnderworld.StgFEM.SolutionVector_LoadCurrentFeVariableValuesOntoVector(
self._solutionVector._cself)
# create force vectors
self._fvector = sle.AssembledVector(temperatureField, tEqNums)
# and matrices
self._kmatrix = sle.AssembledMatrix(self._solutionVector,
self._solutionVector,
rhs=self._fvector)
# we will use voronoi if that has been requested by the user, else use
# gauss integration.
if self._swarm:
intswarm = self._swarm._voronoi_swarm
# need to ensure voronoi is populated now, as assembly terms will call
# initial test functions which may require a valid voronoi swarm
self._swarm._voronoi_swarm.repopulate()
else:
intswarm = uw.swarm.GaussIntegrationSwarm(mesh)
self._kMatTerm = sle.MatrixAssemblyTerm_NA_i__NB_i__Fn(
integrationSwarm=intswarm,
assembledObject=self._kmatrix,
fn=_fn_diffusivity)
self._forceVecTerm = sle.VectorAssemblyTerm_NA__Fn(
integrationSwarm=intswarm,
assembledObject=self._fvector,
fn=fn_heating)
# search for neumann conditions
for cond in conditions:
if isinstance(cond, uw.conditions.NeumannCondition):
#NOTE many NeumannConditions can be used but the _sufaceFluxTerm only records the last
### -VE flux because of the FEM discretisation method of the initial equation
negativeCond = uw.conditions.NeumannCondition(
fn_flux=-1.0 * cond.fn_flux,
variable=cond.variable,
indexSetsPerDof=cond.indexSetsPerDof)
self._surfaceFluxTerm = sle.VectorSurfaceAssemblyTerm_NA__Fn__ni(
assembledObject=self._fvector,
surfaceGaussPoints=2,
nbc=negativeCond)
super(SteadyStateHeat, self).__init__(**kwargs)
def __init__(self,
temperatureField,
fn_diffusivity=None,
fn_heating=0.,
swarm=None,
conditions=[],
conductivityFn=None,
heatingFn=None,
rtolerance=None,
**kwargs):
if conductivityFn:
raise RuntimeError(
"Note that the 'conductivityFn' parameter has been renamed to 'fn_diffusivity'."
)
if heatingFn:
raise RuntimeError(
"Note that the 'heatingFn' parameter has been renamed to 'fn_heating'."
)
if rtolerance:
raise RuntimeError("Note that the 'rtolerance' parameter has been removed.\n" \
"All solver functionality has been moved to underworld.systems.Solver.")
if not isinstance(temperatureField, uw.mesh.MeshVariable):
raise TypeError(
"Provided 'temperatureField' must be of 'MeshVariable' class.")
self._temperatureField = temperatureField
if not fn_diffusivity:
raise ValueError(
"You must specify a diffusivity function via the 'fn_diffusivity' parameter."
)
try:
_fn_diffusivity = uw.function.Function._CheckIsFnOrConvertOrThrow(
fn_diffusivity)
except Exception as e:
raise uw._prepend_message_to_exception(
e,
"Exception encountered. Note that provided 'fn_diffusivity' must be of or convertible to 'Function' class.\nEncountered exception message:\n"
)
try:
_fn_heating = uw.function.Function._CheckIsFnOrConvertOrThrow(
fn_heating)
except Exception as e:
raise uw._prepend_message_to_exception(
e,
"Exception encountered. Note that provided 'fn_heating' must be of or convertible to 'Function' class.\nEncountered exception message:\n"
)
if swarm and not isinstance(swarm, uw.swarm.Swarm):
raise TypeError("Provided 'swarm' must be of 'Swarm' class.")
self._swarm = swarm
if not isinstance(conditions,
(uw.conditions._SystemCondition, list, tuple)):
raise TypeError(
"Provided 'conditions' must be a list '_SystemCondition' objects."
)
if len(conditions) > 1:
raise ValueError(
"Multiple conditions are not currently supported.")
for cond in conditions:
if not isinstance(cond, uw.conditions._SystemCondition):
raise TypeError(
"Provided 'conditions' must be a list '_SystemCondition' objects."
)
# set the bcs on here.. will rearrange this in future.
if cond.variable == self._temperatureField:
libUnderworld.StgFEM.FeVariable_SetBC(
self._temperatureField._cself, cond._cself)
# ok, we've set some bcs, lets recreate eqnumbering
libUnderworld.StgFEM._FeVariable_CreateNewEqnNumber(
self._temperatureField._cself)
self._conditions = conditions
# create solutions vector
self._temperatureSol = sle.SolutionVector(temperatureField)
# create force vectors
self._fvector = sle.AssembledVector(temperatureField)
# and matrices
self._kmatrix = sle.AssembledMatrix(temperatureField,
temperatureField,
rhs=self._fvector)
# create swarm
self._gaussSwarm = uw.swarm.GaussIntegrationSwarm(
self._temperatureField.mesh)
self._PICSwarm = None
if self._swarm:
self._PICSwarm = uw.swarm.PICIntegrationSwarm(self._swarm)
swarmguy = self._PICSwarm
if not swarmguy:
swarmguy = self._gaussSwarm
self._kMatTerm = sle.MatrixAssemblyTerm_NA_i__NB_i__Fn(
integrationSwarm=swarmguy,
assembledObject=self._kmatrix,
fn=_fn_diffusivity)
self._forceVecTerm = sle.VectorAssemblyTerm_NA__Fn(
integrationSwarm=swarmguy,
assembledObject=self._fvector,
fn=fn_heating)
super(SteadyStateHeat, self).__init__(**kwargs)
def __init__(self,
velocityField,
pressureField,
fn_viscosity,
fn_bodyforce=None,
fn_one_on_lambda=None,
fn_lambda=None,
fn_source=None,
voronoi_swarm=None,
conditions=[],
_removeBCs=True,
_fn_viscosity2=None,
_fn_director=None,
fn_stresshistory=None,
_fn_stresshistory=None,
**kwargs):
# DEPRECATION ERROR
if fn_lambda != None:
raise TypeError(
"The parameter 'fn_lambda' has been deprecated. It has been replaced by 'fn_one_on_lambda', a simpler input parameter."
)
if _fn_stresshistory:
raise TypeError(
"The parameter '_fn_stresshistory' has been updated to 'fn_stresshistory'."
)
if not isinstance(velocityField, uw.mesh.MeshVariable):
raise TypeError(
"Provided 'velocityField' must be of 'MeshVariable' class.")
if velocityField.nodeDofCount != velocityField.mesh.dim:
raise ValueError(
"Provided 'velocityField' must be a vector field of same dimensionality as its mesh."
)
self._velocityField = velocityField
if not isinstance(pressureField, uw.mesh.MeshVariable):
raise TypeError(
"Provided 'pressureField' must be of 'MeshVariable' class.")
if pressureField.nodeDofCount != 1:
raise ValueError(
"Provided 'pressureField' must be a scalar field (ie pressureField.nodeDofCount==1)."
)
self._pressureField = pressureField
_fn_viscosity = uw.function.Function.convert(fn_viscosity)
if not isinstance(_fn_viscosity, uw.function.Function):
raise TypeError(
"Provided 'fn_viscosity' must be of or convertible to 'Function' class."
)
if _fn_viscosity2:
_fn_viscosity2 = uw.function.Function.convert(_fn_viscosity2)
if not isinstance(_fn_viscosity2, uw.function.Function):
raise TypeError(
"Provided 'fn_viscosity2' must be of or convertible to 'Function' class."
)
if not isinstance(_removeBCs, bool):
raise TypeError("Provided '_removeBCs' must be of type bool.")
self._removeBCs = _removeBCs
if _fn_director:
_fn_director = uw.function.Function.convert(_fn_director)
if not isinstance(_fn_director, uw.function.Function):
raise TypeError(
"Provided 'fn_director' must be of or convertible to 'Function' class."
)
if fn_stresshistory:
fn_stresshistory = uw.function.Function.convert(fn_stresshistory)
if not isinstance(fn_stresshistory, uw.function.Function):
raise TypeError(
"Provided 'fn_stresshistory' must be of or convertible to 'Function' class."
)
self._fn_minus_one_on_lambda = None
if fn_one_on_lambda != None:
self._fn_minus_one_on_lambda = uw.function.Function.convert(
-1.0 * fn_one_on_lambda)
if not isinstance(self._fn_minus_one_on_lambda,
uw.function.Function):
raise ValueError(
"Provided 'fn_minus_one_on_lambda' must be of, or convertible to, the 'Function' class."
)
if fn_source != None:
self._fn_source = uw.function.Function.convert(fn_source)
if not isinstance(self._fn_source, uw.function.Function):
raise ValueError(
"Provided 'fn_source' must be of, or convertible to, the 'Function' class."
)
if not fn_bodyforce:
if velocityField.mesh.dim == 2:
fn_bodyforce = (0., 0.)
else:
fn_bodyforce = (0., 0., 0.)
_fn_bodyforce = uw.function.Function.convert(fn_bodyforce)
if voronoi_swarm and not isinstance(voronoi_swarm, uw.swarm.Swarm):
raise TypeError(
"Provided 'voronoi_swarm' must be of 'Swarm' class.")
self._swarm = voronoi_swarm
if voronoi_swarm and velocityField.mesh.elementType == 'Q2':
import warnings
warnings.warn(
"Voronoi integration may yield unsatisfactory results for Q2 mesh."
)
mesh = velocityField.mesh
if not isinstance(conditions, (list, tuple)):
conditionslist = []
conditionslist.append(conditions)
conditions = conditionslist
for cond in conditions:
# set the bcs on here
if not isinstance(cond, uw.conditions.SystemCondition):
raise TypeError(
"Provided 'conditions' must be 'SystemCondition' objects.")
elif type(cond) == uw.conditions.DirichletCondition:
if cond.variable == self._velocityField:
libUnderworld.StgFEM.FeVariable_SetBC(
self._velocityField._cself, cond._cself)
elif cond.variable == self._pressureField:
libUnderworld.StgFEM.FeVariable_SetBC(
self._pressureField._cself, cond._cself)
else:
raise ValueError(
"Provided condition does not appear to correspond to the system unknowns."
)
self._conditions = conditions
self._eqNums = dict()
self._eqNums[velocityField] = sle.EqNumber(self._velocityField,
self._removeBCs)
self._eqNums[pressureField] = sle.EqNumber(self._pressureField,
self._removeBCs)
# create solutions vectors and load fevariable values onto them for best first guess
self._velocitySol = sle.SolutionVector(velocityField,
self._eqNums[velocityField])
self._pressureSol = sle.SolutionVector(pressureField,
self._eqNums[pressureField])
libUnderworld.StgFEM.SolutionVector_LoadCurrentFeVariableValuesOntoVector(
self._velocitySol._cself)
libUnderworld.StgFEM.SolutionVector_LoadCurrentFeVariableValuesOntoVector(
self._pressureSol._cself)
# create force vectors
self._fvector = sle.AssembledVector(velocityField,
self._eqNums[velocityField])
self._hvector = sle.AssembledVector(pressureField,
self._eqNums[pressureField])
# and matrices
self._kmatrix = sle.AssembledMatrix(self._velocitySol,
self._velocitySol,
rhs=self._fvector)
self._gmatrix = sle.AssembledMatrix(self._velocitySol,
self._pressureSol,
rhs=self._fvector,
rhs_T=self._hvector)
self._preconditioner = sle.AssembledMatrix(self._pressureSol,
self._pressureSol,
rhs=self._hvector)
# create assembly terms which always use gauss integration
gaussSwarm = uw.swarm.GaussIntegrationSwarm(self._velocityField.mesh)
self._gradStiffMatTerm = sle.GradientStiffnessMatrixTerm(
integrationSwarm=gaussSwarm, assembledObject=self._gmatrix)
self._preCondMatTerm = sle.PreconditionerMatrixTerm(
integrationSwarm=gaussSwarm, assembledObject=self._preconditioner)
# for the following terms, we will use voronoi if that has been requested
# by the user, else use gauss again.
intswarm = gaussSwarm
if self._swarm:
intswarm = self._swarm._voronoi_swarm
# need to ensure voronoi is populated now, as assembly terms will call
# initial test functions which may require a valid voronoi swarm
self._swarm._voronoi_swarm.repopulate()
self._constitMatTerm = sle.ConstitutiveMatrixTerm(
integrationSwarm=intswarm,
assembledObject=self._kmatrix,
fn_visc1=_fn_viscosity,
fn_visc2=_fn_viscosity2,
fn_director=_fn_director)
self._forceVecTerm = sle.VectorAssemblyTerm_NA__Fn(
integrationSwarm=intswarm,
assembledObject=self._fvector,
fn=_fn_bodyforce)
if fn_source:
self._cforceVecTerm = sle.VectorAssemblyTerm_NA__Fn(
integrationSwarm=intswarm,
assembledObject=self._hvector,
fn=self.fn_source)
for cond in self._conditions:
if isinstance(cond, uw.conditions.NeumannCondition):
#NOTE many NeumannConditions can be used but the _sufaceFluxTerm only records the last
self._surfaceFluxTerm = sle.VectorSurfaceAssemblyTerm_NA__Fn__ni(
assembledObject=self._fvector,
surfaceGaussPoints=
3, # increase to resolve stress bc fluctuations
nbc=cond)
if self._fn_minus_one_on_lambda != None:
# add matrix and associated assembly term for compressible stokes formulation
# a mass matrix goes into the lower right block of the stokes system coeff matrix
self._mmatrix = sle.AssembledMatrix(self._pressureSol,
self._pressureSol,
rhs=self._hvector)
# -1. as per Hughes, The Finite Element Method, 1987, Table 4.3.1, [M]
self._compressibleTerm = sle.MatrixAssemblyTerm_NA__NB__Fn(
integrationSwarm=intswarm,
assembledObject=self._mmatrix,
mesh=self._velocityField.mesh,
fn=self._fn_minus_one_on_lambda)
if fn_stresshistory != None:
self._NA_j__Fn_ijTerm = sle.VectorAssemblyTerm_NA_j__Fn_ij(
integrationSwarm=intswarm,
assembledObject=self._fvector,
fn=fn_stresshistory)
super(Stokes, self).__init__(**kwargs)
def __init__(self,
velocityField,
pressureField,
fn_viscosity=None,
fn_bodyforce=None,
swarm=None,
conditions=[],
viscosityFn=None,
bodyForceFn=None,
rtolerance=None,
**kwargs):
# DEPRECATE 1/16
if viscosityFn:
raise RuntimeError(
"Note that the 'viscosityFn' parameter has been renamed to 'fn_viscosity'."
)
if bodyForceFn:
raise RuntimeError(
"Note that the 'bodyForceFn' parameter has been renamed to 'fn_bodyforce'."
)
if rtolerance:
raise RuntimeError("Note that the 'rtolerance' parameter has been removed.\n" \
"All solver functionality has been moved to underworld.systems.Solver.")
if not isinstance(velocityField, uw.mesh.MeshVariable):
raise TypeError(
"Provided 'velocityField' must be of 'MeshVariable' class.")
if velocityField.nodeDofCount != velocityField.mesh.dim:
raise ValueError(
"Provided 'velocityField' must be a vector field of same dimensionality as its mesh."
)
self._velocityField = velocityField
if not isinstance(pressureField, uw.mesh.MeshVariable):
raise TypeError(
"Provided 'pressureField' must be of 'MeshVariable' class.")
if pressureField.nodeDofCount != 1:
raise ValueError(
"Provided 'pressureField' must be a scalar field (ie pressureField.nodeDofCount==1)."
)
self._pressureField = pressureField
if not fn_viscosity:
raise ValueError(
"You must specify a viscosity function via the 'fn_viscosity' parameter."
)
_fn_viscosity = uw.function.Function._CheckIsFnOrConvertOrThrow(
fn_viscosity)
if not isinstance(_fn_viscosity, uw.function.Function):
raise TypeError(
"Provided 'fn_viscosity' must be of or convertible to 'Function' class."
)
if not fn_bodyforce:
if velocityField.mesh.dim == 2:
fn_bodyforce = (0., 0.)
else:
fn_bodyforce = (0., 0., 0.)
_fn_bodyforce = uw.function.Function._CheckIsFnOrConvertOrThrow(
fn_bodyforce)
if swarm and not isinstance(swarm, uw.swarm.Swarm):
raise TypeError("Provided 'swarm' must be of 'Swarm' class.")
self._swarm = swarm
if not isinstance(conditions,
(uw.conditions._SystemCondition, list, tuple)):
raise TypeError(
"Provided 'conditions' must be a list '_SystemCondition' objects."
)
if len(conditions) > 1:
raise ValueError(
"Multiple conditions are not currently supported.")
for cond in conditions:
if not isinstance(cond, uw.conditions._SystemCondition):
raise TypeError(
"Provided 'conditions' must be a list '_SystemCondition' objects."
)
# set the bcs on here.. will rearrange this in future.
if cond.variable == self._velocityField:
libUnderworld.StgFEM.FeVariable_SetBC(
self._velocityField._cself, cond._cself)
elif cond.variable == self._pressureField:
libUnderworld.StgFEM.FeVariable_SetBC(
self._pressureField._cself, cond._cself)
else:
raise ValueError(
"Condition object does not appear to apply to the provided velocityField or pressureField."
)
# ok, we've set some bcs, lets recreate eqnumbering
libUnderworld.StgFEM._FeVariable_CreateNewEqnNumber(
self._pressureField._cself)
libUnderworld.StgFEM._FeVariable_CreateNewEqnNumber(
self._velocityField._cself)
self._conditions = conditions
# create solutions vectors
self._velocitySol = sle.SolutionVector(velocityField)
self._pressureSol = sle.SolutionVector(pressureField)
# create force vectors
self._fvector = sle.AssembledVector(velocityField)
self._hvector = sle.AssembledVector(pressureField)
# and matrices
self._kmatrix = sle.AssembledMatrix(velocityField,
velocityField,
rhs=self._fvector)
self._gmatrix = sle.AssembledMatrix(velocityField,
pressureField,
rhs=self._fvector,
rhs_T=self._hvector)
self._preconditioner = sle.AssembledMatrix(pressureField,
pressureField,
rhs=self._hvector,
allowZeroContrib=True)
# create swarm
self._gaussSwarm = uw.swarm.GaussIntegrationSwarm(
self._velocityField.mesh)
self._PICSwarm = None
if self._swarm:
self._PICSwarm = uw.swarm.PICIntegrationSwarm(self._swarm)
self._PICSwarm.repopulate()
# create assembly terms
self._gradStiffMatTerm = sle.GradientStiffnessMatrixTerm(
integrationSwarm=self._gaussSwarm, assembledObject=self._gmatrix)
self._preCondMatTerm = sle.PreconditionerMatrixTerm(
integrationSwarm=self._gaussSwarm,
assembledObject=self._preconditioner)
swarmguy = self._PICSwarm
if not swarmguy:
swarmguy = self._gaussSwarm
self._constitMatTerm = sle.ConstitutiveMatrixTerm(
integrationSwarm=swarmguy,
assembledObject=self._kmatrix,
fn=_fn_viscosity)
self._forceVecTerm = sle.VectorAssemblyTerm_NA__Fn(
integrationSwarm=swarmguy,
assembledObject=self._fvector,
fn=_fn_bodyforce)
super(Stokes, self).__init__(**kwargs)
def __init__(self,
velocityField,
pressureField,
fn_viscosity,
fn_bodyforce=None,
fn_lambda=None,
voronoi_swarm=None,
conditions=[],
_removeBCs=True,
_fn_viscosity2=None,
_fn_director=None,
_fn_stresshistory=None,
**kwargs):
if not isinstance(velocityField, uw.mesh.MeshVariable):
raise TypeError(
"Provided 'velocityField' must be of 'MeshVariable' class.")
if velocityField.nodeDofCount != velocityField.mesh.dim:
raise ValueError(
"Provided 'velocityField' must be a vector field of same dimensionality as its mesh."
)
self._velocityField = velocityField
if not isinstance(pressureField, uw.mesh.MeshVariable):
raise TypeError(
"Provided 'pressureField' must be of 'MeshVariable' class.")
if pressureField.nodeDofCount != 1:
raise ValueError(
"Provided 'pressureField' must be a scalar field (ie pressureField.nodeDofCount==1)."
)
self._pressureField = pressureField
_fn_viscosity = uw.function.Function.convert(fn_viscosity)
if not isinstance(_fn_viscosity, uw.function.Function):
raise TypeError(
"Provided 'fn_viscosity' must be of or convertible to 'Function' class."
)
if _fn_viscosity2:
_fn_viscosity2 = uw.function.Function.convert(_fn_viscosity2)
if not isinstance(_fn_viscosity2, uw.function.Function):
raise TypeError(
"Provided 'fn_viscosity2' must be of or convertible to 'Function' class."
)
if not isinstance(_removeBCs, bool):
raise TypeError("Provided '_removeBCs' must be of type bool.")
self._removeBCs = _removeBCs
if _fn_director:
_fn_director = uw.function.Function.convert(_fn_director)
if not isinstance(_fn_director, uw.function.Function):
raise TypeError(
"Provided 'fn_director' must be of or convertible to 'Function' class."
)
if _fn_stresshistory:
_fn_stresshistory = uw.function.Function.convert(_fn_stresshistory)
if not isinstance(_fn_stresshistory, uw.function.Function):
raise TypeError(
"Provided '_fn_stresshistory' must be of or convertible to 'Function' class."
)
if fn_lambda != None:
fn_lambda = uw.function.Function.convert(fn_lambda)
if not isinstance(fn_lambda, uw.function.Function):
raise ValueError(
"Provided 'fn_lambda' must be of, or convertible to, the 'Function' class."
)
if not fn_bodyforce:
if velocityField.mesh.dim == 2:
fn_bodyforce = (0., 0.)
else:
fn_bodyforce = (0., 0., 0.)
_fn_bodyforce = uw.function.Function.convert(fn_bodyforce)
if voronoi_swarm and not isinstance(voronoi_swarm, uw.swarm.Swarm):
raise TypeError(
"Provided 'voronoi_swarm' must be of 'Swarm' class.")
self._swarm = voronoi_swarm
if voronoi_swarm and velocityField.mesh.elementType == 'Q2':
import warnings
warnings.warn(
"Voronoi integration may yield unsatisfactory results for Q2 mesh."
)
mesh = velocityField.mesh
if not isinstance(conditions, (list, tuple)):
conditionslist = []
conditionslist.append(conditions)
conditions = conditionslist
for cond in conditions:
# set the bcs on here
if not isinstance(cond, uw.conditions.SystemCondition):
raise TypeError(
"Provided 'conditions' must be 'SystemCondition' objects.")
elif type(cond) == uw.conditions.DirichletCondition:
if cond.variable == self._velocityField:
libUnderworld.StgFEM.FeVariable_SetBC(
self._velocityField._cself, cond._cself)
if cond.variable == self._pressureField:
libUnderworld.StgFEM.FeVariable_SetBC(
self._pressureField._cself, cond._cself)
self._conditions = conditions
self._eqNums = dict()
self._eqNums[velocityField] = sle.EqNumber(self._velocityField,
self._removeBCs)
self._eqNums[pressureField] = sle.EqNumber(self._pressureField,
self._removeBCs)
# create solutions vectors and load fevariable values onto them for best first guess
self._velocitySol = sle.SolutionVector(velocityField,
self._eqNums[velocityField])
self._pressureSol = sle.SolutionVector(pressureField,
self._eqNums[pressureField])
libUnderworld.StgFEM.SolutionVector_LoadCurrentFeVariableValuesOntoVector(
self._velocitySol._cself)
libUnderworld.StgFEM.SolutionVector_LoadCurrentFeVariableValuesOntoVector(
self._pressureSol._cself)
# create force vectors
self._fvector = sle.AssembledVector(velocityField,
self._eqNums[velocityField])
self._hvector = sle.AssembledVector(pressureField,
self._eqNums[pressureField])
# and matrices
self._kmatrix = sle.AssembledMatrix(self._velocitySol,
self._velocitySol,
rhs=self._fvector)
self._gmatrix = sle.AssembledMatrix(self._velocitySol,
self._pressureSol,
rhs=self._fvector,
rhs_T=self._hvector)
self._preconditioner = sle.AssembledMatrix(self._pressureSol,
self._pressureSol,
rhs=self._hvector)
if fn_lambda != None:
self._mmatrix = sle.AssembledMatrix(self._pressureSol,
self._pressureSol,
rhs=self._hvector)
# create assembly terms which always use gauss integration
gaussSwarm = uw.swarm.GaussIntegrationSwarm(self._velocityField.mesh)
self._gradStiffMatTerm = sle.GradientStiffnessMatrixTerm(
integrationSwarm=gaussSwarm, assembledObject=self._gmatrix)
self._preCondMatTerm = sle.PreconditionerMatrixTerm(
integrationSwarm=gaussSwarm, assembledObject=self._preconditioner)
# for the following terms, we will use voronoi if that has been requested
# by the user, else use gauss again.
intswarm = gaussSwarm
if self._swarm:
intswarm = self._swarm._voronoi_swarm
# need to ensure voronoi is populated now, as assembly terms will call
# initial test functions which may require a valid voronoi swarm
self._swarm._voronoi_swarm.repopulate()
self._constitMatTerm = sle.ConstitutiveMatrixTerm(
integrationSwarm=intswarm,
assembledObject=self._kmatrix,
fn_visc1=_fn_viscosity,
fn_visc2=_fn_viscosity2,
fn_director=_fn_director)
self._forceVecTerm = sle.VectorAssemblyTerm_NA__Fn(
integrationSwarm=intswarm,
assembledObject=self._fvector,
fn=_fn_bodyforce)
for cond in self._conditions:
if isinstance(cond, uw.conditions.NeumannCondition):
#NOTE many NeumannConditions can be used but the _sufaceFluxTerm only records the last
self._surfaceFluxTerm = sle.VectorSurfaceAssemblyTerm_NA__Fn__ni(
assembledObject=self._fvector,
surfaceGaussPoints=
3, # increase to resolve stress bc fluctuations
nbc=cond)
if fn_lambda != None:
# some logic for constructing the lower-right [2,2] matrix in the stokes system
# [M] = [Na * 1.0/fn_lambda * Nb], where in our formulation Na and Nb are the pressure shape functions.
# see 4.3.21 of Hughes, Linear static and dynamic finite element analysis
# If fn_lambda is negligable, ie <1.0e-8, then we set the entry to 0.0, ie, incompressible
# otherwise we provide 1.0/lambda to [M]
logicFn = uw.function.branching.conditional([(fn_lambda > 1.0e-8,
1.0 / fn_lambda),
(True, 0.)])
self._compressibleTerm = sle.MatrixAssemblyTerm_NA__NB__Fn(
integrationSwarm=intswarm,
assembledObject=self._mmatrix,
mesh=self._velocityField.mesh,
fn=logicFn)
if _fn_stresshistory != None:
self._vepTerm = sle.VectorAssemblyTerm_VEP__Fn(
integrationSwarm=intswarm,
assembledObject=self._fvector,
fn=_fn_stresshistory)
super(Stokes, self).__init__(**kwargs)
def __init__(self,
phiField,
phiDotField,
velocityField,
fn_diffusivity,
courantFactor=None,
diffusivity=None,
conditions=[],
**kwargs):
if courantFactor:
raise RuntimeError("Note that the 'courantFactor' parameter has been deprecated.\n"\
"If you wish to modify your timestep, do so manually with the value\n"\
"returned from the get_max_dt() method.")
if diffusivity:
raise RuntimeError("Note that the 'diffusivity' parameter has been deprecated.\n"\
"Use the parameter 'fn_diffusivity' instead.")
self._diffusivity = fn_diffusivity
self._diffusivity = fn_diffusivity
self._courantFactor = courantFactor
if not isinstance(phiField, uw.mesh.MeshVariable):
raise TypeError(
"Provided 'phiField' must be of 'MeshVariable' class.")
if phiField.data.shape[1] != 1:
raise TypeError("Provided 'phiField' must be a scalar")
self._phiField = phiField
if not isinstance(phiDotField, (uw.mesh.MeshVariable, type(None))):
raise TypeError(
"Provided 'phiDotField' must be 'None' or of 'MeshVariable' class."
)
if self._phiField.data.shape != phiDotField.data.shape:
raise TypeError(
"Provided 'phiDotField' is not the same shape as the provided 'phiField'"
)
self._phiDotField = phiDotField
# check compatibility of phiField and velocityField
if velocityField.data.shape[1] != self._phiField.mesh.dim:
raise TypeError(
"Provided 'velocityField' must be the same dimensionality as the phiField's mesh"
)
self._velocityField = velocityField
if not isinstance(conditions,
(uw.conditions._SystemCondition, list, tuple)):
raise ValueError(
"Provided 'conditions' must be a list '_SystemCondition' objects."
)
if len(conditions) > 1:
raise ValueError(
"Multiple conditions are not currently supported.")
for cond in conditions:
if not isinstance(cond, uw.conditions._SystemCondition):
raise ValueError(
"Provided 'conditions' must be a list '_SystemCondition' objects."
)
# set the bcs on here.. will rearrange this in future.
if cond.variable == self._phiField:
libUnderworld.StgFEM.FeVariable_SetBC(self._phiField._cself,
cond._cself)
libUnderworld.StgFEM.FeVariable_SetBC(self._phiDotField._cself,
cond._cself)
# ok, we've set some bcs, lets recreate eqnumbering
libUnderworld.StgFEM._FeVariable_CreateNewEqnNumber(
self._phiField._cself)
libUnderworld.StgFEM._FeVariable_CreateNewEqnNumber(
self._phiDotField._cself)
self._conditions = conditions
# create force vectors
self._residualVector = sle.AssembledVector(phiField)
self._massVector = sle.AssembledVector(phiField)
# create swarm
self._gaussSwarm = uw.swarm.GaussIntegrationSwarm(self._phiField.mesh)
super(AdvectionDiffusion, self).__init__(**kwargs)