class CHProblem(NonlinearProblem):
"""Class for interfacing with :py:class:`dolfin.NewtonSolver`."""
def __init__(self, F, bcs, J):
super(SemiDecoupled.CHProblem, self).__init__()
# Assembler for Newton system
self.assembler = SystemAssembler(J, F, bcs)
# Store forms for later
self.forms = {
"F": F,
"J": J,
}
def function_space(self):
return self.forms["F"].arguments()[0].function_space()
def form(self, A, P, b, x):
if A.empty():
matA = as_backend_type(A).mat()
assert not matA.isAssembled()
bs = self.function_space().dofmap().block_size()
matA.setBlockSize(bs)
# matP = as_backend_type(P).mat()
# assert not matP.isAssembled()
# matP.setBlockSize(bs)
def F(self, b, x):
self.assembler.assemble(b, x)
def J(self, A, x):
# matA = as_backend_type(A).mat()
# bs = self.function_space().dofmap().block_size()
# assert matA.getBlockSize() == bs
self.assembler.assemble(A)
def __init__(self, F, bcs, J, J_pc=None):
"""Return subclass of :py:class:`dolfin.NonlinearProblem`
suitable for :py:class:`NewtonSolver` in combination with
:py:class:`muflon.solving.solvers.SemiDecoupled`.
"""
super(CHNonlinearProblem, self).__init__()
# Assembler for Newton system
self.assembler = SystemAssembler(J, F, bcs)
# Assembler for preconditioner
if J_pc is not None:
self.assembler_pc = SystemAssembler(J_pc, F, bcs)
else:
self.assembler_pc = None
# Store bcs
self._bcs = bcs
# Store forms for later
self.forms = {
"F": F,
"J": J,
"J_pc": J_pc,
}
def __init__(self, a, L, bcs, a_pc=None):
self.assembler = SystemAssembler(a, L, bcs)
if a_pc is not None:
self.assembler_pc = SystemAssembler(a_pc, L, bcs)
else:
self.assembler_pc = None
self._bcs = bcs
def __init__(self, F, bcs, J):
super(SemiDecoupled.CHProblem, self).__init__()
# Assembler for Newton system
self.assembler = SystemAssembler(J, F, bcs)
# Store forms for later
self.forms = {
"F": F,
"J": J,
}
def __init__(self, problem, parameters={}, lb=None):
super(DamageSolverSNES, self).__init__()
self.problem = problem
self.energy = problem.energy
self.state = problem.state
self.alpha = problem.state['alpha']
self.alpha_dvec = as_backend_type(self.alpha.vector())
self.alpha_pvec = self.alpha_dvec.vec()
self.bcs = problem.bcs
self.parameters = parameters
comm = self.alpha.function_space().mesh().mpi_comm()
self.comm = comm
V = self.alpha.function_space()
self.V = V
self.Ealpha = derivative(
self.energy, self.alpha,
dolfin.TestFunction(self.alpha.ufl_function_space()))
self.dm = self.alpha.function_space().dofmap()
solver = PETScSNESSolver()
snes = solver.snes()
if lb == None:
lb = interpolate(Constant(0.), V)
ub = interpolate(Constant(1.), V)
prefix = "damage_"
snes.setOptionsPrefix(prefix)
for option, value in self.parameters["snes"].items():
PETScOptions.set(prefix + option, value)
log(LogLevel.DEBUG,
"DEBUG: Set: {} = {}".format(prefix + option, value))
snes.setFromOptions()
(J, F, bcs_alpha) = (problem.J, problem.F, problem.bcs)
self.ass = SystemAssembler(J, F, bcs_alpha)
self.b = self.init_residual()
snes.setFunction(self.residual, self.b.vec())
self.A = self.init_jacobian()
snes.setJacobian(self.jacobian, self.A.mat())
snes.ksp.setOperators(self.A.mat())
snes.setVariableBounds(self.problem.lb.vec(), self.problem.ub.vec()) #
# snes.solve(None, Function(V).vector().vec())
self.solver = snes
class Problem(NonlinearProblem):
"""
Class for interfacing with :py:class:`NewtonSolver`.
"""
def __init__(self, F, bcs, J, null_space=None):
super(Monolithic.Problem, self).__init__()
self.assembler = SystemAssembler(J, F, bcs)
self.null_space = null_space
def F(self, b, x):
self.assembler.assemble(b, x)
if self.null_space:
# Orthogonalize RHS vector b with respect to the null space
self.null_space.orthogonalize(b)
def J(self, A, x):
self.assembler.assemble(A)
if self.null_space:
# Attach null space to PETSc matrix
as_backend_type(A).set_nullspace(self.null_space)
class CHNonlinearProblem(NonlinearProblem):
"""Class for interfacing with :py:class:`CHNewtonSolver`."""
def __init__(self, F, bcs, J, J_pc=None):
"""Return subclass of :py:class:`dolfin.NonlinearProblem`
suitable for :py:class:`NewtonSolver` in combination with
:py:class:`muflon.solving.solvers.SemiDecoupled`.
"""
super(CHNonlinearProblem, self).__init__()
# Assembler for Newton system
self.assembler = SystemAssembler(J, F, bcs)
# Assembler for preconditioner
if J_pc is not None:
self.assembler_pc = SystemAssembler(J_pc, F, bcs)
else:
self.assembler_pc = None
# Store bcs
self._bcs = bcs
# Store forms for later
self.forms = {
"F": F,
"J": J,
"J_pc": J_pc,
}
def get_form(self, key):
form = self.forms.get(key)
if form is None:
raise AttributeError("Form '%s' not available" % key)
return form
def function_space(self):
return self.forms["F"].arguments()[0].function_space()
def form(self, A, P, b, x):
if A.empty():
matA = as_backend_type(A).mat()
assert not matA.isAssembled()
bs = self.function_space().dofmap().block_size()
matA.setBlockSize(bs)
if self.assembler_pc is not None and P.empty():
matP = as_backend_type(P).mat()
assert not matP.isAssembled()
matP.setBlockSize(bs)
def F(self, b, x):
self.assembler.assemble(b, x)
def J(self, A, x):
self.assembler.assemble(A)
def J_pc(self, P, x):
if self.assembler_pc is not None:
self.assembler_pc.assemble(P)
class rmtursAssembler(object):
def __init__(self, a, L, bcs, a_pc=None):
self.assembler = SystemAssembler(a, L, bcs)
if a_pc is not None:
self.assembler_pc = SystemAssembler(a_pc, L, bcs)
else:
self.assembler_pc = None
self._bcs = bcs
def rhs_vector(self, b, x=None):
if x is not None:
self.assembler.assemble(b, x)
else:
self.assembler.assemble(b)
def system_matrix(self, A):
self.assembler.assemble(A)
def pc_matrix(self, P):
if self.assembler_pc is not None:
self.assembler_pc.assemble(P)
def __init__(self, F, bcs, J, null_space=None):
super(Monolithic.Problem, self).__init__()
self.assembler = SystemAssembler(J, F, bcs)
self.null_space = null_space
class DamageSolverSNES:
"""docstring for DamageSolverSNES"""
def __init__(self, problem, parameters={}, lb=None):
super(DamageSolverSNES, self).__init__()
self.problem = problem
self.energy = problem.energy
self.state = problem.state
self.alpha = problem.state['alpha']
self.alpha_dvec = as_backend_type(self.alpha.vector())
self.alpha_pvec = self.alpha_dvec.vec()
self.bcs = problem.bcs
self.parameters = parameters
comm = self.alpha.function_space().mesh().mpi_comm()
self.comm = comm
V = self.alpha.function_space()
self.V = V
self.Ealpha = derivative(
self.energy, self.alpha,
dolfin.TestFunction(self.alpha.ufl_function_space()))
self.dm = self.alpha.function_space().dofmap()
solver = PETScSNESSolver()
snes = solver.snes()
if lb == None:
lb = interpolate(Constant(0.), V)
ub = interpolate(Constant(1.), V)
prefix = "damage_"
snes.setOptionsPrefix(prefix)
for option, value in self.parameters["snes"].items():
PETScOptions.set(prefix + option, value)
log(LogLevel.DEBUG,
"DEBUG: Set: {} = {}".format(prefix + option, value))
snes.setFromOptions()
(J, F, bcs_alpha) = (problem.J, problem.F, problem.bcs)
self.ass = SystemAssembler(J, F, bcs_alpha)
self.b = self.init_residual()
snes.setFunction(self.residual, self.b.vec())
self.A = self.init_jacobian()
snes.setJacobian(self.jacobian, self.A.mat())
snes.ksp.setOperators(self.A.mat())
snes.setVariableBounds(self.problem.lb.vec(), self.problem.ub.vec()) #
# snes.solve(None, Function(V).vector().vec())
self.solver = snes
def update_x(self, x):
"""
Given a PETSc Vec x, update the storage of our solution function alpha.
"""
x.copy(self.alpha_pvec)
self.alpha_dvec.update_ghost_values()
def init_residual(self):
alpha = self.problem.state["alpha"]
b = as_backend_type(Function(alpha.function_space()).vector())
return b
def init_jacobian(self):
A = PETScMatrix(self.comm)
self.ass.init_global_tensor(A, Form(self.problem.J))
return A
def residual(self, snes, x, b):
self.update_x(x)
b_wrap = PETScVector(b)
self.ass.assemble(b_wrap, self.alpha_dvec)
def jacobian(self, snes, x, A, P):
self.update_x(x)
A_wrap = PETScMatrix(A)
self.ass.assemble(A_wrap)
def solve(self):
alpha = self.problem.state["alpha"]
# Need a copy for line searches etc. to work correctly.
x = alpha.copy(deepcopy=True)
xv = as_backend_type(x.vector()).vec()
# Solve the problem
self.solver.solve(None, xv)
def inactive_set_indicator(self, tol=1.0e-5):
Ealpha = assemble(self.Ealpha)
mask_grad = Ealpha[:] < tol
mask_ub = self.alpha.vector()[:] < 1. - tol
mask_lb = self.alpha.vector()[:] > self.problem.lb[:] + tol
local_inactive_set_alpha = set(np.where(mask_ub == True)[0]) \
& set(np.where(mask_grad == True)[0]) \
& set(np.where(mask_lb == True)[0])
_set_alpha = [
self.dm.local_to_global_index(k) for k in local_inactive_set_alpha
]
inactive_set_alpha = set(_set_alpha) | set(self.dm.dofs())
index_set = petsc4py.PETSc.IS()
index_set.createGeneral(list(inactive_set_alpha))
return index_set
def __init__(self, a, L, bcs, a_pc=None,
mp=None, mu=None, ap=None, fp=None, kp=None, gp=None,
bcs_pcd=[]):
"""Collect individual variational forms and boundary conditions
defining a linear problem (system matrix + RHS vector) on the one side
and preconditioning operators on the other side.
*Arguments*
a (:py:class:`dolfin.Form` or :py:class:`ufl.Form`)
Bilinear form representing a system matrix.
L (:py:class:`dolfin.Form` or :py:class:`ufl.Form`)
Linear form representing a right hand side vector.
bcs (:py:class:`list` of :py:class:`dolfin.DirichletBC`)
Boundary conditions applied to ``a``, ``L``, and ``a_pc``.
a_pc (:py:class:`dolfin.Form` or :py:class:`ufl.Form`)
Bilinear form representing a matrix optionally passed to
preconditioner instead of ``a``. In case of PCD, stabilized
00-block can be passed to 00-KSP solver.
mp, mu, ap, fp, kp, gp (:py:class:`dolfin.Form` or :py:class:`ufl.Form`)
Bilinear forms which (some of them) might be used by a
particular PCD(R) preconditioner. Typically they represent "mass
matrix" on pressure, "mass matrix" on velocity, minus Laplacian
operator on pressure, pressure convection-diffusion operator,
pressure convection operator and pressure gradient respectively.
bcs_pcd (:py:class:`list` of :py:class:`dolfin.DirichletBC`)
Artificial boundary conditions used by PCD preconditioner.
All the arguments should be given on the common mixed function space.
All the forms are wrapped using :py:class:`PCDForm` so that each of
them can be endowed with additional set of properties.
By default, ``mp``, ``mu``, ``ap`` and ``gp`` are assumed to be
constant if the preconditioner is used repeatedly in some outer
iterative process (e.g Newton-Raphson method, time-stepping).
As such, the corresponding operators are assembled only once.
On the other hand, ``fp`` and ``kp`` are updated in every
outer iteration.
Also note that ``gp`` is the only form that is by default in a *phantom
mode*. It means that the corresponding operator (if needed) is not
obtained by assembling the form, but it is extracted as the 01-block of
the system matrix.
The default setting can be modified by accessing
a :py:class:`PCDForm` instance via :py:meth:`PCDAssembler.get_pcd_form`
and changing the properties directly.
"""
# Assembler for the linear system of algebraic equations
self.assembler = SystemAssembler(a, L, bcs)
# Assembler for preconditioner
if a_pc is not None:
self.assembler_pc = SystemAssembler(a_pc, L, bcs)
else:
self.assembler_pc = None
# Store bcs
self._bcs = bcs
self._bcs_pcd = bcs_pcd
# Store and initialize forms
self._forms = {
"L": PCDForm(L),
"ap": PCDForm(ap, const=True),
"mp": PCDForm(mp, const=True),
"mu": PCDForm(mu, const=True),
"fp": PCDForm(fp),
"kp": PCDForm(kp),
"gp": PCDForm(gp, const=True, phantom=True),
}
class PCDAssembler(object):
"""Base class for creating linear problems to be solved by application
of the PCD preconditioning strategy. Users are encouraged to use this class
for interfacing with :py:class:`fenapack.field_split.PCDKrylovSolver`.
On request it assembles not only the individual PCD operators but also the
system matrix and the right hand side vector defining the linear problem.
"""
def __init__(self, a, L, bcs, a_pc=None,
mp=None, mu=None, ap=None, fp=None, kp=None, gp=None,
bcs_pcd=[]):
"""Collect individual variational forms and boundary conditions
defining a linear problem (system matrix + RHS vector) on the one side
and preconditioning operators on the other side.
*Arguments*
a (:py:class:`dolfin.Form` or :py:class:`ufl.Form`)
Bilinear form representing a system matrix.
L (:py:class:`dolfin.Form` or :py:class:`ufl.Form`)
Linear form representing a right hand side vector.
bcs (:py:class:`list` of :py:class:`dolfin.DirichletBC`)
Boundary conditions applied to ``a``, ``L``, and ``a_pc``.
a_pc (:py:class:`dolfin.Form` or :py:class:`ufl.Form`)
Bilinear form representing a matrix optionally passed to
preconditioner instead of ``a``. In case of PCD, stabilized
00-block can be passed to 00-KSP solver.
mp, mu, ap, fp, kp, gp (:py:class:`dolfin.Form` or :py:class:`ufl.Form`)
Bilinear forms which (some of them) might be used by a
particular PCD(R) preconditioner. Typically they represent "mass
matrix" on pressure, "mass matrix" on velocity, minus Laplacian
operator on pressure, pressure convection-diffusion operator,
pressure convection operator and pressure gradient respectively.
bcs_pcd (:py:class:`list` of :py:class:`dolfin.DirichletBC`)
Artificial boundary conditions used by PCD preconditioner.
All the arguments should be given on the common mixed function space.
All the forms are wrapped using :py:class:`PCDForm` so that each of
them can be endowed with additional set of properties.
By default, ``mp``, ``mu``, ``ap`` and ``gp`` are assumed to be
constant if the preconditioner is used repeatedly in some outer
iterative process (e.g Newton-Raphson method, time-stepping).
As such, the corresponding operators are assembled only once.
On the other hand, ``fp`` and ``kp`` are updated in every
outer iteration.
Also note that ``gp`` is the only form that is by default in a *phantom
mode*. It means that the corresponding operator (if needed) is not
obtained by assembling the form, but it is extracted as the 01-block of
the system matrix.
The default setting can be modified by accessing
a :py:class:`PCDForm` instance via :py:meth:`PCDAssembler.get_pcd_form`
and changing the properties directly.
"""
# Assembler for the linear system of algebraic equations
self.assembler = SystemAssembler(a, L, bcs)
# Assembler for preconditioner
if a_pc is not None:
self.assembler_pc = SystemAssembler(a_pc, L, bcs)
else:
self.assembler_pc = None
# Store bcs
self._bcs = bcs
self._bcs_pcd = bcs_pcd
# Store and initialize forms
self._forms = {
"L": PCDForm(L),
"ap": PCDForm(ap, const=True),
"mp": PCDForm(mp, const=True),
"mu": PCDForm(mu, const=True),
"fp": PCDForm(fp),
"kp": PCDForm(kp),
"gp": PCDForm(gp, const=True, phantom=True),
}
def get_pcd_form(self, key):
"""Return form wrapped in :py:class:`PCDForm`."""
form = self._forms.get(key)
if form is None:
raise AttributeError("Form '%s' requested by PCD not available" % key)
assert isinstance(form, PCDForm)
return form
def get_dolfin_form(self, key):
"""Return form as :py:class:`dolfin.Form` or :py:class:`ufl.Form`."""
return self.get_pcd_form(key).dolfin_form()
def function_space(self):
return self.get_dolfin_form("L").arguments()[0].function_space()
def rhs_vector(self, b, x=None):
"""Assemble right hand side vector ``b``.
The version with ``x`` is suitable for use inside
a (quasi)-Newton solver.
"""
if x is not None:
self.assembler.assemble(b, x)
else:
self.assembler.assemble(b)
def system_matrix(self, A):
"""Assemble system matrix ``A``."""
self.assembler.assemble(A)
def pc_matrix(self, P):
"""Assemble preconditioning matrix ``P`` whose relevant blocks can be
passed to actual parts of the ``KSP`` solver.
"""
if self.assembler_pc is not None:
self.assembler_pc.assemble(P)
def ap(self, Ap):
assembler = SystemAssembler(self.get_dolfin_form("ap"),
self.get_dolfin_form("L"),
self.pcd_bcs())
assembler.assemble(Ap)
def mp(self, Mp):
assemble(self.get_dolfin_form("mp"), tensor=Mp)
def mu(self, Mu):
assemble(self.get_dolfin_form("mu"), tensor=Mu)
def fp(self, Fp):
assemble(self.get_dolfin_form("fp"), tensor=Fp)
def kp(self, Kp):
assemble(self.get_dolfin_form("kp"), tensor=Kp)
def gp(self, Bt):
"""Assemble discrete pressure gradient. It is crucial to respect any
constraints placed on the velocity test space by Dirichlet boundary
conditions."""
assemble(self.get_dolfin_form("gp"), tensor=Bt)
for bc in self._bcs:
bc.apply(Bt)
# FIXME: Naming
def pcd_bcs(self):
try:
assert self._bcs_pcd is not None
except (AttributeError, AssertionError):
raise AttributeError("BCs requested by PCD not available")
return self._bcs_pcd
def ap(self, Ap):
assembler = SystemAssembler(self.get_dolfin_form("ap"),
self.get_dolfin_form("L"),
self.pcd_bcs())
assembler.assemble(Ap)