def compute_shapes(form: ufl.Form):
"""Computes the shapes of the cell tensor, coefficient & coordinate arrays for a form"""
# Cell tensor
elements = tuple(arg.ufl_element() for arg in form.arguments())
fiat_elements = (create_element(element) for element in elements)
element_dims = tuple(fe.space_dimension() for fe in fiat_elements)
A_shape = element_dims
# Coefficient arrays
ws_shapes = []
for coefficient in form.coefficients():
w_element = coefficient.ufl_element()
w_dim = create_element(w_element).space_dimension()
ws_shapes.append((w_dim,))
if len(ws_shapes) > 0:
max_w_dim = sorted(ws_shapes, key=lambda w_dim: np.prod(w_dim))[-1]
w_full_shape = (len(ws_shapes), ) + max_w_dim
else:
w_full_shape = (0,)
# Coordinate dofs array
num_vertices_per_cell = form.ufl_cell().num_vertices()
gdim = form.ufl_cell().geometric_dimension()
coords_shape = (num_vertices_per_cell, gdim)
return A_shape, w_full_shape, coords_shape
def adjoint(form: ufl.Form, reordered_arguments=None) -> ufl.Form:
"""Compute adjoint of a bilinear form by changing the ordering (count)
of the test and trial functions.
The functions wraps ``ufl.adjoint``, and by default UFL will create new
``Argument`` s. To specify the ``Argument`` s rather than creating new ones,
pass a tuple of ``Argument`` s as ``reordered_arguments``.
See the documentation for ``ufl.adjoint`` for more details.
"""
if reordered_arguments is not None:
return ufl.adjoint(form, reordered_arguments=reordered_arguments)
# Extract form arguments
arguments = form.arguments()
if len(arguments) != 2:
raise RuntimeError(
"Cannot compute adjoint of form, form is not bilinear")
if any(arg.part() is not None for arg in arguments):
raise RuntimeError(
"Cannot compute adjoint of form, parts not supported")
# Create new Arguments in the same spaces (NB: Order does not matter
# anymore here because number is absolute)
v1 = function.Argument(arguments[1].function_space,
arguments[0].number(), arguments[0].part())
v0 = function.Argument(arguments[0].function_space,
arguments[1].number(), arguments[1].part())
# Return form with swapped arguments as new arguments
return ufl.adjoint(form, reordered_arguments=(v1, v0))
def __init__(self, form: ufl.Form, form_compiler_parameters: dict = {}, jit_parameters: dict = {}):
"""Create dolfinx Form
Parameters
----------
form
Pure UFL form
form_compiler_parameters
See :py:func:`ffcx_jit <dolfinx.jit.ffcx_jit>`
jit_parameters
See :py:func:`ffcx_jit <dolfinx.jit.ffcx_jit>`
Note
----
This wrapper for UFL form is responsible for the actual FFCX compilation
and attaching coefficients and domains specific data to the underlying
C++ Form.
"""
# Extract subdomain data from UFL form
sd = form.subdomain_data()
self._subdomains, = list(sd.values()) # Assuming single domain
domain, = list(sd.keys()) # Assuming single domain
mesh = domain.ufl_cargo()
if mesh is None:
raise RuntimeError("Expecting to find a Mesh in the form.")
# Compile UFL form with JIT
ufc_form = jit.ffcx_jit(
mesh.mpi_comm(),
form,
form_compiler_parameters=form_compiler_parameters,
jit_parameters=jit_parameters)
# For every argument in form extract its function space
function_spaces = [
func.ufl_function_space()._cpp_object for func in form.arguments()
]
# Prepare coefficients data. For every coefficient in form take
# its C++ object.
original_coefficients = form.coefficients()
coeffs = [original_coefficients[ufc_form.original_coefficient_position(
i)]._cpp_object for i in range(ufc_form.num_coefficients)]
# Create dictionary of of subdomain markers (possible None for
# some dimensions
subdomains = {cpp.fem.IntegralType.cell: self._subdomains.get("cell"),
cpp.fem.IntegralType.exterior_facet: self._subdomains.get("exterior_facet"),
cpp.fem.IntegralType.interior_facet: self._subdomains.get("interior_facet"),
cpp.fem.IntegralType.vertex: self._subdomains.get("vertex")}
# Prepare dolfinx.cpp.fem.Form and hold it as a member
ffi = cffi.FFI()
self._cpp_object = cpp.fem.create_form(ffi.cast("uintptr_t", ufc_form),
function_spaces, coeffs,
[c._cpp_object for c in form.constants()], subdomains, mesh)
def __init__(self, form: ufl.Form, form_compiler_parameters: dict = None):
"""Create dolfin Form
Parameters
----------
form
Pure UFL form
form_compiler_parameters
Parameters used in JIT FFC compilation of this form
Note
----
This wrapper for UFL form is responsible for the actual FFC compilation
and attaching coefficients and domains specific data to the underlying
C++ Form.
"""
self.form_compiler_parameters = form_compiler_parameters
# Extract subdomain data from UFL form
sd = form.subdomain_data()
self._subdomains, = list(sd.values()) # Assuming single domain
domain, = list(sd.keys()) # Assuming single domain
mesh = domain.ufl_cargo()
# Compile UFL form with JIT
ufc_form = jit.ffc_jit(
form,
form_compiler_parameters=self.form_compiler_parameters,
mpi_comm=mesh.mpi_comm())
# Cast compiled library to pointer to ufc_form
ffi = cffi.FFI()
ufc_form = fem.dofmap.make_ufc_form(ffi.cast("uintptr_t", ufc_form))
# For every argument in form extract its function space
function_spaces = [
func.function_space()._cpp_object for func in form.arguments()
]
# Prepare dolfin.Form and hold it as a member
self._cpp_object = cpp.fem.create_form(ufc_form, function_spaces)
# Need to fill the form with coefficients data
# For every coefficient in form take its CPP object
original_coefficients = form.coefficients()
for i in range(self._cpp_object.num_coefficients()):
j = self._cpp_object.original_coefficient_position(i)
self._cpp_object.set_coefficient(
i, original_coefficients[j]._cpp_object)
if mesh is None:
raise RuntimeError("Expecting to find a Mesh in the form.")
# Attach mesh (because function spaces and coefficients may be
# empty lists)
if not function_spaces:
self._cpp_object.set_mesh(mesh)
# Attach subdomains to C++ Form if we have them
subdomains = self._subdomains.get("cell")
if subdomains:
self._cpp_object.set_cell_domains(subdomains)
subdomains = self._subdomains.get("exterior_facet")
if subdomains:
self._cpp_object.set_exterior_facet_domains(subdomains)
subdomains = self._subdomains.get("interior_facet")
if subdomains:
self._cpp_object.set_interior_facet_domains(subdomains)
subdomains = self._subdomains.get("vertex")
if subdomains:
self._cpp_object.set_vertex_domains(subdomains)
def __init__(self, form: ufl.Form, form_compiler_parameters: dict = None):
"""Create dolfin Form
Parameters
----------
form
Pure UFL form
form_compiler_parameters
Parameters used in JIT FFC compilation of this form
Note
----
This wrapper for UFL form is responsible for the actual FFC compilation
and attaching coefficients and domains specific data to the underlying
C++ Form.
"""
self.form_compiler_parameters = form_compiler_parameters
# Add DOLFIN include paths (just the Boost path for special
# math functions is really required)
# FIXME: move getting include paths to elsewhere
if self.form_compiler_parameters is None:
self.form_compiler_parameters = {
"external_include_dirs": jit.dolfin_pc["include_dirs"]
}
else:
# FIXME: add paths if dict entry already exists
self.form_compiler_parameters[
"external_include_dirs"] = jit.dolfin_pc["include_dirs"]
# Extract subdomain data from UFL form
sd = form.subdomain_data()
self._subdomains, = list(sd.values()) # Assuming single domain
domain, = list(sd.keys()) # Assuming single domain
mesh = domain.ufl_cargo()
# Compile UFL form with JIT
ufc_form = jit.ffc_jit(
form,
form_compiler_parameters=self.form_compiler_parameters,
mpi_comm=mesh.mpi_comm())
# Cast compiled library to pointer to ufc_form
ufc_form = fem.dofmap.make_ufc_form(ufc_form[0])
# For every argument in form extract its function space
function_spaces = [
func.function_space()._cpp_object for func in form.arguments()
]
# Prepare dolfin.Form and hold it as a member
self._cpp_object = cpp.fem.Form(ufc_form, function_spaces)
# Need to fill the form with coefficients data
# For every coefficient in form take its CPP object
original_coefficients = form.coefficients()
for i in range(self._cpp_object.num_coefficients()):
j = self._cpp_object.original_coefficient_position(i)
self._cpp_object.set_coefficient(
j, original_coefficients[i]._cpp_object)
if mesh is None:
raise RuntimeError("Expecting to find a Mesh in the form.")
# Attach mesh (because function spaces and coefficients may be
# empty lists)
if not function_spaces:
self._cpp_object.set_mesh(mesh)
# Attach subdomains to C++ Form if we have them
subdomains = self._subdomains.get("cell")
self._cpp_object.set_cell_domains(subdomains)
subdomains = self._subdomains.get("exterior_facet")
self._cpp_object.set_exterior_facet_domains(subdomains)
subdomains = self._subdomains.get("interior_facet")
self._cpp_object.set_interior_facet_domains(subdomains)
subdomains = self._subdomains.get("vertex")
self._cpp_object.set_vertex_domains(subdomains)
def __init__(self,
a: ufl.Form,
L: ufl.Form,
bcs: typing.List[fem.DirichletBC] = [],
u: fem.Function = None,
petsc_options={},
form_compiler_parameters={},
jit_parameters={}):
"""Initialize solver for a linear variational problem.
Parameters
----------
a
A bilinear UFL form, the left hand side of the variational problem.
L
A linear UFL form, the right hand side of the variational problem.
bcs
A list of Dirichlet boundary conditions.
u
The solution function. It will be created if not provided.
petsc_options
Parameters that is passed to the linear algebra backend PETSc.
For available choices for the 'petsc_options' kwarg, see the
`PETSc-documentation <https://www.mcs.anl.gov/petsc/documentation/index.html>`.
form_compiler_parameters
Parameters used in FFCx compilation of this form. Run `ffcx --help` at
the commandline to see all available options. Takes priority over all
other parameter values, except for `scalar_type` which is determined by
DOLFINx.
jit_parameters
Parameters used in CFFI JIT compilation of C code generated by FFCx.
See `python/dolfinx/jit.py` for all available parameters.
Takes priority over all other parameter values.
.. code-block:: python
problem = LinearProblem(a, L, [bc0, bc1], petsc_options={"ksp_type": "preonly", "pc_type": "lu"})
"""
self._a = fem.Form(a,
form_compiler_parameters=form_compiler_parameters,
jit_parameters=jit_parameters)
self._A = fem.create_matrix(self._a)
self._L = fem.Form(L,
form_compiler_parameters=form_compiler_parameters,
jit_parameters=jit_parameters)
self._b = fem.create_vector(self._L)
if u is None:
# Extract function space from TrialFunction (which is at the
# end of the argument list as it is numbered as 1, while the
# Test function is numbered as 0)
self.u = fem.Function(a.arguments()[-1].ufl_function_space())
else:
self.u = u
self.bcs = bcs
self._solver = PETSc.KSP().create(
self.u.function_space.mesh.mpi_comm())
self._solver.setOperators(self._A)
# Give PETSc solver options a unique prefix
solver_prefix = "dolfinx_solve_{}".format(id(self))
self._solver.setOptionsPrefix(solver_prefix)
# Set PETSc options
opts = PETSc.Options()
opts.prefixPush(solver_prefix)
for k, v in petsc_options.items():
opts[k] = v
opts.prefixPop()
self._solver.setFromOptions()
def __init__(self, form: ufl.Form, form_compiler_parameters: dict = {}, jit_parameters: dict = {}):
"""Create dolfinx Form
Parameters
----------
form
Pure UFL form
form_compiler_parameters
Parameters used in FFCX compilation of this form. Run `ffcx --help` in the commandline
to see all available options.
jit_parameters
Parameters controlling JIT compilation of C code.
Note
----
This wrapper for UFL form is responsible for the actual FFCX compilation
and attaching coefficients and domains specific data to the underlying
C++ Form.
"""
# Extract subdomain data from UFL form
sd = form.subdomain_data()
self._subdomains, = list(sd.values()) # Assuming single domain
domain, = list(sd.keys()) # Assuming single domain
mesh = domain.ufl_cargo()
# Compile UFL form with JIT
ufc_form = jit.ffcx_jit(
form,
form_compiler_parameters=form_compiler_parameters,
jit_parameters=jit_parameters,
mpi_comm=mesh.mpi_comm())
# For every argument in form extract its function space
function_spaces = [
func.ufl_function_space()._cpp_object for func in form.arguments()
]
# Prepare dolfinx.Form and hold it as a member
ffi = cffi.FFI()
self._cpp_object = cpp.fem.create_form(ffi.cast("uintptr_t", ufc_form), function_spaces)
# Need to fill the form with coefficients data
# For every coefficient in form take its C++ object
original_coefficients = form.coefficients()
for i in range(self._cpp_object.num_coefficients()):
j = self._cpp_object.original_coefficient_position(i)
self._cpp_object.set_coefficient(
i, original_coefficients[j]._cpp_object)
# Constants are set based on their position in original form
original_constants = [c._cpp_object for c in form.constants()]
self._cpp_object.set_constants(original_constants)
if mesh is None:
raise RuntimeError("Expecting to find a Mesh in the form.")
# Attach mesh (because function spaces and coefficients may be
# empty lists)
if not function_spaces:
self._cpp_object.set_mesh(mesh)
# Attach subdomains to C++ Form if we have them
subdomains = self._subdomains.get("cell")
if subdomains:
self._cpp_object.set_cell_domains(subdomains)
subdomains = self._subdomains.get("exterior_facet")
if subdomains:
self._cpp_object.set_exterior_facet_domains(subdomains)
subdomains = self._subdomains.get("interior_facet")
if subdomains:
self._cpp_object.set_interior_facet_domains(subdomains)
subdomains = self._subdomains.get("vertex")
if subdomains:
self._cpp_object.set_vertex_domains(subdomains)
def __init__(self,
a: ufl.Form,
L: ufl.Form,
bcs: typing.List[DirichletBCMetaClass] = [],
u: _Function = None,
petsc_options={},
form_compiler_params={},
jit_params={}):
"""Initialize solver for a linear variational problem.
Args:
a: A bilinear UFL form, the left hand side of the variational problem.
L: A linear UFL form, the right hand side of the variational problem.
bcs: A list of Dirichlet boundary conditions.
u: The solution function. It will be created if not provided.
petsc_options: Parameters that is passed to the linear
algebra backend PETSc. For available choices for the
'petsc_options' kwarg, see the `PETSc documentation
<https://petsc4py.readthedocs.io/en/stable/manual/ksp/>`_.
form_compiler_params: Parameters used in FFCx compilation of
this form. Run ``ffcx --help`` at the commandline to see
all available options.
jit_params: Parameters used in CFFI JIT compilation of C
code generated by FFCx. See `python/dolfinx/jit.py` for
all available parameters. Takes priority over all other
parameter values.
Example::
problem = LinearProblem(a, L, [bc0, bc1], petsc_options={"ksp_type": "preonly", "pc_type": "lu"})
"""
self._a = _create_form(a,
form_compiler_params=form_compiler_params,
jit_params=jit_params)
self._A = create_matrix(self._a)
self._L = _create_form(L,
form_compiler_params=form_compiler_params,
jit_params=jit_params)
self._b = create_vector(self._L)
if u is None:
# Extract function space from TrialFunction (which is at the
# end of the argument list as it is numbered as 1, while the
# Test function is numbered as 0)
self.u = _Function(a.arguments()[-1].ufl_function_space())
else:
self.u = u
self._x = _cpp.la.petsc.create_vector_wrap(self.u.x)
self.bcs = bcs
self._solver = PETSc.KSP().create(self.u.function_space.mesh.comm)
self._solver.setOperators(self._A)
# Give PETSc solver options a unique prefix
problem_prefix = "dolfinx_solve_{}".format(id(self))
self._solver.setOptionsPrefix(problem_prefix)
# Set PETSc options
opts = PETSc.Options()
opts.prefixPush(problem_prefix)
for k, v in petsc_options.items():
opts[k] = v
opts.prefixPop()
self._solver.setFromOptions()
# Set matrix and vector PETSc options
self._A.setOptionsPrefix(problem_prefix)
self._A.setFromOptions()
self._b.setOptionsPrefix(problem_prefix)
self._b.setFromOptions()