# Source code for dolfinx.fem.assemble

```
# Copyright (C) 2018-2022 Garth N. Wells, Jack S. Hale
#
# This file is part of DOLFINx (https://www.fenicsproject.org)
#
# SPDX-License-Identifier: LGPL-3.0-or-later
"""Assembly functions for variational forms."""
from __future__ import annotations
import collections
import functools
import typing
import warnings
import numpy as np
import dolfinx
from dolfinx import cpp as _cpp
from dolfinx import la
from dolfinx.cpp.fem import pack_coefficients as _pack_coefficients
from dolfinx.cpp.fem import pack_constants as _pack_constants
from dolfinx.fem.bcs import DirichletBC
from dolfinx.fem.forms import Form
def pack_constants(
form: typing.Union[Form, typing.Sequence[Form]],
) -> typing.Union[np.ndarray, typing.Sequence[np.ndarray]]:
"""Compute form constants.
Pack the `constants` that appear in forms. The packed constants can
be passed to an assembler. This is a performance optimisation for
cases where a form is assembled multiple times and (some) constants
do not change.
If ``form`` is an array of forms, this function returns an array of
form constants with the same shape as form.
Args:
form: A single form or array of forms to pack the constants for.
Returns:
A `constant` array for each form.
"""
def _pack(form):
if form is None:
return None
elif isinstance(form, collections.abc.Iterable):
return list(map(lambda sub_form: _pack(sub_form), form))
else:
return _pack_constants(form)
return _pack(form)
def pack_coefficients(form: typing.Union[Form, typing.Sequence[Form]]):
"""Compute form coefficients.
Pack the `coefficients` that appear in forms. The packed
coefficients can be passed to an assembler. This is a
performance optimisation for cases where a form is assembled
multiple times and (some) coefficients do not change.
If ``form`` is an array of forms, this function returns an array of
form coefficients with the same shape as form.
Args:
form: A single form or array of forms to pack the constants for.
Returns:
Coefficients for each form.
"""
def _pack(form):
if form is None:
return {}
elif isinstance(form, collections.abc.Iterable):
return list(map(lambda sub_form: _pack(sub_form), form))
else:
return _pack_coefficients(form)
return _pack(form)
# -- Vector and matrix instantiation -----------------------------------------
[docs]
def create_vector(L: Form) -> la.Vector:
"""Create a Vector that is compatible with a given linear form"""
dofmap = L.function_spaces[0].dofmap
return la.vector(dofmap.index_map, dofmap.index_map_bs, dtype=L.dtype)
[docs]
def create_matrix(a: Form, block_mode: typing.Optional[la.BlockMode] = None) -> la.MatrixCSR:
"""Create a sparse matrix that is compatible with a given bilinear form.
Args:
a: Bilinear form to assemble.
block_mode: Block mode of the CSR matrix. If ``None``, default
is used.
Returns:
Assembled sparse matrix.
"""
sp = dolfinx.fem.create_sparsity_pattern(a)
sp.finalize()
if block_mode is not None:
return la.matrix_csr(sp, block_mode=block_mode, dtype=a.dtype)
else:
return la.matrix_csr(sp, dtype=a.dtype)
# -- Scalar assembly ---------------------------------------------------------
[docs]
def assemble_scalar(M: Form, constants=None, coeffs=None):
"""Assemble functional. The returned value is local and not
accumulated across processes.
Args:
M: The functional to compute.
constants: Constants that appear in the form. If not provided,
any required constants will be computed.
coeffs: Coefficients that appear in the form. If not provided,
any required coefficients will be computed.
Returns:
The computed scalar on the calling rank.
Note:
Passing `constants` and `coefficients` is a performance
optimisation for when a form is assembled multiple times and
when (some) constants and coefficients are unchanged.
To compute the functional value on the whole domain, the output
of this function is typically summed across all MPI ranks.
"""
constants = constants or _pack_constants(M._cpp_object)
coeffs = coeffs or _pack_coefficients(M._cpp_object)
return _cpp.fem.assemble_scalar(M._cpp_object, constants, coeffs)
# -- Vector assembly ---------------------------------------------------------
[docs]
@functools.singledispatch
def assemble_vector(L: typing.Any, constants=None, coeffs=None):
return _assemble_vector_form(L, constants, coeffs)
@assemble_vector.register(Form)
def _assemble_vector_form(L: Form, constants=None, coeffs=None) -> la.Vector:
"""Assemble linear form into a new Vector.
Args:
L: The linear form to assemble.
constants: Constants that appear in the form. If not provided,
any required constants will be computed.
coeffs: Coefficients that appear in the form. If not provided,
any required coefficients will be computed.
Returns:
The assembled vector for the calling rank.
Note:
Passing `constants` and `coefficients` is a performance
optimisation for when a form is assembled multiple times and
when (some) constants and coefficients are unchanged.
Note:
The returned vector is not finalised, i.e. ghost values are not
accumulated on the owning processes. Calling
:func:`dolfinx.la.Vector.scatter_reverse` on the
return vector can accumulate ghost contributions.
"""
b = create_vector(L)
b.array[:] = 0
constants = constants or _pack_constants(L._cpp_object)
coeffs = coeffs or _pack_coefficients(L._cpp_object)
_assemble_vector_array(b.array, L, constants, coeffs)
return b
@assemble_vector.register(np.ndarray)
def _assemble_vector_array(b: np.ndarray, L: Form, constants=None, coeffs=None):
"""Assemble linear form into an existing array.
Args:
b: The array to assemble the contribution from the calling MPI
rank into. It must have the required size.
L: The linear form assemble.
constants: Constants that appear in the form. If not provided,
any required constants will be computed.
coeffs: Coefficients that appear in the form. If not provided,
any required coefficients will be computed.
Note:
Passing `constants` and `coefficients` is a performance
optimisation for when a form is assembled multiple times and
when (some) constants and coefficients are unchanged.
Note:
The returned vector is not finalised, i.e. ghost values are not
accumulated on the owning processes. Calling
:func:`dolfinx.la.Vector.scatter_reverse` on the
return vector can accumulate ghost contributions.
"""
constants = _pack_constants(L._cpp_object) if constants is None else constants
coeffs = _pack_coefficients(L._cpp_object) if coeffs is None else coeffs
_cpp.fem.assemble_vector(b, L._cpp_object, constants, coeffs)
return b
# -- Matrix assembly ---------------------------------------------------------
[docs]
@functools.singledispatch
def assemble_matrix(
a: typing.Any,
bcs: typing.Optional[list[DirichletBC]] = None,
diagonal: float = 1.0,
constants=None,
coeffs=None,
block_mode: typing.Optional[la.BlockMode] = None,
):
"""Assemble bilinear form into a matrix.
Args:
a: The bilinear form assemble.
bcs: Boundary conditions that affect the assembled matrix.
Degrees-of-freedom constrained by a boundary condition will
have their rows/columns zeroed and the value ``diagonal``
set on on the matrix diagonal.
diagonal: Value to set on the matrix diagonal for Dirichlet boundary
condition constrained degrees-of-freedom belonging to the same trial and test space.
constants: Constants that appear in the form. If not provided,
any required constants will be computed.
coeffs: Coefficients that appear in the form. If not provided,
any required coefficients will be computed.
block_mode: Block size mode for the returned space matrix. If
``None``, default is used.
Returns:
Matrix representation of the bilinear form ``a``.
Note:
The returned matrix is not finalised, i.e. ghost values are not
accumulated.
"""
bcs = [] if bcs is None else bcs
A: la.MatrixCSR = create_matrix(a, block_mode)
_assemble_matrix_csr(A, a, bcs, diagonal, constants, coeffs)
return A
@assemble_matrix.register
def _assemble_matrix_csr(
A: la.MatrixCSR,
a: Form,
bcs: typing.Optional[list[DirichletBC]] = None,
diagonal: float = 1.0,
constants=None,
coeffs=None,
) -> la.MatrixCSR:
"""Assemble bilinear form into a matrix.
Args:
A: The matrix to assemble into. It must have been initialized
with the correct sparsity pattern.
a: The bilinear form assemble.
bcs: Boundary conditions that affect the assembled matrix.
Degrees-of-freedom constrained by a boundary condition will
have their rows/columns zeroed and the value ``diagonal``
set on on
diagonal: Value to set on the matrix diagonal for Dirichlet boundary
condition constrained degrees-of-freedom belonging to the same trial and test space.
constants: Constants that appear in the form. If not provided,
any required constants will be computed.
the matrix diagonal.
coeffs: Coefficients that appear in the form. If not provided,
any required coefficients will be computed.
Note:
The returned matrix is not finalised, i.e. ghost values are not
accumulated.
"""
bcs = [] if bcs is None else [bc._cpp_object for bc in bcs]
constants = _pack_constants(a._cpp_object) if constants is None else constants
coeffs = _pack_coefficients(a._cpp_object) if coeffs is None else coeffs
_cpp.fem.assemble_matrix(A._cpp_object, a._cpp_object, constants, coeffs, bcs)
# If matrix is a 'diagonal'block, set diagonal entry for constrained
# dofs
if a.function_spaces[0] is a.function_spaces[1]:
_cpp.fem.insert_diagonal(A._cpp_object, a.function_spaces[0], bcs, diagonal)
return A
# -- Modifiers for Dirichlet conditions ---------------------------------------
[docs]
def apply_lifting(
b: np.ndarray,
a: list[Form],
bcs: list[list[DirichletBC]],
x0: typing.Optional[list[np.ndarray]] = None,
alpha: float = 1,
constants=None,
coeffs=None,
) -> None:
"""Modify RHS vector b for lifting of Dirichlet boundary conditions.
It modifies b such that:
.. math::
b \\leftarrow b - \\text{scale} * A_j (g_j - x0_j)
where j is a block (nest) index. For a non-blocked problem j = 0.
The boundary conditions bcs are on the trial spaces V_j. The forms
in [a] must have the same test space as L (from which b was built),
but the trial space may differ. If x0 is not supplied, then it is
treated as zero.
Note:
Ghost contributions are not accumulated (not sent to owner).
Caller is responsible for calling VecGhostUpdateBegin/End.
"""
x0 = [] if x0 is None else x0
constants = (
[
_pack_constants(form._cpp_object) if form is not None else np.array([], dtype=b.dtype)
for form in a
]
if constants is None
else constants
)
coeffs = (
[{} if form is None else _pack_coefficients(form._cpp_object) for form in a]
if coeffs is None
else coeffs
)
_a = [None if form is None else form._cpp_object for form in a]
_bcs = [[bc._cpp_object for bc in bcs0] for bcs0 in bcs]
_cpp.fem.apply_lifting(b, _a, constants, coeffs, _bcs, x0, alpha)
[docs]
def set_bc(
b: np.ndarray,
bcs: list[DirichletBC],
x0: typing.Optional[np.ndarray] = None,
scale: float = 1,
) -> None:
"""Insert boundary condition values into vector.
Note:
This function is deprecated.
Only local (owned) entries are set, hence communication after
calling this function is not required unless ghost entries need to
be updated to the boundary condition value.
"""
warnings.warn(
"dolfinx.fem.assembler.set_bc is deprecated. Use dolfinx.fem.DirichletBC.set instead.",
DeprecationWarning,
)
for bc in bcs:
bc.set(b, x0, scale)
```