def weak_form(self):
"""Return the weak form."""
from bempp.api.assembly.discrete_boundary_operator import \
SparseDiscreteBoundaryOperator
if self._sparse_mat is not None:
return SparseDiscreteBoundaryOperator(self._sparse_mat)
backend = parameters['linear_algebra_backend']
if backend not in ['PETSc', 'uBLAS']:
parameters['linear_algebra_backend'] = 'PETSc'
if parameters['linear_algebra_backend'] == 'PETSc':
mat = as_backend_type(assemble(self._fenics_weak_form)).mat()
(indptr, indices, data) = mat.getValuesCSR()
self._sparse_mat = csr_matrix((data, indices, indptr),
shape=mat.size)
elif parameters['linear_algebra_backend'] == 'uBLAS':
self._sparse_mat = assemble(self._fenics_weak_form).sparray()
else:
raise ValueError(
"This should not happen! Backend type is %s. " +
"Default backend should have been set to 'PETSc'.",
str(parameters['linear_algebra_backend']))
parameters['linear_algebra_backend'] = backend
return SparseDiscreteBoundaryOperator(self._sparse_mat)
def assemble(self, operator_descriptor, device_interface, precision, *args,
**kwargs):
"""Assemble the singular part."""
from bempp.api.assembly.discrete_boundary_operator import (
SparseDiscreteBoundaryOperator, )
from bempp.api.utils.helpers import promote_to_double_precision
from scipy.sparse import coo_matrix, csr_matrix
from bempp.api.space.space import return_compatible_representation
domain, dual_to_range = return_compatible_representation(
self.domain, self.dual_to_range)
row_dof_count = dual_to_range.global_dof_count
col_dof_count = domain.global_dof_count
row_grid_dofs = dual_to_range.grid_dof_count
col_grid_dofs = domain.grid_dof_count
if domain.grid != dual_to_range.grid:
return SparseDiscreteBoundaryOperator(
csr_matrix((row_dof_count, col_dof_count), dtype="float64"))
trial_local2global = domain.local2global.ravel()
test_local2global = dual_to_range.local2global.ravel()
trial_multipliers = domain.local_multipliers.ravel()
test_multipliers = dual_to_range.local_multipliers.ravel()
rows, cols, values = assemble_singular_part(
domain.localised_space,
dual_to_range.localised_space,
self.parameters,
operator_descriptor,
device_interface,
)
global_rows = test_local2global[rows]
global_cols = trial_local2global[cols]
global_values = values * trial_multipliers[cols] * test_multipliers[
rows]
if self.parameters.assembly.always_promote_to_double:
values = promote_to_double_precision(values)
mat = coo_matrix(
(global_values, (global_rows, global_cols)),
shape=(row_grid_dofs, col_grid_dofs),
).tocsr()
if domain.requires_dof_transformation:
mat = mat @ domain.dof_transformation
if dual_to_range.requires_dof_transformation:
mat = dual_to_range.dof_transformation.T @ mat
return SparseDiscreteBoundaryOperator(mat)
def assemble(self, operator_descriptor, device_interface, precision, *args,
**kwargs):
"""Sparse assembly of operators."""
from bempp.api.utils.helpers import promote_to_double_precision
from bempp.api.space.space import return_compatible_representation
from .numba_kernels import select_numba_kernels
from scipy.sparse import coo_matrix
from bempp.api.assembly.discrete_boundary_operator import (
SparseDiscreteBoundaryOperator, )
domain, dual_to_range = return_compatible_representation(
self.domain, self.dual_to_range)
row_grid_dofs = dual_to_range.grid_dof_count
col_grid_dofs = domain.grid_dof_count
if domain.grid != dual_to_range.grid:
raise ValueError(
"For sparse operators the domain and dual_to_range grids must be identical."
)
trial_local2global = domain.local2global.ravel()
test_local2global = dual_to_range.local2global.ravel()
trial_multipliers = domain.local_multipliers.ravel()
test_multipliers = dual_to_range.local_multipliers.ravel()
numba_assembly_function, numba_kernel_function = select_numba_kernels(
operator_descriptor, mode="sparse")
rows, cols, values = assemble_sparse(
domain.localised_space,
dual_to_range.localised_space,
self.parameters,
operator_descriptor,
numba_assembly_function,
numba_kernel_function,
)
global_rows = test_local2global[rows]
global_cols = trial_local2global[cols]
global_values = values * trial_multipliers[cols] * test_multipliers[
rows]
if self.parameters.assembly.always_promote_to_double:
values = promote_to_double_precision(values)
mat = coo_matrix(
(global_values, (global_rows, global_cols)),
shape=(row_grid_dofs, col_grid_dofs),
).tocsr()
if domain.requires_dof_transformation:
mat = mat @ domain.dof_transformation
if dual_to_range.requires_dof_transformation:
mat = dual_to_range.dof_transformation.T @ mat
return SparseDiscreteBoundaryOperator(mat)
def weak_form(self):
"""Return the weak form."""
from bempp.api.assembly.discrete_boundary_operator import (
SparseDiscreteBoundaryOperator, )
from dolfin import as_backend_type, assemble, parameters
from scipy.sparse import csr_matrix
if self._sparse_mat is not None:
return SparseDiscreteBoundaryOperator(self._sparse_mat)
backend = parameters["linear_algebra_backend"]
if backend != "PETSc":
raise ValueError(
"Only the PETSc linear algebra backend is supported.")
mat = as_backend_type(assemble(self._fenics_weak_form)).mat()
(indptr, indices, data) = mat.getValuesCSR()
self._sparse_mat = csr_matrix((data, indices, indptr), shape=mat.size)
return SparseDiscreteBoundaryOperator(self._sparse_mat)
def assemble_weak_form(self, parameters):
"""Assemble the local operator and return the assembled operator."""
#pylint: disable=no-name-in-module
from bempp.core.assembly.discrete_boundary_operator import \
convert_to_sparse
from bempp.api.assembly.discrete_boundary_operator import \
SparseDiscreteBoundaryOperator
discrete_operator = SparseDiscreteBoundaryOperator(
convert_to_sparse(self._impl.assemble_weak_form(parameters)))
return discrete_operator
def weak_form(self):
"""Return the weak form."""
from bempp.api.assembly.discrete_boundary_operator import (
SparseDiscreteBoundaryOperator, )
from dolfinx.fem import assemble_matrix
from scipy.sparse import csr_matrix
if self._sparse_mat is None:
mat = assemble_matrix(self._fenics_weak_form)
mat.assemble()
(indptr, indices, data) = mat.getValuesCSR()
self._sparse_mat = csr_matrix((data, indices, indptr),
shape=mat.size)
return SparseDiscreteBoundaryOperator(self._sparse_mat)
def _matrix_from_integration_pairs(
assembler,
all_test_trial_function_pairs,
dof_map, dof_count, weak_form_lookup):
"""Create a sparse matrix from integration pairs."""
#pylint: disable=too-many-locals
import numpy as np
from scipy.sparse import csc_matrix
from bempp.api.assembly.discrete_boundary_operator import \
SparseDiscreteBoundaryOperator
data = np.zeros(len(all_test_trial_function_pairs),
dtype=assembler.dtype)
row_indices = np.zeros(len(all_test_trial_function_pairs),
dtype=np.int)
col_indices = np.zeros(len(all_test_trial_function_pairs),
dtype=np.int)
for index, (test_index, trial_index) in enumerate(
all_test_trial_function_pairs):
row_indices[index] = test_index
col_indices[index] = trial_index
# Get local dofs and dof_weights
test_dofs, test_weights = (dof_map['test'][0][test_index],
dof_map['test'][1][test_index])
trial_dofs, trial_weights = (dof_map['trial'][0][trial_index],
dof_map['trial'][1][trial_index])
for i, test_dof in enumerate(test_dofs):
for j, trial_dof in enumerate(trial_dofs):
element_pair = (test_dof.entity_index,
trial_dof.entity_index)
weak_form_data = weak_form_lookup.get(element_pair)
data[index] += (weak_form_data[test_dof.dof_index,
trial_dof.dof_index] *
#pylint: disable=no-member
np.conj(test_weights[i]) *
#pylint: disable=no-member
np.conj(trial_weights[j]))
return SparseDiscreteBoundaryOperator(
csc_matrix((data, (row_indices, col_indices)),
shape=(dof_count['test'], dof_count['trial'])))
def assemble_singular_part(operator):
"""Assemble the singular part of an integral operator."""
#pylint: disable=too-many-locals
from scipy.sparse import csc_matrix
from bempp.api.assembly.discrete_boundary_operator import \
SparseDiscreteBoundaryOperator
test_space = operator.dual_to_range
trial_space = operator.domain
test_dof_count = operator.dual_to_range.global_dof_count
trial_dof_count = operator.domain.global_dof_count
# If the test and trial grid are different return a zero matrix
if operator.domain.grid != operator.dual_to_range.grid:
return SparseDiscreteBoundaryOperator(
csc_matrix((test_dof_count, trial_dof_count)))
# Cache the global to local accesses
test_dof_map = test_space.global_to_local_dofs(range(test_dof_count))
trial_dof_map = trial_space.global_to_local_dofs(range(trial_dof_count))
grid = operator.domain.grid
# Now get adjacent element pairs
vertex_to_element_matrix = grid.leaf_view.vertex_to_element_matrix
element_to_element_matrix = vertex_to_element_matrix.transpose().dot(
vertex_to_element_matrix)
nonzero_pairs = element_to_element_matrix.nonzero()
index_pairs = zip(nonzero_pairs[0], nonzero_pairs[1])
# Now get all pairs of basis functions who partially
# overlap via adjacent elements
all_test_trial_function_pairs = []
for pair in index_pairs:
test_element = grid.leaf_view.element_from_index(pair[0])
trial_element = grid.leaf_view.element_from_index(pair[1])
global_test_dofs = test_space.get_global_dofs(test_element)
global_trial_dofs = trial_space.get_global_dofs(trial_element)
for test_dof_index in global_test_dofs:
if test_dof_index > -1:
for trial_dof_index in global_trial_dofs:
if trial_dof_index > -1:
all_test_trial_function_pairs.append(
(test_dof_index, trial_dof_index))
# Remove duplicates
all_test_trial_function_pairs = list(set(all_test_trial_function_pairs))
# Now get all integraton element pairs associated
all_integration_element_pairs = []
for function_pair in all_test_trial_function_pairs:
test_local_dofs = test_dof_map[0][function_pair[0]]
trial_local_dofs = trial_dof_map[0][function_pair[1]]
for test_dof in test_local_dofs:
for trial_dof in trial_local_dofs:
all_integration_element_pairs.append(
(test_dof.entity_index, trial_dof.entity_index))
# Remove duplicates
all_integration_element_pairs = list(set(all_integration_element_pairs))
# Now compute all local dof interactions
assembler = operator.local_assembler
weak_forms = assembler.evaluate_local_weak_forms(
all_integration_element_pairs)
# Create a dictionary
weak_form_lookup = dict(zip(all_integration_element_pairs, weak_forms))
# Now need to create the sparse matrix
return _matrix_from_integration_pairs(
operator.local_assembler,
all_test_trial_function_pairs,
{'test': test_dof_map, 'trial': trial_dof_map},
{'test': test_dof_count, 'trial': trial_dof_count},
weak_form_lookup)
def assemble_diagonal(operator):
"""Assemble the singular part of an integral operator."""
from scipy.sparse import csc_matrix
from bempp.api.assembly.discrete_boundary_operator import SparseDiscreteBoundaryOperator
test_space = operator.dual_to_range
trial_space = operator.domain
test_dof_count = operator.dual_to_range.global_dof_count
trial_dof_count = operator.domain.global_dof_count
# If the test and trial grid are different return a zero matrix
#if operator.domain.grid != operator.dual_to_range.grid:
#return SparseDiscreteBoundaryOperator(csc_matrix((test_dof_count, trial_dof_count)))
grid = operator.domain.grid
# Now get adjacent element pairs
vertex_to_element_matrix = grid.leaf_view.vertex_to_element_matrix
element_to_element_matrix = vertex_to_element_matrix.transpose().dot(
vertex_to_element_matrix)
#element_to_element_matrix2 = np.dot(element_to_element_matrix,element_to_element_matrix)
nonzero_pairs = element_to_element_matrix.nonzero()
index_pairs = zip(nonzero_pairs[0], nonzero_pairs[1])
# Now get all pairs of basis functions who partially overlap via adjacent elements
all_test_trial_function_pairs = []
for pair in index_pairs:
test_element = grid.leaf_view.element_from_index(pair[0])
trial_element = grid.leaf_view.element_from_index(pair[1])
global_test_dofs = test_space.get_global_dofs(test_element)
global_trial_dofs = trial_space.get_global_dofs(trial_element)
#for test_dof_index in global_test_dofs:
#if test_dof_index > -1:
#for trial_dof_index in global_trial_dofs:
#if trial_dof_index > -1:
#all_test_trial_function_pairs.append((test_dof_index, trial_dof_index))
for test_dof_index in global_test_dofs:
#for trial_dof_index in global_trial_dofs:
if test_dof_index > -1:
all_test_trial_function_pairs.append(
(test_dof_index, test_dof_index))
# Remove duplicates
all_test_trial_function_pairs = list(set(all_test_trial_function_pairs))
# Now get all integraton element pairs associated
all_integration_element_pairs = []
for function_pair in all_test_trial_function_pairs:
local_dofs = test_space.global_to_local_dofs(function_pair)[0]
test_local_dofs = local_dofs[0]
trial_local_dofs = local_dofs[1]
for test_dof in test_local_dofs:
for trial_dof in trial_local_dofs:
all_integration_element_pairs.append(
(test_dof.entity_index, trial_dof.entity_index))
# Remove duplicates
all_integration_element_pairs = list(set(all_integration_element_pairs))
# Now compute all local dof interactions
assembler = operator.local_assembler
weak_forms = assembler.evaluate_local_weak_forms(
all_integration_element_pairs)
# Create a dictionary
weak_form_lookup = dict(zip(all_integration_element_pairs, weak_forms))
# Now need to create the sparse matrix
data = np.zeros(len(all_test_trial_function_pairs), dtype=assembler.dtype)
row_indices = np.zeros(len(all_test_trial_function_pairs), dtype=np.int)
col_indices = np.zeros(len(all_test_trial_function_pairs), dtype=np.int)
#import ipdb; ipdb.set_trace()
for index, (test_index,
trial_index) in enumerate(all_test_trial_function_pairs):
row_indices[index] = test_index
col_indices[index] = trial_index
# Get local dofs and dof_weights
local_dofs, weights = test_space.global_to_local_dofs(
[test_index, trial_index])
test_dofs, trial_dofs = local_dofs
test_weights, trial_weights = weights
for i, test_dof in enumerate(test_dofs):
for j, trial_dof in enumerate(trial_dofs):
element_pair = (test_dof.entity_index, trial_dof.entity_index)
data[index] += (
weak_form_lookup[element_pair][test_dof.dof_index,
trial_dof.dof_index] *
np.conj(test_weights[i]) * np.conj(trial_weights[j]))
return SparseDiscreteBoundaryOperator(
csc_matrix((data, (row_indices, col_indices)),
shape=(test_dof_count, trial_dof_count)))
def _assemble(self):
"""Assemble the operator."""
from bempp.api.space.space import return_compatible_representation
from bempp.api.assembly.discrete_boundary_operator import (
SparseDiscreteBoundaryOperator, )
from bempp.api.integration.triangle_gauss import rule
from scipy.sparse import coo_matrix
import numpy as _np
points, weights = rule(self._parameters.quadrature.regular)
npoints = len(weights)
comp_trial, comp_test, comp_fun = return_compatible_representation(
self.domain, self.dual_to_range, self._grid_fun.space)
grid = comp_trial.grid
if self._mode == "component":
op = _np.multiply
elif self._mode == "inner":
op = lambda x, y: _np.sum(
x * y.reshape[:, _np.newaxis, :], axis=0, keepdims=True)
elements = (set(comp_test.support_elements).intersection(
set(comp_trial.support_elements)).intersection(
set(comp_fun.support_elements)))
elements = _np.flatnonzero(comp_trial.support * comp_test.support *
comp_fun.support)
number_of_elements = len(elements)
nshape_trial = comp_trial.shapeset.number_of_shape_functions
nshape_test = comp_test.shapeset.number_of_shape_functions
nshape = nshape_trial * nshape_test
data = _np.zeros(number_of_elements * nshape_trial * nshape_test)
for index, elem_index in enumerate(elements):
scale_vals = (self._grid_fun.evaluate(elem_index, points) *
weights * grid.integration_elements[index])
domain_vals = comp_trial.evaluate(elem_index, points)
trial_vals = op(domain_vals, scale_vals)
test_vals = _np.conj(comp_test.evaluate(elem_index, points))
res = _np.tensordot(test_vals, trial_vals, axes=([0, 2], [0, 2]))
data[nshape * index:nshape * (1 + index)] = res.ravel()
irange = _np.arange(nshape_test)
jrange = _np.arange(nshape_trial)
rows = _np.tile(_np.repeat(irange, nshape_trial),
number_of_elements) + _np.repeat(
elements * nshape_test, nshape)
cols = _np.tile(_np.tile(jrange, nshape_test),
number_of_elements) + _np.repeat(
elements * nshape_trial, nshape)
new_rows = comp_test.local2global.ravel()[rows]
new_cols = comp_trial.local2global.ravel()[cols]
nrows = comp_test.dof_transformation.shape[0]
ncols = comp_trial.dof_transformation.shape[0]
mat = coo_matrix((data, (new_rows, new_cols)),
shape=(nrows, ncols)).tocsr()
if comp_trial.requires_dof_transformation:
mat = mat @ self.domain.dof_transformation
if comp_test.requires_dof_transformation:
mat = self.dual_to_range.dof_transformation.T @ mat
return SparseDiscreteBoundaryOperator(mat)