def test_gram_schmidt():
for i in (1, 32):
b = NumpyVectorArray(np.identity(i, dtype=np.float))
a = gram_schmidt(b)
assert b == a
c = NumpyVectorArray([[1.0, 0], [0., 0]])
a = gram_schmidt(c)
assert (a.data == np.array([[1.0, 0]])).all()
def test_gram_schmidt():
for i in (1, 32):
b = NumpyVectorArray(np.identity(i, dtype=np.float))
a = gram_schmidt.gram_schmidt(b)
assert b == a
c = NumpyVectorArray([[1.0, 0], [0., 0]])
a = gram_schmidt.gram_schmidt(c)
assert (a.data == np.array([[1.0, 0]])).all()
def gram_schmidt_basis_extension(basis,
U,
product=None,
copy_basis=True,
copy_U=True):
"""Extend basis using Gram-Schmidt orthonormalization.
Parameters
----------
basis
|VectorArray| containing the basis to extend.
U
|VectorArray| containing the new basis vectors.
product
The scalar product w.r.t. which to orthonormalize; if `None`, the Euclidean
product is used.
copy_basis
If `copy_basis` is `False`, the old basis is extended in-place.
copy_U
If `copy_U` is `False`, the new basis vectors are removed from `U`.
Returns
-------
new_basis
The extended basis.
extension_data
Dict containing the following fields:
:hierarchic: `True` if `new_basis` contains `basis` as its first vectors.
Raises
------
ExtensionError
Gram-Schmidt orthonormalization fails. This is the case when no
vector in `U` is linearly independent from the basis.
"""
if basis is None:
basis = U.empty(reserve=len(U))
basis_length = len(basis)
new_basis = basis.copy() if copy_basis else basis
new_basis.append(U, remove_from_other=(not copy_U))
gram_schmidt(new_basis, offset=basis_length, product=product, copy=False)
if len(new_basis) <= basis_length:
raise ExtensionError
return new_basis, {'hierarchic': True}
def gram_schmidt_basis_extension(basis, U, product=None, copy_basis=True, copy_U=True):
"""Extend basis using Gram-Schmidt orthonormalization.
Parameters
----------
basis
|VectorArray| containing the basis to extend.
U
|VectorArray| containing the new basis vectors.
product
The scalar product w.r.t. which to orthonormalize; if None, the Euclidean
product is used.
copy_basis
If copy_basis is False, the old basis is extended in-place.
copy_U
If copy_U is False, the new basis vectors are removed from U.
Returns
-------
new_basis
The extended basis.
extension_data
Dict containing the following fields:
:hierarchic: `True` if `new_basis` contains `basis` as its first vectors.
Raises
------
ExtensionError
Gram-Schmidt orthonormalization fails. This is the case when no
vector in U is linearly independent from the basis.
"""
if basis is None:
basis = U.empty(reserve=len(U))
basis_length = len(basis)
new_basis = basis.copy() if copy_basis else basis
new_basis.append(U, remove_from_other=(not copy_U))
gram_schmidt(new_basis, offset=basis_length, product=product, copy=False)
if len(new_basis) <= basis_length:
raise ExtensionError
return new_basis, {'hierarchic': True}
def gram_schmidt_basis_extension(basis, U, U_ind=None, product=None, copy_basis=True, copy_U=True):
'''Extend basis using Gram-Schmidt orthonormalization.
Parameters
----------
basis
The basis to extend.
U
The new basis vectors.
U_ind
Indices of the new basis vectors in U.
product
The scalar product w.r.t. which to orthonormalize; if None, the l2-scalar
product on the coefficient vector is used.
copy_basis
If copy_basis is False, the old basis is extended in-place.
copy_U
If copy_U is False, the new basis vectors are removed from U.
Returns
-------
The new basis.
Raises
------
ExtensionError
Gram-Schmidt orthonormalization fails. Usually this is the case when U
is not linearily independent from the basis. However this can also happen
due to rounding errors ...
'''
if basis is None:
basis = NumpyVectorArray(np.zeros((0, U.dim)))
basis_length = len(basis)
new_basis = basis.copy() if copy_basis else basis
new_basis.append(U, o_ind=U_ind, remove_from_other=(not copy_U))
gram_schmidt(new_basis, offset=len(basis), product=product)
if len(new_basis) <= basis_length:
raise ExtensionError
return new_basis
def pod(A, modes=None, product=None, tol=None, symmetrize=None, orthonormalize=False,
check=None, check_tol=None):
assert isinstance(A, VectorArrayInterface)
assert len(A) > 0
assert modes is None or modes <= len(A)
assert product is None or isinstance(product, OperatorInterface)
tol = defaults.pod_tol if tol is None else tol
symmetrize = defaults.pod_symmetrize if symmetrize is None else symmetrize
orthonormalize = defaults.pod_orthonormalize if orthonormalize is None else orthonormalize
check = defaults.pod_check if check is None else check
check_tol = defaults.pod_check_tol if check_tol is None else check_tol
B = A.gramian() if product is None else product.apply2(A, A, pairwise=False)
if symmetrize: # according to rbmatlab this is necessary due to rounding
B = B + B.T
B *= 0.5
eigvals = None if modes is None else (len(B) - modes, len(B) - 1)
EVALS, EVECS = eigh(B, overwrite_a=True, turbo=True, eigvals=eigvals)
EVALS = EVALS[::-1]
EVECS = EVECS.T[::-1, :] # is this a view?
last_above_tol = np.where(EVALS >= tol)[0][-1]
EVALS = EVALS[:last_above_tol + 1]
EVECS = EVECS[:last_above_tol + 1]
if len(EVALS) == 0:
return type(A).empty(A.dim)
POD = A.lincomb(EVECS / np.sqrt(EVALS[:, np.newaxis]))
if orthonormalize:
POD = gram_schmidt(POD, product=product)
if check:
if not product and not float_cmp_all(POD.dot(POD, pairwise=False), np.eye(len(POD)), check_tol):
err = np.max(np.abs(POD.dot(POD, pairwise=False) - np.eye(len(POD))))
raise AccuracyError('result not orthogonal (max err={})'.format(err))
elif product and not float_cmp_all(product.apply2(POD, POD, pairwise=False), np.eye(len(POD)), check_tol):
err = np.max(np.abs(product.apply2(POD, POD, pairwise=False) - np.eye(len(POD))))
raise AccuracyError('result not orthogonal (max err={})'.format(err))
return POD
def reduce_residual(operator, functional=None, RB=None, product=None, extends=None):
"""Generic reduced basis residual reductor.
Given an operator and a functional, the concatenation of residual operator
with the Riesz isomorphism is given by::
riesz_residual.apply(U, mu)
== product.apply_inverse(operator.apply(U, mu) - functional.as_vector(mu))
This reductor determines a low-dimensional subspace of image of a reduced
basis space under `riesz_residual`, computes an orthonormal basis `residual_range`
of this range spaces and then returns the Petrov-Galerkin projection ::
projected_riesz_residual
=== riesz_residual.projected(source_basis=RB, range_basis=residual_range)
of the `riesz_residual` operator. Given an reduced basis coefficient vector `u`,
the dual norm of the residual can then be computed as ::
projected_riesz_residual.apply(u, mu).l2_norm()
Moreover, a `reconstructor` is provided such that ::
reconstructor.reconstruct(projected_riesz_residual.apply(u, mu))
== riesz_residual.apply(RB.lincomb(u), mu)
Parameters
----------
operator
See definition of `riesz_residual`.
functional
See definition of `riesz_residual`. If `None`, zero right-hand side is assumed.
RB
|VectorArray| containing a basis of the reduced space onto which to project.
product
Scalar product |Operator| w.r.t. which to compute the Riesz representatives.
extends
Set by :meth:`~pymor.algorithms.greedy.greedy` to the result of the
last reduction in case the basis extension was `hierarchic`. Used to prevent
re-computation of `residual_range` basis vectors already obtained from previous
reductions.
Returns
-------
projected_riesz_residual
See above.
reconstructor
See above.
reduction_data
Additional data produced by the reduction process. (Compare the `extends` parameter.)
"""
assert functional is None \
or functional.range == NumpyVectorSpace(1) and functional.source == operator.source and functional.linear
assert RB is None or RB in operator.source
assert product is None or product.source == product.range == operator.range
assert extends is None or len(extends) == 3
logger = getLogger('pymor.reductors.reduce_residual')
if RB is None:
RB = operator.source.empty()
if extends and isinstance(extends[0], NonProjectedResiudalOperator):
extends = None
if extends:
residual_range = extends[1].RB.copy()
residual_range_dims = list(extends[2]['residual_range_dims'])
ind_range = range(extends[0].source.dim, len(RB))
else:
residual_range = operator.range.empty()
residual_range_dims = []
ind_range = range(-1, len(RB))
class CollectionError(Exception):
def __init__(self, op):
super(CollectionError, self).__init__()
self.op = op
def collect_operator_ranges(op, ind, residual_range):
if isinstance(op, LincombOperator):
for o in op.operators:
collect_operator_ranges(o, ind, residual_range)
elif isinstance(op, EmpiricalInterpolatedOperator):
if hasattr(op, 'collateral_basis') and ind == -1:
residual_range.append(op.collateral_basis)
elif op.linear and not op.parametric:
if ind >= 0:
residual_range.append(op.apply(RB, ind=ind))
else:
raise CollectionError(op)
def collect_functional_ranges(op, residual_range):
if isinstance(op, LincombOperator):
for o in op.operators:
collect_functional_ranges(o, residual_range)
elif op.linear and not op.parametric:
residual_range.append(op.as_vector())
else:
raise CollectionError(op)
for i in ind_range:
logger.info('Computing residual range for basis vector {}...'.format(i))
new_residual_range = operator.range.empty()
try:
if i == -1:
collect_functional_ranges(functional, new_residual_range)
collect_operator_ranges(operator, i, new_residual_range)
except CollectionError as e:
logger.warn('Cannot compute range of {}. Evaluation will be slow.'.format(e.op))
operator = operator.projected(RB, None)
return (NonProjectedResiudalOperator(operator, functional, product),
NonProjectedReconstructor(product),
{})
if product:
logger.info('Computing Riesz representatives for basis vector {}...'.format(i))
new_residual_range = product.apply_inverse(new_residual_range)
gram_schmidt_offset = len(residual_range)
residual_range.append(new_residual_range)
logger.info('Orthonormalizing ...')
gram_schmidt(residual_range, offset=gram_schmidt_offset, product=product, copy=False)
residual_range_dims.append(len(residual_range))
logger.info('Projecting ...')
operator = operator.projected(RB, residual_range, product=None) # the product always cancels out.
functional = functional.projected(residual_range, None, product=None)
return (ResidualOperator(operator, functional),
GenericRBReconstructor(residual_range),
{'residual_range_dims': residual_range_dims})
def pod(A, modes=None, product=None, tol=None, symmetrize=None, orthonormalize=None,
check=None, check_tol=None):
'''Proper orthogonal decomposition of `A`.
If the |VectorArray| `A` is viewed as a map ::
A: R^(len(A)) ---> R^(dim(A))
then the return value of this method is simply the array of left-singular
vectors of the singular value decomposition of `A`, where the scalar product
on R^(dim(A) is given by `product` and the scalar product on R^(len(A)) is
the Euclidean product.
Parameters
----------
A
The |VectorArray| for which the POD is to be computed.
modes
If not `None` only the first `modes` POD modes (singular vectors) are
returned.
products
Scalar product given as a linear |Operator| w.r.t. compute the POD.
tol
Squared singular values smaller than this value are ignored. If `None`,
the `pod_tol` |default| value is used.
symmetrize
If `True` symmetrize the gramian again before proceeding. If `None`,
the `pod_symmetrize` |default| value is chosen.
orthonormalize
If `True`, orthonormalize the computed POD modes again using
:func:`la.gram_schmidt.gram_schmidt`. If `None`, the `pod_orthonormalize`
|default| value is used.
check
If `True`, check the computed POD modes for orthonormality. If `None`,
the `pod_check` |default| value is used.
check_tol
Tolerance for the orthonormality check. If `None`, the `pod_check_tol`
|default| value is used.
Returns
-------
|VectorArray| of POD modes.
'''
assert isinstance(A, VectorArrayInterface)
assert len(A) > 0
assert modes is None or modes <= len(A)
assert product is None or isinstance(product, OperatorInterface)
tol = defaults.pod_tol if tol is None else tol
symmetrize = defaults.pod_symmetrize if symmetrize is None else symmetrize
orthonormalize = defaults.pod_orthonormalize if orthonormalize is None else orthonormalize
check = defaults.pod_check if check is None else check
check_tol = defaults.pod_check_tol if check_tol is None else check_tol
B = A.gramian() if product is None else product.apply2(A, A, pairwise=False)
if symmetrize: # according to rbmatlab this is necessary due to rounding
B = B + B.T
B *= 0.5
eigvals = None if modes is None else (len(B) - modes, len(B) - 1)
EVALS, EVECS = eigh(B, overwrite_a=True, turbo=True, eigvals=eigvals)
EVALS = EVALS[::-1]
EVECS = EVECS.T[::-1, :] # is this a view? yes it is!
above_tol = np.where(EVALS >= tol)[0]
if len(above_tol) == 0:
return type(A).empty(A.dim)
last_above_tol = above_tol[-1]
EVALS = EVALS[:last_above_tol + 1]
EVECS = EVECS[:last_above_tol + 1]
POD = A.lincomb(EVECS / np.sqrt(EVALS[:, np.newaxis]))
if orthonormalize:
POD = gram_schmidt(POD, product=product, copy=False)
if check:
if not product and not float_cmp_all(POD.dot(POD, pairwise=False), np.eye(len(POD)), check_tol):
err = np.max(np.abs(POD.dot(POD, pairwise=False) - np.eye(len(POD))))
raise AccuracyError('result not orthogonal (max err={})'.format(err))
elif product and not float_cmp_all(product.apply2(POD, POD, pairwise=False), np.eye(len(POD)), check_tol):
err = np.max(np.abs(product.apply2(POD, POD, pairwise=False) - np.eye(len(POD))))
raise AccuracyError('result not orthogonal (max err={})'.format(err))
return POD
def pod_basis_extension(basis, U, count=1, copy_basis=True, product=None, orthonormalize=True):
"""Extend basis with the first `count` POD modes of the projection of U onto the
orthogonal complement of the basis.
Note that the provided basis is assumed to be orthonormal w.r.t. the provided
scalar product!
Parameters
----------
basis
|VectorArray| containing the basis to extend. The basis is expected to be
orthonormal w.r.t. `product`.
U
|VectorArray| containing the vectors to which the POD is applied.
count
Number of POD modes that are to be appended to the basis.
product
The scalar product w.r.t. which to orthonormalize; if None, the Euclidean
product is used.
copy_basis
If copy_basis is False, the old basis is extended in-place.
orthonormalize
If `True`, re-orthonormalize the new basis vectors obtained by the POD
in order to improve numerical accuracy.
Returns
-------
new_basis
The extended basis.
extension_data
Dict containing the following fields:
:hierarchic: `True` if `new_basis` contains `basis` as its first vectors.
Raises
------
ExtensionError
POD produces no new vectors. This is the case when no vector in U
is linearly independent from the basis.
"""
if basis is None:
return pod(U, modes=count, product=product)[0], {'hierarchic': True}
basis_length = len(basis)
new_basis = basis.copy() if copy_basis else basis
if product is None:
U_proj_err = U - basis.lincomb(U.dot(basis, pairwise=False))
else:
U_proj_err = U - basis.lincomb(product.apply2(U, basis, pairwise=False))
new_basis.append(pod(U_proj_err, modes=count, product=product, orthonormalize=False)[0])
if orthonormalize:
gram_schmidt(new_basis, offset=len(basis), product=product, copy=False)
if len(new_basis) <= basis_length:
raise ExtensionError
return new_basis, {'hierarchic': True}
def pod(A, modes=None, product=None, tol=4e-8, symmetrize=False, orthonormalize=True,
check=True, check_tol=1e-10):
"""Proper orthogonal decomposition of `A`.
If the |VectorArray| `A` is viewed as a linear map ::
A: R^(len(A)) ---> R^(dim(A))
then the return value of this method is simply the |VectorArray| of left-singular
vectors of the singular value decomposition of `A` with the scalar product
on R^(dim(A) given by `product` and the scalar product on R^(len(A)) being
the Euclidean product.
Parameters
----------
A
The |VectorArray| for which the POD is to be computed.
modes
If not `None` only the first `modes` POD modes (singular vectors) are
returned.
products
Scalar product |Operator| w.r.t. which the POD is computed.
tol
Singular values smaller than this value multiplied by the largest singular
value are ignored.
symmetrize
If `True`, symmetrize the gramian again before proceeding.
orthonormalize
If `True`, orthonormalize the computed POD modes again using
:func:`la.gram_schmidt.gram_schmidt`.
check
If `True`, check the computed POD modes for orthonormality.
check_tol
Tolerance for the orthonormality check.
Returns
-------
POD
|VectorArray| of POD modes.
SVALS
Sequence of singular values.
"""
assert isinstance(A, VectorArrayInterface)
assert len(A) > 0
assert modes is None or modes <= len(A)
assert product is None or isinstance(product, OperatorInterface)
B = A.gramian() if product is None else product.apply2(A, A, pairwise=False)
if symmetrize: # according to rbmatlab this is necessary due to rounding
B = B + B.T
B *= 0.5
eigvals = None if modes is None else (len(B) - modes, len(B) - 1)
EVALS, EVECS = eigh(B, overwrite_a=True, turbo=True, eigvals=eigvals)
EVALS = EVALS[::-1]
EVECS = EVECS.T[::-1, :] # is this a view? yes it is!
above_tol = np.where(EVALS >= tol ** 2 * EVALS[0])[0]
if len(above_tol) == 0:
return type(A).empty(A.dim)
last_above_tol = above_tol[-1]
SVALS = np.sqrt(EVALS[:last_above_tol + 1])
EVECS = EVECS[:last_above_tol + 1]
POD = A.lincomb(EVECS / SVALS[:, np.newaxis])
if orthonormalize:
POD = gram_schmidt(POD, product=product, copy=False)
if check:
if not product and not float_cmp_all(POD.dot(POD, pairwise=False), np.eye(len(POD)),
atol=check_tol, rtol=0.):
err = np.max(np.abs(POD.dot(POD, pairwise=False) - np.eye(len(POD))))
raise AccuracyError('result not orthogonal (max err={})'.format(err))
elif product and not float_cmp_all(product.apply2(POD, POD, pairwise=False), np.eye(len(POD)),
atol=check_tol, rtol=0.):
err = np.max(np.abs(product.apply2(POD, POD, pairwise=False) - np.eye(len(POD))))
raise AccuracyError('result not orthogonal (max err={})'.format(err))
if len(POD) < len(EVECS):
raise AccuracyError('additional orthonormalization removed basis vectors')
return POD, SVALS
def reduce_residual(operator, functional=None, RB=None, product=None, extends=None):
"""Generic reduced basis residual reductor.
"""
assert functional == None \
or functional.range == NumpyVectorSpace(1) and functional.source == operator.source and functional.linear
assert RB is None or RB in operator.source
assert product is None or product.source == product.range == operator.range
assert extends is None or len(extends) == 3
logger = getLogger('pymor.reductors.reduce_residual')
if RB is None:
RB = operator.source.empty()
if extends and isinstance(extends[0], NonProjectedResiudalOperator):
extends = None
if extends:
residual_range = extends[1].RB.copy()
residual_range_dims = list(extends[2]['residual_range_dims'])
ind_range = range(extends[0].source.dim, len(RB))
else:
residual_range = operator.range.empty()
residual_range_dims = []
ind_range = range(-1, len(RB))
class CollectionError(Exception):
def __init__(self, op):
super(CollectionError, self).__init__()
self.op = op
def collect_operator_ranges(op, ind, residual_range):
if isinstance(op, LincombOperator):
for o in op.operators:
collect_operator_ranges(o, ind, residual_range)
elif isinstance(op, EmpiricalInterpolatedOperator):
if hasattr(op, 'collateral_basis') and ind == -1:
residual_range.append(op.collateral_basis)
elif op.linear and not op.parametric:
if ind >= 0:
residual_range.append(op.apply(RB, ind=ind))
else:
raise CollectionError(op)
def collect_functional_ranges(op, residual_range):
if isinstance(op, LincombOperator):
for o in op.operators:
collect_functional_ranges(o, residual_range)
elif op.linear and not op.parametric:
residual_range.append(op.as_vector())
else:
raise CollectionError(op)
for i in ind_range:
logger.info('Computing residual range for basis vector {}...'.format(i))
new_residual_range = operator.range.empty()
try:
if i == -1:
collect_functional_ranges(functional, new_residual_range)
collect_operator_ranges(operator, i, new_residual_range)
except CollectionError as e:
logger.warn('Cannot compute range of {}. Evaluation will be slow.'.format(e.op))
operator = operator.projected(RB, None)
return (NonProjectedResiudalOperator(operator, functional, product),
NonProjectedReconstructor(product),
{})
if product:
logger.info('Computing Riesz representatives for basis vector {}...'.format(i))
new_residual_range = product.apply_inverse(new_residual_range)
gram_schmidt_offset = len(residual_range)
residual_range.append(new_residual_range)
logger.info('Orthonormalizing ...')
gram_schmidt(residual_range, offset=gram_schmidt_offset, product=product, copy=False)
residual_range_dims.append(len(residual_range))
logger.info('Projecting ...')
operator = operator.projected(RB, residual_range, product=None) # the product always cancels out.
functional = functional.projected(residual_range, None, product=None)
return (ResidualOperator(operator, functional),
GenericRBReconstructor(residual_range),
{'residual_range_dims': residual_range_dims})
def pod_basis_extension(basis,
U,
count=1,
copy_basis=True,
product=None,
orthonormalize=True):
"""Extend basis with the first `count` POD modes of the projection of `U` onto the
orthogonal complement of the basis.
Note that the provided basis is assumed to be orthonormal w.r.t. the provided
scalar product!
Parameters
----------
basis
|VectorArray| containing the basis to extend. The basis is expected to be
orthonormal w.r.t. `product`.
U
|VectorArray| containing the vectors to which the POD is applied.
count
Number of POD modes that are to be appended to the basis.
product
The scalar product w.r.t. which to orthonormalize; if `None`, the Euclidean
product is used.
copy_basis
If `copy_basis` is `False`, the old basis is extended in-place.
orthonormalize
If `True`, re-orthonormalize the new basis vectors obtained by the POD
in order to improve numerical accuracy.
Returns
-------
new_basis
The extended basis.
extension_data
Dict containing the following fields:
:hierarchic: `True` if `new_basis` contains `basis` as its first vectors.
Raises
------
ExtensionError
POD produces no new vectors. This is the case when no vector in `U`
is linearly independent from the basis.
"""
if basis is None:
return pod(U, modes=count, product=product)[0], {'hierarchic': True}
basis_length = len(basis)
new_basis = basis.copy() if copy_basis else basis
if product is None:
U_proj_err = U - basis.lincomb(U.dot(basis, pairwise=False))
else:
U_proj_err = U - basis.lincomb(product.apply2(U, basis,
pairwise=False))
new_basis.append(
pod(U_proj_err, modes=count, product=product, orthonormalize=False)[0])
if orthonormalize:
gram_schmidt(new_basis, offset=len(basis), product=product, copy=False)
if len(new_basis) <= basis_length:
raise ExtensionError
return new_basis, {'hierarchic': True}