def test_slepc(backends):
"""Check for petsc + slepc."""
from dolfin import has_linear_algebra_backend, has_slepc
if has_linear_algebra_backend("PETSc") and has_slepc():
backends.append("petsc")
else:
print "Petsc + slepc not found."
import re
try:
from dolfin import __version__ as dolfin_version
from dolfin import has_linear_algebra_backend, has_slepc
except ImportError:
raise
else:
fenics_version_major = int(dolfin_version[0:4])
if (fenics_version_major < 2016 or fenics_version_major >= 2018):
raise Exception(
'hIPPYlib requires FEniCS versions 2016.x.x or 2017.x.x')
if not has_linear_algebra_backend("PETSc"):
raise Exception(
'hIPPYlib requires FEniCS to be installed with PETSc support')
if not has_slepc():
raise Exception(
'hIPPYlib requires FEniCS to be installed with SLEPc support')
here = path.abspath(path.dirname(__file__))
with open(path.join(here, 'README.md'), encoding='utf-8') as f:
long_description = f.read()
version = {}
with open(path.join(here, 'hippylib/version.py')) as f:
exec(f.read(), version)
VERSION = version['__version__']
REQUIREMENTS = ['mpi4py', 'numpy', 'matplotlib', 'scipy']
import numpy as np
from spuq.utils.testing import *
try:
import dolfin
from dolfin import (UnitSquare, FunctionSpace, Expression, interpolate, dx,
inner, nabla_grad, TrialFunction, TestFunction,
assemble, Constant, DirichletBC, Mesh, PETScMatrix,
SLEPcEigenSolver, Function, solve)
from spuq.fem.fenics.fenics_basis import FEniCSBasis
from spuq.fem.fenics.fenics_vector import FEniCSVector
from spuq.fem.fenics.fenics_operator import FEniCSOperator, FEniCSSolveOperator
HAVE_FENICS = True
# Test for PETSc and SLEPc
HAVE_SLEPC = dolfin.has_linear_algebra_backend("PETSc") and dolfin.has_slepc()
TestFunction = no_test(TestFunction)
except:
HAVE_FENICS = False
def homogeneous_bc(V):
# define boundary conditions
def u0_boundary(x, on_boundary):
return on_boundary
u0 = Constant(0.0)
bc = DirichletBC(V, u0, u0_boundary)
return bc
def assemble_lhs(coeff, V):
"""Assemble the discrete problem (i.e. the stiffness matrix)."""
def eigen_xct(V, A, B=None, k=100, spect='LM', **kwargs):
"""
Get eigen-pairs of A (or generalized eigen-pairs for (A,B)) for the first k in the spectrum spect.
"""
if 'mpi_comm' in kwargs:
mpi_comm = kwargs['mpi_comm']
else:
mpi_comm = df.mpi_comm_world()
# mixed functions to store eigenfunctions
try:
M = df.FunctionSpace(V.mesh(), df.MixedElement([V.ufl_element()] * k))
except:
print('Warning: '
'MixedFunctionSpace'
' has been deprecated after DOLFIN version 1.6.0.')
M = df.MixedFunctionSpace([V] * k)
# Extract subfunction dofs
eigf_dofs = [M.sub(i).dofmap().dofs() for i in range(k)]
eigf = df.Function(M)
# try reading eigen-pairs from file
eig_files = [
f for f in os.listdir(os.getcwd())
if f.startswith('prior_' + spect + 'eig')
]
found_eigv = False
found_eigf = False
if any(eig_files):
for f_i in eig_files:
if int(f_i.split("_k")[-1].split(".")[0]) >= k:
if f_i.endswith('.txt'):
try:
eigv_ = np.loadtxt(os.path.join(os.getcwd(), f_i),
delimiter=',')
eigv = eigv_[:k]
found_eigv = True
except:
pass
if f_i.endswith('.h5'):
try:
f = df.HDF5File(mpi_comm,
os.path.join(os.getcwd(), f_i), "r")
eigf_i = df.Function(V, name='eigenfunction')
for i, dof_i in enumerate(eigf_dofs):
f.read(eigf_i, 'eigf_{0}'.format(i))
eigf.vector()[dof_i] = eigf_i.vector()
f.close()
found_eigf = True
except:
f.close()
pass
if found_eigv and found_eigf:
break
if found_eigv and found_eigf:
print('Read the first %d eigen-pairs with ' % k + {
'LM': 'largest magnitude',
'SM': 'smallest magnitude'
}[spect] + ' successfully!')
return (eigv, eigf), eigf_dofs
else:
# solve the associated eigen-problem
f = df.HDF5File(
mpi_comm,
os.path.join(os.getcwd(),
'prior_' + spect + 'eigf_k' + str(k) + '.h5'), "w")
eigf_i = df.Function(V, name='eigenfunction')
if type(A) is df.PETScMatrix and df.has_slepc():
# using SLEPc
print("Computing the first %d eigenvalues with " % k + {
'LM': 'largest magnitude',
'SM': 'smallest magnitude'
}[spect] + "...")
# Create eigen-solver
if B is not None and type(B) is df.PETScMatrix:
eigen = df.SLEPcEigenSolver(A, B)
eigen.parameters['problem_type'] = 'gen_hermitian'
else:
eigen = df.SLEPcEigenSolver(A)
# eigen.parameters['problem_type']='hermitian'
eigen.parameters['spectrum'] = {
'LM': 'largest magnitude',
'SM': 'smallest magnitude'
}[spect]
if spect is 'SM':
eigen.parameters['tolerance'] = 1e-10
eigen.parameters['maximum_iterations'] = 100
eigen.parameters['spectral_transform'] = 'shift-and-invert'
eigen.parameters['spectral_shift'] = 10.0 * df.DOLFIN_EPS
eigen.solve(k)
print(
'Total number of iterations: %d, and total number of convergences: %d.'
% (eigen.get_iteration_number(), eigen.get_number_converged()))
# get eigen-pairs
eigv = np.zeros(k)
for i, dof_i in enumerate(eigf_dofs):
eigv[i], _, eigf_vec_i, _ = eigen.get_eigenpair(i)
eigf_i.vector()[:] = eigf_vec_i[:]
f.write(eigf_i, 'eigf_{0}'.format(i))
eigf.vector()[dof_i] = eigf_i.vector()
else:
warnings.warn(
'petsc4py or SLEPc not found! Using scipy.sparse.linalg.eigsh...'
)
import scipy.sparse.linalg as spsla
eigv, eigf_vec = spsla.eigsh(A, k=k, M=B, which=spect)
dsc_ord = eigv.argsort()[::-1]
eigv = eigv[dsc_ord]
eigf_vec = eigf_vec[:, dsc_ord]
for i, dof_i in enumerate(eigf_dofs):
eigf_i.vector()[:] = eigf_vec[:, i]
f.write(eigf_i, 'eigf_{0}'.format(i))
eigf.vector()[dof_i] = eigf_i.vector()
f.close()
np.savetxt(os.path.join(os.getcwd(),
'prior_' + spect + 'eigv_k' + str(k) + '.txt'),
eigv,
delimiter=',')
return (eigv, eigf), eigf_dofs
#
# RBniCS is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public License
# along with RBniCS. If not, see <http://www.gnu.org/licenses/>.
#
# Check that dolfin has been compiled with PETSc and SLEPc
from dolfin import has_petsc, has_linear_algebra_backend, parameters, has_slepc
assert has_petsc()
assert has_linear_algebra_backend("PETSc")
assert parameters["linear_algebra_backend"] == "PETSc"
assert has_slepc()
# Import modules
from rbnics.backends.dolfin.abs import abs
from rbnics.backends.dolfin.affine_expansion_storage import AffineExpansionStorage
from rbnics.backends.dolfin.assign import assign
from rbnics.backends.dolfin.basis_functions_matrix import BasisFunctionsMatrix
from rbnics.backends.dolfin.copy import copy
from rbnics.backends.dolfin.eigen_solver import EigenSolver
from rbnics.backends.dolfin.evaluate import evaluate
from rbnics.backends.dolfin.export import export
from rbnics.backends.dolfin.function import Function
from rbnics.backends.dolfin.functions_list import FunctionsList
from rbnics.backends.dolfin.gram_schmidt import GramSchmidt
from rbnics.backends.dolfin.high_order_proper_orthogonal_decomposition import HighOrderProperOrthogonalDecomposition
from rbnics.backends.dolfin.import_ import import_
## You should have received a copy of the GNU General Public License ## along with SUCEM. If not, see <http://www.gnu.org/licenses/>. ## ## Contact: [email protected] # Authors: # Neilen Marais <*****@*****.**> import dolfin as dol from dolfin import dot, curl, inner, dx from scipy.sparse.linalg.eigen.arpack import speigs # Test for PETSc and SLEPc if not dol.has_la_backend("PETSc"): print "DOLFIN has not been configured with PETSc. Exiting." exit() if not dol.has_slepc(): print "DOLFIN has not been configured with SLEPc. Exiting." exit() class CavityDims(object): pass cdims = CavityDims() cdims.a, cdims.b, cdims.c = 29, 23, 19 # Define mesh, function space mesh = dol.UnitCube(1, 1, 1) mesh.coordinates()[:] *= [cdims.a, cdims.b, cdims.c] V = dol.FunctionSpace(mesh, "Nedelec 1st kind H(curl)", 4)
import os
import dolfin as dol
from dolfin import dot, curl, inner, dx
from scipy.sparse.linalg.eigen.arpack import speigs
from sucemfem.Consts import eps0, mu0, c0
import postproc_eigres
from material_properties import MaterialProperties
# Test for PETSc and SLEPc
if not dol.has_la_backend("PETSc"):
print "DOLFIN has not been configured with PETSc. Exiting."
exit()
if not dol.has_slepc():
print "DOLFIN has not been configured with SLEPc. Exiting."
exit()
# class CavityDims(object): pass
# cdims = CavityDims()
# cdims.a, cdims.b, cdims.c = 29,23,19
# Define mesh
# mesh = dol.UnitCube(1,1,1)
# mesh.coordinates()[:] *= [cdims.a,cdims.b,cdims.c]
#mesh_file = 'lee_mittra92_fig6b.xml'
#mesh_file = 'lee_mittra92_fig6c.xml'
mesh_file = '../examples/albani_bernardi74/mesh/albani_bernardi74_fig2VII.xml'
materials_mesh_file = "%s_physical_region%s" % (os.path.splitext(mesh_file))
