def function_load(fun, directory, filename, suffix=None):
fun_V = fun.function_space()
if (not has_hdf5() or not has_hdf5_parallel() or
fun_V.mesh().geometry().dim() is 1 # due to DOLFIN issue #892 TODO
):
return _read_from_xml_file(fun, directory, filename, suffix)
else:
if hasattr(fun_V, "_index_to_components") and len(
fun_V._index_to_components) > 1:
for (index, components) in fun_V._index_to_components.items():
sub_fun_V = get_function_subspace(fun_V, components)
sub_fun = Function(sub_fun_V)
if not _read_from_xdmf_file(sub_fun, directory, filename,
suffix, components):
return False
else:
extended_sub_fun = function_extend_or_restrict(
sub_fun,
None,
fun_V,
components[0],
weight=None,
copy=True)
fun.vector().add_local(
extended_sub_fun.vector().get_local())
fun.vector().apply("add")
return True
else:
return _read_from_xdmf_file(fun, directory, filename, suffix)
def _write_to_file(fun, directory, filename, suffix, components=None):
if components is not None:
filename = filename + "_component_" + "".join(components)
function_name = "function_" + "".join(components)
else:
function_name = "function"
fun_V_element = fun.function_space().ufl_element()
if isinstance(fun_V_element, MixedElement) and not isinstance(
fun_V_element, (TensorElement, VectorElement)):
funs = fun.split(deepcopy=True)
for (i, fun_i) in enumerate(funs):
if components is not None:
filename_i = filename + "_subcomponent_" + str(i)
else:
filename_i = filename + "_component_" + str(i)
_write_to_file(fun_i, directory, filename_i, suffix, None)
else:
if fun_V_element.family() == "Real":
SolutionFile = SolutionFileXML
else:
if has_hdf5() and has_hdf5_parallel():
SolutionFile = SolutionFileXDMF
else:
SolutionFile = SolutionFileXML
if suffix is not None:
if suffix == 0:
# Remove existing files if any, as new functions should not be appended,
# but rather overwrite existing functions
SolutionFile.remove_files(directory, filename)
# Remove from storage and re-create
try:
del _all_solution_files[(directory, filename)]
except KeyError:
pass
_all_solution_files[(directory, filename)] = SolutionFile(
directory, filename)
file_ = _all_solution_files[(directory, filename)]
file_.write(fun, function_name, suffix)
else:
# Remove existing files if any, as new functions should not be appended,
# but rather overwrite existing functions
SolutionFile.remove_files(directory, filename)
# Write function to file
file_ = SolutionFile(directory, filename)
file_.write(fun, function_name, 0)
def _read_from_file(fun, directory, filename, suffix, components=None):
if components is not None:
filename = filename + "_component_" + "".join(components)
function_name = "function_" + "".join(components)
else:
function_name = "function"
fun_V_element = fun.function_space().ufl_element()
if isinstance(fun_V_element, MixedElement) and not isinstance(
fun_V_element, (TensorElement, VectorElement)):
funs = fun.split(deepcopy=True)
for (i, fun_i) in enumerate(funs):
if components is not None:
filename_i = filename + "_subcomponent_" + str(i)
else:
filename_i = filename + "_component_" + str(i)
_read_from_file(fun_i, directory, filename_i, suffix, None)
assign(fun.sub(i), fun_i)
else:
if fun_V_element.family() == "Real":
SolutionFile = SolutionFileXML
else:
if has_hdf5() and has_hdf5_parallel():
SolutionFile = SolutionFileXDMF
else:
SolutionFile = SolutionFileXML
if suffix is not None:
if suffix == 0:
# Remove from storage and re-create
try:
del _all_solution_files[(directory, filename)]
except KeyError:
pass
_all_solution_files[(directory, filename)] = SolutionFile(
directory, filename)
file_ = _all_solution_files[(directory, filename)]
file_.read(fun, function_name, suffix)
else:
file_ = SolutionFile(directory, filename)
file_.read(fun, function_name, 0)
def function_save(fun, directory, filename, suffix=None):
fun_V = fun.function_space()
if (not has_hdf5() or not has_hdf5_parallel() or
fun_V.mesh().geometry().dim() is 1 # due to DOLFIN issue #892 TODO
):
if hasattr(fun_V, "_index_to_components") and len(
fun_V._index_to_components) > 1:
for (index, components) in fun_V._index_to_components.items():
sub_fun = function_extend_or_restrict(fun,
components[0],
get_function_subspace(
fun_V,
components[0]),
None,
weight=None,
copy=True)
_write_to_pvd_file(sub_fun, directory, filename, suffix,
components)
else:
_write_to_pvd_file(fun, directory, filename, suffix)
_write_to_xml_file(fun, directory, filename, suffix)
else:
if hasattr(fun_V, "_index_to_components") and len(
fun_V._index_to_components) > 1:
for (index, components) in fun_V._index_to_components.items():
sub_fun = function_extend_or_restrict(fun,
components[0],
get_function_subspace(
fun_V,
components[0]),
None,
weight=None,
copy=True)
_write_to_xdmf_file(sub_fun, directory, filename, suffix,
components)
else:
_write_to_xdmf_file(fun, directory, filename, suffix)
def _init_last_index(self):
if IndexIO.exists_file(self._directory, self._filename + "_index.sfx"):
self._last_index = IndexIO.load_file(self._directory,
self._filename + "_index.sfx")
else:
self._last_index = -1
def _write_last_index(self, index):
self._last_index = index
# Write out current index
IndexIO.save_file(index, self._directory,
self._filename + "_index.sfx")
if not has_hdf5() or not has_hdf5_parallel():
class SolutionFile(SolutionFile_Base):
def __init__(self, directory, filename):
SolutionFile_Base.__init__(self, directory, filename)
self._visualization_file = PVDFile(self._full_filename + ".pvd",
"compressed")
@staticmethod
def remove_files(directory, filename):
SolutionFile_Base.remove_files(directory, filename)
# No need to remove further files, PVD and XML will get automatically truncated
def write(self, function, name, index):
assert index in (self._last_index, self._last_index + 1)
if index == self._last_index + 1: # writing out solutions after time stepping
# -*- coding: utf-8 -*-
"""
Checks that this version of FEniCS/DOLFIN was compiled with parallel HDF5 and
a few extra preconditoners and solvers.
"""
import dolfin as df
assert df.has_hdf5_parallel()
assert df.has_krylov_solver_preconditioner('hypre_amg')
assert df.has_krylov_solver_preconditioner('hypre_euclid')
assert df.has_krylov_solver_preconditioner('hypre_parasails')
assert df.has_lu_solver_method('mumps')
assert df.has_petsc()
assert df.has_petsc4py()
def invalid_config(encoding):
return (not has_hdf5() and encoding == XDMFFile.Encoding.HDF5) \
or (encoding == XDMFFile.Encoding.ASCII and MPI.size(MPI.comm_world) > 1) \
or (not has_hdf5_parallel() and MPI.size(MPI.comm_world) > 1)
