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 __load_mesh_function_hdf5(mesh_function, mesh, mf_dim=None):
"""
Load a dolfin mesh function from an HDF5 file.
Parameters
----------
mesh_function : str
Name of the file containing the mesh function information
Returns
-------
mesh_func : dolfin.cpp.mesh.MeshFunctionSizet
This function returns a dolfin mesh function object.
"""
# Check dolfin for HDF5 support
if not dlf.has_hdf5():
msg = 'The current installation of dolfin does not support HDF5 files.'
raise SoftwareNotAvailable(msg)
# Check file extension
if mesh_function[-3:] == '.h5':
f = dlf.HDF5File(MPI_COMM_WORLD, mesh_function, 'r')
# Assume the mesh function has 1 less dimension than mesh.
if mf_dim is None:
mf_dim = mesh.geometry().dim() - 1
mesh_func = dlf.MeshFunction('size_t', mesh, mf_dim)
f.read(mesh_func, 'boundaries')
f.close()
else:
msg = 'The file extension provided must be \'.h5\'.'
raise ValueError(msg)
return mesh_func
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 __load_mesh_hdf5(mesh_file):
"""
Load dolfin mesh from an HDF5 file.
Parameters
----------
mesh_file : str
Name of the file containing the mesh information
Returns
-------
mesh : dolfin.cpp.mesh.Mesh
This function returns a dolfin mesh object.
"""
# Check dolfin for HDF5 support
if not dlf.has_hdf5():
msg = 'The current installation of dolfin does not support HDF5 files.'
raise SoftwareNotAvailable(msg)
# Check file extension
if mesh_file[-3:] == '.h5':
f = dlf.HDF5File(MPI_COMM_WORLD, mesh_file, 'r')
mesh = dlf.Mesh()
f.read(mesh, 'mesh', False)
f.close()
else:
msg = 'The file extension provided must be \'.h5\'.'
raise ValueError(msg)
return mesh
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
# Copyright (C) 2014 Chris Richardson
#
# This file is part of DOLFIN (https://www.fenicsproject.org)
#
# SPDX-License-Identifier: LGPL-3.0-or-later
import os
from dolfin import (UnitSquareMesh, MPI, FunctionSpace, Function, Expression,
has_hdf5)
import dolfin.cpp as cpp
from dolfin_utils.test import (skip_if_not_HDF5, tempdir, xfail_if_complex,
xfail_with_serial_hdf5_in_parallel)
if has_hdf5():
from dolfin.io import HDF5File
assert (tempdir)
@xfail_if_complex
@skip_if_not_HDF5
@xfail_with_serial_hdf5_in_parallel
def test_save_and_read_function_timeseries(tempdir):
filename = os.path.join(tempdir, "function.h5")
mesh = UnitSquareMesh(MPI.comm_world, 10, 10)
Q = FunctionSpace(mesh, "CG", 3)
F0 = Function(Q)
F1 = Function(Q)
E = Expression("t*x[0]", t=0.0, degree=1)
F0.interpolate(E)
# Save to HDF5 File
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)
