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# Copyright (C) 2023 Jørgen Schartum Dokken
#
# This file is part of adios4dolfinx
#
# SPDX-License-Identifier: MIT
"""
Functions to create checkpoints with Legacy dolfin
"""
import argparse
import pathlib
import dolfin
import numpy as np
import ufl_legacy as ufl
def create_reference_data(
h5_file: pathlib.Path,
xdmf_file: pathlib.Path,
mesh_name: str,
function_name: str,
family: str,
degree: int,
function_name_vec: str,
) -> dolfin.Function:
mesh = dolfin.UnitCubeMesh(1, 1, 1)
V = dolfin.FunctionSpace(mesh, family, degree)
W = dolfin.VectorFunctionSpace(mesh, family, degree)
x = dolfin.SpatialCoordinate(mesh)
f0 = ufl.conditional(ufl.gt(x[0], 0.5), x[1], 2 * x[0])
v0 = dolfin.project(f0, V)
w0 = dolfin.interpolate(dolfin.Expression(("x[0]", "3*x[2]", "7*x[1]"), degree=1), W)
v1 = dolfin.interpolate(dolfin.Expression("x[0]", degree=1), V)
w1 = dolfin.interpolate(dolfin.Expression(("x[0]", "0", "x[1]"), degree=1), W)
with dolfin.HDF5File(mesh.mpi_comm(), str(h5_file), "w") as hdf:
hdf.write(mesh, mesh_name)
hdf.write(v0, function_name)
hdf.write(w0, function_name_vec)
with dolfin.XDMFFile(mesh.mpi_comm(), str(xdmf_file)) as xdmf:
xdmf.write(mesh)
xdmf.write_checkpoint(v0, function_name, 0, dolfin.XDMFFile.Encoding.HDF5, append=True)
xdmf.write_checkpoint(w0, function_name_vec, 0, dolfin.XDMFFile.Encoding.HDF5, append=True)
xdmf.write_checkpoint(v1, function_name, 1, dolfin.XDMFFile.Encoding.HDF5, append=True)
xdmf.write_checkpoint(w1, function_name_vec, 1, dolfin.XDMFFile.Encoding.HDF5, append=True)
with dolfin.XDMFFile(mesh.mpi_comm(), "test.xdmf") as xdmf:
xdmf.write(mesh)
return v0, w0, v1, w1
def verify_hdf5(
v_ref: dolfin.Function,
w_ref: dolfin.Function,
h5_file: pathlib.Path,
mesh_name: str,
function_name: str,
family: str,
degree: int,
function_name_vec: str,
):
mesh = dolfin.Mesh()
with dolfin.HDF5File(mesh.mpi_comm(), str(h5_file), "r") as hdf:
hdf.read(mesh, mesh_name, False)
V = dolfin.FunctionSpace(mesh, family, degree)
v = dolfin.Function(V)
hdf.read(v, function_name)
W = dolfin.VectorFunctionSpace(mesh, family, degree)
w = dolfin.Function(W)
hdf.read(w, function_name_vec)
assert np.allclose(v.vector().get_local(), v_ref.vector().get_local())
assert np.allclose(w.vector().get_local(), w_ref.vector().get_local())
def verify_xdmf(
v0_ref: dolfin.Function,
w0_ref: dolfin.Function,
v1_ref: dolfin.Function,
w1_ref: dolfin.Function,
xdmf_file: pathlib.Path,
function_name: str,
family: str,
degree: int,
function_name_vec: str,
):
mesh = dolfin.Mesh()
with dolfin.XDMFFile(mesh.mpi_comm(), str(xdmf_file)) as xdmf:
xdmf.read(mesh)
V = dolfin.FunctionSpace(mesh, family, degree)
v0 = dolfin.Function(V)
xdmf.read_checkpoint(v0, function_name, 0)
v1 = dolfin.Function(V)
xdmf.read_checkpoint(v1, function_name, 1)
W = dolfin.VectorFunctionSpace(mesh, family, degree)
w0 = dolfin.Function(W)
xdmf.read_checkpoint(w0, function_name_vec, 0)
w1 = dolfin.Function(W)
xdmf.read_checkpoint(w1, function_name_vec, 1)
assert np.allclose(v0.vector().get_local(), v0_ref.vector().get_local())
assert np.allclose(w0.vector().get_local(), w0_ref.vector().get_local())
assert np.allclose(v1.vector().get_local(), v1_ref.vector().get_local())
assert np.allclose(w1.vector().get_local(), w1_ref.vector().get_local())
if __name__ == "__main__":
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument("--family", type=str, default="DG")
parser.add_argument("--degree", type=int, default=2)
parser.add_argument("--output-dir", type=str, default="legacy", dest="dir")
parser.add_argument("--mesh-name", type=str, default="mesh", dest="name")
parser.add_argument("--function-name", type=str, default="v", dest="f_name")
parser.add_argument("--function-name-vec", type=str, default="w", dest="f_name_vec")
inputs = parser.parse_args()
path = pathlib.Path(inputs.dir)
path.mkdir(exist_ok=True, parents=True)
h5_filename = path / f"{inputs.name}.h5"
xdmf_filename = path / f"{inputs.name}_checkpoint.xdmf"
v0_ref, w0_ref, v1_ref, w1_ref = create_reference_data(
h5_filename,
xdmf_filename,
inputs.name,
inputs.f_name,
inputs.family,
inputs.degree,
inputs.f_name_vec,
)
verify_hdf5(
v0_ref,
w0_ref,
h5_filename,
inputs.name,
inputs.f_name,
inputs.family,
inputs.degree,
inputs.f_name_vec,
)
verify_xdmf(
v0_ref,
w0_ref,
v1_ref,
w1_ref,
xdmf_filename,
inputs.f_name,
inputs.family,
inputs.degree,
inputs.f_name_vec,
)
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