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// Copyright (C) 2017-2021 Chris N. Richardson Garth N. Wells
//
// This file is part of DOLFINx (https://www.fenicsproject.org)
//
// SPDX-License-Identifier: LGPL-3.0-or-later
#include "array.h"
#include "caster_mpi.h"
#include <basix/mdspan.hpp>
#include <dolfinx/common/defines.h>
#include <dolfinx/fem/Function.h>
#include <dolfinx/fem/FunctionSpace.h>
#include <dolfinx/io/ADIOS2Writers.h>
#include <dolfinx/io/VTKFile.h>
#include <dolfinx/io/XDMFFile.h>
#include <dolfinx/io/cells.h>
#include <dolfinx/io/vtk_utils.h>
#include <dolfinx/io/xdmf_utils.h>
#include <dolfinx/mesh/Mesh.h>
#include <dolfinx/mesh/MeshTags.h>
#include <filesystem>
#include <memory>
#include <nanobind/nanobind.h>
#include <nanobind/ndarray.h>
#include <nanobind/stl/complex.h>
#include <nanobind/stl/filesystem.h>
#include <nanobind/stl/pair.h>
#include <nanobind/stl/shared_ptr.h>
#include <nanobind/stl/string.h>
#include <nanobind/stl/variant.h>
#include <nanobind/stl/vector.h>
#include <span>
#include <vector>
namespace nb = nanobind;
namespace dolfinx_wrappers
{
namespace
{
template <typename T, std::size_t ndim>
using mdspan_t = MDSPAN_IMPL_STANDARD_NAMESPACE::mdspan<
const T, MDSPAN_IMPL_STANDARD_NAMESPACE::dextents<std::size_t, ndim>>;
template <typename T>
void xdmf_real_fn(auto&& m)
{
m.def(
"write_mesh",
[](dolfinx::io::XDMFFile& self, const dolfinx::mesh::Mesh<T>& mesh,
std::string xpath) { self.write_mesh(mesh, xpath); },
nb::arg("mesh"), nb::arg("xpath") = "/Xdmf/Domain");
m.def(
"write_meshtags",
[](dolfinx::io::XDMFFile& self,
const dolfinx::mesh::MeshTags<std::int32_t>& meshtags,
const dolfinx::mesh::Geometry<T>& x, std::string geometry_xpath,
std::string xpath)
{ self.write_meshtags(meshtags, x, geometry_xpath, xpath); },
nb::arg("meshtags"), nb::arg("x"), nb::arg("geometry_xpath"),
nb::arg("xpath") = "/Xdmf/Domain");
}
template <typename T, typename U>
void xdmf_scalar_fn(auto&& m)
{
m.def(
"write_function",
[](dolfinx::io::XDMFFile& self, const dolfinx::fem::Function<T, U>& u,
double t, std::string mesh_xpath)
{ self.write_function(u, t, mesh_xpath); },
nb::arg("u"), nb::arg("t"),
nb::arg("mesh_xpath") = "/Xdmf/Domain/Grid[@GridType='Uniform'][1]");
}
template <typename T>
void vtk_real_fn(auto&& m)
{
m.def(
"write",
[](dolfinx::io::VTKFile& self, const dolfinx::mesh::Mesh<T>& mesh,
double t) { self.write(mesh, t); },
nb::arg("mesh"), nb::arg("t") = 0.0);
}
template <typename T, typename U>
void vtk_scalar_fn(auto&& m)
{
m.def(
"write",
[](dolfinx::io::VTKFile& self,
const std::vector<std::shared_ptr<const dolfinx::fem::Function<T, U>>>
u_ptr,
double t)
{
std::vector<std::reference_wrapper<const dolfinx::fem::Function<T, U>>>
u;
for (auto q : u_ptr)
u.push_back(*q);
self.write(u, t);
},
nb::arg("u"), nb::arg("t") = 0.0);
}
template <typename T>
void declare_vtx_writer(nb::module_& m, std::string type)
{
#ifdef HAS_ADIOS2
{
std::string pyclass_name = "VTXWriter_" + type;
nb::class_<dolfinx::io::VTXWriter<T>>(m, pyclass_name.c_str())
.def(
"__init__",
[](dolfinx::io::VTXWriter<T>* self, MPICommWrapper comm,
std::filesystem::path filename,
std::shared_ptr<const dolfinx::mesh::Mesh<T>> mesh,
std::string engine) {
new (self)
dolfinx::io::VTXWriter<T>(comm.get(), filename, mesh, engine);
},
nb::arg("comm"), nb::arg("filename"), nb::arg("mesh"),
nb::arg("engine"))
.def(
"__init__",
[](dolfinx::io::VTXWriter<T>* self, MPICommWrapper comm,
std::filesystem::path filename,
const std::vector<std::variant<
std::shared_ptr<const dolfinx::fem::Function<float, T>>,
std::shared_ptr<const dolfinx::fem::Function<double, T>>,
std::shared_ptr<
const dolfinx::fem::Function<std::complex<float>, T>>,
std::shared_ptr<const dolfinx::fem::Function<
std::complex<double>, T>>>>& u,
std::string engine, dolfinx::io::VTXMeshPolicy policy)
{
new (self) dolfinx::io::VTXWriter<T>(comm.get(), filename, u,
engine, policy);
},
nb::arg("comm"), nb::arg("filename"), nb::arg("u"),
nb::arg("engine") = "BPFile",
nb::arg("policy") = dolfinx::io::VTXMeshPolicy::update)
.def("close", [](dolfinx::io::VTXWriter<T>& self) { self.close(); })
.def(
"write", [](dolfinx::io::VTXWriter<T>& self, double t)
{ self.write(t); }, nb::arg("t"));
}
{
std::string pyclass_name = "FidesWriter_" + type;
nb::class_<dolfinx::io::FidesWriter<T>>(m, pyclass_name.c_str(),
"FidesWriter object")
.def(
"__init__",
[](dolfinx::io::FidesWriter<T>* self, MPICommWrapper comm,
std::filesystem::path filename,
std::shared_ptr<const dolfinx::mesh::Mesh<T>> mesh,
std::string engine) {
new (self) dolfinx::io::FidesWriter<T>(comm.get(), filename, mesh,
engine);
},
nb::arg("comm"), nb::arg("filename"), nb::arg("mesh"),
nb::arg("engine") = "BPFile")
.def(
"__init__",
[](dolfinx::io::FidesWriter<T>* self, MPICommWrapper comm,
std::filesystem::path filename,
const std::vector<std::variant<
std::shared_ptr<const dolfinx::fem::Function<float, T>>,
std::shared_ptr<const dolfinx::fem::Function<double, T>>,
std::shared_ptr<
const dolfinx::fem::Function<std::complex<float>, T>>,
std::shared_ptr<const dolfinx::fem::Function<
std::complex<double>, T>>>>& u,
std::string engine, dolfinx::io::FidesMeshPolicy policy)
{
new (self) dolfinx::io::FidesWriter<T>(comm.get(), filename, u,
engine, policy);
},
nb::arg("comm"), nb::arg("filename"), nb::arg("u"),
nb::arg("engine") = "BPFile",
nb::arg("policy") = dolfinx::io::FidesMeshPolicy::update)
.def("close", [](dolfinx::io::FidesWriter<T>& self) { self.close(); })
.def(
"write", [](dolfinx::io::FidesWriter<T>& self, double t)
{ self.write(t); }, nb::arg("t"));
}
#endif
}
template <typename T>
void declare_data_types(nb::module_& m)
{
m.def(
"distribute_entity_data",
[](const dolfinx::mesh::Topology topology,
nb::ndarray<const std::int64_t, nb::ndim<1>, nb::c_contig>
input_global_indices,
std::int64_t num_nodes_g, const fem::ElementDofLayout& cmap_dof_layout,
nb::ndarray<const std::int32_t, nb::ndim<2>, nb::c_contig> xdofmap,
int entity_dim,
nb::ndarray<const std::int64_t, nb::ndim<2>, nb::c_contig> entities,
nb::ndarray<const T, nb::ndim<1>, nb::c_contig> values)
{
assert(entities.shape(0) == values.size());
mdspan_t<const std::int64_t, 2> entities_span(
entities.data(), entities.shape(0), entities.shape(1));
mdspan_t<const std::int32_t, 2> xdofmap_span(
xdofmap.data(), xdofmap.shape(0), xdofmap.shape(1));
std::span<const std::int64_t> input_global_indices_span(
input_global_indices.data(), input_global_indices.size());
std::pair<std::vector<std::int32_t>, std::vector<T>> entities_values
= dolfinx::io::xdmf_utils::distribute_entity_data<T>(
topology, input_global_indices_span, num_nodes_g,
cmap_dof_layout, xdofmap_span, entity_dim, entities_span,
std::span(values.data(), values.size()));
std::size_t num_vert_per_entity = dolfinx::mesh::cell_num_entities(
dolfinx::mesh::cell_entity_type(topology.cell_type(), entity_dim,
0),
0);
return std::pair(
as_nbarray(std::move(entities_values.first),
{entities_values.first.size() / num_vert_per_entity,
num_vert_per_entity}),
as_nbarray(std::move(entities_values.second)));
},
nb::arg("topology"), nb::arg("input_global_indices"),
nb::arg("num_nodes_g"), nb::arg("cmap_dof_layout"), nb::arg("xdofmap"),
nb::arg("entity_dim"), nb::arg("entities"),
nb::arg("values").noconvert());
}
} // namespace
void io(nb::module_& m)
{
// dolfinx::io::cell vtk cell type converter
m.def("get_vtk_cell_type", &dolfinx::io::cells::get_vtk_cell_type,
nb::arg("cell"), nb::arg("dim"), "Get VTK cell identifier");
m.def(
"extract_vtk_connectivity",
[](nb::ndarray<const std::int32_t, nb::ndim<2>, nb::c_contig> dofmap,
dolfinx::mesh::CellType cell)
{
mdspan_t<const std::int32_t, 2> _dofmap(dofmap.data(), dofmap.shape(0),
dofmap.shape(1));
auto [cells, shape]
= dolfinx::io::extract_vtk_connectivity(_dofmap, cell);
return as_nbarray(std::move(cells), shape.size(), shape.data());
},
nb::arg("dofmap"), nb::arg("celltype"),
"Extract the mesh topology with VTK ordering using "
"geometry indices");
// dolfinx::io::cell permutation functions
m.def("perm_vtk", &dolfinx::io::cells::perm_vtk, nb::arg("type"),
nb::arg("num_nodes"),
"Permutation array to map from VTK to DOLFINx node ordering");
m.def("perm_gmsh", &dolfinx::io::cells::perm_gmsh, nb::arg("type"),
nb::arg("num_nodes"),
"Permutation array to map from Gmsh to DOLFINx node ordering");
// dolfinx::io::XDMFFile
nb::class_<dolfinx::io::XDMFFile> xdmf_file(m, "XDMFFile");
// dolfinx::io::XDMFFile::Encoding enums
nb::enum_<dolfinx::io::XDMFFile::Encoding>(xdmf_file, "Encoding")
.value("HDF5", dolfinx::io::XDMFFile::Encoding::HDF5, "HDF5 encoding")
.value("ASCII", dolfinx::io::XDMFFile::Encoding::ASCII,
"Plain text encoding");
xdmf_file
.def(
"__init__",
[](dolfinx::io::XDMFFile* x, MPICommWrapper comm,
std::filesystem::path filename, std::string file_mode,
dolfinx::io::XDMFFile::Encoding encoding) {
new (x) dolfinx::io::XDMFFile(comm.get(), filename, file_mode,
encoding);
},
nb::arg("comm"), nb::arg("filename"), nb::arg("file_mode"),
nb::arg("encoding") = dolfinx::io::XDMFFile::Encoding::HDF5)
.def("close", &dolfinx::io::XDMFFile::close)
.def("write_geometry", &dolfinx::io::XDMFFile::write_geometry,
nb::arg("geometry"), nb::arg("name") = "geometry",
nb::arg("xpath") = "/Xdmf/Domain")
.def(
"read_topology_data",
[](dolfinx::io::XDMFFile& self, std::string name, std::string xpath)
{
auto [cells, shape] = self.read_topology_data(name, xpath);
return as_nbarray(std::move(cells), shape.size(), shape.data());
},
nb::arg("name") = "mesh", nb::arg("xpath") = "/Xdmf/Domain")
.def(
"read_geometry_data",
[](dolfinx::io::XDMFFile& self, std::string name, std::string xpath)
{
auto [x, shape] = self.read_geometry_data(name, xpath);
std::vector<double>& _x = std::get<std::vector<double>>(x);
return as_nbarray(std::move(_x), shape.size(), shape.data());
},
nb::arg("name") = "mesh", nb::arg("xpath") = "/Xdmf/Domain")
.def("read_geometry_data", &dolfinx::io::XDMFFile::read_geometry_data,
nb::arg("name") = "mesh", nb::arg("xpath") = "/Xdmf/Domain")
.def("read_cell_type", &dolfinx::io::XDMFFile::read_cell_type,
nb::arg("name") = "mesh", nb::arg("xpath") = "/Xdmf/Domain")
.def("read_meshtags", &dolfinx::io::XDMFFile::read_meshtags,
nb::arg("mesh"), nb::arg("name"), nb::arg("xpath") = "/Xdmf/Domain")
.def("write_information", &dolfinx::io::XDMFFile::write_information,
nb::arg("name"), nb::arg("value"), nb::arg("xpath") = "/Xdmf/Domain")
.def("read_information", &dolfinx::io::XDMFFile::read_information,
nb::arg("name"), nb::arg("xpath") = "/Xdmf/Domain")
.def_prop_ro(
"comm", [](dolfinx::io::XDMFFile& self)
{ return MPICommWrapper(self.comm()); }, nb::keep_alive<0, 1>());
xdmf_real_fn<float>(xdmf_file);
xdmf_real_fn<double>(xdmf_file);
xdmf_scalar_fn<float, float>(xdmf_file);
xdmf_scalar_fn<double, double>(xdmf_file);
xdmf_scalar_fn<std::complex<float>, float>(xdmf_file);
xdmf_scalar_fn<std::complex<double>, double>(xdmf_file);
// dolfinx::io::VTKFile
nb::class_<dolfinx::io::VTKFile> vtk_file(m, "VTKFile");
vtk_file
.def(
"__init__",
[](dolfinx::io::VTKFile* v, MPICommWrapper comm,
std::filesystem::path filename, std::string mode)
{ new (v) dolfinx::io::VTKFile(comm.get(), filename, mode); },
nb::arg("comm"), nb::arg("filename"), nb::arg("mode"))
.def("close", &dolfinx::io::VTKFile::close);
vtk_real_fn<float>(vtk_file);
vtk_real_fn<double>(vtk_file);
vtk_scalar_fn<float, float>(vtk_file);
vtk_scalar_fn<double, double>(vtk_file);
vtk_scalar_fn<std::complex<float>, float>(vtk_file);
vtk_scalar_fn<std::complex<double>, double>(vtk_file);
#ifdef HAS_ADIOS2
nb::enum_<dolfinx::io::FidesMeshPolicy>(m, "FidesMeshPolicy")
.value("update", dolfinx::io::FidesMeshPolicy::update)
.value("reuse", dolfinx::io::FidesMeshPolicy::reuse);
nb::enum_<dolfinx::io::VTXMeshPolicy>(m, "VTXMeshPolicy")
.value("update", dolfinx::io::VTXMeshPolicy::update)
.value("reuse", dolfinx::io::VTXMeshPolicy::reuse);
#endif
declare_vtx_writer<float>(m, "float32");
declare_vtx_writer<double>(m, "float64");
declare_data_types<std::int32_t>(m);
declare_data_types<float>(m);
declare_data_types<std::complex<float>>(m);
declare_data_types<double>(m);
declare_data_types<std::complex<double>>(m);
}
} // namespace dolfinx_wrappers
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