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Make read_meshtags a template function #3533

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Make read_meshtags a template function #3533

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35a65b4
Safe default value for unbound variables in dolfinx.conf
mleoni-pf Oct 14, 2024
dfca9ce
Merge branch 'FEniCS:main' into main
mleoni-pf Nov 21, 2024
8de82a7
Merge branch 'main' of github.com:FEniCS/dolfinx
mleoni-pf Nov 22, 2024
a095f16
Merge branch 'FEniCS:main' into main
mleoni-pf Nov 24, 2024
f892d40
Merge branch 'main' of github.com:FEniCS/dolfinx
mleoni-pf Nov 25, 2024
2700ed7
Make read_meshtags a template function
mleoni-pf Nov 25, 2024
20924b1
Merge branch 'main' into mleoni/make_read_meshtags_a_template_function
mleoni-pf Nov 25, 2024
8d7c60c
Fix signature of explicit template instantiation
mleoni-pf Nov 25, 2024
0c5c541
Merge branch 'main' into mleoni/make_read_meshtags_a_template_function
mleoni-pf Nov 25, 2024
087e384
Merge branch 'main' into mleoni/make_read_meshtags_a_template_function
mleoni-pf Nov 28, 2024
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25 changes: 19 additions & 6 deletions cpp/dolfinx/io/XDMFFile.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -333,7 +333,8 @@ template void XDMFFile::write_meshtags(const mesh::MeshTags<std::int32_t>&,
std::string, std::string);
/// @endcond
//-----------------------------------------------------------------------------
mesh::MeshTags<std::int32_t>
template <typename T>
mesh::MeshTags<T>
XDMFFile::read_meshtags(const mesh::Mesh<double>& mesh, std::string name,
std::optional<std::string> attribute_name,
std::string xpath)
Expand Down Expand Up @@ -365,8 +366,8 @@ XDMFFile::read_meshtags(const mesh::Mesh<double>& mesh, std::string name,
else
values_data_node = attribute_node.child("DataItem");
}
const std::vector values = xdmf_utils::get_dataset<std::int32_t>(
_comm.comm(), values_data_node, _h5_id);
const std::vector values
= xdmf_utils::get_dataset<T>(_comm.comm(), values_data_node, _h5_id);

const std::pair<std::string, int> cell_type_str
= xdmf_utils::get_cell_type(grid_node.child("Topology"));
Expand All @@ -380,8 +381,8 @@ XDMFFile::read_meshtags(const mesh::Mesh<double>& mesh, std::string name,
const std::int64_t,
MDSPAN_IMPL_STANDARD_NAMESPACE::dextents<std::size_t, 2>>
entities_span(entities1.data(), eshape);
std::pair<std::vector<std::int32_t>, std::vector<std::int32_t>>
entities_values = xdmf_utils::distribute_entity_data<std::int32_t>(
std::pair<std::vector<std::int32_t>, std::vector<T>> entities_values
= xdmf_utils::distribute_entity_data<T>(
*mesh.topology(), mesh.geometry().input_global_indices(),
mesh.geometry().index_map()->size_global(),
mesh.geometry().cmap().create_dof_layout(), mesh.geometry().dofmap(),
Expand All @@ -397,12 +398,24 @@ XDMFFile::read_meshtags(const mesh::Mesh<double>& mesh, std::string name,
num_vertices_per_entity);
mesh::MeshTags meshtags = mesh::create_meshtags(
mesh.topology(), mesh::cell_dim(cell_type), entities_adj,
std::span<const std::int32_t>(entities_values.second));
std::span<const T>(entities_values.second));
meshtags.name = name;

return meshtags;
}
//-----------------------------------------------------------------------------
// Instantiation for different types
/// @cond
template mesh::MeshTags<std::int32_t>
XDMFFile::read_meshtags(const mesh::Mesh<double>& mesh, std::string name,
std::optional<std::string> attribute_name,
std::string xpath);
template mesh::MeshTags<double>
XDMFFile::read_meshtags(const mesh::Mesh<double>& mesh, std::string name,
std::optional<std::string> attribute_name,
std::string xpath);
/// @endcond
//-----------------------------------------------------------------------------
std::pair<mesh::CellType, int> XDMFFile::read_cell_type(std::string grid_name,
std::string xpath)
{
Expand Down
9 changes: 5 additions & 4 deletions cpp/dolfinx/io/XDMFFile.h
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Original file line number Diff line number Diff line change
Expand Up @@ -170,10 +170,11 @@ class XDMFFile
/// GridType="Uniform"
/// @param[in] attribute_name Name of the attribute to read
/// @param[in] xpath XPath where MeshTags Grid is stored in file
mesh::MeshTags<std::int32_t>
read_meshtags(const mesh::Mesh<double>& mesh, std::string name,
std::optional<std::string> attribute_name,
std::string xpath = "/Xdmf/Domain");
template <typename T = std::int32_t>
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What types are supported? If the type in the file can't be checked it can lead to all sorts of crashes and mis-behaviours.

What is needed for this to be robust is a function for querying the data type in the file. I started this ages ago for HDF5 files, but it wasn't trivial to make it precise, but getting the type size was easy and may be adequate.

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We hit the same issue with the recent checkpointing project. We should have a chat in #developmemt about the best ways to tackle this.

mesh::MeshTags<T> read_meshtags(const mesh::Mesh<double>& mesh,
std::string name,
std::optional<std::string> attribute_name,
std::string xpath = "/Xdmf/Domain");

/// Write Information
/// @param[in] name
Expand Down
2 changes: 1 addition & 1 deletion python/dolfinx/wrappers/io.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -271,7 +271,7 @@ void io(nb::module_& m)
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,
.def("read_meshtags", &dolfinx::io::XDMFFile::read_meshtags<std::int32_t>,
nb::arg("mesh"), nb::arg("name"), nb::arg("attribute_name").none(),
nb::arg("xpath"))
.def("write_information", &dolfinx::io::XDMFFile::write_information,
Expand Down
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