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HDF XDMF entry: store reference cell #14056

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Jul 6, 2022
Merged

HDF XDMF entry: store reference cell #14056

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885f234
Revert "Remove deprecated XDMFEntry::get_xdmf_content"
tjhei Jun 28, 2022
7c09264
XDMF changes
tjhei Jun 24, 2022
cb2ad0a
remove serialization text from test output
tjhei Jun 26, 2022
9cb9ec6
use the new constructor
tjhei Jun 26, 2022
3b9663d
address comment
tjhei Jun 29, 2022
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4 changes: 0 additions & 4 deletions doc/news/changes/incompatibilities/20220627Arndt-1
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64 changes: 60 additions & 4 deletions include/deal.II/base/data_out_base.h
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Original file line number Diff line number Diff line change
Expand Up @@ -3322,15 +3322,28 @@ class XDMFEntry
* cases where <code>solution_filename == mesh_filename</code>, and
* <code>dim==spacedim</code>.
*/
XDMFEntry(const std::string & filename,
const double time,
const std::uint64_t nodes,
const std::uint64_t cells,
const unsigned int dim,
const ReferenceCell &cell_type);

/**
* Deprecated constructor.
*
* @deprecated Use the constructor that additionally takes a ReferenceCell.
*/
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Suggested change
*/
*/
DEAL_II_DEPRECATED_EARLY

or the other one.

XDMFEntry(const std::string & filename,
const double time,
const std::uint64_t nodes,
const std::uint64_t cells,
const unsigned int dim);

/**
* Simplified constructor that calls the complete constructor for
* cases where <code>dim==spacedim</code>.
* Deprecated constructor.
*
* @deprecated Use the constructor that additionally takes a ReferenceCell.
*/
XDMFEntry(const std::string & mesh_filename,
const std::string & solution_filename,
Expand All @@ -3340,8 +3353,23 @@ class XDMFEntry
const unsigned int dim);

/**
* Constructor that sets all members to provided parameters.
* Simplified constructor that calls the complete constructor for
* cases where <code>dim==spacedim</code>.
*/
XDMFEntry(const std::string & mesh_filename,
const std::string & solution_filename,
const double time,
const std::uint64_t nodes,
const std::uint64_t cells,
const unsigned int dim,
const ReferenceCell &cell_type);

/**
* Deprecated constructor.
*
* @deprecated Use the constructor that additionally takes a ReferenceCell.
*/
DEAL_II_DEPRECATED
XDMFEntry(const std::string & mesh_filename,
const std::string & solution_filename,
const double time,
Expand All @@ -3350,6 +3378,18 @@ class XDMFEntry
const unsigned int dim,
const unsigned int spacedim);

/**
* Constructor that sets all members to provided parameters.
*/
XDMFEntry(const std::string & mesh_filename,
const std::string & solution_filename,
const double time,
const std::uint64_t nodes,
const std::uint64_t cells,
const unsigned int dim,
const unsigned int spacedim,
const ReferenceCell &cell_type);

/**
* Record an attribute and associated dimensionality.
*/
Expand All @@ -3366,14 +3406,24 @@ class XDMFEntry
serialize(Archive &ar, const unsigned int /*version*/)
{
ar &valid &h5_sol_filename &h5_mesh_filename &entry_time &num_nodes
&num_cells &dimension &space_dimension &attribute_dims;
&num_cells &dimension &space_dimension &cell_type &attribute_dims;
}

/**
* Get the XDMF content associated with this entry.
* If the entry is not valid, this returns an empty string.
*/
std::string
get_xdmf_content(const unsigned int indent_level) const;

/**
* Get the XDMF content associated with this entry.
* If the entry is not valid, this returns an empty string.
*
* @deprecated Use the other function instead.
*/
DEAL_II_DEPRECATED
std::string
get_xdmf_content(const unsigned int indent_level,
const ReferenceCell &reference_cell) const;

Expand Down Expand Up @@ -3419,6 +3469,12 @@ class XDMFEntry
*/
unsigned int space_dimension;

/**
* The type of cell in deal.II language. We currently only support
* xdmf entries where all cells have the same type.
*/
ReferenceCell cell_type;

/**
* The attributes associated with this entry and their dimension.
*/
Expand Down
148 changes: 125 additions & 23 deletions source/base/data_out_base.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -7985,13 +7985,24 @@ DataOutInterface<dim, spacedim>::create_xdmf_entry(
// Output the XDMF file only on the root process
if (myrank == 0)
{
const auto &patches = get_patches();
Assert(patches.size() > 0, DataOutBase::ExcNoPatches());
// We currently don't support writing mixed meshes:
#ifdef DEBUG
for (const auto &patch : patches)
Assert(patch.reference_cell == patches[0].reference_cell,
ExcNotImplemented());
#endif


XDMFEntry entry(h5_mesh_filename,
h5_solution_filename,
cur_time,
global_node_cell_count[0],
global_node_cell_count[1],
dim,
spacedim);
spacedim,
patches[0].reference_cell);
unsigned int n_data_sets = data_filter.n_data_sets();

// The vector names generated here must match those generated in the HDF5
Expand Down Expand Up @@ -8037,20 +8048,9 @@ DataOutInterface<dim, spacedim>::write_xdmf_file(
xdmf_file
<< " <Grid Name=\"CellTime\" GridType=\"Collection\" CollectionType=\"Temporal\">\n";

// Write out all the entries indented
const auto &patches = get_patches();
Assert(patches.size() > 0, DataOutBase::ExcNoPatches());

// We currently don't support writing mixed meshes:
#ifdef DEBUG
for (const auto &patch : patches)
Assert(patch.reference_cell == patches[0].reference_cell,
ExcNotImplemented());
#endif

for (const auto &entry : entries)
{
xdmf_file << entry.get_xdmf_content(3, patches[0].reference_cell);
xdmf_file << entry.get_xdmf_content(3);
}

xdmf_file << " </Grid>\n";
Expand Down Expand Up @@ -9129,6 +9129,7 @@ XDMFEntry::XDMFEntry()
, num_cells(numbers::invalid_unsigned_int)
, dimension(numbers::invalid_unsigned_int)
, space_dimension(numbers::invalid_unsigned_int)
, cell_type()
{}


Expand All @@ -9138,7 +9139,16 @@ XDMFEntry::XDMFEntry(const std::string & filename,
const std::uint64_t nodes,
const std::uint64_t cells,
const unsigned int dim)
: XDMFEntry(filename, filename, time, nodes, cells, dim, dim)
: XDMFEntry(filename, filename, time, nodes, cells, dim, dim, ReferenceCell())
{}

XDMFEntry::XDMFEntry(const std::string & filename,
const double time,
const std::uint64_t nodes,
const std::uint64_t cells,
const unsigned int dim,
const ReferenceCell &cell_type)
: XDMFEntry(filename, filename, time, nodes, cells, dim, dim, cell_type)
{}


Expand All @@ -9149,7 +9159,33 @@ XDMFEntry::XDMFEntry(const std::string & mesh_filename,
const std::uint64_t nodes,
const std::uint64_t cells,
const unsigned int dim)
: XDMFEntry(mesh_filename, solution_filename, time, nodes, cells, dim, dim)
: XDMFEntry(mesh_filename,
solution_filename,
time,
nodes,
cells,
dim,
dim,
ReferenceCell())
{}



XDMFEntry::XDMFEntry(const std::string & mesh_filename,
const std::string & solution_filename,
const double time,
const std::uint64_t nodes,
const std::uint64_t cells,
const unsigned int dim,
const ReferenceCell &cell_type)
: XDMFEntry(mesh_filename,
solution_filename,
time,
nodes,
cells,
dim,
dim,
cell_type)
{}


Expand All @@ -9161,6 +9197,59 @@ XDMFEntry::XDMFEntry(const std::string & mesh_filename,
const std::uint64_t cells,
const unsigned int dim,
const unsigned int spacedim)
: XDMFEntry(mesh_filename,
solution_filename,
time,
nodes,
cells,
dim,
spacedim,
ReferenceCell())
{}



namespace
{
/**
* Deprecated XDMFEntry constructors do not fill the cell_type, so we use this
* little helper to convert it to the appropriate hex cell.
*/
ReferenceCell
cell_type_hex_if_invalid(const ReferenceCell &cell_type,
const unsigned int dimension)
{
if (cell_type == ReferenceCells::Invalid)
{
switch (dimension)
{
case 0:
return ReferenceCells::get_hypercube<0>();
case 1:
return ReferenceCells::get_hypercube<1>();
case 2:
return ReferenceCells::get_hypercube<2>();
case 3:
return ReferenceCells::get_hypercube<3>();
default:
AssertThrow(false, ExcMessage("Invalid dimension"));
}
}
else
return cell_type;
}
} // namespace



XDMFEntry::XDMFEntry(const std::string & mesh_filename,
const std::string & solution_filename,
const double time,
const std::uint64_t nodes,
const std::uint64_t cells,
const unsigned int dim,
const unsigned int spacedim,
const ReferenceCell &cell_type_)
: valid(true)
, h5_sol_filename(solution_filename)
, h5_mesh_filename(mesh_filename)
Expand All @@ -9169,6 +9258,7 @@ XDMFEntry::XDMFEntry(const std::string & mesh_filename,
, num_cells(cells)
, dimension(dim)
, space_dimension(spacedim)
, cell_type(cell_type_hex_if_invalid(cell_type_, dim))
{}


Expand Down Expand Up @@ -9202,6 +9292,18 @@ namespace
std::string
XDMFEntry::get_xdmf_content(const unsigned int indent_level,
const ReferenceCell &reference_cell) const
{
// We now store the type of cell in the XDMFEntry:
(void)reference_cell;
Assert(cell_type == reference_cell,
ExcMessage("Incorrect ReferenceCell type passed in."));
return get_xdmf_content(indent_level);
}



std::string
XDMFEntry::get_xdmf_content(const unsigned int indent_level) const
{
if (!valid)
return "";
Expand Down Expand Up @@ -9234,26 +9336,26 @@ XDMFEntry::get_xdmf_content(const unsigned int indent_level,
}
else if (dimension == 2)
{
Assert(reference_cell == ReferenceCells::Quadrilateral ||
reference_cell == ReferenceCells::Triangle,
Assert(cell_type == ReferenceCells::Quadrilateral ||
cell_type == ReferenceCells::Triangle,
ExcNotImplemented());

if (reference_cell == ReferenceCells::Quadrilateral)
if (cell_type == ReferenceCells::Quadrilateral)
{
ss << "Quadrilateral";
}
else // if (reference_cell == ReferenceCells::Triangle)
else // if (cell_type == ReferenceCells::Triangle)
{
ss << "Triangle";
}
}
else if (dimension == 3)
{
Assert(reference_cell == ReferenceCells::Hexahedron ||
reference_cell == ReferenceCells::Tetrahedron,
Assert(cell_type == ReferenceCells::Hexahedron ||
cell_type == ReferenceCells::Tetrahedron,
ExcNotImplemented());

if (reference_cell == ReferenceCells::Hexahedron)
if (cell_type == ReferenceCells::Hexahedron)
{
ss << "Hexahedron";
}
Expand All @@ -9273,7 +9375,7 @@ XDMFEntry::get_xdmf_content(const unsigned int indent_level,
ss << "\">\n";

ss << indent(indent_level + 2) << "<DataItem Dimensions=\"" << num_cells
<< " " << reference_cell.n_vertices()
<< " " << cell_type.n_vertices()
<< "\" NumberType=\"UInt\" Format=\"HDF\">\n";

ss << indent(indent_level + 3) << h5_mesh_filename << ":/cells\n";
Expand Down
2 changes: 1 addition & 1 deletion tests/data_out/data_out_hdf5_02.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -134,7 +134,7 @@ check()
<< " <Grid Name=\"CellTime\" GridType=\"Collection\" CollectionType=\"Temporal\">\n";

// Write out the entry
xdmf_file << entry.get_xdmf_content(3, ReferenceCells::get_hypercube<dim>());
xdmf_file << entry.get_xdmf_content(3);

xdmf_file << " </Grid>\n";
xdmf_file << " </Domain>\n";
Expand Down
2 changes: 1 addition & 1 deletion tests/mpi/data_out_hdf5_02.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -86,7 +86,7 @@ check()
<< " <Grid Name=\"CellTime\" GridType=\"Collection\" CollectionType=\"Temporal\">\n";

// Write out the entry
xdmf_file << entry.get_xdmf_content(3, ReferenceCells::get_hypercube<dim>());
xdmf_file << entry.get_xdmf_content(3);

xdmf_file << " </Grid>\n";
xdmf_file << " </Domain>\n";
Expand Down
7 changes: 2 additions & 5 deletions tests/serialization/xdmf_entry.cc
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Expand Up @@ -43,7 +43,6 @@ test()
oa << entry1;
// archive and stream closed when destructors are called
}
deallog << oss.str() << std::endl;

// verify correctness of the serialization
{
Expand All @@ -54,13 +53,11 @@ test()

deallog << "XDMFEntry before serialization: " << std::endl
<< std::endl
<< entry1.get_xdmf_content(0, ReferenceCells::get_hypercube<dim>())
<< std::endl;
<< entry1.get_xdmf_content(0) << std::endl;

deallog << "XDMFEntry after de-serialization: " << std::endl
<< std::endl
<< entry2.get_xdmf_content(0, ReferenceCells::get_hypercube<dim>())
<< std::endl;
<< entry2.get_xdmf_content(0) << std::endl;
}


Expand Down