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// Copyright (C) 2012-2020 Chris N. Richardson, Garth N. Wells and Michal Habera
//
// This file is part of DOLFINx (https://www.fenicsproject.org)
//
// SPDX-License-Identifier: LGPL-3.0-or-later
#include "xdmf_function.h"
#include "xdmf_mesh.h"
#include "xdmf_utils.h"
#include <basix/mdspan.hpp>
#include <boost/lexical_cast.hpp>
#include <dolfinx/common/IndexMap.h>
#include <dolfinx/fem/DofMap.h>
#include <dolfinx/fem/FiniteElement.h>
#include <dolfinx/fem/Function.h>
#include <dolfinx/fem/FunctionSpace.h>
#include <dolfinx/mesh/Mesh.h>
#include <dolfinx/mesh/Topology.h>
#include <pugixml.hpp>
#include <string>
using namespace dolfinx;
using namespace dolfinx::io;
namespace
{
/// Convert a shape to the XDMF string description (Scalar, Vector,
/// Tensor).
std::string shape_to_string(std::span<const std::size_t> shape)
{
if (shape.empty())
return "Scalar";
else if (shape.size() == 1 and shape[0] == 1)
return "Scalar";
else if (shape.size() == 1)
return "Vector";
else if (shape.size() == 2)
return "Tensor";
else
throw std::runtime_error("Unsupported value shape");
}
} // namespace
//-----------------------------------------------------------------------------
template <dolfinx::scalar T, std::floating_point U>
void xdmf_function::add_function(MPI_Comm comm, const fem::Function<T, U>& u,
double t, pugi::xml_node& xml_node,
hid_t h5_id)
{
spdlog::info("Adding function to node \"{}\"", xml_node.path('/'));
assert(u.function_space());
auto mesh = u.function_space()->mesh();
assert(mesh);
std::shared_ptr<const fem::FiniteElement<U>> element
= u.function_space()->element();
assert(element);
// FIXME: is the below check adequate for detecting a Lagrange
// element?
// Check that element is Lagrange
if (!element->interpolation_ident())
{
throw std::runtime_error("Only Lagrange functions are supported. "
"Interpolate Functions before output.");
}
auto map_c = mesh->topology()->index_map(mesh->topology()->dim());
assert(map_c);
auto map_x = mesh->geometry().index_map();
assert(map_x);
auto dofmap = u.function_space()->dofmap();
assert(dofmap);
const int bs = dofmap->bs();
// Pad to 3D if vector/tensor is product of dimensions is smaller than 3**rank
// to ensure that we can visualize them correctly in Paraview
std::span<const std::size_t> value_shape = u.function_space()->value_shape();
int rank = value_shape.size();
int num_components = std::reduce(value_shape.begin(), value_shape.end(), 1,
std::multiplies{});
if (num_components < std::pow(3, rank))
num_components = std::pow(3, rank);
// Get fem::Function data values and shape
std::vector<T> data_values;
std::span<const T> x = u.x()->array();
const bool cell_centred
= element->space_dimension() / element->block_size() == 1;
if (cell_centred)
{
// Get dof array and pack into array (padded where appropriate)
const std::int32_t num_local_cells = map_c->size_local();
data_values.resize(num_local_cells * num_components, 0);
for (std::int32_t c = 0; c < num_local_cells; ++c)
{
auto dofs = dofmap->cell_dofs(c);
assert(dofs.size() == 1);
for (std::size_t i = 0; i < dofs.size(); ++i)
for (int j = 0; j < bs; ++j)
data_values[num_components * c + j] = x[bs * dofs[i] + j];
}
}
else
{
// Get number of geometry nodes per cell
const auto& geometry = mesh->geometry();
auto& cmap = geometry.cmap();
int cmap_dim = cmap.dim();
int cell_dim = element->space_dimension() / element->block_size();
if (cmap_dim != cell_dim)
{
throw std::runtime_error(
"Degree of output Function must be same as mesh degree. Maybe the "
"Function needs to be interpolated?");
}
// Check that dofmap layouts are equal and check Lagrange variants
if (dofmap->element_dof_layout() != cmap.create_dof_layout())
{
throw std::runtime_error("Function and Mesh dof layouts do not match. "
"Maybe the Function needs to be interpolated?");
}
if (cmap.degree() > 2
and element->basix_element().lagrange_variant() != cmap.variant())
{
throw std::runtime_error("Mis-match in Lagrange family. Maybe the "
"Function needs to be interpolated?");
}
std::int32_t num_cells = map_c->size_local() + map_c->num_ghosts();
std::int32_t num_local_points = map_x->size_local();
// Get dof array and pack into array (padded where appropriate)
auto dofmap_x = geometry.dofmap();
data_values.resize(num_local_points * num_components, 0);
for (std::int32_t c = 0; c < num_cells; ++c)
{
auto dofs = dofmap->cell_dofs(c);
auto dofs_x = MDSPAN_IMPL_STANDARD_NAMESPACE::submdspan(
dofmap_x, c, MDSPAN_IMPL_STANDARD_NAMESPACE::full_extent);
assert(dofs.size() == dofs_x.size());
for (std::size_t i = 0; i < dofs.size(); ++i)
{
if (dofs_x[i] < num_local_points)
{
for (int j = 0; j < bs; ++j)
data_values[num_components * dofs_x[i] + j] = x[bs * dofs[i] + j];
}
}
}
}
// Global size
const std::int64_t num_values
= cell_centred ? map_c->size_global() : map_x->size_global();
const std::int64_t num_local = data_values.size() / num_components;
std::int64_t offset = 0;
MPI_Exscan(&num_local, &offset, 1, MPI_INT64_T, MPI_SUM, comm);
const bool use_mpi_io = dolfinx::MPI::size(comm) > 1;
std::vector<std::string> components = {""};
if constexpr (!std::is_scalar_v<T>)
components = {"real_", "imag_"};
std::string t_str = boost::lexical_cast<std::string>(t);
std::replace(t_str.begin(), t_str.end(), '.', '_');
for (auto component : components)
{
std::string attr_name = component + u.name;
std::string dataset_name
= std::string("/Function/") + attr_name + std::string("/") + t_str;
// Add attribute node
pugi::xml_node attr_node = xml_node.append_child("Attribute");
assert(attr_node);
attr_node.append_attribute("Name") = attr_name.c_str();
attr_node.append_attribute("AttributeType")
= shape_to_string(value_shape).c_str();
attr_node.append_attribute("Center") = cell_centred ? "Cell" : "Node";
std::span<const scalar_value_type_t<T>> u;
std::vector<scalar_value_type_t<T>> _data;
if constexpr (!std::is_scalar_v<T>)
{
// Complex-valued case
_data.resize(data_values.size());
if (component == "real_")
{
std::ranges::transform(data_values, _data.begin(),
[](auto x) { return x.real(); });
}
else if (component == "imag_")
{
std::ranges::transform(data_values, _data.begin(),
[](auto x) { return x.imag(); });
}
u = std::span<const scalar_value_type_t<T>>(_data);
}
else
u = std::span<const T>(data_values);
// -- Real case, add data item
xdmf_utils::add_data_item(attr_node, h5_id, dataset_name, u, offset,
{num_values, num_components}, "", use_mpi_io);
}
}
//-----------------------------------------------------------------------------
// Instantiation for different types
/// @cond
template void xdmf_function::add_function(MPI_Comm,
const fem::Function<float, float>&,
double, pugi::xml_node&, hid_t);
template void xdmf_function::add_function(MPI_Comm,
const fem::Function<double, double>&,
double, pugi::xml_node&, hid_t);
template void
xdmf_function::add_function(MPI_Comm,
const fem::Function<std::complex<float>, float>&,
double, pugi::xml_node&, hid_t);
template void
xdmf_function::add_function(MPI_Comm,
const fem::Function<std::complex<double>, double>&,
double, pugi::xml_node&, hid_t);
/// @endcond
//-----------------------------------------------------------------------------
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