xdmf_utils.h

// Copyright (C) 2012 Chris N. Richardson
//
// This file is part of DOLFINx (https://www.fenicsproject.org)
//
// SPDX-License-Identifier:    LGPL-3.0-or-later
 
#pragma once
 
#include "HDF5Interface.h"
#include "pugixml.hpp"
#include <array>
#include <dolfinx/common/utils.h>
#include <dolfinx/mesh/cell_types.h>
#include <filesystem>
#include <string>
#include <utility>
#include <vector>
#include <xtl/xspan.hpp>
 
namespace pugi
{
class xml_node;
} // namespace pugi
 
namespace dolfinx
{
 
namespace fem
{
template <typename T>
class Function;
} // namespace fem
 
namespace fem
{
class CoordinateElement;
}
 
namespace mesh
{
class Mesh;
}
 
namespace io::xdmf_utils
{
 
// Get DOLFINx cell type string from XML topology node
// @return DOLFINx cell type and polynomial degree
std::pair<std::string, int> get_cell_type(const pugi::xml_node& topology_node);
 
// Return (0) HDF5 filename and (1) path in HDF5 file from a DataItem
// node
std::array<std::string, 2> get_hdf5_paths(const pugi::xml_node& dataitem_node);
 
std::filesystem::path
get_hdf5_filename(const std::filesystem::path& xdmf_filename);
 
std::vector<std::int64_t> get_dataset_shape(const pugi::xml_node& dataset_node);
 
std::int64_t get_num_cells(const pugi::xml_node& topology_node);
 
std::vector<double> get_point_data_values(const fem::Function<double>& u);
std::vector<std::complex<double>>
get_point_data_values(const fem::Function<std::complex<double>>& u);
 
std::vector<double> get_cell_data_values(const fem::Function<double>& u);
std::vector<std::complex<double>>
get_cell_data_values(const fem::Function<std::complex<double>>& u);
 
std::string vtk_cell_type_str(mesh::CellType cell_type, int num_nodes);
 
std::pair<std::vector<std::int32_t>, std::vector<std::int32_t>>
distribute_entity_data(const mesh::Mesh& mesh, int entity_dim,
                       const xtl::span<const std::int64_t>& entities,
                       const xtl::span<const std::int32_t>& data);
 
template <typename T>
void add_data_item(pugi::xml_node& xml_node, const hid_t h5_id,
                   const std::string& h5_path, const T& x, std::int64_t offset,
                   const std::vector<std::int64_t>& shape,
                   const std::string& number_type, bool use_mpi_io)
{
  // Add DataItem node
  assert(xml_node);
  pugi::xml_node data_item_node = xml_node.append_child("DataItem");
  assert(data_item_node);
 
  // Add dimensions attribute
  std::string dims;
  for (auto d : shape)
    dims += std::to_string(d) + std::string(" ");
  dims.pop_back();
  data_item_node.append_attribute("Dimensions") = dims.c_str();
 
  // Set type for topology data (needed by XDMF to prevent default to
  // float)
  if (!number_type.empty())
    data_item_node.append_attribute("NumberType") = number_type.c_str();
 
  // Add format attribute
  if (h5_id < 0)
  {
    data_item_node.append_attribute("Format") = "XML";
    assert(shape.size() == 2);
    std::ostringstream s;
    s.precision(16);
    for (std::size_t i = 0; i < (std::size_t)x.size(); ++i)
    {
      if ((i + 1) % shape[1] == 0 and shape[1] != 0)
        s << x.data()[i] << std::endl;
      else
        s << x.data()[i] << " ";
    }
 
    data_item_node.append_child(pugi::node_pcdata).set_value(s.str().c_str());
  }
  else
  {
    data_item_node.append_attribute("Format") = "HDF";
 
    // Get name of HDF5 file, including path
    const std::filesystem::path p = HDF5Interface::get_filename(h5_id);
    const std::filesystem::path filename = p.filename().c_str();
 
    // Add HDF5 filename and HDF5 internal path to XML file
    const std::string xdmf_path
        = filename.string() + std::string(":") + h5_path;
    data_item_node.append_child(pugi::node_pcdata).set_value(xdmf_path.c_str());
 
    // Compute data offset and range of values
    std::int64_t local_shape0 = x.size();
    for (std::size_t i = 1; i < shape.size(); ++i)
    {
      assert(local_shape0 % shape[i] == 0);
      local_shape0 /= shape[i];
    }
 
    const std::array local_range{offset, offset + local_shape0};
    HDF5Interface::write_dataset(h5_id, h5_path, x.data(), local_range, shape,
                                 use_mpi_io, false);
 
    // Add partitioning attribute to dataset
    // std::vector<std::size_t> partitions;
    // std::vector<std::size_t> offset_tmp(1, offset);
    // dolfinx::MPI::gather(comm, offset_tmp, partitions);
    // dolfinx::MPI::broadcast(comm, partitions);
    // HDF5Interface::add_attribute(h5_id, h5_path, "partition", partitions);
  }
}
 
} // namespace io::xdmf_utils
} // namespace dolfinx