/usr/include/dolfin/io/HDF5Utility.h is in libdolfin-dev 1.4.0+dfsg-4.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 | // Copyright (C) 2013 Chris N. Richardson
//
// This file is part of DOLFIN.
//
// DOLFIN is free software: you can redistribute it and/or modify
// it under the terms of the GNU Lesser General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.
//
// DOLFIN is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public License
// along with DOLFIN. If not, see <http://www.gnu.org/licenses/>.
//
//
// First added: 2013-05-07
// Last changed: 2013-06-18
#ifndef __DOLFIN_HDF5UTILITY_H
#define __DOLFIN_HDF5UTILITY_H
#ifdef HAS_HDF5
#include <string>
#include <vector>
#include "dolfin/common/types.h"
namespace dolfin
{
class GenericDofMap;
class Mesh;
/// This class contains some algorithms which do not explicitly
/// depend on the HDF5 file format, mostly to do with reorganising
/// Mesh entities with MPI
class HDF5Utility
{
public:
/// Generate two vectors, in the range of "vector_range"
/// of the global DOFs.
/// global_cells is a list of cells which point to the DOF (non-unique)
/// and remote_local_dofi is the pertinent local_dof of the cell.
/// input_cells is a list of cells held on this process, and
/// input_cell_dofs/x_cell_dofs list their local_dofs.
static void
map_gdof_to_cell(const MPI_Comm mpi_comm,
const std::vector<std::size_t>& input_cells,
const std::vector<dolfin::la_index>& input_cell_dofs,
const std::vector<std::size_t>& x_cell_dofs,
const std::pair<dolfin::la_index, dolfin::la_index>
vector_range,
std::vector<std::size_t>& global_cells,
std::vector<std::size_t>& remote_local_dofi);
/// Given the cell dof index specified
/// as (process, local_cell_index, local_cell_dof_index)
/// get the global_dof index from that location, and return it for all
/// DOFs in the range of "vector_range"
static void get_global_dof(const MPI_Comm mpi_comm,
const std::vector<std::pair<std::size_t, std::size_t> >& cell_ownership,
const std::vector<std::size_t>& remote_local_dofi,
const std::pair<std::size_t, std::size_t> vector_range,
const GenericDofMap& dofmap,
std::vector<dolfin::la_index>& global_dof);
/// Get cell owners for an arbitrary set of cells.
/// Returns (process, local index) pairs
static std::vector<std::pair<std::size_t, std::size_t> >
cell_owners(const Mesh&mesh, const std::vector<std::size_t> cells);
/// Get mapping of cells in the assigned global range of the
/// current process to remote process and remote local index.
static void cell_owners_in_range(std::vector<std::pair<std::size_t,
std::size_t> >& global_owner,
const Mesh& mesh);
/// Convert LocalMeshData structure to a Mesh, used when running
/// in serial
static void build_local_mesh(Mesh& mesh, const LocalMeshData& mesh_data);
/// Reorder vertices into global index order, so they can be saved
/// correctly for HDF5 mesh output
static std::vector<double>
reorder_vertices_by_global_indices(const Mesh& mesh);
/// Reorder data values of type double into global index order
/// Shape of 2D array is given in global_size
static void reorder_values_by_global_indices(const Mesh& mesh,
std::vector<double>& data,
std::size_t width);
};
}
#endif
#endif
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