nemesis_io.h

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// The libMesh Finite Element Library.
// Copyright (C) 2002-2025 Benjamin S. Kirk, John W. Peterson, Roy H. Stogner

// This library 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 2.1 of the License, or (at your option) any later version.

// This library 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 this library; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA



#ifndef LIBMESH_NEMESIS_IO_H
#define LIBMESH_NEMESIS_IO_H


// Local includes
#include "libmesh/libmesh_common.h"
#include "libmesh/mesh_input.h"
#include "libmesh/mesh_output.h"
#include "libmesh/parallel_object.h"

// C++ includes

namespace libMesh
{

// Forward declarations
class Nemesis_IO_Helper;
class System;

class Nemesis_IO : public MeshInput<MeshBase>,
                   public MeshOutput<MeshBase>,
                   public ParallelObject
{

public:

  explicit
  Nemesis_IO (MeshBase & mesh, bool single_precision=false);

  explicit
  Nemesis_IO (const MeshBase & mesh, bool single_precision=false);

  virtual ~Nemesis_IO ();

  virtual void read (const std::string & base_filename) override;

  virtual void write (const std::string & base_filename) override;

  void write_timestep (const std::string & fname,
                       const EquationSystems & es,
                       const int timestep,
                       const Real time);

  void set_output_variables(const std::vector<std::string> & output_variables,
                            bool allow_empty = true);

  virtual void write_nodal_data (const std::string & fname,
                                 const std::vector<Number> & soln,
                                 const std::vector<std::string> & names) override;

  virtual void write_nodal_data (const std::string & fname,
                                 const EquationSystems & es,
                                 const std::set<std::string> * system_names) override;

  virtual void write_nodal_data (const std::string & fname,
                                 const NumericVector<Number> & parallel_soln,
                                 const std::vector<std::string> & names) override;

  void write_element_data (const EquationSystems & es);

  void verbose (bool set_verbosity);

  void write_complex_magnitude (bool val);

  void write_global_data (const std::vector<Number> &,
                          const std::vector<std::string> &);

  void write_information_records (const std::vector<std::string> &);

  void append(bool val);

  const std::vector<std::string> & get_nodal_var_names();

  void copy_nodal_solution(System & system,
                           std::string system_var_name,
                           std::string exodus_var_name,
                           unsigned int timestep=1);

  void copy_elemental_solution(System & system,
                               std::string system_var_name,
                               std::string exodus_var_name,
                               unsigned int timestep=1);

  void copy_scalar_solution(System & system,
                            std::vector<std::string> system_var_names,
                            std::vector<std::string> exodus_var_names,
                            unsigned int timestep=1);

  void read_global_variable(std::vector<std::string> global_var_names,
                            unsigned int timestep,
                            std::vector<Real> & global_values);

  void set_hdf5_writing(bool write_hdf5);

private:

  /*
   * A helper function for use in debug and devel modes, for asserting
   * that we get symmetric communication maps from a file we read
   * and/or that we're writing them out in a symmetric fashion
   * ourselves.
   */
  void assert_symmetric_cmaps();

#if defined(LIBMESH_HAVE_EXODUS_API) && defined(LIBMESH_HAVE_NEMESIS_API)
  std::unique_ptr<Nemesis_IO_Helper> nemhelper;

  int _timestep;
#endif

  bool _verbose;

  bool _append;

  void prepare_to_write_nodal_data (const std::string & fname,
                                    const std::vector<std::string> & names);

  std::vector<std::string> _output_variables;

  bool _allow_empty_variables;
};


} // namespace libMesh


#endif // LIBMESH_NEMESIS_IO_H