visualization.C

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//-----------------------------------------------------------------------bl-
//--------------------------------------------------------------------------
//
// GRINS - General Reacting Incompressible Navier-Stokes
//
// Copyright (C) 2014-2016 Paul T. Bauman, Roy H. Stogner
// Copyright (C) 2010-2013 The PECOS Development Team
//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the Version 2.1 GNU Lesser General
// Public License as published by the Free Software Foundation.
//
// 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. 51 Franklin Street, Fifth Floor,
// Boston, MA  02110-1301  USA
//
//-----------------------------------------------------------------------el-


// This class
#include "grins/visualization.h"

// GRINS
#include "grins/grins_enums.h"
#include "grins/multiphysics_sys.h"

// libMesh
#include "libmesh/getpot.h"
#include "libmesh/gmv_io.h"
#include "libmesh/exodusII_io.h"
#include "libmesh/mesh.h"
#include "libmesh/nemesis_io.h"
#include "libmesh/tecplot_io.h"
#include "libmesh/vtk_io.h"

// POSIX
#include <sys/errno.h>
#include <sys/stat.h>
#include <sys/types.h>

namespace GRINS
{

  Visualization::Visualization( const GetPot& input,
                                const libMesh::Parallel::Communicator &comm )
    : _vis_output_file_prefix( input("vis-options/vis_output_file_prefix", "unknown" ) )
  {
    unsigned int num_formats = input.vector_variable_size("vis-options/output_format");

    // If no format specified, default to ExodusII only
    if( num_formats == 0 )
      {
        // Were we specifically asked to use a ParallelMesh or SerialMesh?
        std::string mesh_class = input("mesh-options/mesh_class", "default");

        if (mesh_class == "parallel")
          _output_format.push_back("Nemesis");
        else if (mesh_class == "serial")
          _output_format.push_back("ExodusII");
        else if (mesh_class == "default")
          {
            // Is our default Mesh distributable?
            libMesh::Mesh testdefault(comm);
            testdefault.delete_remote_elements();
            if (testdefault.is_serial())
              _output_format.push_back("ExodusII");
            else
              _output_format.push_back("Nemesis");
          }
        else
          {
            std::cerr << " Visualization::Visualization:"
                      << " mesh-options/mesh_class had invalid value " << mesh_class
                      << std::endl;
            libmesh_error();
          }
      }

    for( unsigned int i = 0; i < num_formats; i++ )
      {
        _output_format.push_back( input("vis-options/output_format", "DIE", i ) );
      }

    return;
  }

  Visualization::~Visualization()
  {
    return;
  }

  void Visualization::output( SharedPtr<libMesh::EquationSystems> equation_system )
  {
    this->dump_visualization( equation_system, _vis_output_file_prefix, 0.0 );

    return;
  }

  void Visualization::output
    ( SharedPtr<libMesh::EquationSystems> equation_system,
      const unsigned int time_step,
      const libMesh::Real time )
  {
    std::stringstream suffix;

    suffix << time_step;

    std::string filename = this->_vis_output_file_prefix;
    filename+="."+suffix.str();

    this->dump_visualization( equation_system, filename, time );

    return;
  }

  void Visualization::output_residual( SharedPtr<libMesh::EquationSystems> equation_system,
                                       MultiphysicsSystem* system )
  {
    this->output_residual( equation_system, system, 0, 0.0 );
    return;
  }

  void Visualization::output_residual_sensitivities
    (SharedPtr<libMesh::EquationSystems> equation_system,
     MultiphysicsSystem* system,
     const libMesh::ParameterVector & params)
  {
    this->output_residual_sensitivities
      ( equation_system, system, params, 0, 0.0 );
  }

  void Visualization::output_adjoint( SharedPtr<libMesh::EquationSystems> equation_system,
                                      MultiphysicsSystem* system )
  {
    this->output_adjoint( equation_system, system, 0, 0.0 );
  }

  void Visualization::output_solution_sensitivities
    (SharedPtr<libMesh::EquationSystems> equation_system,
     MultiphysicsSystem* system,
     const libMesh::ParameterVector & params)
  {
    this->output_solution_sensitivities
      ( equation_system, system, params, 0, 0.0 );
  }

  void Visualization::dump_visualization
    ( SharedPtr<libMesh::EquationSystems> equation_system,
      const std::string& filename_prefix,
      const libMesh::Real time )
  {
    libMesh::MeshBase& mesh = equation_system->get_mesh();

    if( this->_vis_output_file_prefix == "unknown" )
      {
        // TODO: Need consisent way to print warning messages.
        std::cout << " WARNING in Visualization::dump_visualization :"
                  << " using 'unknown' as file prefix since it was not set "
                  << std::endl;
      }

    // If we're asked to put files in a subdirectory, let's make sure
    // it exists
    if (!mesh.comm().rank())
      for (std::size_t pos = this->_vis_output_file_prefix.find('/');
           pos != std::string::npos;
           pos = this->_vis_output_file_prefix.find('/',++pos))
        if (mkdir(this->_vis_output_file_prefix.substr(0,pos).c_str(),
                  0777) != 0 && errno != EEXIST)
          libmesh_file_error(this->_vis_output_file_prefix.substr(0,pos));

    for( std::vector<std::string>::const_iterator format = _output_format.begin();
         format != _output_format.end();
         format ++ )
      {
        // The following is a modifed copy from the FIN-S code.
        if ((*format) == "tecplot" ||
            (*format) == "dat")
          {
            std::string filename = filename_prefix+".dat";
            libMesh::TecplotIO(mesh,false).write_equation_systems( filename,
                                                                   *equation_system );
          }
        else if ((*format) == "tecplot_binary" ||
                 (*format) == "plt")
          {
            std::string filename = filename_prefix+".plt";
            libMesh::TecplotIO(mesh,true).write_equation_systems( filename,
                                                                  *equation_system );
          }
        else if ((*format) == "gmv")
          {
            std::string filename = filename_prefix+".gmv";
            libMesh::GMVIO(mesh).write_equation_systems( filename,
                                                *equation_system );
          }
        else if ((*format) == "pvtu")
          {
            std::string filename = filename_prefix+".pvtu";
            libMesh::VTKIO(mesh).write_equation_systems( filename,
                                                *equation_system );
          }
        else if ((*format) == "ExodusII")
          {
            std::string filename = filename_prefix+".exo";

            // The "1" is hardcoded for the number of time steps because the ExodusII manual states that
            // it should be the number of timesteps within the file. Here, we are explicitly only doing
            // one timestep per file.
            libMesh::ExodusII_IO(mesh).write_timestep
              ( filename, *equation_system, 1, time );
          }
        else if ((*format) == "Nemesis")
          {
            std::string filename = filename_prefix+".nem";

            // The "1" is hardcoded for the number of time steps because the ExodusII manual states that
            // it should be the number of timesteps within the file. Here, we are explicitly only doing
            // one timestep per file.
            libMesh::Nemesis_IO(mesh).write_timestep
              ( filename, *equation_system, 1, time );
          }
        else if ((*format).find("xda") != std::string::npos ||
                 (*format).find("xdr") != std::string::npos)
          {
            std::string filename = filename_prefix+"."+(*format);
            const bool binary = ((*format).find("xdr") != std::string::npos);
            equation_system->write( filename,
                                    binary ? GRINSEnums::ENCODE : GRINSEnums::WRITE,
                                    libMesh::EquationSystems::WRITE_DATA |
                                    libMesh::EquationSystems::WRITE_ADDITIONAL_DATA );
          }
        else if ((*format) == "mesh_only" )
          {
            std::string filename = filename_prefix+"_mesh.xda";
            equation_system->get_mesh().write( filename );
          }
        else
          {
            // TODO: Do we want to use this to error throughout the code?
            // TODO: (at least need to pass/print some message/string) - sahni
            libmesh_error();
          }
      } // End loop over formats

    return;
  }

} // namespace GRINS