equation_systems_io.C

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// The libMesh Finite Element Library.
// Copyright (C) 2002-2018 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


#include "libmesh/libmesh_common.h"
#include "libmesh/libmesh_logging.h"


// C++ Includes
#include <cstdio> // for std::sprintf
#include <sstream>

// Local Includes
#include "libmesh/libmesh_version.h"
#include "libmesh/equation_systems.h"
#include "libmesh/mesh_base.h"
#include "libmesh/mesh_tools.h"
#include "libmesh/parallel.h"
#include "libmesh/xdr_cxx.h"
#include "libmesh/mesh_refinement.h"

namespace libMesh
{

// Forward Declarations

// Anonymous namespace for implementation details.
namespace {
std::string local_file_name (const unsigned int processor_id,
                             const std::string & name)
{
  std::string basename(name);
  char buf[256];

  if (basename.size() - basename.rfind(".bz2") == 4)
    {
      basename.erase(basename.end()-4, basename.end());
      std::sprintf(buf, "%s.%04u.bz2", basename.c_str(), processor_id);
    }
  else if (basename.size() - basename.rfind(".gz") == 3)
    {
      basename.erase(basename.end()-3, basename.end());
      std::sprintf(buf, "%s.%04u.gz", basename.c_str(), processor_id);
    }
  else
    std::sprintf(buf, "%s.%04u", basename.c_str(), processor_id);

  return std::string(buf);
}
}




// ------------------------------------------------------------
// EquationSystem class implementation
template <typename InValType>
void EquationSystems::read (const std::string & name,
                            const unsigned int read_flags,
                            bool partition_agnostic)
{
  XdrMODE mode = READ;
  if (name.find(".xdr") != std::string::npos)
    mode = DECODE;
  this->read(name, mode, read_flags, partition_agnostic);

#ifdef LIBMESH_ENABLE_AMR
  MeshRefinement mesh_refine(_mesh);
  mesh_refine.clean_refinement_flags();
#endif
}



template <typename InValType>
void EquationSystems::read (const std::string & name,
                            const XdrMODE mode,
                            const unsigned int read_flags,
                            bool partition_agnostic)
{
  // If we have exceptions enabled we can be considerate and try
  // to read old restart files which contain infinite element
  // information but do not have the " with infinite elements"
  // string in the version information.

  // First try the read the user requested
  libmesh_try
    {
      this->_read_impl<InValType> (name, mode, read_flags, partition_agnostic);
    }

  // If that fails, try it again but explicitly request we look for infinite element info
  libmesh_catch (...)
    {
      libMesh::out << "\n*********************************************************************\n"
                   << "READING THE FILE \"" << name << "\" FAILED.\n"
                   << "It is possible this file contains infinite element information,\n"
                   << "but the version string does not contain \" with infinite elements\"\n"
                   << "Let's try this again, but looking for infinite element information...\n"
                   << "*********************************************************************\n"
                   << std::endl;

      libmesh_try
        {
          this->_read_impl<InValType> (name, mode, read_flags | EquationSystems::TRY_READ_IFEMS, partition_agnostic);
        }

      // If all that failed, we are out of ideas here...
      libmesh_catch (...)
        {
          libMesh::out << "\n*********************************************************************\n"
                       << "Well, at least we tried!\n"
                       << "Good Luck!!\n"
                       << "*********************************************************************\n"
                       << std::endl;
          LIBMESH_THROW();
        }
    }

#ifdef LIBMESH_ENABLE_AMR
  MeshRefinement mesh_refine(_mesh);
  mesh_refine.clean_refinement_flags();
#endif
}



template <typename InValType>
void EquationSystems::_read_impl (const std::string & name,
                                  const XdrMODE mode,
                                  const unsigned int read_flags,
                                  bool partition_agnostic)
{
  // Set booleans from the read_flags argument
  const bool read_header          = read_flags & EquationSystems::READ_HEADER;
  const bool read_data            = read_flags & EquationSystems::READ_DATA;
  const bool read_additional_data = read_flags & EquationSystems::READ_ADDITIONAL_DATA;
  const bool read_legacy_format   = read_flags & EquationSystems::READ_LEGACY_FORMAT;
  const bool try_read_ifems       = read_flags & EquationSystems::TRY_READ_IFEMS;
  const bool read_basic_only      = read_flags & EquationSystems::READ_BASIC_ONLY;
  bool read_parallel_files  = false;

  std::vector<std::pair<std::string, System *>> xda_systems;

  // This will unzip a file with .bz2 as the extension, otherwise it
  // simply returns the name if the file need not be unzipped.
  Xdr io ((this->processor_id() == 0) ? name : "", mode);
  libmesh_assert (io.reading());

  {
    // 1.)
    // Read the version header.
    std::string version = "legacy";
    if (!read_legacy_format)
      {
        if (this->processor_id() == 0) io.data(version);
        this->comm().broadcast(version);

        // All processors have the version header, if it does not contain
        // the libMesh_label string then it is a legacy file.
        const std::string libMesh_label = "libMesh-";
        std::string::size_type lm_pos = version.find(libMesh_label);
        if (lm_pos==std::string::npos)
          {
            io.close();

            // Recursively call this read() function but with the
            // EquationSystems::READ_LEGACY_FORMAT bit set.
            this->read (name, mode, (read_flags | EquationSystems::READ_LEGACY_FORMAT), partition_agnostic);
            return;
          }

        // Figure out the libMesh version that created this file
        std::istringstream iss(version.substr(lm_pos + libMesh_label.size()));
        int ver_major = 0, ver_minor = 0, ver_patch = 0;
        char dot;
        iss >> ver_major >> dot >> ver_minor >> dot >> ver_patch;
        io.set_version(LIBMESH_VERSION_ID(ver_major, ver_minor, ver_patch));


        read_parallel_files = (version.rfind(" parallel") < version.size());

        // If requested that we try to read infinite element information,
        // and the string " with infinite elements" is not in the version,
        // then tack it on.  This is for compatibility reading ifem
        // files written prior to 11/10/2008 - BSK
        if (try_read_ifems)
          if (!(version.rfind(" with infinite elements") < version.size()))
            version += " with infinite elements";

      }
    else
      libmesh_deprecated();

    START_LOG("read()","EquationSystems");

    // 2.)
    // Read the number of equation systems
    unsigned int n_sys=0;
    if (this->processor_id() == 0) io.data (n_sys);
    this->comm().broadcast(n_sys);

    for (unsigned int sys=0; sys<n_sys; sys++)
      {
        // 3.)
        // Read the name of the sys-th equation system
        std::string sys_name;
        if (this->processor_id() == 0) io.data (sys_name);
        this->comm().broadcast(sys_name);

        // 4.)
        // Read the type of the sys-th equation system
        std::string sys_type;
        if (this->processor_id() == 0) io.data (sys_type);
        this->comm().broadcast(sys_type);

        if (read_header)
          this->add_system (sys_type, sys_name);

        // 5.) - 9.)
        // Let System::read_header() do the job
        System & new_system = this->get_system(sys_name);
        new_system.read_header (io,
                                version,
                                read_header,
                                read_additional_data,
                                read_legacy_format);

        xda_systems.push_back(std::make_pair(sys_name, &new_system));

        // If we're only creating "basic" systems, we need to tell
        // each system that before we call init() later.
        if (read_basic_only)
          new_system.set_basic_system_only();
      }
  }



  // Now we are ready to initialize the underlying data
  // structures. This will initialize the vectors for
  // storage, the dof_map, etc...
  if (read_header)
    this->init();

  // 10.) & 11.)
  // Read and set the numeric vector values
  if (read_data)
    {
      // the EquationSystems::read() method should look constant from the mesh
      // perspective, but we need to assign a temporary numbering to the nodes
      // and elements in the mesh, which requires that we abuse const_cast
      if (!read_legacy_format && partition_agnostic)
        {
          MeshBase & mesh = const_cast<MeshBase &>(this->get_mesh());
          MeshTools::Private::globally_renumber_nodes_and_elements(mesh);
        }

      Xdr local_io (read_parallel_files ? local_file_name(this->processor_id(),name) : "", mode);

      for (auto & pr : xda_systems)
        if (read_legacy_format)
          {
            libmesh_deprecated();
#ifdef LIBMESH_ENABLE_DEPRECATED
            pr.second->read_legacy_data (io, read_additional_data);
#endif
          }
        else
          if (read_parallel_files)
            pr.second->read_parallel_data<InValType>   (local_io, read_additional_data);
          else
            pr.second->read_serialized_data<InValType> (io, read_additional_data);


      // Undo the temporary numbering.
      if (!read_legacy_format && partition_agnostic)
        _mesh.fix_broken_node_and_element_numbering();
    }

  STOP_LOG("read()","EquationSystems");

  // Localize each system's data
  this->update();
}



void EquationSystems::write(const std::string & name,
                            const unsigned int write_flags,
                            bool partition_agnostic) const
{
  XdrMODE mode = WRITE;
  if (name.find(".xdr") != std::string::npos)
    mode = ENCODE;
  this->write(name, mode, write_flags, partition_agnostic);
}



void EquationSystems::write(const std::string & name,
                            const XdrMODE mode,
                            const unsigned int write_flags,
                            bool partition_agnostic) const
{
  // the EquationSystems::write() method should look constant,
  // but we need to assign a temporary numbering to the nodes
  // and elements in the mesh, which requires that we abuse const_cast
  if (partition_agnostic)
    {
      MeshBase & mesh = const_cast<MeshBase &>(this->get_mesh());
      MeshTools::Private::globally_renumber_nodes_and_elements(mesh);
    }

  // set booleans from write_flags argument
  const bool write_data            = write_flags & EquationSystems::WRITE_DATA;
  const bool write_additional_data = write_flags & EquationSystems::WRITE_ADDITIONAL_DATA;

  // always write parallel files if we're instructed to write in
  // parallel
  const bool write_parallel_files  =
    (write_flags & EquationSystems::WRITE_PARALLEL_FILES)
    // Even if we're on a distributed mesh, we may or may not have a
    // consistent way of reconstructing the same mesh partitioning
    // later, but we need the same mesh partitioning if we want to
    // reread the parallel solution safely, so let's write a serial file
    // unless specifically requested not to.
    // ||
    // // but also write parallel files if we haven't been instructed to
    // // write in serial and we're on a distributed mesh
    // (!(write_flags & EquationSystems::WRITE_SERIAL_FILES) &&
    // !this->get_mesh().is_serial())
    ;

  // New scope so that io will close before we try to zip the file
  {
    Xdr io((this->processor_id()==0) ? name : "", mode);
    libmesh_assert (io.writing());

    LOG_SCOPE("write()", "EquationSystems");

    const unsigned int proc_id = this->processor_id();

    unsigned int n_sys = 0;
    for (auto & pr : _systems)
      if (!pr.second->hide_output())
        n_sys++;

    // set the version number in the Xdr object
    io.set_version(LIBMESH_VERSION_ID(LIBMESH_MAJOR_VERSION,
                                      LIBMESH_MINOR_VERSION,
                                      LIBMESH_MICRO_VERSION));

    // Only write the header information
    // if we are processor 0.
    if (proc_id == 0)
      {
        std::string comment;
        char buf[256];

        // 1.)
        // Write the version header
        std::string version("libMesh-" + libMesh::get_io_compatibility_version());
        if (write_parallel_files) version += " parallel";

#ifdef LIBMESH_ENABLE_INFINITE_ELEMENTS
        version += " with infinite elements";
#endif
        io.data (version, "# File Format Identifier");

        // 2.)
        // Write the number of equation systems
        io.data (n_sys, "# No. of Equation Systems");

        for (auto & pr : _systems)
          {
            // Ignore this system if it has been marked as hidden
            if (pr.second->hide_output()) continue;

            // 3.)
            // Write the name of the sys_num-th system
            {
              const unsigned int sys_num = pr.second->number();
              std::string sys_name       = pr.first;

              comment =  "# Name, System No. ";
              std::sprintf(buf, "%u", sys_num);
              comment += buf;

              io.data (sys_name, comment.c_str());
            }

            // 4.)
            // Write the type of system handled
            {
              const unsigned int sys_num = pr.second->number();
              std::string sys_type       = pr.second->system_type();

              comment =  "# Type, System No. ";
              std::sprintf(buf, "%u", sys_num);
              comment += buf;

              io.data (sys_type, comment.c_str());
            }

            // 5.) - 9.)
            // Let System::write_header() do the job
            pr.second->write_header (io, version, write_additional_data);
          }
      }

    // Start from the first system, again,
    // to write vectors to disk, if wanted
    if (write_data)
      {
        // open a parallel buffer if warranted.
        Xdr local_io (write_parallel_files ? local_file_name(this->processor_id(),name) : "", mode);

        for (auto & pr : _systems)
          {
            // Ignore this system if it has been marked as hidden
            if (pr.second->hide_output()) continue;

            // 10.) + 11.)
            if (write_parallel_files)
              pr.second->write_parallel_data (local_io,write_additional_data);
            else
              pr.second->write_serialized_data (io,write_additional_data);
          }
      }
  }

  // the EquationSystems::write() method should look constant,
  // but we need to undo the temporary numbering of the nodes
  // and elements in the mesh, which requires that we abuse const_cast
  if (partition_agnostic)
    const_cast<MeshBase &>(_mesh).fix_broken_node_and_element_numbering();
}



// template specialization

template void EquationSystems::read<Number> (const std::string & name, const unsigned int read_flags, bool partition_agnostic);
template void EquationSystems::read<Number> (const std::string & name, const XdrMODE mode, const unsigned int read_flags, bool partition_agnostic);
template void EquationSystems::_read_impl<Number> (const std::string & name, const XdrMODE mode, const unsigned int read_flags, bool partition_agnostic);
#ifdef LIBMESH_USE_COMPLEX_NUMBERS
template void EquationSystems::read<Real> (const std::string & name, const unsigned int read_flags, bool partition_agnostic);
template void EquationSystems::read<Real> (const std::string & name, const XdrMODE mode, const unsigned int read_flags, bool partition_agnostic);
template void EquationSystems::_read_impl<Real> (const std::string & name, const XdrMODE mode, const unsigned int read_flags, bool partition_agnostic);
#endif

} // namespace libMesh