datacollection.cpp

Go to the documentation of this file.

// Copyright (c) 2010, Lawrence Livermore National Security, LLC. Produced at
// the Lawrence Livermore National Laboratory. LLNL-CODE-443211. All Rights
// reserved. See file COPYRIGHT for details.
//
// This file is part of the MFEM library. For more information and source code
// availability see http://mfem.org.
//
// MFEM 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) version 2.1 dated February 1999.

#include "fem.hpp"
#include "../general/text.hpp"
#include "picojson.h"

#include <fstream>
#include <cerrno>      // errno
#include <sstream>

#ifndef _WIN32
#include <sys/stat.h>  // mkdir
#else
#include <direct.h>    // _mkdir
#define mkdir(dir, mode) _mkdir(dir)
#endif

namespace mfem
{

// static method
int DataCollection::create_directory(const std::string &dir_name,
                                     const Mesh *mesh, int myid)
{
   // create directories recursively
   const char path_delim = '/';
   std::string::size_type pos = 0;
   int err;
#ifdef MFEM_USE_MPI
   const ParMesh *pmesh = dynamic_cast<const ParMesh*>(mesh);
#endif

   do
   {
      pos = dir_name.find(path_delim, pos+1);
      std::string subdir = dir_name.substr(0, pos);

#ifndef MFEM_USE_MPI
      err = mkdir(subdir.c_str(), 0777);
      err = (err && (errno != EEXIST)) ? 1 : 0;
#else
      if (myid == 0 || pmesh == NULL)
      {
         err = mkdir(subdir.c_str(), 0777);
         err = (err && (errno != EEXIST)) ? 1 : 0;
      }
#endif
   }
   while ( pos != std::string::npos );

#ifdef MFEM_USE_MPI
   if (pmesh)
   {
      MPI_Bcast(&err, 1, MPI_INT, 0, pmesh->GetComm());
   }
#endif

   return err;
}

// class DataCollection implementation

DataCollection::DataCollection(const std::string& collection_name, Mesh *mesh_)
{
   name = collection_name;
   // leave prefix_path empty
   mesh = mesh_;
   myid = 0;
   num_procs = 1;
   serial = true;
   appendRankToFileName = false;

#ifdef MFEM_USE_MPI
   ParMesh *par_mesh = dynamic_cast<ParMesh*>(mesh);
   if (par_mesh)
   {
      myid = par_mesh->GetMyRank();
      num_procs = par_mesh->GetNRanks();
      serial = false;
      appendRankToFileName = true;
   }
#endif
   own_data = false;
   cycle = -1;
   time = 0.0;
   time_step = 0.0;
   precision = precision_default;
   pad_digits = pad_digits_default;
   format = 0; // use older serial mesh format
   error = NO_ERROR;
}

void DataCollection::SetMesh(Mesh *new_mesh)
{
   if (own_data && new_mesh != mesh) { delete mesh; }
   mesh = new_mesh;
   myid = 0;
   num_procs = 1;
   serial = true;
   appendRankToFileName = false;

#ifdef MFEM_USE_MPI
   ParMesh *par_mesh = dynamic_cast<ParMesh*>(mesh);
   if (par_mesh)
   {
      myid = par_mesh->GetMyRank();
      num_procs = par_mesh->GetNRanks();
      serial = false;
      appendRankToFileName = true;
   }
#endif
}

void DataCollection::RegisterField(const std::string& name, GridFunction *gf)
{
   GridFunction *&ref = field_map[name];
   if (own_data)
   {
      delete ref; // if newly allocated -> ref is null -> OK
   }
   ref = gf;
}

void DataCollection::DeregisterField(const std::string& name)
{
   FieldMapIterator it = field_map.find(name);
   if (it != field_map.end())
   {
      if (own_data)
      {
         delete it->second;
      }
      field_map.erase(it);
   }
}

void DataCollection::RegisterQField(const std::string& q_field_name,
                                    QuadratureFunction *qf)
{
   QuadratureFunction *&ref = q_field_map[q_field_name];
   if (own_data)
   {
      delete ref; // if newly allocated -> ref is null -> OK
   }
   ref = qf;
}

void DataCollection::DeregisterQField(const std::string& name)
{
   QFieldMapIterator it = q_field_map.find(name);
   if (it != q_field_map.end())
   {
      if (own_data)
      {
         delete it->second;
      }
      q_field_map.erase(it);
   }
}

GridFunction *DataCollection::GetField(const std::string& field_name)
{
   FieldMapConstIterator it = field_map.find(field_name);

   return (it != field_map.end()) ? it->second : NULL;
}

QuadratureFunction *DataCollection::GetQField(const std::string& q_field_name)
{
   QFieldMapConstIterator it = q_field_map.find(q_field_name);

   return (it != q_field_map.end()) ? it->second : NULL;
}

void DataCollection::SetPrefixPath(const std::string& prefix)
{
   if (!prefix.empty())
   {
      prefix_path = prefix;
      if (!prefix_path.empty() && prefix_path[prefix_path.size()-1] != '/')
      {
         prefix_path += '/';
      }
   }
   else
   {
      prefix_path.clear();
   }
}

void DataCollection::Load(int cycle)
{
   MFEM_ABORT("this method is not implemented");
}

void DataCollection::Save()
{
   SaveMesh();

   if (error) { return; }

   for (FieldMapIterator it = field_map.begin(); it != field_map.end(); ++it)
   {
      SaveOneField(it);
      // Even if there is an error, try saving the other fields
   }

   for (QFieldMapIterator it = q_field_map.begin(); it != q_field_map.end();
        ++it)
   {
      SaveOneQField(it);
   }
}

void DataCollection::SaveMesh()
{
   int err;

   std::string dir_name = prefix_path + name;
   if (cycle != -1)
   {
      dir_name += "_" + to_padded_string(cycle, pad_digits);
   }
   err = create_directory(dir_name, mesh, myid);
   if (err)
   {
      error = WRITE_ERROR;
      MFEM_WARNING("Error creating directory: " << dir_name);
      return; // do not even try to write the mesh
   }

   std::string mesh_name = dir_name +
                           ((serial || format == 0 )? "/mesh" : "/pmesh");
   if (appendRankToFileName)
   {
      mesh_name += "." + to_padded_string(myid, pad_digits);
   }
   std::ofstream mesh_file(mesh_name.c_str());
   mesh_file.precision(precision);
#ifdef MFEM_USE_MPI
   const ParMesh *pmesh = dynamic_cast<const ParMesh*>(mesh);
   if (pmesh && format == 1 )
   {
      pmesh->ParPrint(mesh_file);
   }
   else
#endif
   {
      mesh->Print(mesh_file);
   }
   if (!mesh_file)
   {
      error = WRITE_ERROR;
      MFEM_WARNING("Error writing mesh to file: " << mesh_name);
   }
}

std::string DataCollection::GetFieldFileName(const std::string &field_name)
{
   std::string dir_name = prefix_path + name;
   if (cycle != -1)
   {
      dir_name += "_" + to_padded_string(cycle, pad_digits);
   }
   std::string file_name = dir_name + "/" + field_name;
   if (appendRankToFileName)
   {
      file_name += "." + to_padded_string(myid, pad_digits);
   }
   return file_name;
}

void DataCollection::SaveOneField(const FieldMapIterator &it)
{
   std::ofstream field_file(GetFieldFileName(it->first).c_str());
   field_file.precision(precision);
   (it->second)->Save(field_file);
   if (!field_file)
   {
      error = WRITE_ERROR;
      MFEM_WARNING("Error writing field to file: " << it->first);
   }
}

void DataCollection::SaveOneQField(const QFieldMapIterator &it)
{
   std::ofstream q_field_file(GetFieldFileName(it->first).c_str());
   q_field_file.precision(precision);
   (it->second)->Save(q_field_file);
   if (!q_field_file)
   {
      error = WRITE_ERROR;
      MFEM_WARNING("Error writing q-field to file: " << it->first);
   }
}

void DataCollection::SaveField(const std::string &field_name)
{
   FieldMapIterator it = field_map.find(field_name);
   if (it != field_map.end())
   {
      SaveOneField(it);
   }
}

void DataCollection::SaveQField(const std::string &q_field_name)
{
   QFieldMapIterator it = q_field_map.find(q_field_name);
   if (it != q_field_map.end())
   {
      SaveOneQField(it);
   }
}

void DataCollection::DeleteData()
{
   if (own_data) { delete mesh; }
   mesh = NULL;

   for (FieldMapIterator it = field_map.begin(); it != field_map.end(); ++it)
   {
      if (own_data) { delete it->second; }
      it->second = NULL;
   }
   for (QFieldMapIterator it = q_field_map.begin();
        it != q_field_map.end(); ++it)
   {
      if (own_data) { delete it->second; }
      it->second = NULL;
   }
   own_data = false;
}

void DataCollection::DeleteAll()
{
   DeleteData();
   field_map.clear();
   q_field_map.clear();
}

DataCollection::~DataCollection()
{
   DeleteData();
}


// class VisItDataCollection implementation

VisItDataCollection::VisItDataCollection(const std::string& collection_name,
                                         Mesh *mesh)
   : DataCollection(collection_name, mesh)
{
   appendRankToFileName = true; // always include rank in file names
   cycle = 0;                   // always include cycle in directory names

   if (mesh)
   {
      spatial_dim = mesh->SpaceDimension();
      topo_dim = mesh->Dimension();
   }
   else
   {
      spatial_dim = 0;
      topo_dim = 0;
   }
   visit_max_levels_of_detail = 32;
}

void VisItDataCollection::SetMesh(Mesh *new_mesh)
{
   DataCollection::SetMesh(new_mesh);
   appendRankToFileName = true;
   spatial_dim = mesh->SpaceDimension();
   topo_dim = mesh->Dimension();
}

void VisItDataCollection::RegisterField(const std::string& name,
                                        GridFunction *gf)
{
   DataCollection::RegisterField(name, gf);
   field_info_map[name] = VisItFieldInfo("nodes", gf->VectorDim());
}

void VisItDataCollection::SetMaxLevelsOfDetail(int max_levels_of_detail)
{
   visit_max_levels_of_detail = max_levels_of_detail;
}

void VisItDataCollection::DeleteAll()
{
   field_info_map.clear();
   DataCollection::DeleteAll();
}

void VisItDataCollection::Save()
{
   DataCollection::Save();
   SaveRootFile();
}

void VisItDataCollection::SaveRootFile()
{
   if (myid != 0) { return; }

   std::string root_name = prefix_path + name + "_" +
                           to_padded_string(cycle, pad_digits) + ".mfem_root";
   std::ofstream root_file(root_name.c_str());
   root_file << GetVisItRootString();
   if (!root_file)
   {
      error = WRITE_ERROR;
      MFEM_WARNING("Error writting VisIt Root file: " << root_name);
   }
}

void VisItDataCollection::Load(int cycle_)
{
   DeleteAll();
   cycle = cycle_;
   std::string root_name = prefix_path + name + "_" +
                           to_padded_string(cycle, pad_digits) + ".mfem_root";
   LoadVisItRootFile(root_name);
   if (!error)
   {
      LoadMesh();
   }
   if (!error)
   {
      LoadFields();
   }
   if (!error)
   {
      own_data = true;
   }
   else
   {
      DeleteAll();
   }
}

void VisItDataCollection::LoadVisItRootFile(const std::string& root_name)
{
   std::ifstream root_file(root_name.c_str());
   std::stringstream buffer;
   buffer << root_file.rdbuf();
   if (!buffer)
   {
      error = READ_ERROR;
      MFEM_WARNING("Error reading the VisIt Root file: " << root_name);
   }
   else
   {
      ParseVisItRootString(buffer.str());
   }
}

void VisItDataCollection::LoadMesh()
{
   std::string mesh_fname = prefix_path + name + "_" +
                            to_padded_string(cycle, pad_digits) +
                            "/mesh." + to_padded_string(myid, pad_digits);
   named_ifgzstream file(mesh_fname.c_str());
   if (!file)
   {
      error = READ_ERROR;
      MFEM_WARNING("Unable to open mesh file: " << mesh_fname);
      return;
   }
   // TODO: 1) load parallel mesh on one processor
   //       2) load parallel mesh on the same number of processors
   mesh = new Mesh(file, 1, 1);
   spatial_dim = mesh->SpaceDimension();
   topo_dim = mesh->Dimension();
}

void VisItDataCollection::LoadFields()
{
   std::string path_left = prefix_path + name + "_" +
                           to_padded_string(cycle, pad_digits) + "/";
   std::string path_right = "." + to_padded_string(myid, pad_digits);

   field_map.clear();
   for (FieldInfoMapIterator it = field_info_map.begin();
        it != field_info_map.end(); ++it)
   {
      std::string fname = path_left + it->first + path_right;
      std::ifstream file(fname.c_str());
      if (!file)
      {
         error = READ_ERROR;
         MFEM_WARNING("Unable to open field file: " << fname);
         return;
      }
      // TODO: 1) load parallel GridFunction on one processor
      //       2) load parallel GridFunction on the same number of processors
      field_map[it->first] = new GridFunction(mesh, file);
   }
}

std::string VisItDataCollection::GetVisItRootString()
{
   // Get the path string (relative to where the root file is, i.e. no prefix).
   std::string path_str = name + "_" + to_padded_string(cycle, pad_digits) + "/";

   // We have to build the json tree inside out to get all the values in there
   picojson::object top, dsets, main, mesh, fields, field, mtags, ftags;

   // Build the mesh data
   std::string file_ext_format = ".%0" + to_string(pad_digits) + "d";
   mtags["spatial_dim"] = picojson::value(to_string(spatial_dim));
   mtags["topo_dim"] = picojson::value(to_string(topo_dim));
   mtags["max_lods"] = picojson::value(to_string(visit_max_levels_of_detail));
   mesh["path"] = picojson::value(path_str + ((format==0)?"":"p") + "mesh" +
                                  file_ext_format);
   mesh["tags"] = picojson::value(mtags);

   // Build the fields data entries
   for (FieldInfoMapIterator it = field_info_map.begin();
        it != field_info_map.end(); ++it)
   {
      ftags["assoc"] = picojson::value((it->second).association);
      ftags["comps"] = picojson::value(to_string((it->second).num_components));
      field["path"] = picojson::value(path_str + it->first + file_ext_format);
      field["tags"] = picojson::value(ftags);
      fields[it->first] = picojson::value(field);
   }

   main["cycle"] = picojson::value(double(cycle));
   main["time"] = picojson::value(time);
   main["domains"] = picojson::value(double(num_procs));
   main["mesh"] = picojson::value(mesh);
   if (!field_info_map.empty())
   {
      main["fields"] = picojson::value(fields);
   }

   dsets["main"] = picojson::value(main);
   top["dsets"] = picojson::value(dsets);

   return picojson::value(top).serialize(true);
}

void VisItDataCollection::ParseVisItRootString(const std::string& json)
{
   picojson::value top, dsets, main, mesh, fields;
   std::string parse_err = picojson::parse(top, json);
   if (!parse_err.empty())
   {
      error = READ_ERROR;
      MFEM_WARNING("Unable to parse visit root data.");
      return;
   }

   // Process "main"
   dsets = top.get("dsets");
   main = dsets.get("main");
   cycle = int(main.get("cycle").get<double>());
   time = main.get("time").get<double>();
   num_procs = int(main.get("domains").get<double>());
   mesh = main.get("mesh");
   fields = main.get("fields");

   // ... Process "mesh"

   // Set the DataCollection::name using the mesh path
   std::string path = mesh.get("path").get<std::string>();
   size_t right_sep = path.find('_');
   if (right_sep == std::string::npos)
   {
      error = READ_ERROR;
      MFEM_WARNING("Unable to parse visit root data.");
      return;
   }
   name = path.substr(0, right_sep);

   spatial_dim = to_int(mesh.get("tags").get("spatial_dim").get<std::string>());
   topo_dim = to_int(mesh.get("tags").get("topo_dim").get<std::string>());
   visit_max_levels_of_detail =
      to_int(mesh.get("tags").get("max_lods").get<std::string>());

   // ... Process "fields"
   field_info_map.clear();
   if (fields.is<picojson::object>())
   {
      picojson::object fields_obj = fields.get<picojson::object>();
      for (picojson::object::iterator it = fields_obj.begin();
           it != fields_obj.end(); ++it)
      {
         picojson::value tags = it->second.get("tags");
         field_info_map[it->first] =
            VisItFieldInfo(tags.get("assoc").get<std::string>(),
                           to_int(tags.get("comps").get<std::string>()));
      }
   }
}

}  // end namespace MFEM