datacollection.cpp

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// 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.googlecode.com.
//
// 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 "picojson.h"

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

namespace mfem
{

using namespace std;

// Helper string functions. Will go away in C++11

string to_string(int i)
{
   stringstream ss;
   ss << i;

   // trim leading spaces
   string out_str = ss.str();
   out_str = out_str.substr(out_str.find_first_not_of(" \t"));
   return out_str;
}

string to_padded_string(int i, int digits)
{
   ostringstream oss;
   oss << setw(digits) << setfill('0') << i;
   return oss.str();
}

int to_int(string str)
{
   int i;
   stringstream(str) >> i;
   return i;
}

// class DataCollection implementation

DataCollection::DataCollection(const char *collection_name)
{
   name = collection_name;
   mesh = NULL;
   myid = 0;
   num_procs = 1;
   serial = true;
   own_data = false;
   cycle = -1;
   time = 0.0;
   pad_digits = pad_digits_default;
   error = NO_ERROR;
}

DataCollection::DataCollection(const char *collection_name, Mesh *_mesh)
{
   name = collection_name;
   mesh = _mesh;
   myid = 0;
   num_procs = 1;
   serial = true;
#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;
   }
#endif
   own_data = false;
   cycle = -1;
   time = 0.0;
   pad_digits = pad_digits_default;
   error = NO_ERROR;
}

void DataCollection::RegisterField(const char* name, GridFunction *gf)
{
   field_map[name] = gf;
}

GridFunction *DataCollection::GetField(const char *field_name)
{
   if (HasField(field_name))
      return field_map[field_name];
   else
      return NULL;
}

void DataCollection::Save()
{
   string dir_name;
   if (cycle == -1)
      dir_name = name;
   else
      dir_name = name + "_" + to_padded_string(cycle, pad_digits);
   int err;
#ifndef MFEM_USE_MPI
   err = mkdir(dir_name.c_str(), 0777);
   err = (err && (errno != EEXIST)) ? 1 : 0;
#else
   ParMesh *pmesh = dynamic_cast<ParMesh*>(mesh);
   if (myid == 0 || pmesh == NULL)
   {
      err = mkdir(dir_name.c_str(), 0777);
      err = (err && (errno != EEXIST)) ? 1 : 0;
      if (pmesh)
         MPI_Bcast(&err, 1, MPI_INT, 0, pmesh->GetComm());
   }
   else
   {
      // Wait for rank 0 to create the directory
      MPI_Bcast(&err, 1, MPI_INT, 0, pmesh->GetComm());
   }
#endif
   if (err)
   {
      error = WRITE_ERROR;
      MFEM_WARNING("Error creating directory: " << dir_name);
      return; // do not even try to write mesh or fields
   }

   string mesh_name;
   if (serial)
      mesh_name = dir_name + "/mesh";
   else
      mesh_name = dir_name + "/mesh." + to_padded_string(myid, pad_digits);
   ofstream mesh_file(mesh_name.c_str());
   mesh->Print(mesh_file);
   if (!mesh_file)
   {
      error = WRITE_ERROR;
      MFEM_WARNING("Error writing mesh to file: " << mesh_name);
   }
   mesh_file.close();

   string field_name;
   for (map<string,GridFunction*>::iterator it = field_map.begin();
        it != field_map.end(); ++it)
   {
      if (serial)
         field_name = dir_name + "/" + it->first;
      else
         field_name = dir_name + "/" + it->first + "." +
            to_padded_string(myid, pad_digits);
      ofstream field_file(field_name.c_str());
      (it->second)->Save(field_file);
      if (!field_file)
      {
         error = WRITE_ERROR;
         MFEM_WARNING("Error writting field to file: " << field_name);
      }
   }
}

void DataCollection::DeleteData()
{
   if (own_data)
      delete mesh;
   mesh = NULL;
   for (map<string,GridFunction*>::iterator it = field_map.begin();
        it != field_map.end(); ++it)
   {
      if (own_data)
         delete it->second;
      it->second = NULL;
   }
   own_data = false;
}

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

DataCollection::~DataCollection()
{
   if (own_data)
   {
      delete mesh;
      for (map<string,GridFunction*>::iterator it = field_map.begin();
           it != field_map.end(); ++it)
         delete it->second;
   }
}


// class VisItDataCollection implementation

VisItDataCollection::VisItDataCollection(const char *collection_name)
   : DataCollection(collection_name)
{
   serial = false; // always include rank in file names
   cycle  = 0;     // always include cycle in directory names

   spatial_dim = 0;
   topo_dim = 0;
   visit_max_levels_of_detail = 32;
}

VisItDataCollection::VisItDataCollection(const char *collection_name,
                                         Mesh *mesh)
   : DataCollection(collection_name, mesh)
{
   serial = false; // always include rank in file names
   cycle  = 0;     // always include cycle in directory names

   spatial_dim = mesh->SpaceDimension();
   topo_dim = mesh->Dimension();
   visit_max_levels_of_detail = 32;
}

void VisItDataCollection::RegisterField(const char* 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()
{
   if (myid == 0)
   {
      string root_name = name + "_" + to_padded_string(cycle, pad_digits) +
         ".mfem_root";
      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);
      }
   }
   DataCollection::Save();
}

void VisItDataCollection::Load(int _cycle)
{
   DeleteAll();
   cycle = _cycle;
   string root_name = 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(string root_name)
{
   ifstream root_file(root_name.c_str());
   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()
{
   string mesh_fname = name + "_" + to_padded_string(cycle, pad_digits) +
      "/mesh." + to_padded_string(myid, pad_digits);
   ifstream 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()
{
   string path_left = name + "_" + to_padded_string(cycle, pad_digits) + "/";
   string path_right = "." + to_padded_string(myid, pad_digits);

   field_map.clear();
   for (map<string,VisItFieldInfo>::iterator it = field_info_map.begin();
        it != field_info_map.end(); ++it)
   {
      string fname = path_left + it->first + path_right;
      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);
   }
}

string VisItDataCollection::GetVisItRootString()
{
   // Get the path string
   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
   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 + "mesh" + file_ext_format);
   mesh["tags"] = picojson::value(mtags);

   // Build the fields data entries
   for (map<string,VisItFieldInfo>::iterator 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(string json)
{
   picojson::value top, dsets, main, mesh, fields;
   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
   string path = mesh.get("path").get<string>();
   size_t right_sep = path.find('_');
   if (right_sep == 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<string>());
   topo_dim = to_int(mesh.get("tags").get("topo_dim").get<string>());
   visit_max_levels_of_detail =
      to_int(mesh.get("tags").get("max_lods").get<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<string>(),
                           to_int(tags.get("comps").get<string>()));
      }
   }
}

}