get-values.cpp

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// Copyright (c) 2010-2022, Lawrence Livermore National Security, LLC. Produced
// at the Lawrence Livermore National Laboratory. All Rights reserved. See files
// LICENSE and NOTICE for details. LLNL-CODE-806117.
//
// This file is part of the MFEM library. For more information and source code
// availability visit https://mfem.org.
//
// MFEM is free software; you can redistribute it and/or modify it under the
// terms of the BSD-3 license. We welcome feedback and contributions, see file
// CONTRIBUTING.md for details.
//
//    --------------------------------------------------------------------
//    Get Values Miniapp:  Extract field values via DataCollection classes
//    --------------------------------------------------------------------
//
// This miniapp loads previously saved data using DataCollection sub-classes,
// see e.g. load-dc miniapp and Example 5/5p, and output field values at a
// set of points. Currently, only the VisItDataCollection class is supported.
//
// Compile with: make get-values
//
// Serial sample runs:
//   > get-values -r ../../examples/Example5 -p "0 0 0.1 0" -fn pressure
//
// Parallel sample runs:
//   > mpirun -np 4 get-values -r ../electromagnetics/Volta-AMR-Parallel
//           -c 1 -p "0 0 0 0.1 0.1 0.1" -fn ALL
//
// Point locations can be specified on the command line using -p or within a
// data file whose name can be given with option -pf.  The data file format is:
//
// number_of_points space_dimension
// x_0 y_0 ...
// x_1 y_1 ...
// etc.
//
// By default all available fields are evaluated.  The list of fields can be
// reduced by specifying the desired field names with -fn. The -fn option
// takes a space separated list of field names surrounded by quotes.  Field
// names containing spaces, such as "Field 1" and "Field 2", can be entered as:
//    get-values -fn "Field\ 1 Field\ 2"
//
// By default the data is written to standard out.  This can be overwritten
// with the -o [filename] option.
//
// The output format contains comments as well as sizing information to aid in
// subsequent processing.  The bulk of the data consists of one line per point
// with a 0-based integer index followed by the point coordinates and then the
// field data.  A legend, appearing before the bulk data, shows the order of
// the fields along with the number of values per field (for vector data).
//
#include "mfem.hpp"

#include <fstream>
#include <set>
#include <string>

using namespace std;
using namespace mfem;

void parseFieldNames(const char * field_name_c_str, set<string> &field_names);
void parsePoints(int spaceDim, const char *pts_file_c_str, Vector &pts);
/// @cond Suppress_Doxygen_warnings
void writeLegend(const DataCollection::FieldMapType &fields,
                 const set<string> & field_names, int spaceDim);
/// @endcond

int main(int argc, char *argv[])
{
#ifdef MFEM_USE_MPI
   Mpi::Init();
   if (!Mpi::Root()) { mfem::out.Disable(); mfem::err.Disable(); }
   Hypre::Init();
#endif

   // Parse command-line options.
   const char *coll_name = NULL;
   int cycle = 0;
   int pad_digits_cycle = 6;
   int pad_digits_rank = 6;

   const char *field_name_c_str = "ALL";
   const char *pts_file_c_str = "";
   Vector pts;

   const char *out_file_c_str = "";

   OptionsParser args(argc, argv);
   args.AddOption(&coll_name, "-r", "--root-file",
                  "Set the VisIt data collection root file prefix.", true);
   args.AddOption(&cycle, "-c", "--cycle", "Set the cycle index to read.");
   args.AddOption(&pad_digits_cycle, "-pdc", "--pad-digits-cycle",
                  "Number of digits in cycle.");
   args.AddOption(&pad_digits_rank, "-pdr", "--pad-digits-rank",
                  "Number of digits in MPI rank.");
   args.AddOption(&pts, "-p", "--points", "List of points.");
   args.AddOption(&field_name_c_str, "-fn", "--field-names",
                  "List of field names to get values from.");
   args.AddOption(&pts_file_c_str, "-pf", "--point-file",
                  "Filename containing a list of points.");
   args.AddOption(&out_file_c_str, "-o", "--output-file",
                  "Output filename.");
   args.Parse();
   if (!args.Good())
   {
      args.PrintUsage(mfem::out);
      return 1;
   }
   args.PrintOptions(mfem::out);

#ifdef MFEM_USE_MPI
   VisItDataCollection dc(MPI_COMM_WORLD, coll_name);
#else
   VisItDataCollection dc(coll_name);
#endif
   dc.SetPadDigitsCycle(pad_digits_cycle);
   dc.SetPadDigitsRank(pad_digits_rank);
   dc.Load(cycle);

   if (dc.Error() != DataCollection::NO_ERROR)
   {
      mfem::out << "Error loading VisIt data collection: " << coll_name << endl;
      return 1;
   }

   int spaceDim = dc.GetMesh()->SpaceDimension();

   mfem::out << endl;
   mfem::out << "Collection Name: " << dc.GetCollectionName() << endl;
   mfem::out << "Space Dimension: " << spaceDim << endl;
   mfem::out << "Cycle:           " << dc.GetCycle() << endl;
   mfem::out << "Time:            " << dc.GetTime() << endl;
   mfem::out << "Time Step:       " << dc.GetTimeStep() << endl;
   mfem::out << endl;

   typedef DataCollection::FieldMapType fields_t;
   const fields_t &fields = dc.GetFieldMap();
   // Print the names of all fields.
   mfem::out << "fields: [ ";
   for (fields_t::const_iterator it = fields.begin(); it != fields.end(); ++it)
   {
      if (it != fields.begin()) { mfem::out << ", "; }
      mfem::out << it->first;
   }
   mfem::out << " ]" << endl;

   // Parsing desired field names
   set<string> field_names;
   parseFieldNames(field_name_c_str, field_names);

   // Print field names to be extracted
   mfem::out << "Extracting fields: ";
   for (set<string>::iterator it=field_names.begin();
        it!=field_names.end(); it++)
   {
      mfem::out << " \"" << *it << "\"";
   }
   mfem::out << endl;

   parsePoints(spaceDim, pts_file_c_str, pts);
   int npts = pts.Size() / spaceDim;

   DenseMatrix pt_mat(pts.GetData(), spaceDim, npts);

   Array<int> elem_ids;
   Array<IntegrationPoint> ip;
   int nfound = dc.GetMesh()->FindPoints(pt_mat, elem_ids, ip);
   mfem::out << "Found " << nfound << " points." << endl;

   ofstream ofs;
   if (strcmp(out_file_c_str,"") != 0
#ifdef MFEM_USE_MPI
       && Mpi::Root()
#endif
      )
   {
      ofs.open(out_file_c_str);
      if (!ofs)
      {
         MFEM_ABORT("Failed to open output file: " << out_file_c_str << '\n');
      }

      mfem::out.SetStream(ofs);
   }

   // Write legend showing the order of the fields and their sizes
   writeLegend(fields, field_names, spaceDim);

   mfem::out << "# Number of points\n" << nfound << endl;

   for (int e=0; e<elem_ids.Size(); e++)
   {
      if (elem_ids[e] >= 0)
      {
         mfem::out << e;
         for (int d=0; d<spaceDim; d++)
         {
            mfem::out << ' ' << pt_mat(d, e);
         }

         // Loop over all fields.
         for (fields_t::const_iterator it = fields.begin();
              it != fields.end(); ++it)
         {
            if (field_names.find("ALL") != field_names.end() ||
                field_names.find(it->first) != field_names.end())
            {
               if (it->second->VectorDim() == 1)
               {
                  mfem::out << ' ' << it->second->GetValue(elem_ids[e], ip[e]);
               }
               else
               {
                  Vector val;
                  it->second->GetVectorValue(elem_ids[e], ip[e], val);
                  for (int d=0; d<it->second->VectorDim(); d++)
                  {
                     mfem::out << ' ' << val[d];
                  }
               }
            }
         }
         mfem::out << endl;
      }
   }
   if (ofs) { ofs.close(); }

   return 0;
}

void parseFieldNames(const char * field_name_c_str, set<string> &field_names)
{
   string field_name_str(field_name_c_str);
   string field_name;

   for (string::iterator it=field_name_str.begin();
        it!=field_name_str.end(); it++)
   {
      if (*it == '\\')
      {
         it++;
         field_name.push_back(*it);
      }
      else if (*it == ' ')
      {
         if (!field_name.empty())
         {
            field_names.insert(field_name);
         }
         field_name.clear();
      }
      else if (it == field_name_str.end() - 1)
      {
         field_name.push_back(*it);
         field_names.insert(field_name);
      }
      else
      {
         field_name.push_back(*it);
      }
   }
   if (field_names.size() == 0)
   {
      field_names.insert("ALL");
   }
}

void parsePoints(int spaceDim, const char *pts_file_c_str, Vector &pts)
{
   if (strcmp(pts_file_c_str,"") == 0) { return; }

   ifstream ifs(pts_file_c_str);

   if (!ifs)
   {
      MFEM_ABORT("Failed to open point file: " << pts_file_c_str << '\n');
   }

   int o, n, dim;
   ifs >> n >> dim;

   MFEM_VERIFY(dim == spaceDim, "Mismatch in mesh's space dimension "
               "and point dimension.");

   if (pts.Size() > 0 && pts.Size() % spaceDim == 0)
   {
      int size = pts.Size() + n * dim;
      Vector tmp(size);
      for (int i=0; i<pts.Size(); i++)
      {
         tmp[i] = pts[i];
      }
      o = pts.Size();
      pts.Swap(tmp);
   }
   else
   {
      pts.SetSize(n * dim);
      o = 0;
   }

   for (int i=0; i<n; i++)
   {
      for (int d=0; d<dim; d++)
      {
         ifs >> pts[o + i * dim + d];
      }
   }

   ifs.close();
}

void writeLegend(const DataCollection::FieldMapType &fields,
                 const set<string> & field_names, int spaceDim)
{
   typedef DataCollection::FieldMapType fields_t;

   // Count the number of fields to be output
   int nfields = 1;
   for (fields_t::const_iterator it = fields.begin();
        it != fields.end(); ++it)
   {
      if (field_names.find("ALL") != field_names.end() ||
          field_names.find(it->first) != field_names.end())
      {
         nfields++;
      }
   }

   // Write the legend showing each field name and its number of entries
   mfem::out << "# Number of fields" << endl << nfields << endl;
   mfem::out << "# Legend" << endl;
   mfem::out << "# \"Index\" \"Location\":" << spaceDim;
   for (fields_t::const_iterator it = fields.begin();
        it != fields.end(); ++it)
   {
      if (field_names.find("ALL") != field_names.end() ||
          field_names.find(it->first) != field_names.end())
      {
         mfem::out << " \"" << it->first << "\":" << it->second->VectorDim();
      }
   }
   mfem::out << endl;

   // Write the number of entries for each field without the names
   // which should be more convenient for parsing the output file.
   mfem::out << spaceDim;
   for (fields_t::const_iterator it = fields.begin();
        it != fields.end(); ++it)
   {
      if (field_names.find("ALL") != field_names.end() ||
          field_names.find(it->first) != field_names.end())
      {
         mfem::out << " " << it->second->VectorDim();
      }
   }
   mfem::out << endl;
}