ElementFileWriter.cc

//
// Software License for AMDiS
//
// Copyright (c) 2010 Dresden University of Technology 
// All rights reserved.
// Authors: Simon Vey, Thomas Witkowski et al.
//
// This file is part of AMDiS
//
// See also license.opensource.txt in the distribution.


#include <boost/iostreams/filtering_stream.hpp>
#include <boost/iostreams/device/file_descriptor.hpp>
#include <boost/filesystem/operations.hpp>
#include <boost/filesystem/convenience.hpp>
#include <boost/lexical_cast.hpp>

#include "io/VtkWriter.h"
#include "ElementFileWriter.h"
#include "BasisFunction.h"
#include "Initfile.h"
#include "Traverse.h"
#include "AdaptInfo.h"

namespace AMDiS {

  using namespace std;

  ElementFileWriter::ElementFileWriter(string name_, 
				       Mesh *mesh_,
				       map<int, double> &mapvec)
    : name(name_),
      amdisMeshDatExt(".elem.mesh"),
      vtkExt(".vtu"),
      writeAMDiSFormat(0),
      writeVtkFormat(0),
      appendIndex(0),
      indexLength(5),
      indexDecimals(3),
      tsModulo(1),
      timestepNumber(-1),
      mesh(mesh_),
      vec(mapvec)
  {
    if (name != "") {
      Parameters::get(name + "->output->filename", filename);
      Parameters::get(name + "->output->AMDiS format", writeAMDiSFormat);
      Parameters::get(name + "->output->AMDiS mesh-dat ext", amdisMeshDatExt);
      Parameters::get(name + "->output->ParaView format", writeVtkFormat);
      Parameters::get(name + "->output->append index", appendIndex);
      Parameters::get(name + "->output->index length", indexLength);
      Parameters::get(name + "->output->index decimals", indexDecimals);
      Parameters::get(name + "->output->write every i-th timestep", tsModulo);
    }
  }


  void ElementFileWriter::writeFiles(AdaptInfo *adaptInfo, bool force,
				     int level, Flag traverseFlag, 
				     bool (*writeElem)(ElInfo*))
  {
    FUNCNAME("ElementFileWriter::writeFiles()");

    timestepNumber++;
    timestepNumber %= tsModulo;

    if (timestepNumber != 0 && !force) 
      return;

    string fn = filename;

    if (appendIndex) {
      TEST_EXIT(indexLength <= 99)("index lenght > 99\n");
      TEST_EXIT(indexDecimals <= 97)("index decimals > 97\n");
      TEST_EXIT(indexDecimals < indexLength)("index length <= index decimals\n");
    
      char formatStr[9];
      sprintf(formatStr, "%%0%d.%df", indexLength, indexDecimals);

      char timeStr[20];
      sprintf(timeStr, formatStr, adaptInfo ? adaptInfo->getTime() : 0.0);

      fn += timeStr;
    }

    if (writeAMDiSFormat) {
      TEST_EXIT(mesh)("no mesh\n");
    
      writeMeshDatValues(const_cast<char*>((fn + amdisMeshDatExt).c_str()),
			 adaptInfo ? adaptInfo->getTime() : 0.0);
      MSG("MeshDat file written to %s\n", (fn + amdisMeshDatExt).c_str());
    }

    if (writeVtkFormat) {
      TEST_EXIT(mesh)("no mesh\n");

      writeVtkValues(fn, vtkExt);
      MSG("VTK file written to %s\n", (fn + vtkExt).c_str());		     
    }
  }


  void ElementFileWriter::writeFile(map<int, double> &vec,
				    Mesh *mesh,
				    string filename,
				    string postfix,
				    int level)
  {
    ElementFileWriter efw("", mesh, vec);
    efw.writeVtkValues(filename, postfix, level);
  }
  

  void ElementFileWriter::writeMeshDatValues(string filename, double time)
  {
    FUNCNAME("ElementFileWriter::writeMeshDatValues()");

    boost::iostreams::filtering_ostream file;
    {
      //boost::iostreams seems not to truncate the file
      ofstream swapfile(filename.c_str(), ios::out | ios::trunc);
      TEST_EXIT(swapfile.is_open())
	("Cannot open file %s for writing!\n", name.c_str());
      swapfile.close();
    }
    file.push(boost::iostreams::file_descriptor_sink(filename, ios::trunc));

    int dim = mesh->getDim();
    double val;

    // === Write header. ===
    file << "mesh name: " << mesh->getName().c_str() << "\n\n";
    file << "time: " << time << "\n\n"; 
    file << "DIM: " << dim << "\n";
    file << "DIM_OF_WORLD: " << Global::getGeo(WORLD) << "\n\n";
    file << "number of vertices: " << (dim+1)*mesh->getNumberOfLeaves() << "\n";
    file << "number of elements: " << mesh->getNumberOfLeaves() << "\n\n";


    // === Write vertex coordinates (every vertex for every element). ===
    file << "vertex coordinates:\n";
    TraverseStack stack;

    ElInfo *elInfo = stack.traverseFirst(mesh,
					 -1, 
					 Mesh::CALL_LEAF_EL | 
					 Mesh::FILL_COORDS);

    while (elInfo) {

      // Write coordinates of all element vertices.
      for (int i = 0; i <= dim; ++i) {     
	for (int j = 0; j < dim; ++j) {
	  file << elInfo->getCoord(i)[j] << " ";
	}
	file << "\n";
      }
    
      elInfo = stack.traverseNext(elInfo);
    }


    // === Write elements. ===
    int numLeaves = mesh->getNumberOfLeaves();
    int vertCntr = 0;
    file << "\n";
    file << "element vertices:\n";
    for (int i = 0; i < numLeaves; ++i) {
      for (int j = 0; j <= dim; ++j) {
	file << vertCntr << " ";
	++vertCntr;
      }
      file << "\n";
    }


    // === Write values. ===

    // Write values header.
    file << "\n";
    file << "number of values: 1\n\n";
    file << "value description: " << name.c_str() << "\n";
    file << "number of interpolation points: 0" << "\n";
    file << "type: scalar" << "\n";
    file << "interpolation type: lagrange" << "\n";
    file << "interpolation degree: 1" << "\n";
    file << "end of description: " << name.c_str() << "\n\n";

    // Write values.
    file << "vertex values: " << name.c_str() << "\n";

    file.setf(ios::scientific,ios::floatfield);

    elInfo = stack.traverseFirst(mesh,
				 -1, 
				 Mesh::CALL_LEAF_EL);

    while (elInfo) {
      // Get element value.
      val = vec[elInfo->getElement()->getIndex()];
    
      // Write value for each vertex of each element.
      for (int i = 0; i <= dim; ++i) {      
	file << val << "\n";
      }
    
      elInfo = stack.traverseNext(elInfo);
    }  // end of: mesh traverse


    // Write values trailor.
    file << "\n";
    file << "interpolation values: " << name.c_str() << "\n\n\n";
    file << "element interpolation points: " << name.c_str() << "\n";
  }


  void ElementFileWriter::writeVtkValues(string fname, 
					 string postfix, 
					 int level)
  {
    FUNCNAME("ElementFileWriter::writeVtkValues()");

#if HAVE_PARALLEL_DOMAIN_AMDIS
    string filename = 
      fname  + 
      "-p" + boost::lexical_cast<std::string>(MPI::COMM_WORLD.Get_rank()) + "-" +
      postfix;
#else
    string filename = fname + postfix;
#endif

    boost::iostreams::filtering_ostream file;
    {
      //boost::iostreams seems not to truncate the file
      ofstream swapfile(filename.c_str(), ios::out | ios::trunc);
      TEST_EXIT(swapfile.is_open())
	("Cannot open file %s for writing!\n", name.c_str());
      swapfile.close();
    }
    file.push(boost::iostreams::file_descriptor_sink(filename, ios::trunc));

    int dim = mesh->getDim();
    int dimOfWorld = Global::getGeo(WORLD);
    int vertices = mesh->getGeo(VERTEX);
    int nElements = mesh->getNumberOfLeaves();
    Flag traverseFlag = level == -1 ? Mesh::CALL_LEAF_EL : Mesh::CALL_EL_LEVEL;

    if (level != -1) {
      nElements = 0;

      TraverseStack stack;
      ElInfo *elInfo = stack.traverseFirst(mesh, level, Mesh::CALL_EL_LEVEL);
      while (elInfo) {
	nElements++;
	elInfo = stack.traverseNext(elInfo);
      }
    }

    file << "<?xml version=\"1.0\"?>\n";
    file << "<VTKFile type=\"UnstructuredGrid\" version=\"0.1\" byte_order=\"LittleEndian\">\n";
    file << "  <UnstructuredGrid>\n";
    file << "    <Piece NumberOfPoints=\"" << (dim + 1) * nElements
	 << "\" NumberOfCells=\"" <<  nElements << "\">\n";
    file << "      <Points>\n";
    file << "        <DataArray type=\"Float32\" NumberOfComponents=\"3\" format=\"ascii\">\n";


    // === Write vertex coordinates (every vertex for every element). ===
    TraverseStack stack;
    ElInfo *elInfo = 
      stack.traverseFirst(mesh, level, traverseFlag | Mesh::FILL_COORDS);

    while (elInfo) {
      // Write coordinates of all element vertices.
      for (int i = 0; i <= dim; i++) {     
	for (int j = 0; j < dimOfWorld; j++) 
	  file << elInfo->getCoord(i)[j] << " ";
	
	for (int j = dimOfWorld; j < 3; j++) 
	  file << "0.0";
	
	file << "\n";
      }
   
      elInfo = stack.traverseNext(elInfo);
    }

    file << "        </DataArray>\n";
    file << "      </Points>\n";
    file << "      <Cells>\n";

    file << "        <DataArray type=\"Int32\" Name=\"offsets\">\n";
    for (int i = 0; i < nElements; i++) 
      file << " " << (i + 1) * vertices << "\n";    
    file << "        </DataArray>\n";


    file << "        <DataArray type=\"UInt8\" Name=\"types\">\n";
    for (int i = 0; i < nElements; i++) {
      switch (vertices) {
      case 2:
	file << " 3\n";
	break;
      case 3: 
	file << " 5\n";
	break;
      case 4:
	file << " 10\n";
	break;		    
      default:
	break;
      }	   
    }
    file << "        </DataArray>\n";

    file << "        <DataArray type=\"Int32\" Name=\"connectivity\">\n";
    int vertCntr = 0;
    for (int i = 0; i < nElements; ++i) {
      for (int j = 0; j <= dim; ++j) {
	file << vertCntr << " ";
	++vertCntr;
      }
      file << "\n";
    }
    file << "        </DataArray>\n";
    
    file << "      </Cells>\n";
    file << "      <PointData>\n";
    file << "        <DataArray type=\"Float32\" Name=\"value\" format=\"ascii\">\n";

    file.setf(ios::scientific,ios::floatfield);

    elInfo = stack.traverseFirst(mesh, level, traverseFlag | Mesh::FILL_COORDS);
    int vc = 0;
    while (elInfo) {
      // Get element value.
      double val = vec[elInfo->getElement()->getIndex()];
   
      // Write value for each vertex of each element.
      for (int i = 0; i <= dim; i++) 
	file << (fabs(val) < 1e-40 ? 0.0 : val) << "\n";
      
      vc++;
      elInfo = stack.traverseNext(elInfo);
    } 

    file << "        </DataArray>\n";
    

    file << "      </PointData>\n";
    file << "    </Piece>\n";
    file << "  </UnstructuredGrid>\n";
    file << "</VTKFile>\n";

#if HAVE_PARALLEL_DOMAIN_AMDIS
    if (MPI::COMM_WORLD.Get_rank() == 0)
      VtkWriter::writeParallelFile(fname + ".pvtu", MPI::COMM_WORLD.Get_size(),
				   fname, ".vtu", 1);
#endif
  }
}