Initialize at openlb-1-3

1 files changed, 439 insertions, 0 deletions

diff --git a/src/io/superVtmWriter3D.hh b/src/io/superVtmWriter3D.hh
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+/*  This file is part of the OpenLB library
+ *
+ *  Copyright (C) 2016-2017 Albert Mink, Maximilian Gaedtke, Markus Morhard Mathias J. Krause
+ *  E-mail contact: info@openlb.net
+ *  The most recent release of OpenLB can be downloaded at
+ *  <http://www.openlb.net/>
+ *
+ *  This program is free software; you can redistribute it and/or
+ *  modify it under the terms of the GNU General Public License
+ *  as published by the Free Software Foundation; either version 2
+ *  of the License, or (at your option) any later version.
+ *
+ *  This program 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 General Public License for more details.
+ *
+ *  You should have received a copy of the GNU General Public
+ *  License along with this program; if not, write to the Free
+ *  Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
+ *  Boston, MA  02110-1301, USA.
+*/
+
+/** \file
+ * A method to write vtk data for cuboid geometries
+ * (only for uniform grids) -- generic implementation.
+ */
+
+#ifndef SUPER_VTM_WRITER_3D_HH
+#define SUPER_VTM_WRITER_3D_HH
+
+#include <fstream>
+#include <iostream>
+#include <iomanip>
+#include <string>
+#include "core/singleton.h"
+#include "communication/loadBalancer.h"
+#include "geometry/cuboidGeometry3D.h"
+#include "communication/mpiManager.h"
+#include "io/fileName.h"
+#include "io/superVtmWriter3D.h"
+#include "io/base64.h"
+
+#include <stdio.h>
+#include <assert.h>
+#include "zlib.h"
+
+
+
+namespace olb {
+
+
+template<typename T, typename W>
+SuperVTMwriter3D<T,W>::SuperVTMwriter3D( const std::string& name, bool binary, bool compress)
+  : clout( std::cout,"SuperVTMwriter3D" ), _createFile(false), _name(name), _binary(binary), _compress(compress)
+{}
+
+template<typename T, typename W>
+void SuperVTMwriter3D<T,W>::write(int iT)
+{
+  int rank = 0;
+#ifdef PARALLEL_MODE_MPI
+  rank = singleton::mpi().getRank();
+#endif
+
+  //  !!!!!!!!!!! check whether _pointerVec is empty
+  if ( _pointerVec.empty() ) {
+    clout << "Error: Did you add a Functor ?";
+  } else {
+    // to get first element _pointerVec
+    // problem if functors with different SuperStructure are stored
+    // since till now, there is only one origin
+    const auto it_begin = _pointerVec.cbegin();
+    CuboidGeometry3D<T> const& cGeometry = (**it_begin).getSuperStructure().getCuboidGeometry();
+    // no gaps between vti files (cuboids)
+    (**it_begin).getSuperStructure().communicate();
+    LoadBalancer<T>& load = (**it_begin).getSuperStructure().getLoadBalancer();
+    const T delta = cGeometry.getMotherCuboid().getDeltaR();
+
+    // PVD, owns all
+    if ( rank == 0 ) {
+      const std::string pathPVD = singleton::directories().getVtkOutDir()
+                            + createFileName( _name ) + ".pvd";
+      dataPVDmaster( iT, pathPVD,  "data/" + createFileName( _name, iT ) + ".vtm" );
+
+      const std::string pathVTM = singleton::directories().getVtkOutDir()
+                            + "data/" + createFileName( _name, iT ) + ".vtm";
+      preambleVTM(pathVTM);
+      for (int iC = 0; iC < cGeometry.getNc(); iC++) {
+        dataVTM( iC, pathVTM, createFileName( _name, iT, iC) + ".vti" );
+      }
+      closeVTM(pathVTM);
+    }
+    // VTI, each process writes its cuboids
+    for (int iCloc = 0; iCloc < load.size(); iCloc++) {
+    // get piece/whole extent
+      const Vector<int,3> extent0(-1,-1,-1);
+      const Vector<int,3> extent1( cGeometry.get(load.glob(iCloc)).getExtend() );
+
+      const std::string fullNameVTI = singleton::directories().getVtkOutDir() + "data/"
+                                + createFileName( _name, iT, load.glob(iCloc) ) + ".vti";
+
+      // get dimension/extent for each cuboid
+      const int originLatticeR[4] = {load.glob(iCloc),0,0,0};
+      T originPhysR[3] = {T()};
+      cGeometry.getPhysR(originPhysR,originLatticeR);
+
+      preambleVTI(fullNameVTI, extent0, extent1, originPhysR, delta);
+      for (auto it : _pointerVec) {
+        dataArray(fullNameVTI, *it, load.glob(iCloc), extent1);
+      }
+      closePiece(fullNameVTI);
+      closeVTI(fullNameVTI);
+    }
+  }
+}
+
+template<typename T, typename W>
+void SuperVTMwriter3D<T,W>::write(SuperF3D<T,W>& f, int iT)
+{
+  CuboidGeometry3D<T> const& cGeometry = f.getSuperStructure().getCuboidGeometry();
+  LoadBalancer<T>& load = f.getSuperStructure().getLoadBalancer();
+  // no gaps between vti files (cuboids)
+  f.getSuperStructure().communicate();
+  const T delta = cGeometry.getMotherCuboid().getDeltaR();
+
+  int rank = 0;
+#ifdef PARALLEL_MODE_MPI
+  rank = singleton::mpi().getRank();
+#endif
+
+  // write a pvd file, which links all vti files
+  // each vti file is written by one thread, which may own severals cuboids
+  if ( rank == 0 ) {
+    // master only
+    const std::string pathVTM = singleton::directories().getVtkOutDir()
+                          + createFileName( f.getName(), iT )  + ".vtm";
+
+    preambleVTM(pathVTM);
+    for (int iC = 0; iC < cGeometry.getNc(); iC++) {
+      const std::string nameVTI = "data/" + createFileName( f.getName(), iT, iC) + ".vti";
+      // puts name of .vti piece to a .pvd file [fullNamePVD]
+      dataVTM( iC, pathVTM, nameVTI );
+    }
+    closeVTM(pathVTM);
+  } // master only
+
+  for (int iCloc = 0; iCloc < load.size(); iCloc++) {
+    // get piece/whole extent
+    const Vector<int,3> extent0(-1,-1,-1);
+    const Vector<int,3> extent1( cGeometry.get(load.glob(iCloc)).getExtend() );
+
+    const std::string fullNameVTI = singleton::directories().getVtkOutDir() + "data/"
+                              + createFileName( f.getName(), iT, load.glob(iCloc) ) + ".vti";
+
+    // get dimension/extent for each cuboid
+    const int originLatticeR[4] = {load.glob(iCloc),0,0,0};
+    T originPhysR[3] = {T()};
+    cGeometry.getPhysR(originPhysR,originLatticeR);
+
+    preambleVTI(fullNameVTI, extent0, extent1, originPhysR, delta);
+
+    dataArray(fullNameVTI, f, load.glob(iCloc), extent1);
+    closePiece(fullNameVTI);
+    closeVTI(fullNameVTI);
+  } // cuboid
+}
+
+
+template<typename T, typename W>
+void SuperVTMwriter3D<T,W>::write(std::shared_ptr<SuperF3D<T,W>> ptr_f, int iT)
+{
+  write(*ptr_f, iT);
+}
+
+template<typename T, typename W>
+void SuperVTMwriter3D<T,W>::createMasterFile()
+{
+  int rank = 0;
+#ifdef PARALLEL_MODE_MPI
+  rank = singleton::mpi().getRank();
+#endif
+  if ( rank == 0 ) {
+    const std::string fullNamePVDmaster = singleton::directories().getVtkOutDir()
+                                    + createFileName( _name ) + ".pvd";
+    preamblePVD(fullNamePVDmaster);
+    closePVD(fullNamePVDmaster);
+    _createFile = true;
+  }
+}
+
+template<typename T, typename W>
+void SuperVTMwriter3D<T,W>::addFunctor(SuperF3D<T,W>& f)
+{
+  _pointerVec.push_back(&f);
+}
+
+template<typename T, typename W>
+void SuperVTMwriter3D<T,W>::clearAddedFunctors()
+{
+  _pointerVec.clear();
+}
+
+template<typename T, typename W>
+std::string SuperVTMwriter3D<T,W>::getName() const
+{
+  return _name;
+}
+
+
+
+
+////////////////////private member functions///////////////////////////////////
+template<typename T, typename W>
+void SuperVTMwriter3D<T,W>::preambleVTI (const std::string& fullName,
+    const Vector<int,3> extent0, const Vector<int,3> extent1, T origin[], T delta)
+{
+  double d_delta = delta;
+  double d_origin[3] = {origin[0], origin[1], origin[2]};
+
+  std::ofstream fout(fullName, std::ios::trunc);
+  if (!fout) {
+    clout << "Error: could not open " << fullName << std::endl;
+  }
+  fout << "<?xml version=\"1.0\"?>\n";
+  fout << "<VTKFile type=\"ImageData\" version=\"0.1\" ";
+  if (_compress) {
+    fout << "byte_order=\"LittleEndian\" compressor=\"vtkZLibDataCompressor\">\n";
+  } else {
+    fout << "byte_order=\"LittleEndian\">\n";
+  }
+  fout << "<ImageData WholeExtent=\""
+       << extent0[0] <<" "<< extent1[0] <<" "
+       << extent0[1] <<" "<< extent1[1] <<" "
+       << extent0[2] <<" "<< extent1[2]
+       << "\" Origin=\"" << d_origin[0] << " " << d_origin[1] << " " << d_origin[2]
+       << "\" Spacing=\"" << d_delta << " " << d_delta << " " << d_delta << "\">\n";
+  fout << "<Piece Extent=\""
+       << extent0[0] <<" "<< extent1[0] <<" "
+       << extent0[1] <<" "<< extent1[1] <<" "
+       << extent0[2] <<" "<< extent1[2] <<"\">\n";
+  fout << "<PointData>\n";
+  fout.close();
+}
+
+template<typename T, typename W>
+void SuperVTMwriter3D<T,W>::closeVTI(const std::string& fullNamePiece)
+{
+  std::ofstream fout(fullNamePiece, std::ios::app );
+  if (!fout) {
+    clout << "Error: could not open " << fullNamePiece << std::endl;
+  }
+  fout << "</ImageData>\n";
+  fout << "</VTKFile>\n";
+  fout.close();
+}
+
+template<typename T, typename W>
+void SuperVTMwriter3D<T,W>::preamblePVD(const std::string& fullNamePVD)
+{
+  std::ofstream fout(fullNamePVD, std::ios::trunc);
+  if (!fout) {
+    clout << "Error: could not open " << fullNamePVD << std::endl;
+  }
+  fout << "<?xml version=\"1.0\"?>\n";
+  fout << "<VTKFile type=\"Collection\" version=\"0.1\" "
+       << "byte_order=\"LittleEndian\">\n"
+       << "<Collection>\n";
+  fout.close();
+}
+
+template<typename T, typename W>
+void SuperVTMwriter3D<T,W>::closePVD(const std::string& fullNamePVD)
+{
+  std::ofstream fout(fullNamePVD, std::ios::app );
+  if (!fout) {
+    clout << "Error: could not open " << fullNamePVD << std::endl;
+  }
+  fout << "</Collection>\n";
+  fout << "</VTKFile>\n";
+  fout.close();
+}
+
+template<typename T, typename W>
+void SuperVTMwriter3D<T,W>::preambleVTM(const std::string& fullNamePVD)
+{
+  std::ofstream fout(fullNamePVD, std::ios::trunc);
+  if (!fout) {
+    clout << "Error: could not open " << fullNamePVD << std::endl;
+  }
+  fout << "<?xml version=\"1.0\"?>\n";
+  fout << "<VTKFile type=\"vtkMultiBlockDataSet\" version=\"1.0\" "
+       << "byte_order=\"LittleEndian\">\n"
+       << "<vtkMultiBlockDataSet>\n" ;
+  fout.close();
+}
+
+template<typename T, typename W>
+void SuperVTMwriter3D<T,W>::closeVTM(const std::string& fullNamePVD)
+{
+  std::ofstream fout(fullNamePVD, std::ios::app );
+  if (!fout) {
+    clout << "Error: could not open " << fullNamePVD << std::endl;
+  }
+  fout << "</vtkMultiBlockDataSet>\n";
+  fout << "</VTKFile>\n";
+  fout.close();
+}
+
+template<typename T, typename W>
+void SuperVTMwriter3D<T,W>::dataVTM(int iC, const std::string& fullNamePVD,
+                                    const std::string& namePiece)
+{
+  std::ofstream fout(fullNamePVD, std::ios::app);
+  if (!fout) {
+    clout << "Error: could not open " << fullNamePVD << std::endl;
+  }
+  fout << "<Block index=\"" << iC << "\" >\n";
+  fout << "<DataSet index= \"0\" " << "file=\"" << namePiece << "\">\n"
+       << "</DataSet>\n";
+  fout << "</Block>\n";
+  fout.close();
+}
+
+template<typename T, typename W>
+void SuperVTMwriter3D<T,W>::dataPVDmaster(int iT,
+    const std::string& fullNamePVDMaster,
+    const std::string& namePiece)
+{
+  std::ofstream fout(fullNamePVDMaster, std::ios::in | std::ios::out | std::ios::ate);
+  if (fout) {
+    fout.seekp(-25,std::ios::end);    // jump -25 form the end of file to overwrite closePVD
+
+    fout << "<DataSet timestep=\"" << iT << "\" "
+         << "group=\"\" part=\"\" "
+         << "file=\"" << namePiece << "\"/>\n";
+    fout.close();
+    closePVD(fullNamePVDMaster);
+  } else {
+    clout << "Error: could not open " << fullNamePVDMaster << std::endl;
+  }
+}
+
+template<typename T, typename W>
+void SuperVTMwriter3D<T,W>::dataArray(const std::string& fullName,
+                                      SuperF3D<T,W>& f, int iC, const Vector<int,3> extent1)
+{
+  std::ofstream fout( fullName, std::ios::out | std::ios::app );
+  if (!fout) {
+    clout << "Error: could not open " << fullName << std::endl;
+  }
+
+  fout << "<DataArray type=\"Float32\" Name=\"" << f.getName() << "\" NumberOfComponents=\"" << f.getTargetDim() << "\" ";
+  if (_compress || _binary) {
+    fout << "format=\"binary\" encoding=\"base64\">\n";
+  } else {
+    fout << ">\n";
+  }
+
+  int i[4] = {iC, 0, 0, 0};
+  W evaluated[f.getTargetDim()];
+  for (int iDim = 0; iDim < f.getTargetDim(); ++iDim) {
+    evaluated[iDim] = W();
+  }
+
+  size_t numberOfFloats = f.getTargetDim() * (extent1[0]+2) * (extent1[1]+2) * (extent1[2]+2);
+  uint32_t binarySize = static_cast<uint32_t>( numberOfFloats*sizeof(float) );
+
+  std::unique_ptr<float[]> streamFloat(new float[numberOfFloats]);    // stack may be too small
+  int itter = 0;
+  // fill buffer with functor data
+  for (i[3] = -1; i[3] < extent1[2]+1; ++i[3]) {
+    for (i[2] = -1; i[2] < extent1[1]+1; ++i[2]) {
+      for (i[1] = -1; i[1] < extent1[0]+1; ++i[1]) {
+        f(evaluated,i);
+        for (int iDim = 0; iDim < f.getTargetDim(); ++iDim) {
+          streamFloat[itter] = float( evaluated[iDim] );
+          ++itter;
+        }
+      }
+    }
+  }
+
+  if (_compress) {
+    // char buffer for functor data
+    const unsigned char* charData = reinterpret_cast<unsigned char*>(streamFloat.get());
+    // buffer for compression
+    std::unique_ptr<unsigned char[]> comprData(new unsigned char[ binarySize ]);    // stack may be too small
+
+    // compress data (not yet decoded as base64) by zlib
+    uLongf sizeCompr = compressBound(binarySize);
+    compress2( comprData.get(), &sizeCompr, charData, binarySize, -1);
+
+    // encode prefix to base64 documented in  http://www.earthmodels.org/software/vtk-and-paraview/vtk-file-formats
+    Base64Encoder<uint32_t> prefixEncoder(fout, 4);
+    uint32_t prefix[4] = {1,binarySize,binarySize,static_cast<uint32_t>(sizeCompr)};
+    prefixEncoder.encode(prefix, 4);
+
+    // encode compressed data to base64
+    Base64Encoder<unsigned char> dataEncoder( fout, sizeCompr );
+    dataEncoder.encode(comprData.get(), sizeCompr);
+  } else if(_binary) {
+    // encode prefix to base64 documented in  http://www.earthmodels.org/software/vtk-and-paraview/vtk-file-formats
+    Base64Encoder<uint32_t> prefixEncoder(fout, 1);
+    prefixEncoder.encode(&binarySize, 1);
+    //  write numbers from functor
+    Base64Encoder<float> dataEncoder(fout, numberOfFloats);
+    dataEncoder.encode(streamFloat.get(),numberOfFloats);
+  } else {
+    for( size_t iOut = 0; iOut < numberOfFloats; ++iOut ) {
+      fout << streamFloat[iOut] << " ";
+    }
+  }
+  fout.close();
+
+  std::ofstream ffout( fullName,  std::ios::out | std::ios::app );
+  if (!ffout) {
+    clout << "Error: could not open " << fullName << std::endl;
+  }
+  ffout << "\n</DataArray>\n";
+  ffout.close();
+}
+
+template<typename T, typename W>
+void SuperVTMwriter3D<T,W>::closePiece(const std::string& fullNamePiece)
+{
+  std::ofstream fout(fullNamePiece, std::ios::app );
+  if (!fout) {
+    clout << "Error: could not open " << fullNamePiece << std::endl;
+  }
+  fout << "</PointData>\n";
+  fout << "</Piece>\n";
+  fout.close();
+}
+
+
+}  // namespace olb
+
+#endif