FileReaderHDF5.h

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// This file is part of the Peano project. For conditions of distribution and
// use, please see the copyright notice at www.peano-framework.org
#pragma once
 
#include "config.h"
#include "peano4/utils/Globals.h"
#include "peano4/datamanagement/CellMarker.h"
 
#include "tarch/logging/Log.h"
 
#include <list> 
#include <vector> 
 
#ifdef UseHDF5
#include "H5Cpp.h"
#endif
 
namespace toolbox {
  namespace particles {
    class FileReaderHDF5;
  }
}
 
 
class toolbox::particles::FileReaderHDF5 {
  private:
    static tarch::logging::Log                           _log;
 
    /* Coordinates */
    std::list< tarch::la::Vector<Dimensions,double> >    _Coordinates;
 
    /* Other fields in the HDF5 file */
    std::vector< tarch::la::Vector<Dimensions,double> >  _Velocity;
    std::vector<double>                                  _Mass;
    std::vector<double>                                  _SmoothingLength;
    std::vector<double>                                  _InternalEnergy;
    std::vector<int>                                     _ParticleIDs;
 
    /* If we are removing read-in particles on-the-fly while sorting
     * them into voxels, we need to keep track of their index to access
     * the other particle quantities correctly. This list keeps these indexes.*/
    std::list<int>                                       _ParticleIndex;
 
    /* Copies that hold the data only for particles within the voxel */
    /* If you are adding additional quantities, don't forget to update them
     * in FileReaderHDF5.clearVoxel() and FileReaderHDF5.isVoxelEmpty() 
     * as well */
    std::vector< tarch::la::Vector<Dimensions,double> >  _VelocityWithinVoxel;
    std::vector<double>                                  _MassWithinVoxel;
    std::vector<double>                                  _SmoothingLengthWithinVoxel;
    std::vector<double>                                  _InternalEnergyWithinVoxel;
    std::vector<int>                                     _ParticleIDsWithinVoxel;
 
  public:
    void readHDF5File( const std::string& filename );
 
#ifdef UseHDF5
 
    std::vector< int > readIntScalar( 
       const H5::H5File&   file, 
       const H5std_string& groupName, 
       const H5std_string& datasetName );
 
    std::vector< double > readDoubleScalar( 
       const H5::H5File&   file, 
       const H5std_string& groupName, 
       const H5std_string& datasetName );
 
    std::list< tarch::la::Vector<Dimensions,double> > readDoubleArray( 
       const H5::H5File&   file, 
       const H5std_string& groupName, 
       const H5std_string& datasetName );
 
    std::vector< tarch::la::Vector<Dimensions,double> > readFloatArray( 
       const H5::H5File&   file, 
       const H5std_string& groupName, 
       const H5std_string& datasetName );
 
#endif   
 
    std::list< tarch::la::Vector<Dimensions,double> > getParticlesWithinVoxel(
      const tarch::la::Vector<Dimensions,double>&  x,
      const tarch::la::Vector<Dimensions,double>&  h,
      bool remove
    );
 
 
    void clear();
 
    bool empty() const;
 
    bool getNumberOfCoordinates() const;
 
    void clearVoxel();
 
    bool isVoxelEmpty() const;
 
    /* 
     * Get methods for data other than Coordinates.
     */
    std::vector< tarch::la::Vector<Dimensions,double> > getVelocityWithinVoxel() const;
    std::vector<double>                                 getMassWithinVoxel() const;
    std::vector<double>                                 getSmoothingLengthWithinVoxel() const;
    std::vector<double>                                 getInternalEnergyWithinVoxel() const;
    std::vector<int>                                    getParticleIDsWithinVoxel() const;
 
};