Hdf5DataWriter.hpp

/*

Copyright (C) University of Oxford, 2005-2009

University of Oxford means the Chancellor, Masters and Scholars of the
University of Oxford, having an administrative office at Wellington
Square, Oxford OX1 2JD, UK.

This file is part of Chaste.

Chaste 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, either version 2.1 of the License, or
(at your option) any later version.

Chaste 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 Lesser General Public
License for more details. The offer of Chaste under the terms of the
License is subject to the License being interpreted in accordance with
English Law and subject to any action against the University of Oxford
being under the jurisdiction of the English Courts.

You should have received a copy of the GNU Lesser General Public License
along with Chaste. If not, see <http://www.gnu.org/licenses/>.

*/
#ifndef HDF5DATAWRITER_HPP_
#define HDF5DATAWRITER_HPP_

#include <hdf5.h>
#include <petscvec.h>
#include <cassert>
#include <vector>
#include "Exception.hpp"
#include "AbstractDataWriter.hpp"
#include "DataWriterVariable.hpp"
#include "OutputFileHandler.hpp"

class Hdf5DataWriter//  : public AbstractDataWriter
{
private:
    bool mAmMaster;          
    std::string mDirectory; 
    std::string mBaseName; 
    bool mCleanDirectory;   
    bool mIsInDefineMode; 
    bool mIsFixedDimensionSet; 
    bool mIsUnlimitedDimensionSet; 
    std::string mUnlimitedDimensionName;
    std::string mUnlimitedDimensionUnit;
    unsigned mFileFixedDimensionSize; 
    unsigned mDataFixedDimensionSize; 
    unsigned mLo, mHi; 
    unsigned mNumberOwned, mOffset; 
    bool mIsDataComplete;
    bool mNeedExtend; 
    std::vector<unsigned> mIncompleteNodeIndices;

    std::vector<DataWriterVariable> mVariables; 
    void CheckVariableName(std::string name); 
    void CheckUnitsName(std::string name); 
    hid_t mFileId;
    hid_t mDatasetId;
    hid_t mTimeDatasetId;

    long mCurrentTimeStep;

    const static unsigned DATASET_DIMS=3;
    hsize_t mDatasetDims[DATASET_DIMS];

public:
    Hdf5DataWriter(std::string directory, std::string baseName, bool cleanDirectory=true);
    virtual ~Hdf5DataWriter();

    void DefineFixedDimension(long dimensionSize);
    void DefineFixedDimension(std::vector<unsigned> nodesToOuput, long vecSize);
    void DefineUnlimitedDimension(std::string variableName, std::string variableUnits);
    void AdvanceAlongUnlimitedDimension();
    int DefineVariable(std::string variableName, std::string variableUnits);
    virtual void EndDefineMode();
    void PossiblyExtend();
    void PutVector(int variableID, Vec petscVector);
    void PutStripedVector(int firstVariableID, int secondVariableID, Vec petscVector);
    void PutUnlimitedVariable(double value);

    void Close();
};

#endif /*HDF5DATAWRITER_HPP_*/

---