DumpWriter.hpp

/*
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 * modification, are permitted provided that the following conditions are met:
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 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *
 * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [4] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [5] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [6] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [7] Lamichhane, Newman & Gezelter, J. Chem. Phys. 141, 134110 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 */
 
#ifndef IO_DUMPWRITER_HPP
#define IO_DUMPWRITER_HPP
 
#define _LARGEFILE_SOURCE64
#ifndef _FILE_OFFSET_BITS
#define _FILE_OFFSET_BITS 64
#endif
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include <fstream>
#include <iostream>
#include <string>
 
#include <sys/stat.h>
#include <sys/types.h>
 
#include "brains/SimInfo.hpp"
#include "brains/Thermo.hpp"
#include "primitives/Atom.hpp"
#include "primitives/StuntDouble.hpp"
 
namespace OpenMD {
 
  /**
   * @class DumpWriter DumpWriter.hpp "io/DumpWriter.hpp"
   * @todo
   */
  class DumpWriter {
  public:
    DumpWriter(SimInfo* info);
    DumpWriter(SimInfo* info, const std::string& filename);
    DumpWriter(SimInfo* info, const std::string& filename, bool writeDumpFile);
    ~DumpWriter();
 
    void writeDumpAndEor();
    void writeDump();
    void writeEor();
 
  private:
    void writeFrame(std::ostream& os);
    void writeFrameProperties(std::ostream& os, Snapshot* s);
    std::string prepareDumpLine(StuntDouble* sd);
    std::string prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex);
    std::ostream* createOStream(const std::string& filename);
    void writeClosing(std::ostream& os);
 
    SimInfo* info_ {nullptr};
    std::string filename_;
    std::ostream* dumpFile_;
    std::string eorFilename_;
    bool needCompression_;
    bool needForceVector_;
    bool needParticlePot_;
    bool needFlucQ_;
    bool needElectricField_;
    bool needSitePotential_;
    bool needDensity_;
    bool doSiteData_;
    bool createDumpFile_;
  };
}  // namespace OpenMD
 
#endif  // #define IO_DUMPWRITER_HPP