DumpReader.hpp

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/*
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 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the following paper when you publish your work:
 *
 * [1] Drisko et al., J. Open Source Softw. 9, 7004 (2024).
 *
 * Good starting points for code and simulation methodology are:
 *
 * [2] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [3] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [4] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [6] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [7] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 * [9] Drisko & Gezelter, J. Chem. Theory Comput. 20, 4986-4997 (2024).
 */
 
/**
 * @file DumpReader.hpp
 * @author tlin
 * @date 11/15/2004
 * @version 2.0
 */
 
#ifndef IO_DUMPREADER_HPP
#define IO_DUMPREADER_HPP
 
#include <cstdio>
#include <string>
 
#include "brains/SimInfo.hpp"
#include "primitives/StuntDouble.hpp"
 
namespace OpenMD {
 
  /**
   * @class DumpReader DumpReader.hpp "io/DumpReader.hpp"
   * @todo get rid of more junk code from DumpReader
   */
  class DumpReader final {
  public:
    DumpReader(SimInfo* info, const std::string& filename);
    ~DumpReader();
 
    /** Returns the number of frames in the dump file*/
    int getNFrames();
 
    void setNeedCOMprops(bool ncp) { needCOMprops_ = ncp; }
 
    void readFrame(int whichFrame);
 
  protected:
    void scanFile();
    void readSet(int whichFrame);
    void parseDumpLine(const std::string&);
    void parseSiteLine(const std::string&);
    void readFrameProperties(std::istream& inputStream);
    int readStuntDoubles(std::istream& inputStream);
    void readSiteData(std::istream& inputStream);
 
    SimInfo* info_ {nullptr};
 
    std::string filename_;
    bool isScanned_;
 
    int nframes_;
 
    std::ifstream inFile_;
 
    std::vector<std::streampos> framePos_;
 
    bool needPos_;
    bool needVel_;
    bool needQuaternion_;
    bool needAngMom_;
    bool needCOMprops_;
    bool readField_;
 
    const static int bufferSize = 4096;
    char buffer[bufferSize];
  };
}  // namespace OpenMD
 
#endif  // IO_DUMPREADER_HPP