RestReader.hpp

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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 RestReader.hpp
 */
 
#ifndef IO_RESTREADER_HPP
#define IO_RESTREADER_HPP
 
#include <cstdio>
#include <string>
 
#include "brains/SimInfo.hpp"
#include "primitives/StuntDouble.hpp"
 
namespace OpenMD {
 
  /**
   * @class RestReader RestReader.hpp "io/RestReader.hpp"
   */
  class RestReader {
  public:
    RestReader(SimInfo* info, const std::string& filename,
               std::vector<int> stuntDoubleIndex) :
        info_(info),
        stuntDoubleIndex_(stuntDoubleIndex), filename_(filename) {
#ifdef IS_MPI
      if (worldRank == 0) {
#endif
 
        inFile_ = new std::ifstream(filename_.c_str(),
                                    ifstream::in | ifstream::binary);
 
        if (inFile_->fail()) {
          snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
                   "RestReader: Cannot open file: %s\n", filename_.c_str());
          painCave.isFatal = 1;
          simError();
        }
#ifdef IS_MPI
      }
 
      strcpy(checkPointMsg, "Reference file opened for reading successfully.");
      errorCheckPoint();
#endif
    }
 
    void readReferenceStructure(void);
 
    ~RestReader() {
#ifdef IS_MPI
      if (worldRank == 0) {
#endif
 
        delete inFile_;
 
#ifdef IS_MPI
      }
 
      strcpy(checkPointMsg, "Reference file closed successfully.");
      errorCheckPoint();
#endif
    }
 
  protected:
    void parseDumpLine(const std::string& line);
    void readStuntDoubles(std::istream& inpuStream);
    void readFrameProperties(std::istream& inputStream);
    void scanFile(void);
    void readSet(void);
 
  private:
    SimInfo* info_ {nullptr};
 
    std::vector<Vector3d> all_pos_;
    std::vector<int> stuntDoubleIndex_;
 
    std::istream* inFile_;
    std::string filename_;
 
    long long framePos_;
 
    const static int bufferSize = 4096;
    char buffer[bufferSize];
  };
}  // namespace OpenMD
 
#endif  // IO_RESTREADER_HPP