RNEMDStats.hpp

/*
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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 APPLICATIONS_STATICPROPS_RNEMDSTATS_HPP
#define APPLICATIONS_STATICPROPS_RNEMDSTATS_HPP
 
#include <bitset>
#include <string>
#include <utility>
#include <vector>
 
#include "applications/staticProps/SpatialStatistics.hpp"
#include "brains/SimInfo.hpp"
#include "math/Vector3.hpp"
#include "primitives/StuntDouble.hpp"
#include "types/AtomType.hpp"
 
namespace OpenMD {
 
  class RNEMDZ : public SlabStatistics {
  public:
    RNEMDZ(SimInfo* info, const std::string& filename, const std::string& sele,
           int nzbins, int axis = 2);
    void processFrame(int frame);
    void processStuntDouble(StuntDouble*, int) {}
 
  private:
    enum OutputFields {
      BEGININDEX = 0,
      Z          = BEGININDEX,
      TEMPERATURE,
      VELOCITY,
      DENSITY,
      ACTIVITY,
      ELECTRICFIELD,
      ELECTROSTATICPOTENTIAL,
      CHARGE,
      CHARGEVELOCITY,
      ENDINDEX
    };
 
    using OutputBitSet = std::bitset<ENDINDEX - BEGININDEX>;
 
    OutputBitSet outputMask_;
    bool usePeriodicBoundaryConditions_;
  };
 
  class RNEMDR : public ShellStatistics {
  public:
    RNEMDR(SimInfo* info, const std::string& filename, const std::string& sele,
           const std::string& comsele, int nrbins, RealType binWidth);
    void processFrame(int frame);
    void processStuntDouble(StuntDouble*, int) {}
 
  private:
    enum OutputFields {
      BEGININDEX = 0,
      R          = BEGININDEX,
      TEMPERATURE,
      ANGULARVELOCITY,
      DENSITY,
      ENDINDEX
    };
 
    using OutputBitSet = std::bitset<ENDINDEX - BEGININDEX>;
 
    OutputBitSet outputMask_;
  };
 
  class RNEMDRTheta : public ShellStatistics {
  public:
    RNEMDRTheta(SimInfo* info, const std::string& filename,
                const std::string& sele, const std::string& comsele, int nrbins,
                RealType binWidth, int nanglebins);
    void processFrame(int frame);
    void processStuntDouble(StuntDouble*, int) {}
    std::pair<int, int> getBins(Vector3d pos);
    void writeOutput();
 
  private:
    int nAngleBins_;
    Vector3d fluxVector_;
 
    OutputData r_;
    OutputData angularVelocity_;
  };
}  // namespace OpenMD
 
#endif