RNEMDStats.hpp

/*
 * Copyright (c) 2004-present, The University of Notre Dame. All rights
 * reserved.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright notice,
 *    this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright notice,
 *    this list of conditions and the following disclaimer in the documentation
 *    and/or other materials provided with the distribution.
 *
 * 3. Neither the name of the copyright holder nor the names of its
 *    contributors may be used to endorse or promote products derived from
 *    this software without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
 * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 * POSSIBILITY OF SUCH DAMAGE.
 *
 * 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).
 */
 
#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