OHTSTJob.h

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/*
** This file is part of eOn.
**
** SPDX-License-Identifier: BSD-3-Clause
**
** Copyright (c) 2010--present, eOn Development Team
** All rights reserved.
**
** Repo:
** https://github.com/TheochemUI/eOn
*/
#pragma once
#include "eon/Eigen.h"
#include "eon/Job.h"
#include "eon/Matter.h"
#include "eon/Parameters.h"
 
namespace tests {
struct OHTSTPlaneWrapTest;
}
 
namespace eonc {

inline double pmfScanS(long plane, long nScan, double guideLen) {
  const long n = nScan < 2L ? 2L : nScan;
  return static_cast<double>(plane) * guideLen / static_cast<double>(n - 1);
}

class OHTSTJob : public Job {
 
public:
  OHTSTJob(std::unique_ptr<Parameters> parameters, Runtime &rt)
      : Job(std::move(parameters), rt) {}
  ~OHTSTJob(void) = default;
  std::vector<std::string> run(void);
 
private:
  struct PlaneAverages {
    double fn{0.0};   
    VectorXd rotNorm; 
    VectorXd rotRaw;  
    VectorXd pos;     
  };
 
  // x is the unwrapped free configuration. It is not read back from
  // Matter: setPositionsFreeV wraps into the primary cell, and the
  // projection of that image is a different 3N point.
  PlaneAverages samplePlane(Matter &matter, VectorXd &x, const VectorXd &gamma,
                            const VectorXd &normal);
 
  friend struct ::tests::OHTSTPlaneWrapTest;

  double reactantQRatio(Matter &matter, const VectorXd &gammaR,
                        const VectorXd &normal);

  void drawThermalVelocities(VectorXd &vel, const VectorXd *normal);

  bool symmetryReflect(const VectorXd &xR, VectorXd &x, VectorXd &v,
                       const VectorXd &xOld, const VectorXd *normal);
  friend struct OHTSTSymmetryTest;
 
  std::vector<VectorXd> m_symDirs; 
  VectorXd m_symXR;                
 
  VectorXd m_masses3N;        
  double m_dt{0.0};           
  double m_kbt{0.0};          
  double m_andersenProb{0.0}; 
  long m_seedState{12345};    
  double uniformDraw();       
  double gaussDraw();         
  bool m_gaussHave{false};
  double m_gaussSpare{0.0};
};

AtomMatrix minImageRemoveRigidDrift(const Matter &reference, AtomMatrix diff,
                                    Eigen::RowVector3d *totalDrift);
 
} // namespace eonc