TimeCorrFunc.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).
 */
 
#ifndef APPLICATIONS_DYNAMICPROPS_TIMECORRFUNC_HPP
#define APPLICATIONS_DYNAMICPROPS_TIMECORRFUNC_HPP
 
#include <string>
#include <vector>
 
#include "applications/dynamicProps/DynamicProperty.hpp"
#include "brains/SimInfo.hpp"
#include "io/DumpReader.hpp"
#include "primitives/StuntDouble.hpp"
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"
#include "utils/ProgressBar.hpp"
 
namespace OpenMD {
 
  //! Computes a correlation function by scanning a trajectory once to
  //! precompute quantities to be correlated
  
  // There are two modes for carrying out time correleation
  // functions. The default mode allows overlapping origins of the
  // sampling windows. 
  //
  // origin 0:  frames 0,1,2,...,nFrames-1
  // origin 1:  frames 1,2,3,...,nFrames-1
  // origin 2:  frames 2,3,4,...,nFrames-1
  // ...  
  // This gives many samples for short lag times and fewer for long
  // lag times, and we normalize using count_[timeBin]
  //
  // The second approach uses non-overlapping windows:
  // |--ncor--|--nsep--|--ncor--|--nsep--|--ncor--|
  //    avg1              avg2              avg3
  // We accomplish this behavior by setting:
  //
  // nStart_ = frames to skip at beginning (for equilibration)
  // ncor = frames per window (nTimeBins_)
  // nStride_ = frames between window starts (ncor + nsep)
  //
  // This means that the sampling windows look like:
  // origin 0:  frames [nStart_, nStart_ + ncor)
  // origin 1:  frames [nStart_ + nStride_, nStart_ + nStride_ + ncor)
  // origin 2:  frames [nStart_ + 2*nStride_, nStart_ + 2*nStride_ + ncor)
  //
  // nStride_ is the key here:
  // nStride_ = 1             = all overlapping origins
  // nStride_ = nTimeBins_    = tight non-overlapping windows (nsep=0)
  // nStride_ > nTimeBins_    = sampling windows with a decorrelation gap
  // 1 < nStride_ < nTimeBins_ = overlapping fixed-length windows
  //                             (pass tsep_fs < 0 to setWindowingParameters;
  //                              |tsep_fs| is the overlap duration in fs)
 
  template<typename T>
  class TimeCorrFunc : public DynamicProperty {
  public:
    TimeCorrFunc(SimInfo* info, const std::string& filename,
                 const std::string& sele1, const std::string& sele2);
 
    virtual ~TimeCorrFunc() { delete reader_; }
    
    // Setters — call before doCorrelate()
    void setWindowingParameters(RealType tcorr_fs, int nStart, RealType tsep_fs);
    
    virtual void doCorrelate();
 
    const std::string& getCorrFuncType() const { return corrFuncType_; }
 
    void setCorrFuncType(const std::string& type) { corrFuncType_ = type; }
 
    void setParameterString(const std::string& params) {
      paramString_ = params;
    }
 
    void setLabelString(const std::string& label) { labelString_ = label; }
 
  protected:
    virtual void preCorrelate();
    virtual void correlation();
    virtual void postCorrelate();
    virtual void computeFrame(int frame);
    virtual void validateSelection(SelectionManager& seleMan);
    virtual void correlateFrames(int frame1, int frame2, int timeBin);
    virtual void writeCorrelate();
 
    // The pure virtual functions that must be implemented.
 
    // For System Properties:
    virtual void computeProperty1(int frame)      = 0;
    virtual void computeProperty2(int frame)      = 0;
    virtual T calcCorrVal(int frame1, int frame2) = 0;
    // For Molecular Properties
    virtual int computeProperty1(int frame, Molecule* mol) = 0;
    virtual int computeProperty2(int frame, Molecule* mol) = 0;
    // For Object
    virtual int computeProperty1(int frame, StuntDouble* sd) = 0;
    virtual int computeProperty2(int frame, StuntDouble* sd) = 0;
    // For Bond properties
    virtual int computeProperty1(int frame, Bond* b) = 0;
    virtual int computeProperty2(int frame, Bond* b) = 0;
    // For everything except System properties:
    virtual T calcCorrVal(int frame1, int frame2, int id1, int id2) = 0;
 
    RealType deltaTime_;
    unsigned int nTimeBins_;
    int nFrames_;
    std::vector<T> histogram_;
    std::vector<int> count_;
    std::vector<RealType> times_;
    RealType dtMean_ {};
    RealType dtSigma_ {};
 
    SimInfo* info_ {nullptr};
    DumpReader* reader_;
    std::string dumpFilename_;
    SelectionManager seleMan1_;
    SelectionManager seleMan2_;
 
    Snapshot* currentSnapshot_;
 
    std::string selectionScript1_;
    std::string selectionScript2_;
 
    SelectionEvaluator evaluator1_;
    SelectionEvaluator evaluator2_;
 
    bool uniqueSelections_;
    bool autoCorrFunc_;
    bool doSystemProperties_;
    bool doMolecularProperties_;
    bool doObjectProperties_;
    bool doAtomicProperties_;
    bool doBondProperties_;
    bool allowTimeFuzz_;
 
    std::string corrFuncType_;
    std::string paramString_;
    std::string labelString_;
 
    std::vector<std::vector<int>> sele1ToIndex_;
    std::vector<std::vector<int>> sele2ToIndex_;
    std::vector<std::vector<int>> GIDtoSele1_;
    std::vector<std::vector<int>> GIDtoSele2_;
    std::vector<std::vector<int>> selection1StartFrame_;
    std::vector<std::vector<int>> selection2StartFrame_;
 
    ProgressBarPtr progressBar_;
    // --- Windowing parameters -------------------------------------------
    //
    // nStart_  : number of frames to skip at the start of the trajectory
    //            (equilibration period). Default 0.
    //
    // nStride_ : number of frames between the start of successive
    //            correlation windows.
    //
    //   nStride_ = 1          → original overlapping-origin behavior
    //                           (all possible time origins used)
    //
    //   nStride_ = nTimeBins_ → non-overlapping windows, no gap
    //                           (MultiSpec ncor mode)
    //
    //   nStride_ = nTimeBins_ + nSep_
    //                         → non-overlapping windows with a gap
    //                           between them (MultiSpec ncor+nsep mode)
    //
    // nSep_    : gap in frames between end of one window and start of
    //            the next. Only meaningful when nStride_ > nTimeBins_.
    //            Default 0.
    //
    // nTimeBins_ already controls the correlation window length (ncor).
    // It is set from simParams->getSampleTime() and nFrames_ in the
    // existing constructor, but can be overridden by setSampleSize().
    //
    // navg_    : number of windows that fit in the trajectory given
    //            nStart_, nStride_, nTimeBins_, nFrames_.
    //            Computed in preCorrelate(), read-only after that.
    //
    // useWindowing_ : true if nStride_ > 1 or nStart_ > 0.
    //                 Controls which correlation() path is taken.
    // --------------------------------------------------------------------
 
    int  nStart_  {0};      // frames to skip at trajectory start
    int  nSep_    {0};      // signed offset: >0 gap, <0 overlap (frames)
    int  nStride_ {1};      // frames between window origins
    int  navg_    {0};      // number of windows (computed)
    bool useWindowing_ {false};
 
  };
 
  template<typename T>
  class AutoCorrFunc : public TimeCorrFunc<T> {
  public:
    AutoCorrFunc(SimInfo* info, const std::string& filename,
                 const std::string& sele1, const std::string& sele2);
 
  protected:
    virtual void computeProperty1(int frame)                 = 0;
    virtual int computeProperty1(int frame, Molecule* mol)   = 0;
    virtual int computeProperty1(int frame, StuntDouble* sd) = 0;
    virtual int computeProperty1(int frame, Bond* bond)      = 0;
 
    virtual void computeProperty2(int) {}
    virtual int computeProperty2(int, Molecule*) { return -1; }
    virtual int computeProperty2(int, StuntDouble*) { return -1; }
    virtual int computeProperty2(int, Bond*) { return -1; }
  };
 
  template<typename T>
  class CrossCorrFunc : public TimeCorrFunc<T> {
  public:
    CrossCorrFunc(SimInfo* info, const std::string& filename,
                  const std::string& sele1, const std::string& sele2);
 
  protected:
    virtual void computeProperty1(int frame)                 = 0;
    virtual int computeProperty1(int frame, Molecule* mol)   = 0;
    virtual int computeProperty1(int frame, StuntDouble* sd) = 0;
    virtual int computeProperty1(int frame, Bond* bond)      = 0;
    virtual void computeProperty2(int frame)                 = 0;
    virtual int computeProperty2(int frame, Molecule* mol)   = 0;
    virtual int computeProperty2(int frame, StuntDouble* sd) = 0;
    virtual int computeProperty2(int frame, Bond* bond)      = 0;
  };
 
  template<typename T>
  class SystemACF : public AutoCorrFunc<T> {
  public:
    SystemACF(SimInfo* info, const std::string& filename,
              const std::string& sele1, const std::string& sele2);
 
  protected:
    virtual void computeProperty1(int frame)      = 0;
    virtual T calcCorrVal(int frame1, int frame2) = 0;
 
    virtual int computeProperty1(int, Molecule*) { return -1; }
    virtual int computeProperty1(int, StuntDouble*) { return -1; }
    virtual int computeProperty1(int, Bond*) { return -1; }
 
    virtual void computeProperty2(int) {}
    virtual int computeProperty2(int, Molecule*) { return -1; }
    virtual int computeProperty2(int, StuntDouble*) { return -1; }
    virtual int computeProperty2(int, Bond*) { return -1; }
 
    T calcCorrVal(int, int, int, int) { return T(0.0); }
  };
 
  template<typename T>
  class SystemCCF : public CrossCorrFunc<T> {
  public:
    SystemCCF(SimInfo* info, const std::string& filename,
              const std::string& sele1, const std::string& sele2);
 
  protected:
    virtual void computeProperty1(int frame)      = 0;
    virtual void computeProperty2(int frame)      = 0;
    virtual T calcCorrVal(int frame1, int frame2) = 0;
 
    virtual int computeProperty1(int, Molecule*) { return -1; }
    virtual int computeProperty1(int, StuntDouble*) { return -1; }
    virtual int computeProperty1(int, Bond*) { return -1; }
 
    virtual int computeProperty2(int, Molecule*) { return -1; }
    virtual int computeProperty2(int, StuntDouble*) { return -1; }
    virtual int computeProperty2(int, Bond*) { return -1; }
 
    T calcCorrVal(int, int, int, int) { return T(0.0); }
  };
 
  template<typename T>
  class ObjectACF : public AutoCorrFunc<T> {
  public:
    ObjectACF(SimInfo* info, const std::string& filename,
              const std::string& sele1, const std::string& sele2);
 
  protected:
    virtual int computeProperty1(int frame, StuntDouble* sd)        = 0;
    virtual T calcCorrVal(int frame1, int frame2, int id1, int id2) = 0;
 
    virtual void computeProperty1(int) { return; }
    virtual int computeProperty1(int, Molecule*) { return -1; }
    virtual int computeProperty1(int, Bond*) { return -1; }
 
    virtual void computeProperty2(int) { return; }
    virtual int computeProperty2(int, Molecule*) { return -1; }
    virtual int computeProperty2(int, StuntDouble*) { return -1; }
    virtual int computeProperty2(int, Bond*) { return -1; }
 
    virtual T calcCorrVal(int, int) { return T(0.0); }
  };
 
  template<typename T>
  class ObjectCCF : public CrossCorrFunc<T> {
  public:
    ObjectCCF(SimInfo* info, const std::string& filename,
              const std::string& sele1, const std::string& sele2);
 
  protected:
    virtual int computeProperty1(int frame, StuntDouble* sd)        = 0;
    virtual int computeProperty2(int frame, StuntDouble* sd)        = 0;
    virtual T calcCorrVal(int frame1, int frame2, int id1, int id2) = 0;
 
    virtual void computeProperty1(int) { return; }
    virtual int computeProperty1(int, Molecule*) { return -1; }
    virtual int computeProperty1(int, Bond*) { return -1; }
 
    virtual void computeProperty2(int) {}
    virtual int computeProperty2(int, Molecule*) { return -1; }
    virtual int computeProperty2(int, Bond*) { return -1; }
 
    virtual T calcCorrVal(int, int) { return T(0.0); }
  };
 
  template<typename T>
  class MoleculeACF : public AutoCorrFunc<T> {
  public:
    MoleculeACF(SimInfo* info, const std::string& filename,
                const std::string& sele1, const std::string& sele2);
 
  protected:
    virtual int computeProperty1(int frame, Molecule* mol)          = 0;
    virtual T calcCorrVal(int frame1, int frame2, int id1, int id2) = 0;
 
    virtual void computeProperty1(int) { return; }
    virtual int computeProperty1(int, StuntDouble*) { return -1; }
    virtual int computeProperty1(int, Bond*) { return -1; }
 
    virtual void computeProperty2(int) { return; }
    virtual int computeProperty2(int, Molecule*) { return -1; }
    virtual int computeProperty2(int, StuntDouble*) { return -1; }
    virtual int computeProperty2(int, Bond*) { return -1; }
 
    virtual T calcCorrVal(int, int) { return T(0.0); }
  };
 
  template<typename T>
  class MoleculeCCF : public CrossCorrFunc<T> {
  public:
    MoleculeCCF(SimInfo* info, const std::string& filename,
                const std::string& sele1, const std::string& sele2);
 
  protected:
    virtual int computeProperty1(int frame, Molecule* mol)          = 0;
    virtual int computeProperty2(int frame, Molecule* mol)          = 0;
    virtual T calcCorrVal(int frame1, int frame2, int id1, int id2) = 0;
 
    virtual void computeProperty1(int) { return; }
    virtual int computeProperty1(int, StuntDouble*) { return -1; }
    virtual int computeProperty1(int, Bond*) { return -1; }
 
    virtual void computeProperty2(int) {}
    virtual int computeProperty2(int, StuntDouble*) { return -1; }
    virtual int computeProperty2(int, Bond*) { return -1; }
 
    virtual T calcCorrVal(int, int) { return T(0.0); }
  };
}  // namespace OpenMD
 
#endif