NitrileFrequencyMap.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_STATICPROPS_NITRILEFREQUENCYMAP_HPP
#define APPLICATIONS_STATICPROPS_NITRILEFREQUENCYMAP_HPP
 
#include <string>
#include <vector>
 
#include "applications/staticProps/StaticAnalyser.hpp"
#include "nonbonded/Electrostatic.hpp"
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"
 
using namespace std;
namespace OpenMD {
 
  class NitrileFrequencyMap : public StaticAnalyser {
  public:
    NitrileFrequencyMap(SimInfo* info, const string& filename,
                        const string& sele1, int nbins);
 
    virtual void process();
 
  private:
    bool excludeAtomPair(int atom1, int atom2);
    void processHistogram();
    void writeProbs();
 
    SimInfo* info_ {nullptr};
    Snapshot* currentSnapshot_ {};
 
    string selectionScript1_;
    SelectionManager seleMan1_;
    SelectionEvaluator evaluator1_;
 
    int nProcessed_ {};
    vector<int> count_;
    vector<RealType> histogram_;
    vector<RealType> freqs_;
    map<string, RealType> frequencyMap_;
    RealType minFreq_;
    RealType maxFreq_;
    int nBins_ {};
    vector<vector<int>> excludesForAtom;
    Electrostatic* electrostatic_;
    Vector3d EF_;
  };
}  // namespace OpenMD
 
#endif