ChargeDensityZ.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_CHARGEDENSITYZ_HPP
#define APPLICATIONS_STATICPROPS_CHARGEDENSITYZ_HPP
 
#include <map>
#include <set>
 
#include "applications/staticProps/StaticAnalyser.hpp"
#include "brains/Thermo.hpp"
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"
#include "utils/ElementsTable.hpp"
 
namespace OpenMD {
 
  class ChargeDensityZ : public StaticAnalyser {
  public:
    ChargeDensityZ(SimInfo* info, const std::string& filename,
                   const std::string& sele, int nzbins, RealType vRadius,
                   std::string atomName = "Au", bool xyzGen = false,
                   int axis = 2);
    virtual void process();
 
  private:
    virtual void writeDensity();
    virtual void generateXYZForLastFrame();
 
    Snapshot* currentSnapshot_;
    int nProcessed_;
    std::string selectionScript_;
    SelectionEvaluator evaluator_;
    SelectionManager seleMan_;
    Thermo thermo_;
 
    std::vector<RealType> zBox_;
    std::vector<RealType> densityZAverageAllFrame_;
    std::vector<RealType> averageDensityZ_;
    std::vector<RealType> flucDensityZAverageAllFrame_;
    std::vector<RealType> densityFlucZAverageAllFrame_;
    std::vector<RealType> absDensityFlucZAverageAllFrame_;
    std::vector<RealType> densityFlucZAverageFirstFrame_;
    std::vector<RealType> absDensityFlucZAverageFirstFrame_;
 
    int axis_, x_, y_;
    RealType vRadius_;
    std::string fileName_;
    std::string atomFlucCharge_;
    bool genXYZ_;
 
    Mat3x3d hmat_;
 
    std::map<std::string, RealType> vander_waals_r;
    std::map<std::string, RealType> averageChargeForEachType_;
    std::map<std::string, int> SDCount_;
    std::string axisLabel_;
 
    std::map<int, RealType> averageChargeUsingGlobalIndex_;
    std::map<int, std::vector<RealType>> totalChargeUsingGlobalIndex_;
    std::map<int, RealType> totalChargeFluctationsUsingGlobalIndex_;
    std::map<int, std::vector<RealType>> zPosUsingGlobalIndex_;
    std::map<int, std::vector<RealType>> xPosUsingGlobalIndex_;
    std::map<int, std::vector<RealType>> yPosUsingGlobalIndex_;
    std::map<int, int> countUsingGlobalIndex_;
    std::map<int, RealType> vanderRUsingGlobalIndex_;
    std::map<int, std::string> atomNameGlobalIndex_;
  };
}  // namespace OpenMD
 
#endif