PositionZ.hpp

/*
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 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *
 * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [4] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [5] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [6] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [7] Lamichhane, Newman & Gezelter, J. Chem. Phys. 141, 134110 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 */
 
/*
 * Computes the position distribution along preferred axis for the selected atom
 * Created by Hemanta Bhattarai on 02/20/20.
 */
 
#ifndef APPLICATIONS_STATICPROPS_POSITIONZ_HPP
#define APPLICATIONS_STATICPROPS_POSITIONZ_HPP
 
#include <string>
#include <vector>
 
#include "applications/staticProps/StaticAnalyser.hpp"
#include "brains/SimInfo.hpp"
#include "brains/Thermo.hpp"
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"
 
namespace OpenMD {
 
  class PositionZ : public StaticAnalyser {
  public:
    PositionZ(SimInfo* info, const std::string& filename,
              const std::string& sele, int nzbins, int axis = 2);
 
    virtual void process();
 
  private:
    virtual void writePositionZ();
 
    Snapshot* currentSnapshot_;
    int nProcessed_;
    std::string selectionScript_;
    SelectionEvaluator evaluator_;
    SelectionManager seleMan_;
    Thermo thermo_;
 
    std::vector<RealType> sliceSDCount_;
    std::vector<RealType> flucSliceSDCount_;
 
    std::vector<RealType> zBox_;
    std::vector<RealType> positionZ_;
    int axis_;
    std::string axisLabel_;
  };
}  // namespace OpenMD
 
#endif