AtomData.hpp

/*
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 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
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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 VISITOR_ATOMDATA_HPP
#define VISITOR_ATOMDATA_HPP
 
#include <memory>
#include <string>
#include <vector>
 
#include "math/Vector3.hpp"
#include "utils/GenericData.hpp"
 
namespace OpenMD {
 
  struct AtomInfo {
    AtomInfo() :
        pos(V3Zero), vec(V3Zero), vel(V3Zero), frc(V3Zero), eField(V3Zero),
        charge(0.0), hasCharge(false), hasVector(false), hasVelocity(false),
        hasForce(false), hasElectricField(false), hasGlobalID(false) {}
 
    std::string atomTypeName;
    int globalID;
    Vector3d pos;
    Vector3d vec;
    Vector3d vel;
    Vector3d frc;
    Vector3d eField;
    RealType charge;
    bool hasCharge;
    bool hasVector;
    bool hasVelocity;
    bool hasForce;
    bool hasElectricField;
    bool hasGlobalID;
  };
 
  class AtomData : public GenericData {
  public:
    AtomData(const std::string& id = "ATOMDATA") : GenericData(id) {}
 
    void addAtomInfo(std::shared_ptr<AtomInfo> info) { data.push_back(info); }
 
    void clearAllAtomInfo();
 
    std::shared_ptr<AtomInfo> beginAtomInfo(
        std::vector<std::shared_ptr<AtomInfo>>::iterator& i) {
      i = data.begin();
      return i != data.end() ? *i : nullptr;
    }
 
    std::shared_ptr<AtomInfo> nextAtomInfo(
        std::vector<std::shared_ptr<AtomInfo>>::iterator& i) {
      ++i;
      return i != data.end() ? *i : nullptr;
    }
 
    std::vector<std::shared_ptr<AtomInfo>> getData() { return data; }
 
    size_t getSize() { return data.size(); }
 
  protected:
    std::vector<std::shared_ptr<AtomInfo>> data;
  };
}  // namespace OpenMD
 
#endif  // VISITOR_ATOMDATA_HPP