LipidTransVisitor.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 VISITORS_LIPIDTRANSVISITOR_HPP
#define VISITORS_LIPIDTRANSVISITOR_HPP
 
#include "brains/SimInfo.hpp"
#include "primitives/Molecule.hpp"
#include "primitives/StuntDouble.hpp"
#include "selection/SelectionEvaluator.hpp"
#include "selection/SelectionManager.hpp"
#include "visitors/AtomData.hpp"
#include "visitors/BaseVisitor.hpp"
 
namespace OpenMD {
 
  class LipidTransVisitor : public BaseVisitor {
  public:
    using BaseVisitor::visit;
    LipidTransVisitor(SimInfo* info, const std::string& originSeleScript,
                      const std::string& refSeleScript);
 
    virtual void visit(Atom* atom) { internalVisit(atom); }
    virtual void visit(DirectionalAtom* datom) { internalVisit(datom); }
    virtual void visit(RigidBody* rb) { internalVisit(rb); }
 
    virtual const std::string toString();
 
    void update();
 
  protected:
    void internalVisit(StuntDouble* sd);
    SimInfo* info_ {nullptr};
    SelectionEvaluator originEvaluator_;
    SelectionManager originSeleMan_;
    DirectionalAtom* originDatom_;
    SelectionEvaluator refEvaluator_;
    SelectionManager refSeleMan_;
    StuntDouble* refSd_;
    RotMat3x3d rotMat_;
    Vector3d origin_;
  };
}  // namespace OpenMD
 
#endif