MoLocator.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 UTILS_MOLOCATOR_HPP
#define UTILS_MOLOCATOR_HPP
 
#include <vector>
 
#include "brains/ForceField.hpp"
#include "math/SquareMatrix3.hpp"
#include "math/Vector3.hpp"
#include "primitives/Atom.hpp"
#include "primitives/DirectionalAtom.hpp"
#include "primitives/Molecule.hpp"
#include "types/MoleculeStamp.hpp"
 
namespace OpenMD {
 
  class MoLocator {
  public:
    MoLocator(MoleculeStamp* theStamp, ForceField* theFF);
    void placeMol(const Vector3d& offset, const Vector3d& ort, Molecule* mol);
    static RealType getMolMass(MoleculeStamp* molStamp, ForceField* myFF);
 
  private:
    void calcRef(void);
    static RealType getAtomMass(const std::string& at, ForceField* myFF);
    RotMat3x3d latVec2RotMat(
        const Vector3d& lv);  ///< convert lattice vector to rotation matrix
 
    MoleculeStamp* myStamp;
 
    ForceField* myFF;
    std::vector<Vector3d> refCoords;
    unsigned int nIntegrableObjects;
  };
}  // namespace OpenMD
 
#endif