MoleculeCreator.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).
 */
 
/**
 * @file MoleculeCreator.hpp
 * @author tlin
 * @date 11/04/2004
 * @version 1.0
 */
 
#ifndef BRAINS_MOLECULECREATOR_HPP
#define BRAINS_MOLECULECREATOR_HPP
 
#include "brains/SimInfo.hpp"
#include "primitives/Molecule.hpp"
#include "types/AtomStamp.hpp"
#include "types/BendStamp.hpp"
#include "types/BondStamp.hpp"
#include "types/CutoffGroupStamp.hpp"
#include "types/InversionStamp.hpp"
#include "types/RigidBodyStamp.hpp"
#include "types/TorsionStamp.hpp"
 
namespace OpenMD {
 
  /**
   * @class MoleculeCreator MoleculeCreator.hpp "brains/MoleculeCreator.hpp"
   * @brief
   */
  class MoleculeCreator {
  public:
    virtual void createOverrideAtomTypes(ForceField* ff, MoleculeStamp* molStamp);
    
    virtual Molecule* createMolecule(ForceField* ff, MoleculeStamp* molStamp,
                                     int globalIndex,
                                     LocalIndexManager* localIndexMan);
 
  protected:
    /** Create an atom by its stamp */
    virtual Atom* createAtom(ForceField* ff, AtomStamp* stamp,
                             LocalIndexManager* localIndexMan);
    virtual RigidBody* createRigidBody(MoleculeStamp* molStamp, Molecule* mol,
                                       RigidBodyStamp* rbStamp,
                                       LocalIndexManager* localIndexMan);
    virtual Bond* createBond(ForceField* ff, Molecule* mol, BondStamp* stamp,
                             LocalIndexManager* localIndexMan);
    virtual Bend* createBend(ForceField* ff, Molecule* mol, BendStamp* stamp,
                             LocalIndexManager* localIndexMan);
    virtual Torsion* createTorsion(ForceField* ff, Molecule* mol,
                                   TorsionStamp* stamp,
                                   LocalIndexManager* localIndexMan);
    virtual Inversion* createInversion(ForceField* ff, Molecule* mol,
                                       InversionStamp* stamp,
                                       LocalIndexManager* localIndexMan);
    virtual CutoffGroup* createCutoffGroup(Molecule* mol,
                                           CutoffGroupStamp* stamp,
                                           LocalIndexManager* localIndexMan);
    virtual CutoffGroup* createCutoffGroup(Molecule*, Atom* atom,
                                           LocalIndexManager* localIndexMan);
    virtual void createConstraintPair(Molecule* mol);
    virtual void createConstraintElem(Molecule* mol);
  };
}  // namespace OpenMD
 
#endif  // BRAINS_MOLECULECREATOR_HPP