src/brains/MoleculeCreator.hpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
/**
 * @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 "types/AtomStamp.hpp"
#include "types/BondStamp.hpp"
#include "types/BendStamp.hpp"
#include "types/CutoffGroupStamp.hpp"
#include "types/RigidBodyStamp.hpp"
#include "types/TorsionStamp.hpp"
#include "types/InversionStamp.hpp"
#include "primitives/Molecule.hpp"
namespace OpenMD {

  /**
   * @class MoleculeCreator MoleculeCreator.hpp "brains/MoleculeCreator.hpp"
   * @brief
   */
  class MoleculeCreator {
  public:
    virtual Molecule* createMolecule(ForceField* ff, MoleculeStamp *molStamp,
                                     int stampId, int globalIndex,  
                                     LocalIndexManager* localIndexMan);

  protected:
        
    /** Create an atom by its stamp */
    virtual Atom* createAtom(ForceField* ff, Molecule* mol, 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 * mol, Atom* atom, 
                                           LocalIndexManager* localIndexMan);
    virtual void createConstraintPair(Molecule* mol);     
    virtual void createConstraintElem(Molecule* mol);
  };


}
#endif //BRAINS_MOLECULECREATOR_HPP
Revision:	1953
Committed:	Thu Dec 5 18:19:26 2013 UTC (11 years, 10 months ago) by gezelter
File size:	4574 byte(s)
Log Message:	Rewrote much of selection module, added a bond correlation function
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43	gezelter	507	/**
44			* @file MoleculeCreator.hpp
45			* @author tlin
46			* @date 11/04/2004
47			* @version 1.0
48			*/
49	gezelter	246
50			#ifndef BRAINS_MOLECULECREATOR_HPP
51			#define BRAINS_MOLECULECREATOR_HPP
52
53			#include "brains/SimInfo.hpp"
54			#include "types/AtomStamp.hpp"
55			#include "types/BondStamp.hpp"
56			#include "types/BendStamp.hpp"
57			#include "types/CutoffGroupStamp.hpp"
58			#include "types/RigidBodyStamp.hpp"
59			#include "types/TorsionStamp.hpp"
60	gezelter	1277	#include "types/InversionStamp.hpp"
61	gezelter	246	#include "primitives/Molecule.hpp"
62	gezelter	1390	namespace OpenMD {
63	gezelter	246
64	gezelter	507	/**
65			* @class MoleculeCreator MoleculeCreator.hpp "brains/MoleculeCreator.hpp"
66			* @brief
67			*/
68			class MoleculeCreator {
69			public:
70			virtual Molecule* createMolecule(ForceField* ff, MoleculeStamp *molStamp,
71	gezelter	1277	int stampId, int globalIndex,
72			LocalIndexManager* localIndexMan);
73	gezelter	246
74	gezelter	507	protected:
75	gezelter	246
76	gezelter	507	/** Create an atom by its stamp */
77			virtual Atom* createAtom(ForceField* ff, Molecule* mol, AtomStamp* stamp,
78			LocalIndexManager* localIndexMan);
79			virtual RigidBody* createRigidBody(MoleculeStamp molStamp, Molecule mol,
80	gezelter	1277	RigidBodyStamp* rbStamp,
81			LocalIndexManager* localIndexMan);
82	gezelter	1953	virtual Bond* createBond(ForceField* ff, Molecule* mol, BondStamp* stamp,
83			LocalIndexManager* localIndexMan);
84			virtual Bend* createBend(ForceField* ff, Molecule* mol, BendStamp* stamp,
85			LocalIndexManager* localIndexMan);
86	gezelter	1277	virtual Torsion* createTorsion(ForceField* ff, Molecule* mol,
87	gezelter	1953	TorsionStamp* stamp,
88			LocalIndexManager* localIndexMan);
89	gezelter	1277	virtual Inversion* createInversion(ForceField* ff, Molecule* mol,
90	gezelter	1953	InversionStamp* stamp,
91			LocalIndexManager* localIndexMan);
92	gezelter	1277	virtual CutoffGroup* createCutoffGroup(Molecule* mol,
93	gezelter	1782	CutoffGroupStamp* stamp,
94			LocalIndexManager* localIndexMan);
95			virtual CutoffGroup* createCutoffGroup(Molecule * mol, Atom* atom,
96			LocalIndexManager* localIndexMan);
97	gezelter	507	virtual void createConstraintPair(Molecule* mol);
98			virtual void createConstraintElem(Molecule* mol);
99			};
100	gezelter	246
101
102			}
103			#endif //BRAINS_MOLECULECREATOR_HPP