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root/OpenMD/trunk/src/brains/MoleculeCreator.hpp

Comparing trunk/src/brains/MoleculeCreator.hpp (file contents):
Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
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	+	*
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	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43	<	/**
44	<	* @file MoleculeCreator.hpp
45	<	* @author tlin
46	<	* @date 11/04/2004
47	<	* @time 13:51am
48	<	* @version 1.0
48	<	*/
43	>	/**
44	>	* @file MoleculeCreator.hpp
45	>	* @author tlin
46	>	* @date 11/04/2004
47	>	* @version 1.0
48	>	*/
49
50		#ifndef BRAINS_MOLECULECREATOR_HPP
51		#define BRAINS_MOLECULECREATOR_HPP
#	Line 57 | Line 57
57		#include "types/CutoffGroupStamp.hpp"
58		#include "types/RigidBodyStamp.hpp"
59		#include "types/TorsionStamp.hpp"
60	+	#include "types/InversionStamp.hpp"
61		#include "primitives/Molecule.hpp"
62	<	namespace oopse {
62	>	namespace OpenMD {
63
64	<	/**
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	<	int stampId, int globalIndex,  LocalIndexManager* localIndexMan);
64	>	/**
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	>	int stampId, int globalIndex,
72	>	LocalIndexManager* localIndexMan);
73
74	<	protected:
74	>	protected:
75
76	<	/** Create an atom by its stamp */
77	<	virtual Atom* createAtom(ForceField* ff, Molecule* mol, AtomStamp* stamp,
78	<	LocalIndexManager* localIndexMan);
76	>	/** 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	>	RigidBodyStamp* rbStamp,
81	>	LocalIndexManager* localIndexMan);
82	>	virtual Bond* createBond(ForceField* ff, Molecule* mol, BondStamp* stamp);
83	>	virtual Bend* createBend(ForceField* ff, Molecule* mol, BendStamp* stamp);
84	>	virtual Torsion* createTorsion(ForceField* ff, Molecule* mol,
85	>	TorsionStamp* stamp);
86	>	virtual Inversion* createInversion(ForceField* ff, Molecule* mol,
87	>	InversionStamp* stamp);
88	>	virtual CutoffGroup* createCutoffGroup(Molecule* mol,
89	>	CutoffGroupStamp* stamp,
90	>	LocalIndexManager* localIndexMan);
91	>	virtual CutoffGroup* createCutoffGroup(Molecule * mol, Atom* atom,
92	>	LocalIndexManager* localIndexMan);
93	>	virtual void createConstraintPair(Molecule* mol);
94	>	virtual void createConstraintElem(Molecule* mol);
95	>	};
96
78	–	virtual RigidBody* createRigidBody(MoleculeStamp *molStamp, Molecule* mol,
79	–	RigidBodyStamp* rbStamp,  LocalIndexManager* localIndexMan);
97
81	–	virtual Bond* createBond(ForceField* ff, Molecule* mol, BondStamp* stamp);
82	–	virtual Bend* createBend(ForceField* ff, Molecule* mol, BendStamp* stamp);
83	–	virtual Torsion* createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp);
84	–	virtual CutoffGroup* createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp);
85	–	virtual CutoffGroup* createCutoffGroup(Molecule * mol, Atom* atom);
86	–	virtual void createConstraintPair(Molecule* mol);
87	–	virtual void createConstraintElem(Molecule* mol);
88	–	};
89	–
90	–
98		}
99		#endif //BRAINS_MOLECULECREATOR_HPP

Comparing trunk/src/brains/MoleculeCreator.hpp (property svn:keywords):
Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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