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root/OpenMD/trunk/src/brains/MoleculeCreator.hpp
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Comparing trunk/src/brains/MoleculeCreator.hpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# 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, 24107 (2008).          
39 + * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42   /**
# 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"
# Line 67 | Line 68 | namespace oopse {
68    class MoleculeCreator {
69    public:
70      virtual Molecule* createMolecule(ForceField* ff, MoleculeStamp *molStamp,
71 <                                     int stampId, int globalIndex,  LocalIndexManager* localIndexMan);
71 >                                     int stampId, int globalIndex,  
72 >                                     LocalIndexManager* localIndexMan);
73  
74    protected:
75          
76      /** Create an atom by its stamp */
77      virtual Atom* createAtom(ForceField* ff, Molecule* mol, AtomStamp* stamp,
78                               LocalIndexManager* localIndexMan);
77 –
79      virtual RigidBody* createRigidBody(MoleculeStamp *molStamp, Molecule* mol,
80 <                                       RigidBodyStamp* rbStamp,  LocalIndexManager* localIndexMan);
81 <
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, TorsionStamp* stamp);
85 <    virtual CutoffGroup* createCutoffGroup(Molecule* mol, CutoffGroupStamp* 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      virtual CutoffGroup* createCutoffGroup(Molecule * mol, Atom* atom);
91      virtual void createConstraintPair(Molecule* mol);    
92      virtual void createConstraintElem(Molecule* mol);

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