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Comparing trunk/src/utils/MoLocator.hpp (file contents):
Revision 483 by gezelter, Tue Apr 12 21:28:07 2005 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 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   #ifndef UTILS_MOLOCATOR_HPP
43 –
44   #define UTILS_MOLOCATOR_HPP
45  
46   #include <vector>
# Line 51 | Line 51
51   #include "primitives/Molecule.hpp"
52   #include "math/SquareMatrix3.hpp"
53   #include "math/Vector3.hpp"
54 < #include "UseTheForce/ForceField.hpp"
55 < namespace oopse {
56 < //convert lattice vector to rotation matrix
57 < double getAtomMass(const std::string& at, ForceField* myFF);
58 < double getMolMass(MoleculeStamp *molStamp, ForceField *myFF);
59 < RotMat3x3d latVec2RotMat(const Vector3d& lv);
60 < class MoLocator{
61 <    public:
62 <        MoLocator( MoleculeStamp* theStamp, ForceField* theFF);
63 <        void placeMol( const Vector3d& offset, const Vector3d& ort, Molecule* mol);
64 <    private:
65 <        void calcRef( void );
66 <        MoleculeStamp* myStamp;
54 > #include "brains/ForceField.hpp"
55  
56 <        ForceField* myFF;
69 <        std::vector<Vector3d> refCoords;
70 <        int nIntegrableObjects;
56 > namespace OpenMD {
57  
58 < };
58 >  class MoLocator{
59 >  public:
60 >    MoLocator( MoleculeStamp* theStamp, ForceField* theFF);
61 >    void placeMol( const Vector3d& offset, const Vector3d& ort, Molecule* mol);
62 >    static RealType getMolMass(MoleculeStamp *molStamp, ForceField *myFF);
63  
64 +  private:
65 +    void calcRef( void );
66 +    static RealType getAtomMass(const std::string& at, ForceField* myFF);
67 +    RotMat3x3d latVec2RotMat(const Vector3d& lv); ///< convert lattice vector to rotation matrix
68 +    
69 +    MoleculeStamp* myStamp;
70 +
71 +    ForceField* myFF;
72 +    std::vector<Vector3d> refCoords;
73 +    unsigned int nIntegrableObjects;
74 +  };
75   }
76   #endif
77  

Comparing trunk/src/utils/MoLocator.hpp (property svn:keywords):
Revision 483 by gezelter, Tue Apr 12 21:28:07 2005 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

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