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Comparing trunk/src/primitives/Atom.hpp (file contents):
Revision 963 by tim, Wed May 17 21:51:42 2006 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 52 | Line 52
52   #include "primitives/StuntDouble.hpp"
53   #include "types/AtomType.hpp"
54  
55 < namespace oopse{
55 > namespace OpenMD{
56    class Atom : public StuntDouble {
57    public:
58      Atom(AtomType* at);
59 <
59 >    
60      virtual std::string getType() {return atomType_->getName();}
61 <        
61 >    
62      /**
63       * Returns the inertia tensor of this stuntdouble
64       * @return the inertia tensor of this stuntdouble
65       */
66      virtual Mat3x3d getI();
67 <
67 >    
68      /**
69       * Returns the gradient of this stuntdouble
70       * @return the inertia tensor of this stuntdouble
71       */
72      virtual std::vector<RealType> getGrad();
73 <
73 >    
74      virtual void accept(BaseVisitor* v);
75 <
75 >    
76      /**
77       * Returns the AtomType of this Atom.
78       * @return the atom type of this atom
# Line 80 | Line 80 | namespace oopse{
80      AtomType* getAtomType() {
81        return atomType_;
82      }
83 <            
83 >    
84      //forward  functions of AtomType class
85 <    bool    isCharge()  {
85 >    bool isCharge()  {
86        return atomType_->isCharge();
87      }
88 <            
89 <    bool    isDirectional() {
88 >    
89 >    bool isDirectional() {
90        return atomType_->isDirectional();
91      }
92 <
93 <    bool    isDipole()  {
92 >    
93 >    bool isDipole()  {
94        return atomType_->isDipole();
95      }
96  
97 <    bool    isQudrapole()  {
97 >    bool isQudrapole()  {
98        return atomType_->isQuadrupole();
99      }
100 <            
101 <    bool    isMultipole()  {
100 >    
101 >    bool isMultipole()  {
102        return atomType_->isMultipole();
103      }
104 <            
105 <    bool    isGayBerne()  {
104 >    
105 >    bool isGayBerne()  {
106        return atomType_->isGayBerne();
107      }
108              
109 <    bool    isSticky()  {
109 >    bool isSticky()  {
110        return atomType_->isSticky();
111      }
112  
113 <    bool    isShape()  {
113 >    bool isShape()  {
114        return atomType_->isShape();
115      }            
116 +    
117 +    bool isMetal() {
118 +      return atomType_->isMetal();
119 +    }
120  
121      int getIdent() {
122        return atomType_->getIdent();
123      }
124 <            
124 >    
125    protected:
126      AtomType* atomType_;
127    };
128 +  
129 + }//namespace OpenMD
130  
125 – }//namepace oopse
126 –
131   #endif //PRIMITIVES_ATOM_HPP

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