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Comparing trunk/src/primitives/Inversion.hpp (file contents):
Revision 1275 by cli2, Fri Jul 4 20:54:29 2008 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 2013 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, 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   /**
# Line 49 | Line 50
50   #ifndef PRIMITIVES_INVERSION_HPP
51   #define PRIMITIVES_INVERSION_HPP
52  
53 + #include "primitives/ShortRangeInteraction.hpp"
54   #include "primitives/Atom.hpp"
53 –
55   #include "types/InversionType.hpp"
56  
57 < namespace oopse {
57 > namespace OpenMD {
58    struct InversionData {
59      RealType angle;
60      RealType potential;
# Line 65 | Line 66 | namespace oopse {
66      InversionData curr;
67    };
68  
68 –  
69    /**
70     * @class Inversion Inversion.hpp "primitives/Inversion.hpp"
71     */
72 <  class Inversion {
72 >  class Inversion : public ShortRangeInteraction {
73    public:
74      Inversion(Atom* atom1, Atom* atom2, Atom* atom3, Atom* atom4, InversionType* it);
75      virtual ~Inversion() {}
76 <    virtual void calcForce(RealType& angle);
76 >    virtual void calcForce(RealType& angle, bool doParticlePot);
77          
78 +    RealType getValue(int snapshotNo) {
79 +      // In OpenMD's version of an inversion, the central atom
80 +      // comes first.  However, to get the planarity in a typical cosine
81 +      // version of this potential (i.e. Amber-style), the central atom
82 +      // is treated as atom *3* in a standard torsion form:
83 +      
84 +      Vector3d pos1 = atoms_[1]->getPos(snapshotNo);
85 +      Vector3d pos2 = atoms_[2]->getPos(snapshotNo);
86 +      Vector3d pos3 = atoms_[0]->getPos(snapshotNo);
87 +      Vector3d pos4 = atoms_[3]->getPos(snapshotNo);
88 +      
89 +      Vector3d r31 = pos1 - pos3;
90 +      Vector3d r23 = pos3 - pos2;
91 +      Vector3d r43 = pos3 - pos4;
92 +      
93 +      //  Calculate the cross products and distances
94 +      Vector3d A = cross(r31, r43);
95 +      RealType rA = A.length();
96 +      Vector3d B = cross(r43, r23);
97 +      RealType rB = B.length();
98 +      //Vector3d C = cross(r23, A);
99 +      //RealType rC = C.length();
100 +      
101 +      A.normalize();
102 +      B.normalize();
103 +      //C.normalize();
104 +      
105 +      //  Calculate the sin and cos
106 +      RealType cos_phi = dot(A, B) ;
107 +      if (cos_phi > 1.0) cos_phi = 1.0;
108 +      if (cos_phi < -1.0) cos_phi = -1.0;
109 +      return acos(cos_phi);
110 +    }
111 +
112 +
113      RealType getPotential() {
114        return potential_;
115      }
116  
117      Atom* getAtomA() {
118 <      return atom1_;
118 >      return atoms_[0];
119      }
120  
121      Atom* getAtomB() {
122 <      return atom2_;
122 >      return atoms_[1];
123      }
124  
125      Atom* getAtomC() {
126 <      return atom3_;
126 >      return atoms_[2];
127      }
128  
129      Atom* getAtomD() {
130 <      return atom4_;
130 >      return atoms_[3];
131      }
132  
133      InversionType * getInversionType() {
134        return inversionType_;
135      }
136 <        
137 <  protected:
136 >    virtual std::string getName() { return name_;}        
137 >    /** Sets the name of this inversion for selections */
138 >    virtual void setName(const std::string& name) { name_ = name;}
139  
140 <    Atom* atom1_;
141 <    Atom* atom2_;
142 <    Atom* atom3_;
107 <    Atom* atom4_;
140 >    void accept(BaseVisitor* v) {
141 >      v->visit(this);
142 >    }    
143  
144 +  protected:
145      InversionType* inversionType_;
146 +    InversionKey inversionKey_;
147 +    std::string name_;        
148  
149      RealType potential_;
150    };    

Comparing trunk/src/primitives/Inversion.hpp (property svn:keywords):
Revision 1275 by cli2, Fri Jul 4 20:54:29 2008 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 2013 UTC

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