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Comparing trunk/src/primitives/Inversion.cpp (file contents):
Revision 1290 by cli2, Wed Sep 10 19:51:45 2008 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   #include "primitives/Inversion.hpp"
43 – #include "fstream"
43  
44 < namespace oopse {
44 > namespace OpenMD {
45  
46    Inversion::Inversion(Atom *atom1, Atom *atom2, Atom *atom3,
47                         Atom *atom4, InversionType *it) :
# Line 51 | Line 50 | namespace oopse {
50    
51    void Inversion::calcForce(RealType& angle) {
52      
53 <    // In OOPSE's version of an inversion, the central atom
53 >    // In OpenMD's version of an inversion, the central atom
54      // comes first.  However, to get the planarity in a typical cosine
55      // version of this potential (i.e. Amber-style), the central atom
56      // is treated as atom *3* in a standard torsion form:
57  
58      Vector3d pos1 = atom2_->getPos();
59 <    Vector3d pos2 = atom1_->getPos();
60 <    Vector3d pos3 = atom4_->getPos();
61 <    Vector3d pos4 = atom3_->getPos();
59 >    Vector3d pos2 = atom3_->getPos();
60 >    Vector3d pos3 = atom1_->getPos();
61 >    Vector3d pos4 = atom4_->getPos();
62  
63 <   /*std::ofstream myfile;
64 <   myfile.open("Inversion", std::ios::app);      
65 <   myfile << atom1_->getType() << " - atom1; "
67 <              << atom2_->getType() << " - atom2; "
68 <              << atom3_->getType() << " - atom3; "
69 <              << atom4_->getType() << " - atom4; "
70 <              << std::endl;
71 < */
72 <    Vector3d r21 = pos1 - pos2;
73 <    Vector3d r32 = pos2 - pos3;
74 <    Vector3d r42 = pos2 - pos4;
63 >    Vector3d r31 = pos1 - pos3;
64 >    Vector3d r23 = pos3 - pos2;
65 >    Vector3d r43 = pos3 - pos4;
66  
67      //  Calculate the cross products and distances
68 <    Vector3d A = cross(r21, r32);
68 >    Vector3d A = cross(r31, r43);
69      RealType rA = A.length();
70 <    Vector3d B = cross(r32, r42);
70 >    Vector3d B = cross(r43, r23);
71      RealType rB = B.length();
72      //Vector3d C = cross(r23, A);
73      //RealType rC = C.length();
# Line 87 | Line 78 | namespace oopse {
78      
79      //  Calculate the sin and cos
80      RealType cos_phi = dot(A, B) ;
81 <    if (cos_phi > 1.0) {cos_phi = 1.0; std::cout << "!!!! cos_phi is bigger than 1.0"
82 <                                                 << std::endl;}
92 <    if (cos_phi < -1.0) {cos_phi = -1.0; std::cout << "!!!! cos_phi is less than -1.0"
93 <                                                   << std::endl;}
94 <    //std::cout << "We actually use this inversion!!!!" << std::endl;
81 >    if (cos_phi > 1.0) cos_phi = 1.0;
82 >    if (cos_phi < -1.0) cos_phi = -1.0;
83  
84      RealType dVdcosPhi;
97 –    //cos_phi = 2.0*cos_phi*cos_phi - 1.0;
85      inversionType_->calcForce(cos_phi, potential_, dVdcosPhi);
86      Vector3d f1 ;
87      Vector3d f2 ;
# Line 103 | Line 90 | namespace oopse {
90      Vector3d dcosdA = (cos_phi * A - B) /rA;
91      Vector3d dcosdB = (cos_phi * B - A) /rB;
92  
93 <    f1 = dVdcosPhi * cross(r32, dcosdA);
94 <    f2 = dVdcosPhi * ( cross(r42, dcosdB) - cross(r21, dcosdA));
95 <    f3 = dVdcosPhi * cross(dcosdB, r32);
93 >    f1 = dVdcosPhi * cross(r43, dcosdA);
94 >    f2 = dVdcosPhi * ( cross(r23, dcosdB) - cross(r31, dcosdA));
95 >    f3 = dVdcosPhi * cross(dcosdB, r43);
96  
97 <    // In OOPSE's version of an improper torsion, the central atom
97 >    // In OpenMD's version of an improper torsion, the central atom
98      // comes first.  However, to get the planarity in a typical cosine
99      // version of this potential (i.e. Amber-style), the central atom
100      // is treated as atom *3* in a standard torsion form:
101  
102      //  AMBER:   I - J - K - L   (e.g. K is sp2 hybridized carbon)
103 <    //  OOPSE:   I - (J - K - L)  (e.g. I is sp2 hybridized carbon)
103 >    //  OpenMD:  I - (J - K - L)  (e.g. I is sp2 hybridized carbon)
104  
105      // Confusing enough?  Good.
106  
# Line 122 | Line 109 | namespace oopse {
109      atom4_->addFrc(-f2);
110      atom3_->addFrc(-f3);
111  
112 +    atom1_->addParticlePot(potential_);
113 +    atom2_->addParticlePot(potential_);
114 +    atom3_->addParticlePot(potential_);
115 +    atom4_->addParticlePot(potential_);
116 +
117      angle = acos(cos_phi) /M_PI * 180.0;
118    }
119  

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