src/primitives/Torsion.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#include "config.h"
#include <cmath>

#include "primitives/Torsion.hpp"

namespace OpenMD {

  Torsion::Torsion(Atom *atom1, Atom *atom2, Atom *atom3, Atom *atom4,
                   TorsionType *tt) : ShortRangeInteraction(),
                                      torsionType_(tt) {
    atoms_.resize(4);
    atoms_[0] = atom1;
    atoms_[1] = atom2;
    atoms_[2] = atom3;
    atoms_[3] = atom4;
  }

  void Torsion::calcForce(RealType& angle, bool doParticlePot) {

    Vector3d pos1 = atoms_[0]->getPos();
    Vector3d pos2 = atoms_[1]->getPos();
    Vector3d pos3 = atoms_[2]->getPos();
    Vector3d pos4 = atoms_[3]->getPos();

    Vector3d r21 = pos1 - pos2;
    Vector3d r32 = pos2 - pos3;
    Vector3d r43 = pos3 - pos4;

    //  Calculate the cross products and distances
    Vector3d A = cross(r21, r32);
    RealType rA = A.length();
    Vector3d B = cross(r32, r43);
    RealType rB = B.length();

    /* 
       If either of the two cross product vectors is tiny, that means
       the three atoms involved are colinear, and the torsion angle is
       going to be undefined.  The easiest check for this problem is
       to use the product of the two lengths.
    */
    if (rA * rB < OpenMD::epsilon) return;
    
    A.normalize();
    B.normalize();  
    
    //  Calculate the sin and cos
    RealType cos_phi = dot(A, B) ;
    if (cos_phi > 1.0) cos_phi = 1.0;
    if (cos_phi < -1.0) cos_phi = -1.0; 
    
    RealType dVdcosPhi;
    torsionType_->calcForce(cos_phi, potential_, dVdcosPhi);
    Vector3d f1 ;
    Vector3d f2 ;
    Vector3d f3 ;
    
    Vector3d dcosdA = (cos_phi * A - B) /rA;
    Vector3d dcosdB = (cos_phi * B - A) /rB;
    
    f1 = dVdcosPhi * cross(r32, dcosdA);
    f2 = dVdcosPhi * ( cross(r43, dcosdB) - cross(r21, dcosdA));
    f3 = dVdcosPhi * cross(dcosdB, r32);
    
    atoms_[0]->addFrc(f1);
    atoms_[1]->addFrc(f2 - f1);
    atoms_[2]->addFrc(f3 - f2);
    atoms_[3]->addFrc(-f3);
    
    if (doParticlePot) {
      atoms_[0]->addParticlePot(potential_);
      atoms_[1]->addParticlePot(potential_);
      atoms_[2]->addParticlePot(potential_);
      atoms_[3]->addParticlePot(potential_);
    }
    
    angle = acos(cos_phi) /M_PI * 180.0;    
  }  
}
Revision:	1953
Committed:	Thu Dec 5 18:19:26 2013 UTC (11 years, 4 months ago) by gezelter
File size:	4382 byte(s)
Log Message:	Rewrote much of selection module, added a bond correlation function
#	Content
1	/*
2	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
6	* redistribute this software in source and binary code form, provided
7	* that the following conditions are met:
8	*
9	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
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.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
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	#include "config.h"
44	#include <cmath>
45
46	#include "primitives/Torsion.hpp"
47
48	namespace OpenMD {
49
50	Torsion::Torsion(Atom atom1, Atom atom2, Atom atom3, Atom atom4,
51	TorsionType *tt) : ShortRangeInteraction(),
52	torsionType_(tt) {
53	atoms_.resize(4);
54	atoms_[0] = atom1;
55	atoms_[1] = atom2;
56	atoms_[2] = atom3;
57	atoms_[3] = atom4;
58	}
59
60	void Torsion::calcForce(RealType& angle, bool doParticlePot) {
61
62	Vector3d pos1 = atoms_[0]->getPos();
63	Vector3d pos2 = atoms_[1]->getPos();
64	Vector3d pos3 = atoms_[2]->getPos();
65	Vector3d pos4 = atoms_[3]->getPos();
66
67	Vector3d r21 = pos1 - pos2;
68	Vector3d r32 = pos2 - pos3;
69	Vector3d r43 = pos3 - pos4;
70
71	// Calculate the cross products and distances
72	Vector3d A = cross(r21, r32);
73	RealType rA = A.length();
74	Vector3d B = cross(r32, r43);
75	RealType rB = B.length();
76
77	/*
78	If either of the two cross product vectors is tiny, that means
79	the three atoms involved are colinear, and the torsion angle is
80	going to be undefined. The easiest check for this problem is
81	to use the product of the two lengths.
82	*/
83	if (rA * rB < OpenMD::epsilon) return;
84
85	A.normalize();
86	B.normalize();
87
88	// Calculate the sin and cos
89	RealType cos_phi = dot(A, B) ;
90	if (cos_phi > 1.0) cos_phi = 1.0;
91	if (cos_phi < -1.0) cos_phi = -1.0;
92
93	RealType dVdcosPhi;
94	torsionType_->calcForce(cos_phi, potential_, dVdcosPhi);
95	Vector3d f1 ;
96	Vector3d f2 ;
97	Vector3d f3 ;
98
99	Vector3d dcosdA = (cos_phi * A - B) /rA;
100	Vector3d dcosdB = (cos_phi * B - A) /rB;
101
102	f1 = dVdcosPhi * cross(r32, dcosdA);
103	f2 = dVdcosPhi * ( cross(r43, dcosdB) - cross(r21, dcosdA));
104	f3 = dVdcosPhi * cross(dcosdB, r32);
105
106	atoms_[0]->addFrc(f1);
107	atoms_[1]->addFrc(f2 - f1);
108	atoms_[2]->addFrc(f3 - f2);
109	atoms_[3]->addFrc(-f3);
110
111	if (doParticlePot) {
112	atoms_[0]->addParticlePot(potential_);
113	atoms_[1]->addParticlePot(potential_);
114	atoms_[2]->addParticlePot(potential_);
115	atoms_[3]->addParticlePot(potential_);
116	}
117
118	angle = acos(cos_phi) /M_PI * 180.0;
119	}
120	}