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, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
 
#include "primitives/Torsion.hpp"

namespace OpenMD {

  Torsion::Torsion(Atom *atom1, Atom *atom2, Atom *atom3, Atom *atom4,
                   TorsionType *tt) :
    atom1_(atom1), atom2_(atom2), atom3_(atom3), atom4_(atom4), torsionType_(tt) { }

  void Torsion::calcForce(RealType& angle) {

    Vector3d pos1 = atom1_->getPos();
    Vector3d pos2 = atom2_->getPos();
    Vector3d pos3 = atom3_->getPos();
    Vector3d pos4 = atom4_->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);
    
    atom1_->addFrc(f1);
    atom2_->addFrc(f2 - f1);
    atom3_->addFrc(f3 - f2);
    atom4_->addFrc(-f3);
    
    atom1_->addParticlePot(potential_);
    atom2_->addParticlePot(potential_);
    atom3_->addParticlePot(potential_);
    atom4_->addParticlePot(potential_);
    
    angle = acos(cos_phi) /M_PI * 180.0;    
  }  
}
Revision:	1446
Committed:	Thu Jun 17 14:48:02 2010 UTC (14 years, 10 months ago) by gezelter
Original Path:	*trunk/src/primitives/Torsion.cpp*
File size:	4067 byte(s)
Log Message:	Fixed a bug in Torsion (and GhostTorsion) which is triggered by a configuration with colinear atoms. The problem was discovered by Brett Donovan. Thanks, Brett!
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* 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	gezelter	1390	*
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	gezelter	246	*/
41
42			#include "primitives/Torsion.hpp"
43	gezelter	2
44	gezelter	1390	namespace OpenMD {
45	gezelter	2
46	gezelter	507	Torsion::Torsion(Atom atom1, Atom atom2, Atom atom3, Atom atom4,
47			TorsionType *tt) :
48	gezelter	246	atom1_(atom1), atom2_(atom2), atom3_(atom3), atom4_(atom4), torsionType_(tt) { }
49	gezelter	2
50	tim	963	void Torsion::calcForce(RealType& angle) {
51	tim	749
52	gezelter	246	Vector3d pos1 = atom1_->getPos();
53			Vector3d pos2 = atom2_->getPos();
54			Vector3d pos3 = atom3_->getPos();
55			Vector3d pos4 = atom4_->getPos();
56	gezelter	2
57	gezelter	246	Vector3d r21 = pos1 - pos2;
58			Vector3d r32 = pos2 - pos3;
59			Vector3d r43 = pos3 - pos4;
60	gezelter	2
61	gezelter	246	// Calculate the cross products and distances
62			Vector3d A = cross(r21, r32);
63	tim	963	RealType rA = A.length();
64	gezelter	246	Vector3d B = cross(r32, r43);
65	tim	963	RealType rB = B.length();
66	gezelter	2
67	gezelter	1446	/*
68			If either of the two cross product vectors is tiny, that means
69			the three atoms involved are colinear, and the torsion angle is
70			going to be undefined. The easiest check for this problem is
71			to use the product of the two lengths.
72			*/
73			if (rA * rB < OpenMD::epsilon) return;
74
75	gezelter	246	A.normalize();
76	gezelter	1446	B.normalize();
77	gezelter	246
78			// Calculate the sin and cos
79	tim	963	RealType cos_phi = dot(A, B) ;
80	tim	749	if (cos_phi > 1.0) cos_phi = 1.0;
81			if (cos_phi < -1.0) cos_phi = -1.0;
82	gezelter	1446
83	tim	963	RealType dVdcosPhi;
84	tim	749	torsionType_->calcForce(cos_phi, potential_, dVdcosPhi);
85	cli2	1290	Vector3d f1 ;
86			Vector3d f2 ;
87			Vector3d f3 ;
88	gezelter	1446
89	gezelter	507	Vector3d dcosdA = (cos_phi * A - B) /rA;
90			Vector3d dcosdB = (cos_phi * B - A) /rB;
91	gezelter	1446
92	gezelter	507	f1 = dVdcosPhi * cross(r32, dcosdA);
93			f2 = dVdcosPhi * ( cross(r43, dcosdB) - cross(r21, dcosdA));
94			f3 = dVdcosPhi * cross(dcosdB, r32);
95	tim	749
96	gezelter	246	atom1_->addFrc(f1);
97			atom2_->addFrc(f2 - f1);
98			atom3_->addFrc(f3 - f2);
99			atom4_->addFrc(-f3);
100	gezelter	1446
101	gezelter	1309	atom1_->addParticlePot(potential_);
102			atom2_->addParticlePot(potential_);
103			atom3_->addParticlePot(potential_);
104			atom4_->addParticlePot(potential_);
105	gezelter	1446
106			angle = acos(cos_phi) /M_PI * 180.0;
107			}
108	gezelter	2	}