src/primitives/GhostTorsion.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/GhostTorsion.hpp"

namespace OpenMD {
  
  GhostTorsion::GhostTorsion(Atom *atom1, Atom *atom2,  
                             DirectionalAtom* ghostAtom, TorsionType *tt) 
    : Torsion(atom1, atom2, ghostAtom, ghostAtom, tt) {}
  
  void GhostTorsion::calcForce(RealType& angle) {
    DirectionalAtom* ghostAtom = static_cast<DirectionalAtom*>(atom3_);    
    
    Vector3d pos1 = atom1_->getPos();
    Vector3d pos2 = atom2_->getPos();
    Vector3d pos3 = ghostAtom->getPos();
    
    Vector3d r21 = pos1 - pos2;
    Vector3d r32 = pos2 - pos3;
    Vector3d r43 = ghostAtom->getA().getColumn(2);
    
    //  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) ;
    
    RealType dVdcosPhi;
    torsionType_->calcForce(cos_phi, potential_, dVdcosPhi);
    
    Vector3d dcosdA = (cos_phi * A - B) /rA;
    Vector3d dcosdB = (cos_phi * B - A) /rB;
    
    Vector3d f1 = dVdcosPhi * cross(r32, dcosdA);
    Vector3d f2 = dVdcosPhi * ( cross(r43, dcosdB) - cross(r21, dcosdA));
    Vector3d f3 = dVdcosPhi * cross(dcosdB, r32);
    
    atom1_->addFrc(f1);
    atom2_->addFrc(f2 - f1);
    
    ghostAtom->addFrc(-f2);
    
    f3.negate();
    ghostAtom->addTrq(cross(r43, f3));    
    
    atom1_->addParticlePot(potential_);
    atom2_->addParticlePot(potential_);
    ghostAtom->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/GhostTorsion.cpp*
File size:	4052 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	tim	273	* 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	tim	273	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	tim	273	* 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	tim	273	*/
41
42			#include "primitives/GhostTorsion.hpp"
43
44	gezelter	1390	namespace OpenMD {
45	gezelter	1211
46			GhostTorsion::GhostTorsion(Atom atom1, Atom atom2,
47			DirectionalAtom* ghostAtom, TorsionType *tt)
48			: Torsion(atom1, atom2, ghostAtom, ghostAtom, tt) {}
49
50	tim	963	void GhostTorsion::calcForce(RealType& angle) {
51	tim	275	DirectionalAtom* ghostAtom = static_cast<DirectionalAtom*>(atom3_);
52	gezelter	1211
53	tim	273	Vector3d pos1 = atom1_->getPos();
54			Vector3d pos2 = atom2_->getPos();
55			Vector3d pos3 = ghostAtom->getPos();
56	gezelter	1211
57	tim	273	Vector3d r21 = pos1 - pos2;
58			Vector3d r32 = pos2 - pos3;
59	gezelter	1443	Vector3d r43 = ghostAtom->getA().getColumn(2);
60	gezelter	1211
61	tim	273	// Calculate the cross products and distances
62			Vector3d A = cross(r21, r32);
63	tim	963	RealType rA = A.length();
64	tim	273	Vector3d B = cross(r32, r43);
65	tim	963	RealType rB = B.length();
66	gezelter	1446
67			/*
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	gezelter	1211
75	tim	273	A.normalize();
76			B.normalize();
77
78			// Calculate the sin and cos
79	tim	963	RealType cos_phi = dot(A, B) ;
80	gezelter	1211
81	tim	963	RealType dVdcosPhi;
82	tim	749	torsionType_->calcForce(cos_phi, potential_, dVdcosPhi);
83	gezelter	1211
84	tim	273	Vector3d dcosdA = (cos_phi * A - B) /rA;
85			Vector3d dcosdB = (cos_phi * B - A) /rB;
86	gezelter	1211
87	tim	273	Vector3d f1 = dVdcosPhi * cross(r32, dcosdA);
88			Vector3d f2 = dVdcosPhi * ( cross(r43, dcosdB) - cross(r21, dcosdA));
89			Vector3d f3 = dVdcosPhi * cross(dcosdB, r32);
90	gezelter	1211
91	tim	273	atom1_->addFrc(f1);
92			atom2_->addFrc(f2 - f1);
93	gezelter	1211
94	tim	273	ghostAtom->addFrc(-f2);
95	gezelter	1211
96	tim	273	f3.negate();
97			ghostAtom->addTrq(cross(r43, f3));
98	gezelter	1211
99	gezelter	1309	atom1_->addParticlePot(potential_);
100			atom2_->addParticlePot(potential_);
101			ghostAtom->addParticlePot(potential_);
102
103	tim	749	angle = acos(cos_phi) /M_PI * 180.0;
104	gezelter	507	}
105	tim	273	}
106