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, 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/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, bool doParticlePot) {
    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().transpose().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));    
    
    if (doParticlePot) {
      atom1_->addParticlePot(potential_);
      atom2_->addParticlePot(potential_);
      ghostAtom->addParticlePot(potential_);
    }

    angle = acos(cos_phi) /M_PI * 180.0;
  }
}

Revision:	1850
Committed:	Wed Feb 20 15:39:39 2013 UTC (12 years, 2 months ago) by gezelter
File size:	4226 byte(s)
Log Message:	Fixed a widespread typo in the license
#	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	gezelter	1850	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	tim	273	*/
42
43	gezelter	1767	#include "config.h"
44			#include <cmath>
45
46	tim	273	#include "primitives/GhostTorsion.hpp"
47
48	gezelter	1390	namespace OpenMD {
49	gezelter	1211
50			GhostTorsion::GhostTorsion(Atom atom1, Atom atom2,
51			DirectionalAtom* ghostAtom, TorsionType *tt)
52			: Torsion(atom1, atom2, ghostAtom, ghostAtom, tt) {}
53
54	gezelter	1712	void GhostTorsion::calcForce(RealType& angle, bool doParticlePot) {
55	tim	275	DirectionalAtom* ghostAtom = static_cast<DirectionalAtom*>(atom3_);
56	gezelter	1211
57	tim	273	Vector3d pos1 = atom1_->getPos();
58			Vector3d pos2 = atom2_->getPos();
59			Vector3d pos3 = ghostAtom->getPos();
60	gezelter	1211
61	tim	273	Vector3d r21 = pos1 - pos2;
62			Vector3d r32 = pos2 - pos3;
63	gezelter	1459	Vector3d r43 = ghostAtom->getA().transpose().getColumn(2);
64	gezelter	1211
65	tim	273	// Calculate the cross products and distances
66			Vector3d A = cross(r21, r32);
67	tim	963	RealType rA = A.length();
68	tim	273	Vector3d B = cross(r32, r43);
69	tim	963	RealType rB = B.length();
70	gezelter	1446
71			/*
72			If either of the two cross product vectors is tiny, that means
73			the three atoms involved are colinear, and the torsion angle is
74			going to be undefined. The easiest check for this problem is
75			to use the product of the two lengths.
76			*/
77			if (rA * rB < OpenMD::epsilon) return;
78	gezelter	1211
79	tim	273	A.normalize();
80			B.normalize();
81
82			// Calculate the sin and cos
83	tim	963	RealType cos_phi = dot(A, B) ;
84	gezelter	1211
85	tim	963	RealType dVdcosPhi;
86	tim	749	torsionType_->calcForce(cos_phi, potential_, dVdcosPhi);
87	gezelter	1211
88	tim	273	Vector3d dcosdA = (cos_phi * A - B) /rA;
89			Vector3d dcosdB = (cos_phi * B - A) /rB;
90	gezelter	1211
91	tim	273	Vector3d f1 = dVdcosPhi * cross(r32, dcosdA);
92			Vector3d f2 = dVdcosPhi * ( cross(r43, dcosdB) - cross(r21, dcosdA));
93			Vector3d f3 = dVdcosPhi * cross(dcosdB, r32);
94	gezelter	1211
95	tim	273	atom1_->addFrc(f1);
96			atom2_->addFrc(f2 - f1);
97	gezelter	1211
98	tim	273	ghostAtom->addFrc(-f2);
99	gezelter	1211
100	tim	273	f3.negate();
101			ghostAtom->addTrq(cross(r43, f3));
102	gezelter	1211
103	gezelter	1712	if (doParticlePot) {
104			atom1_->addParticlePot(potential_);
105			atom2_->addParticlePot(potential_);
106			ghostAtom->addParticlePot(potential_);
107			}
108	gezelter	1309
109	tim	749	angle = acos(cos_phi) /M_PI * 180.0;
110	gezelter	507	}
111	tim	273	}
112