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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
 
#include "primitives/Torsion.hpp"

namespace oopse {

  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() {
    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);
    double rA = A.length();
    Vector3d B = cross(r32, r43);
    double rB = B.length();
    Vector3d C = cross(r32, A);
    double rC = C.length();

    A.normalize();
    B.normalize();
    C.normalize();
    
    //  Calculate the sin and cos
    double cos_phi = dot(A, B) ;
    double sin_phi = dot(C, B);

    double dVdPhi;
    torsionType_->calcForce(cos_phi, sin_phi, potential_, dVdPhi);

    Vector3d f1;
    Vector3d f2;
    Vector3d f3;

    if (fabs(sin_phi) > 0.5) {
    //use the sin version to  prevent potential singularities

    Vector3d dcosdA = (cos_phi * A - B) /rA;
    Vector3d dcosdB = (cos_phi * B - A) /rB;

    double dVdcosPhi = -dVdPhi / sin_phi;

    f1 = dVdcosPhi * cross(r32, dcosdA);
    f2 = dVdcosPhi * ( cross(r43, dcosdB) - cross(r21, dcosdA));
    f3 = dVdcosPhi * cross(dcosdB, r32);

    } else {
    //use the cos version to  prevent potential singularities

    double dVdsinPhi = dVdPhi /cos_phi;
    Vector3d dsindB = (sin_phi * B - C) /rB;
    Vector3d dsindC = (sin_phi * C - B) /rC;

    f1.x() = dVdsinPhi*((r32.y()*r32.y() + r32.z()*r32.z())*dsindC.x() - r32.x()*r32.y()*dsindC.y() - r32.x()*r32.z()*dsindC.z());

    f1.y() = dVdsinPhi*((r32.z()*r32.z() + r32.x()*r32.x())*dsindC.y() - r32.y()*r32.z()*dsindC.z() - r32.y()*r32.x()*dsindC.x());

    f1.z() = dVdsinPhi*((r32.x()*r32.x() + r32.y()*r32.y())*dsindC.z() - r32.z()*r32.x()*dsindC.x() - r32.z()*r32.y()*dsindC.y());

    f2.x() = dVdsinPhi*(-(r32.y()*r21.y() + r32.z()*r21.z())*dsindC.x() + (2.0*r32.x()*r21.y() - r21.x()*r32.y())*dsindC.y()
    + (2.0*r32.x()*r21.z() - r21.x()*r32.z())*dsindC.z() + dsindB.z()*r43.y() - dsindB.y()*r43.z());

    f2.y() = dVdsinPhi*(-(r32.z()*r21.z() + r32.x()*r21.x())*dsindC.y() + (2.0*r32.y()*r21.z() - r21.y()*r32.z())*dsindC.z()
    + (2.0*r32.y()*r21.x() - r21.y()*r32.x())*dsindC.x() + dsindB.x()*r43.z() - dsindB.z()*r43.x());

    f2.z() = dVdsinPhi*(-(r32.x()*r21.x() + r32.y()*r21.y())*dsindC.z() + (2.0*r32.z()*r21.x() - r21.z()*r32.x())*dsindC.x()
    +(2.0*r32.z()*r21.y() - r21.z()*r32.y())*dsindC.y() + dsindB.y()*r43.x() - dsindB.x()*r43.y());

    f3 = dVdsinPhi * cross(dsindB, r32);
    }

    atom1_->addFrc(f1);
    atom2_->addFrc(f2 - f1);
    atom3_->addFrc(f3 - f2);
    atom4_->addFrc(-f3);
  }

}
Revision:	2391
Committed:	Thu Oct 20 20:27:34 2005 UTC (18 years, 8 months ago) by tim
File size:	4949 byte(s)
Log Message:	Fix the other branch of force calculation in Torision.cpp
#	User	Rev	Content
1	gezelter	2204	/*
2	gezelter	1930	* 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. 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
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#include "primitives/Torsion.hpp"
43	gezelter	1490
44	gezelter	1930	namespace oopse {
45	gezelter	1490
46	gezelter	2204	Torsion::Torsion(Atom atom1, Atom atom2, Atom atom3, Atom atom4,
47			TorsionType *tt) :
48	gezelter	1930	atom1_(atom1), atom2_(atom2), atom3_(atom3), atom4_(atom4), torsionType_(tt) { }
49	gezelter	1490
50	gezelter	2204	void Torsion::calcForce() {
51	gezelter	1930	Vector3d pos1 = atom1_->getPos();
52			Vector3d pos2 = atom2_->getPos();
53			Vector3d pos3 = atom3_->getPos();
54			Vector3d pos4 = atom4_->getPos();
55	gezelter	1490
56	gezelter	1930	Vector3d r21 = pos1 - pos2;
57			Vector3d r32 = pos2 - pos3;
58			Vector3d r43 = pos3 - pos4;
59	gezelter	1490
60	gezelter	1930	// Calculate the cross products and distances
61			Vector3d A = cross(r21, r32);
62			double rA = A.length();
63			Vector3d B = cross(r32, r43);
64			double rB = B.length();
65			Vector3d C = cross(r32, A);
66			double rC = C.length();
67	gezelter	1490
68	gezelter	1930	A.normalize();
69			B.normalize();
70			C.normalize();
71
72			// Calculate the sin and cos
73			double cos_phi = dot(A, B) ;
74			double sin_phi = dot(C, B);
75	gezelter	1490
76	gezelter	1930	double dVdPhi;
77			torsionType_->calcForce(cos_phi, sin_phi, potential_, dVdPhi);
78	gezelter	1490
79	gezelter	1930	Vector3d f1;
80			Vector3d f2;
81			Vector3d f3;
82	gezelter	1490
83	tim	2391	if (fabs(sin_phi) > 0.5) {
84			//use the sin version to prevent potential singularities
85	gezelter	1490
86	gezelter	2204	Vector3d dcosdA = (cos_phi * A - B) /rA;
87			Vector3d dcosdB = (cos_phi * B - A) /rB;
88	gezelter	1490
89	gezelter	2204	double dVdcosPhi = -dVdPhi / sin_phi;
90	gezelter	1490
91	gezelter	2204	f1 = dVdcosPhi * cross(r32, dcosdA);
92			f2 = dVdcosPhi * ( cross(r43, dcosdB) - cross(r21, dcosdA));
93			f3 = dVdcosPhi * cross(dcosdB, r32);
94	gezelter	1490
95	tim	2391	} else {
96			//use the cos version to prevent potential singularities
97	gezelter	1490
98	tim	2391	double dVdsinPhi = dVdPhi /cos_phi;
99			Vector3d dsindB = (sin_phi * B - C) /rB;
100			Vector3d dsindC = (sin_phi * C - B) /rC;
101	gezelter	1490
102	tim	2391	f1.x() = dVdsinPhi((r32.y()r32.y() + r32.z()r32.z())dsindC.x() - r32.x()r32.y()dsindC.y() - r32.x()r32.z()dsindC.z());
103	gezelter	1490
104	tim	2391	f1.y() = dVdsinPhi((r32.z()r32.z() + r32.x()r32.x())dsindC.y() - r32.y()r32.z()dsindC.z() - r32.y()r32.x()dsindC.x());
105	gezelter	1490
106	tim	2391	f1.z() = dVdsinPhi((r32.x()r32.x() + r32.y()r32.y())dsindC.z() - r32.z()r32.x()dsindC.x() - r32.z()r32.y()dsindC.y());
107	gezelter	1490
108	tim	2391	f2.x() = dVdsinPhi(-(r32.y()r21.y() + r32.z()r21.z())dsindC.x() + (2.0r32.x()r21.y() - r21.x()r32.y())dsindC.y()
109			+ (2.0r32.x()r21.z() - r21.x()r32.z())dsindC.z() + dsindB.z()r43.y() - dsindB.y()r43.z());
110	gezelter	1490
111	tim	2391	f2.y() = dVdsinPhi(-(r32.z()r21.z() + r32.x()r21.x())dsindC.y() + (2.0r32.y()r21.z() - r21.y()r32.z())dsindC.z()
112			+ (2.0r32.y()r21.x() - r21.y()r32.x())dsindC.x() + dsindB.x()r43.z() - dsindB.z()r43.x());
113	gezelter	1490
114	tim	2391	f2.z() = dVdsinPhi(-(r32.x()r21.x() + r32.y()r21.y())dsindC.z() + (2.0r32.z()r21.x() - r21.z()r32.x())dsindC.x()
115			+(2.0r32.z()r21.y() - r21.z()r32.y())dsindC.y() + dsindB.y()r43.x() - dsindB.x()r43.y());
116	gezelter	1490
117	tim	2391	f3 = dVdsinPhi * cross(dsindB, r32);
118			}
119	gezelter	1490
120	gezelter	1930	atom1_->addFrc(f1);
121			atom2_->addFrc(f2 - f1);
122			atom3_->addFrc(f3 - f2);
123			atom4_->addFrc(-f3);
124	gezelter	2204	}
125	gezelter	1490
126			}