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->getElectroFrame().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();
    Vector3d C = cross(r32, A);
    RealType rC = C.length();
    
    A.normalize();
    B.normalize();
    C.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:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 5 months ago) by gezelter
Original Path:	*trunk/src/primitives/GhostTorsion.cpp*
File size:	3829 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	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			Vector3d r43 = ghostAtom->getElectroFrame().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	tim	273	Vector3d C = cross(r32, A);
67	tim	963	RealType rC = C.length();
68	gezelter	1211
69	tim	273	A.normalize();
70			B.normalize();
71			C.normalize();
72
73			// Calculate the sin and cos
74	tim	963	RealType cos_phi = dot(A, B) ;
75	gezelter	1211
76	tim	963	RealType dVdcosPhi;
77	tim	749	torsionType_->calcForce(cos_phi, potential_, dVdcosPhi);
78	gezelter	1211
79	tim	273	Vector3d dcosdA = (cos_phi * A - B) /rA;
80			Vector3d dcosdB = (cos_phi * B - A) /rB;
81	gezelter	1211
82	tim	273	Vector3d f1 = dVdcosPhi * cross(r32, dcosdA);
83			Vector3d f2 = dVdcosPhi * ( cross(r43, dcosdB) - cross(r21, dcosdA));
84			Vector3d f3 = dVdcosPhi * cross(dcosdB, r32);
85	gezelter	1211
86	tim	273	atom1_->addFrc(f1);
87			atom2_->addFrc(f2 - f1);
88	gezelter	1211
89	tim	273	ghostAtom->addFrc(-f2);
90	gezelter	1211
91	tim	273	f3.negate();
92			ghostAtom->addTrq(cross(r43, f3));
93	gezelter	1211
94	gezelter	1309	atom1_->addParticlePot(potential_);
95			atom2_->addParticlePot(potential_);
96			ghostAtom->addParticlePot(potential_);
97
98	tim	749	angle = acos(cos_phi) /M_PI * 180.0;
99	gezelter	507	}
100	tim	273	}
101