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();
    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) ;
    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:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 5 months ago) by gezelter
File size:	3802 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	Content
1	/*
2	* 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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* 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	*
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	*/
41
42	#include "primitives/Torsion.hpp"
43
44	namespace OpenMD {
45
46	Torsion::Torsion(Atom atom1, Atom atom2, Atom atom3, Atom atom4,
47	TorsionType *tt) :
48	atom1_(atom1), atom2_(atom2), atom3_(atom3), atom4_(atom4), torsionType_(tt) { }
49
50	void Torsion::calcForce(RealType& angle) {
51
52	Vector3d pos1 = atom1_->getPos();
53	Vector3d pos2 = atom2_->getPos();
54	Vector3d pos3 = atom3_->getPos();
55	Vector3d pos4 = atom4_->getPos();
56
57	Vector3d r21 = pos1 - pos2;
58	Vector3d r32 = pos2 - pos3;
59	Vector3d r43 = pos3 - pos4;
60
61	// Calculate the cross products and distances
62	Vector3d A = cross(r21, r32);
63	RealType rA = A.length();
64	Vector3d B = cross(r32, r43);
65	RealType rB = B.length();
66	Vector3d C = cross(r32, A);
67	RealType rC = C.length();
68
69	A.normalize();
70	B.normalize();
71	C.normalize();
72
73	// Calculate the sin and cos
74	RealType cos_phi = dot(A, B) ;
75	if (cos_phi > 1.0) cos_phi = 1.0;
76	if (cos_phi < -1.0) cos_phi = -1.0;
77
78	RealType dVdcosPhi;
79	torsionType_->calcForce(cos_phi, potential_, dVdcosPhi);
80	Vector3d f1 ;
81	Vector3d f2 ;
82	Vector3d f3 ;
83
84	Vector3d dcosdA = (cos_phi * A - B) /rA;
85	Vector3d dcosdB = (cos_phi * B - A) /rB;
86
87	f1 = dVdcosPhi * cross(r32, dcosdA);
88	f2 = dVdcosPhi * ( cross(r43, dcosdB) - cross(r21, dcosdA));
89	f3 = dVdcosPhi * cross(dcosdB, r32);
90
91	atom1_->addFrc(f1);
92	atom2_->addFrc(f2 - f1);
93	atom3_->addFrc(f3 - f2);
94	atom4_->addFrc(-f3);
95
96	atom1_->addParticlePot(potential_);
97	atom2_->addParticlePot(potential_);
98	atom3_->addParticlePot(potential_);
99	atom4_->addParticlePot(potential_);
100
101	angle = acos(cos_phi) /M_PI * 180.0;
102	}
103
104	}