src/primitives/Inversion.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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#include "primitives/Inversion.hpp"

namespace OpenMD {

  Inversion::Inversion(Atom *atom1, Atom *atom2, Atom *atom3, 
                       Atom *atom4, InversionType *it) :
    atom1_(atom1), atom2_(atom2), atom3_(atom3), atom4_(atom4), 
    inversionType_(it) { }
  
  void Inversion::calcForce(RealType& angle, bool doParticlePot) {
    
    // In OpenMD's version of an inversion, the central atom
    // comes first.  However, to get the planarity in a typical cosine
    // version of this potential (i.e. Amber-style), the central atom
    // is treated as atom *3* in a standard torsion form:

    Vector3d pos1 = atom2_->getPos();
    Vector3d pos2 = atom3_->getPos();
    Vector3d pos3 = atom1_->getPos();
    Vector3d pos4 = atom4_->getPos();

    Vector3d r31 = pos1 - pos3;
    Vector3d r23 = pos3 - pos2;
    Vector3d r43 = pos3 - pos4;

    //  Calculate the cross products and distances
    Vector3d A = cross(r31, r43);
    RealType rA = A.length();
    Vector3d B = cross(r43, r23);
    RealType rB = B.length();
    //Vector3d C = cross(r23, 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;
    inversionType_->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(r43, dcosdA);
    f2 = dVdcosPhi * ( cross(r23, dcosdB) - cross(r31, dcosdA));
    f3 = dVdcosPhi * cross(dcosdB, r43);

    // In OpenMD's version of an improper torsion, the central atom
    // comes first.  However, to get the planarity in a typical cosine
    // version of this potential (i.e. Amber-style), the central atom
    // is treated as atom *3* in a standard torsion form:

    //  AMBER:   I - J - K - L   (e.g. K is sp2 hybridized carbon)
    //  OpenMD:  I - (J - K - L)  (e.g. I is sp2 hybridized carbon)

    // Confusing enough?  Good.

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

    if (doParticlePot) { 
      atom1_->addParticlePot(potential_);
      atom2_->addParticlePot(potential_);
      atom3_->addParticlePot(potential_);
      atom4_->addParticlePot(potential_);
    }
    
    angle = acos(cos_phi) /M_PI * 180.0;
  }

}
Revision:	1712
Committed:	Sat May 19 13:30:21 2012 UTC (12 years, 11 months ago) by gezelter
File size:	4662 byte(s)
Log Message:	Bugfixes (mostly related to particlePot and storageLayout).
#	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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	#include "primitives/Inversion.hpp"
44
45	namespace OpenMD {
46
47	Inversion::Inversion(Atom atom1, Atom atom2, Atom *atom3,
48	Atom atom4, InversionType it) :
49	atom1_(atom1), atom2_(atom2), atom3_(atom3), atom4_(atom4),
50	inversionType_(it) { }
51
52	void Inversion::calcForce(RealType& angle, bool doParticlePot) {
53
54	// In OpenMD's version of an inversion, the central atom
55	// comes first. However, to get the planarity in a typical cosine
56	// version of this potential (i.e. Amber-style), the central atom
57	// is treated as atom 3 in a standard torsion form:
58
59	Vector3d pos1 = atom2_->getPos();
60	Vector3d pos2 = atom3_->getPos();
61	Vector3d pos3 = atom1_->getPos();
62	Vector3d pos4 = atom4_->getPos();
63
64	Vector3d r31 = pos1 - pos3;
65	Vector3d r23 = pos3 - pos2;
66	Vector3d r43 = pos3 - pos4;
67
68	// Calculate the cross products and distances
69	Vector3d A = cross(r31, r43);
70	RealType rA = A.length();
71	Vector3d B = cross(r43, r23);
72	RealType rB = B.length();
73	//Vector3d C = cross(r23, A);
74	//RealType rC = C.length();
75
76	A.normalize();
77	B.normalize();
78	//C.normalize();
79
80	// Calculate the sin and cos
81	RealType cos_phi = dot(A, B) ;
82	if (cos_phi > 1.0) cos_phi = 1.0;
83	if (cos_phi < -1.0) cos_phi = -1.0;
84
85	RealType dVdcosPhi;
86	inversionType_->calcForce(cos_phi, potential_, dVdcosPhi);
87	Vector3d f1 ;
88	Vector3d f2 ;
89	Vector3d f3 ;
90
91	Vector3d dcosdA = (cos_phi * A - B) /rA;
92	Vector3d dcosdB = (cos_phi * B - A) /rB;
93
94	f1 = dVdcosPhi * cross(r43, dcosdA);
95	f2 = dVdcosPhi * ( cross(r23, dcosdB) - cross(r31, dcosdA));
96	f3 = dVdcosPhi * cross(dcosdB, r43);
97
98	// In OpenMD's version of an improper torsion, the central atom
99	// comes first. However, to get the planarity in a typical cosine
100	// version of this potential (i.e. Amber-style), the central atom
101	// is treated as atom 3 in a standard torsion form:
102
103	// AMBER: I - J - K - L (e.g. K is sp2 hybridized carbon)
104	// OpenMD: I - (J - K - L) (e.g. I is sp2 hybridized carbon)
105
106	// Confusing enough? Good.
107
108	atom2_->addFrc(f1);
109	atom1_->addFrc(f2 - f1 + f3);
110	atom4_->addFrc(-f2);
111	atom3_->addFrc(-f3);
112
113	if (doParticlePot) {
114	atom1_->addParticlePot(potential_);
115	atom2_->addParticlePot(potential_);
116	atom3_->addParticlePot(potential_);
117	atom4_->addParticlePot(potential_);
118	}
119
120	angle = acos(cos_phi) /M_PI * 180.0;
121	}
122
123	}