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, 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/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) { 
    inversionKey_ = inversionType_->getKey();
  }
  
  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;
    switch (inversionKey_) {
    case itCosAngle:
      inversionType_->calcForce(cos_phi, potential_, dVdcosPhi);
      break;
    case itAngle:
      RealType phi = acos(cos_phi);
      RealType dVdPhi;
      inversionType_->calcForce(phi, potential_, dVdPhi);
      RealType sin_phi = sqrt(1.0 - cos_phi * cos_phi);   
      if (fabs(sin_phi) < 1.0E-6) {
        sin_phi = 1.0E-6;
      }
      dVdcosPhi = dVdPhi / sin_phi;
      break;
    }
    
    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:	1890
Committed:	Tue Jun 18 21:06:25 2013 UTC (11 years, 10 months ago) by gezelter
File size:	5139 byte(s)
Log Message:	Adding HarmonicInversionType for GROMOS and CHARMM style force fields.
#	User	Rev	Content
1	cli2	1275	/*
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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	cli2	1275	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	cli2	1275	* 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	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	cli2	1275	*/
42
43	gezelter	1782	#include "config.h"
44			#include <cmath>
45
46	cli2	1275	#include "primitives/Inversion.hpp"
47
48	gezelter	1390	namespace OpenMD {
49	cli2	1275
50			Inversion::Inversion(Atom atom1, Atom atom2, Atom *atom3,
51			Atom atom4, InversionType it) :
52			atom1_(atom1), atom2_(atom2), atom3_(atom3), atom4_(atom4),
53	gezelter	1890	inversionType_(it) {
54			inversionKey_ = inversionType_->getKey();
55			}
56	cli2	1275
57	gezelter	1782	void Inversion::calcForce(RealType& angle, bool doParticlePot) {
58	cli2	1275
59	gezelter	1390	// In OpenMD's version of an inversion, the central atom
60	cli2	1275	// comes first. However, to get the planarity in a typical cosine
61			// version of this potential (i.e. Amber-style), the central atom
62			// is treated as atom 3 in a standard torsion form:
63
64			Vector3d pos1 = atom2_->getPos();
65	cli2	1303	Vector3d pos2 = atom3_->getPos();
66			Vector3d pos3 = atom1_->getPos();
67			Vector3d pos4 = atom4_->getPos();
68	cli2	1275
69	cli2	1303	Vector3d r31 = pos1 - pos3;
70			Vector3d r23 = pos3 - pos2;
71			Vector3d r43 = pos3 - pos4;
72	cli2	1275
73			// Calculate the cross products and distances
74	cli2	1303	Vector3d A = cross(r31, r43);
75	cli2	1275	RealType rA = A.length();
76	cli2	1303	Vector3d B = cross(r43, r23);
77	cli2	1275	RealType rB = B.length();
78	cli2	1290	//Vector3d C = cross(r23, A);
79			//RealType rC = C.length();
80	cli2	1275
81			A.normalize();
82			B.normalize();
83	cli2	1290	//C.normalize();
84	cli2	1275
85			// Calculate the sin and cos
86			RealType cos_phi = dot(A, B) ;
87	gezelter	1309	if (cos_phi > 1.0) cos_phi = 1.0;
88			if (cos_phi < -1.0) cos_phi = -1.0;
89	cli2	1275
90			RealType dVdcosPhi;
91	gezelter	1890	switch (inversionKey_) {
92			case itCosAngle:
93			inversionType_->calcForce(cos_phi, potential_, dVdcosPhi);
94			break;
95			case itAngle:
96			RealType phi = acos(cos_phi);
97			RealType dVdPhi;
98			inversionType_->calcForce(phi, potential_, dVdPhi);
99			RealType sin_phi = sqrt(1.0 - cos_phi * cos_phi);
100			if (fabs(sin_phi) < 1.0E-6) {
101			sin_phi = 1.0E-6;
102			}
103			dVdcosPhi = dVdPhi / sin_phi;
104			break;
105			}
106
107	cli2	1290	Vector3d f1 ;
108			Vector3d f2 ;
109			Vector3d f3 ;
110	cli2	1275
111			Vector3d dcosdA = (cos_phi * A - B) /rA;
112			Vector3d dcosdB = (cos_phi * B - A) /rB;
113
114	cli2	1303	f1 = dVdcosPhi * cross(r43, dcosdA);
115			f2 = dVdcosPhi * ( cross(r23, dcosdB) - cross(r31, dcosdA));
116			f3 = dVdcosPhi * cross(dcosdB, r43);
117	cli2	1275
118	gezelter	1390	// In OpenMD's version of an improper torsion, the central atom
119	cli2	1275	// comes first. However, to get the planarity in a typical cosine
120			// version of this potential (i.e. Amber-style), the central atom
121			// is treated as atom 3 in a standard torsion form:
122
123			// AMBER: I - J - K - L (e.g. K is sp2 hybridized carbon)
124	gezelter	1390	// OpenMD: I - (J - K - L) (e.g. I is sp2 hybridized carbon)
125	cli2	1275
126			// Confusing enough? Good.
127
128	cli2	1290	atom2_->addFrc(f1);
129			atom1_->addFrc(f2 - f1 + f3);
130			atom4_->addFrc(-f2);
131			atom3_->addFrc(-f3);
132
133	gezelter	1782	if (doParticlePot) {
134			atom1_->addParticlePot(potential_);
135			atom2_->addParticlePot(potential_);
136			atom3_->addParticlePot(potential_);
137			atom4_->addParticlePot(potential_);
138			}
139
140	cli2	1275	angle = acos(cos_phi) /M_PI * 180.0;
141			}
142
143			}