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) : 
    ShortRangeInteraction(), inversionType_(it) { 

    atoms_.resize(4);
    atoms_[0] = atom1;
    atoms_[1] = atom2;
    atoms_[2] = atom3;
    atoms_[3] = atom4;
    
    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 = atoms_[1]->getPos();
    Vector3d pos2 = atoms_[2]->getPos();
    Vector3d pos3 = atoms_[0]->getPos();
    Vector3d pos4 = atoms_[3]->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.

    atoms_[1]->addFrc(f1);
    atoms_[0]->addFrc(f2 - f1 + f3);
    atoms_[3]->addFrc(-f2);
    atoms_[2]->addFrc(-f3);

    if (doParticlePot) { 
      atoms_[0]->addParticlePot(potential_);
      atoms_[1]->addParticlePot(potential_);
      atoms_[2]->addParticlePot(potential_);
      atoms_[3]->addParticlePot(potential_);
    }
    
    angle = acos(cos_phi) /M_PI * 180.0;
  }

}
Revision:	1953
Committed:	Thu Dec 5 18:19:26 2013 UTC (11 years, 4 months ago) by gezelter
File size:	5256 byte(s)
Log Message:	Rewrote much of selection module, added a bond correlation function
#	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, 234107 (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 "config.h"
44	#include <cmath>
45
46	#include "primitives/Inversion.hpp"
47
48	namespace OpenMD {
49
50	Inversion::Inversion(Atom atom1, Atom atom2, Atom *atom3,
51	Atom atom4, InversionType it) :
52	ShortRangeInteraction(), inversionType_(it) {
53
54	atoms_.resize(4);
55	atoms_[0] = atom1;
56	atoms_[1] = atom2;
57	atoms_[2] = atom3;
58	atoms_[3] = atom4;
59
60	inversionKey_ = inversionType_->getKey();
61	}
62
63	void Inversion::calcForce(RealType& angle, bool doParticlePot) {
64
65	// In OpenMD's version of an inversion, the central atom
66	// comes first. However, to get the planarity in a typical cosine
67	// version of this potential (i.e. Amber-style), the central atom
68	// is treated as atom 3 in a standard torsion form:
69
70	Vector3d pos1 = atoms_[1]->getPos();
71	Vector3d pos2 = atoms_[2]->getPos();
72	Vector3d pos3 = atoms_[0]->getPos();
73	Vector3d pos4 = atoms_[3]->getPos();
74
75	Vector3d r31 = pos1 - pos3;
76	Vector3d r23 = pos3 - pos2;
77	Vector3d r43 = pos3 - pos4;
78
79	// Calculate the cross products and distances
80	Vector3d A = cross(r31, r43);
81	RealType rA = A.length();
82	Vector3d B = cross(r43, r23);
83	RealType rB = B.length();
84	//Vector3d C = cross(r23, A);
85	//RealType rC = C.length();
86
87	A.normalize();
88	B.normalize();
89	//C.normalize();
90
91	// Calculate the sin and cos
92	RealType cos_phi = dot(A, B) ;
93	if (cos_phi > 1.0) cos_phi = 1.0;
94	if (cos_phi < -1.0) cos_phi = -1.0;
95
96	RealType dVdcosPhi;
97	switch (inversionKey_) {
98	case itCosAngle:
99	inversionType_->calcForce(cos_phi, potential_, dVdcosPhi);
100	break;
101	case itAngle:
102	RealType phi = acos(cos_phi);
103	RealType dVdPhi;
104	inversionType_->calcForce(phi, potential_, dVdPhi);
105	RealType sin_phi = sqrt(1.0 - cos_phi * cos_phi);
106	if (fabs(sin_phi) < 1.0E-6) {
107	sin_phi = 1.0E-6;
108	}
109	dVdcosPhi = dVdPhi / sin_phi;
110	break;
111	}
112
113	Vector3d f1 ;
114	Vector3d f2 ;
115	Vector3d f3 ;
116
117	Vector3d dcosdA = (cos_phi * A - B) /rA;
118	Vector3d dcosdB = (cos_phi * B - A) /rB;
119
120	f1 = dVdcosPhi * cross(r43, dcosdA);
121	f2 = dVdcosPhi * ( cross(r23, dcosdB) - cross(r31, dcosdA));
122	f3 = dVdcosPhi * cross(dcosdB, r43);
123
124	// In OpenMD's version of an improper torsion, the central atom
125	// comes first. However, to get the planarity in a typical cosine
126	// version of this potential (i.e. Amber-style), the central atom
127	// is treated as atom 3 in a standard torsion form:
128
129	// AMBER: I - J - K - L (e.g. K is sp2 hybridized carbon)
130	// OpenMD: I - (J - K - L) (e.g. I is sp2 hybridized carbon)
131
132	// Confusing enough? Good.
133
134	atoms_[1]->addFrc(f1);
135	atoms_[0]->addFrc(f2 - f1 + f3);
136	atoms_[3]->addFrc(-f2);
137	atoms_[2]->addFrc(-f3);
138
139	if (doParticlePot) {
140	atoms_[0]->addParticlePot(potential_);
141	atoms_[1]->addParticlePot(potential_);
142	atoms_[2]->addParticlePot(potential_);
143	atoms_[3]->addParticlePot(potential_);
144	}
145
146	angle = acos(cos_phi) /M_PI * 180.0;
147	}
148
149	}