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. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 */
 
#include "primitives/Inversion.hpp"
#include "fstream"

namespace oopse {

  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) {
    
    // In OOPSE'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();

   /*std::ofstream myfile;
   myfile.open("Inversion", std::ios::app);       
   myfile << atom1_->getType() << " - atom1; "
              << atom2_->getType() << " - atom2; "
              << atom3_->getType() << " - atom3; "
              << atom4_->getType() << " - atom4; "
              << std::endl;
*/
    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; std::cout << "!!!! cos_phi is bigger than 1.0" 
                                                 << std::endl;}
    if (cos_phi < -1.0) {cos_phi = -1.0; std::cout << "!!!! cos_phi is less than -1.0" 
                                                   << std::endl;}
    //std::cout << "We actually use this inversion!!!!" << std::endl;

    RealType dVdcosPhi;
    //cos_phi = 2.0*cos_phi*cos_phi - 1.0;
    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 OOPSE'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)
    //  OOPSE:   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);

    angle = acos(cos_phi) /M_PI * 180.0;
  }

}
Revision:	1303
Committed:	Mon Oct 13 21:35:22 2008 UTC (16 years, 6 months ago) by cli2
Original Path:	*trunk/src/primitives/Inversion.cpp*
File size:	4995 byte(s)
Log Message:	Fixes for Inversions for use with Amber
#	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			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#include "primitives/Inversion.hpp"
43	cli2	1290	#include "fstream"
44	cli2	1275
45			namespace oopse {
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) {
53
54			// In OOPSE'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	cli2	1303	Vector3d pos2 = atom3_->getPos();
61			Vector3d pos3 = atom1_->getPos();
62			Vector3d pos4 = atom4_->getPos();
63	cli2	1275
64	cli2	1290	/*std::ofstream myfile;
65			myfile.open("Inversion", std::ios::app);
66			myfile << atom1_->getType() << " - atom1; "
67			<< atom2_->getType() << " - atom2; "
68			<< atom3_->getType() << " - atom3; "
69			<< atom4_->getType() << " - atom4; "
70			<< std::endl;
71			*/
72	cli2	1303	Vector3d r31 = pos1 - pos3;
73			Vector3d r23 = pos3 - pos2;
74			Vector3d r43 = pos3 - pos4;
75	cli2	1275
76			// Calculate the cross products and distances
77	cli2	1303	Vector3d A = cross(r31, r43);
78	cli2	1275	RealType rA = A.length();
79	cli2	1303	Vector3d B = cross(r43, r23);
80	cli2	1275	RealType rB = B.length();
81	cli2	1290	//Vector3d C = cross(r23, A);
82			//RealType rC = C.length();
83	cli2	1275
84			A.normalize();
85			B.normalize();
86	cli2	1290	//C.normalize();
87	cli2	1275
88			// Calculate the sin and cos
89			RealType cos_phi = dot(A, B) ;
90	cli2	1290	if (cos_phi > 1.0) {cos_phi = 1.0; std::cout << "!!!! cos_phi is bigger than 1.0"
91			<< std::endl;}
92			if (cos_phi < -1.0) {cos_phi = -1.0; std::cout << "!!!! cos_phi is less than -1.0"
93			<< std::endl;}
94			//std::cout << "We actually use this inversion!!!!" << std::endl;
95	cli2	1275
96			RealType dVdcosPhi;
97	cli2	1290	//cos_phi = 2.0cos_phicos_phi - 1.0;
98	cli2	1275	inversionType_->calcForce(cos_phi, potential_, dVdcosPhi);
99	cli2	1290	Vector3d f1 ;
100			Vector3d f2 ;
101			Vector3d f3 ;
102	cli2	1275
103			Vector3d dcosdA = (cos_phi * A - B) /rA;
104			Vector3d dcosdB = (cos_phi * B - A) /rB;
105
106	cli2	1303	f1 = dVdcosPhi * cross(r43, dcosdA);
107			f2 = dVdcosPhi * ( cross(r23, dcosdB) - cross(r31, dcosdA));
108			f3 = dVdcosPhi * cross(dcosdB, r43);
109	cli2	1275
110			// In OOPSE's version of an improper torsion, the central atom
111			// comes first. However, to get the planarity in a typical cosine
112			// version of this potential (i.e. Amber-style), the central atom
113			// is treated as atom 3 in a standard torsion form:
114
115			// AMBER: I - J - K - L (e.g. K is sp2 hybridized carbon)
116			// OOPSE: I - (J - K - L) (e.g. I is sp2 hybridized carbon)
117
118			// Confusing enough? Good.
119
120	cli2	1290	atom2_->addFrc(f1);
121			atom1_->addFrc(f2 - f1 + f3);
122			atom4_->addFrc(-f2);
123			atom3_->addFrc(-f3);
124
125	cli2	1275	angle = acos(cos_phi) /M_PI * 180.0;
126			}
127
128			}