src/primitives/GhostTorsion.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/GhostTorsion.hpp"

namespace oopse {

  GhostTorsion::GhostTorsion(Atom *atom1, Atom *atom2,  DirectionalAtom* ghostAtom,
                             TorsionType *tt) : Torsion(atom1, atom2, ghostAtom, ghostAtom, tt) {}

  void GhostTorsion::calcForce(RealType& angle) {
    DirectionalAtom* ghostAtom = static_cast<DirectionalAtom*>(atom3_);    

    Vector3d pos1 = atom1_->getPos();
    Vector3d pos2 = atom2_->getPos();
    Vector3d pos3 = ghostAtom->getPos();

    Vector3d r21 = pos1 - pos2;
    Vector3d r32 = pos2 - pos3;
    Vector3d r43 = ghostAtom->getElectroFrame().getColumn(2);

    //  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) ;

    RealType dVdcosPhi;
    torsionType_->calcForce(cos_phi, potential_, dVdcosPhi);

    Vector3d dcosdA = (cos_phi * A - B) /rA;
    Vector3d dcosdB = (cos_phi * B - A) /rB;

    Vector3d f1 = dVdcosPhi * cross(r32, dcosdA);
    Vector3d f2 = dVdcosPhi * ( cross(r43, dcosdB) - cross(r21, dcosdA));
    Vector3d f3 = dVdcosPhi * cross(dcosdB, r32);

    atom1_->addFrc(f1);
    atom2_->addFrc(f2 - f1);

    ghostAtom->addFrc(-f2);

    f3.negate();
    ghostAtom->addTrq(cross(r43, f3));    

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

}

Revision:	2759
Committed:	Wed May 17 21:51:42 2006 UTC (18 years, 1 month ago) by tim
File size:	3589 byte(s)
Log Message:	Adding single precision capabilities to c++ side
#	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. 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/GhostTorsion.hpp"
43
44	namespace oopse {
45
46	GhostTorsion::GhostTorsion(Atom atom1, Atom atom2, DirectionalAtom* ghostAtom,
47	TorsionType *tt) : Torsion(atom1, atom2, ghostAtom, ghostAtom, tt) {}
48
49	void GhostTorsion::calcForce(RealType& angle) {
50	DirectionalAtom* ghostAtom = static_cast<DirectionalAtom*>(atom3_);
51
52	Vector3d pos1 = atom1_->getPos();
53	Vector3d pos2 = atom2_->getPos();
54	Vector3d pos3 = ghostAtom->getPos();
55
56	Vector3d r21 = pos1 - pos2;
57	Vector3d r32 = pos2 - pos3;
58	Vector3d r43 = ghostAtom->getElectroFrame().getColumn(2);
59
60	// Calculate the cross products and distances
61	Vector3d A = cross(r21, r32);
62	RealType rA = A.length();
63	Vector3d B = cross(r32, r43);
64	RealType rB = B.length();
65	Vector3d C = cross(r32, A);
66	RealType rC = C.length();
67
68	A.normalize();
69	B.normalize();
70	C.normalize();
71
72	// Calculate the sin and cos
73	RealType cos_phi = dot(A, B) ;
74
75	RealType dVdcosPhi;
76	torsionType_->calcForce(cos_phi, potential_, dVdcosPhi);
77
78	Vector3d dcosdA = (cos_phi * A - B) /rA;
79	Vector3d dcosdB = (cos_phi * B - A) /rB;
80
81	Vector3d f1 = dVdcosPhi * cross(r32, dcosdA);
82	Vector3d f2 = dVdcosPhi * ( cross(r43, dcosdB) - cross(r21, dcosdA));
83	Vector3d f3 = dVdcosPhi * cross(dcosdB, r32);
84
85	atom1_->addFrc(f1);
86	atom2_->addFrc(f2 - f1);
87
88	ghostAtom->addFrc(-f2);
89
90	f3.negate();
91	ghostAtom->addTrq(cross(r43, f3));
92
93	angle = acos(cos_phi) /M_PI * 180.0;
94	}
95
96	}
97