src/primitives/GhostBend.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/GhostBend.hpp"
#include "primitives/DirectionalAtom.hpp"
namespace oopse {

/**@todo still a lot left to improve*/
void GhostBend::calcForce() {
    DirectionalAtom* ghostAtom = static_cast<DirectionalAtom*>(atom2_);
    
    Vector3d pos1 = atom1_->getPos();
    Vector3d pos2 = ghostAtom->getPos();

    Vector3d r12 = pos1 - pos2;
    double d12 = r12.length();

    double d12inv = 1.0 / d12;

    Vector3d r32 = ghostAtom->getElectroFrame().getColumn(2);
    double d32 = r32.length();

    double d32inv = 1.0 / d32;

    double cosTheta = dot(r12, r32) / (d12 * d32);

    //check roundoff     
    if (cosTheta > 1.0) {
        cosTheta = 1.0;
    } else if (cosTheta < -1.0) {
        cosTheta = -1.0;
    }

    double theta = acos(cosTheta);

    double firstDerivative;

    bendType_->calcForce(theta, firstDerivative, potential_);

    double sinTheta = sqrt(1.0 - cosTheta * cosTheta);

    if (fabs(sinTheta) < 1.0E-12) {
        sinTheta = 1.0E-12;
    }

    double commonFactor1 = -firstDerivative / sinTheta * d12inv;
    double commonFactor2 = -firstDerivative / sinTheta * d32inv;

    Vector3d force1 = commonFactor1*(r12*(d12inv*cosTheta) - r32*d32inv);
    Vector3d force3 = commonFactor2*(r32*(d32inv*cosTheta) - r12*d12inv);
    atom1_->addFrc(force1);
    ghostAtom->addFrc(-force1);
    /**@todo test correctness */
    ghostAtom->addTrq(cross(r32, force3) );

}

} //end namespace oopse

Revision:	1927
Committed:	Wed Jan 12 17:14:35 2005 UTC (20 years, 7 months ago) by tim
File size:	3516 byte(s)
Log Message:	change license
#	User	Rev	Content
1	tim	1927	/*
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	tim	1832	#include "primitives/GhostBend.hpp"
43	tim	1782	#include "primitives/DirectionalAtom.hpp"
44	tim	1748	namespace oopse {
45
46			/*@todo still a lot left to improve/
47	tim	1832	void GhostBend::calcForce() {
48	tim	1782	DirectionalAtom* ghostAtom = static_cast<DirectionalAtom*>(atom2_);
49
50	tim	1748	Vector3d pos1 = atom1_->getPos();
51	tim	1782	Vector3d pos2 = ghostAtom->getPos();
52	tim	1748
53			Vector3d r12 = pos1 - pos2;
54			double d12 = r12.length();
55
56	tim	1782	double d12inv = 1.0 / d12;
57	tim	1748
58	tim	1816	Vector3d r32 = ghostAtom->getElectroFrame().getColumn(2);
59	tim	1748	double d32 = r32.length();
60
61	tim	1782	double d32inv = 1.0 / d32;
62	tim	1748
63	tim	1782	double cosTheta = dot(r12, r32) / (d12 * d32);
64	tim	1748
65			//check roundoff
66			if (cosTheta > 1.0) {
67			cosTheta = 1.0;
68			} else if (cosTheta < -1.0) {
69			cosTheta = -1.0;
70			}
71
72			double theta = acos(cosTheta);
73
74			double firstDerivative;
75
76			bendType_->calcForce(theta, firstDerivative, potential_);
77
78			double sinTheta = sqrt(1.0 - cosTheta * cosTheta);
79
80	tim	1782	if (fabs(sinTheta) < 1.0E-12) {
81			sinTheta = 1.0E-12;
82	tim	1748	}
83
84			double commonFactor1 = -firstDerivative / sinTheta * d12inv;
85			double commonFactor2 = -firstDerivative / sinTheta * d32inv;
86
87			Vector3d force1 = commonFactor1(r12(d12invcosTheta) - r32d32inv);
88	tim	1782	Vector3d force3 = commonFactor2(r32(d32invcosTheta) - r12d12inv);
89	tim	1748	atom1_->addFrc(force1);
90	tim	1782	ghostAtom->addFrc(-force1);
91			/*@todo test correctness /
92			ghostAtom->addTrq(cross(r32, force3) );
93
94			}
95
96	tim	1748	} //end namespace oopse
97	tim	1782