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. 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, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
 
#include "primitives/GhostBend.hpp"
#include "primitives/DirectionalAtom.hpp"
namespace OpenMD {

  /**@todo still a lot left to improve*/
  void GhostBend::calcForce(RealType& angle) {
    DirectionalAtom* ghostAtom = static_cast<DirectionalAtom*>(atom2_);
    
    Vector3d pos1 = atom1_->getPos();
    Vector3d pos2 = ghostAtom->getPos();
    
    Vector3d r12 = pos1 - pos2;
    RealType d12 = r12.length();
    
    RealType d12inv = 1.0 / d12;
    
    Vector3d r32 = ghostAtom->getElectroFrame().getColumn(2);
    RealType d32 = r32.length();
    
    RealType d32inv = 1.0 / d32;
    
    RealType cosTheta = dot(r12, r32) / (d12 * d32);
    
    //check roundoff     
    if (cosTheta > 1.0) {
      cosTheta = 1.0;
    } else if (cosTheta < -1.0) {
      cosTheta = -1.0;
    }
    
    RealType theta = acos(cosTheta);
    
    RealType firstDerivative;
    
    bendType_->calcForce(theta, potential_, firstDerivative);
    
    RealType sinTheta = sqrt(1.0 - cosTheta * cosTheta);
    
    if (fabs(sinTheta) < 1.0E-12) {
      sinTheta = 1.0E-12;
    }
    
    RealType commonFactor1 = -firstDerivative / sinTheta * d12inv;
    RealType 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) );    

    atom1_->addParticlePot(potential_);
    ghostAtom->addParticlePot(potential_);

    angle = theta /M_PI * 180.0;
    
  }  
} //end namespace OpenMD

Revision:	1390
Committed:	Wed Nov 25 20:02:06 2009 UTC (15 years, 5 months ago) by gezelter
Original Path:	*trunk/src/primitives/GhostBend.cpp*
File size:	3772 byte(s)
Log Message:	Almost all of the changes necessary to create OpenMD out of our old project (OOPSE-4)
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* 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			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39			* [4] Vardeman & Gezelter, in progress (2009).
40	gezelter	246	*/
41
42			#include "primitives/GhostBend.hpp"
43			#include "primitives/DirectionalAtom.hpp"
44	gezelter	1390	namespace OpenMD {
45	gezelter	2
46	gezelter	507	/*@todo still a lot left to improve/
47	tim	963	void GhostBend::calcForce(RealType& angle) {
48	gezelter	246	DirectionalAtom* ghostAtom = static_cast<DirectionalAtom*>(atom2_);
49	gezelter	2
50	gezelter	246	Vector3d pos1 = atom1_->getPos();
51			Vector3d pos2 = ghostAtom->getPos();
52	gezelter	1211
53	gezelter	246	Vector3d r12 = pos1 - pos2;
54	tim	963	RealType d12 = r12.length();
55	gezelter	1211
56	tim	963	RealType d12inv = 1.0 / d12;
57	gezelter	1211
58	gezelter	246	Vector3d r32 = ghostAtom->getElectroFrame().getColumn(2);
59	tim	963	RealType d32 = r32.length();
60	gezelter	1211
61	tim	963	RealType d32inv = 1.0 / d32;
62	gezelter	1211
63	tim	963	RealType cosTheta = dot(r12, r32) / (d12 * d32);
64	gezelter	1211
65	gezelter	246	//check roundoff
66			if (cosTheta > 1.0) {
67	gezelter	507	cosTheta = 1.0;
68	gezelter	246	} else if (cosTheta < -1.0) {
69	gezelter	507	cosTheta = -1.0;
70	gezelter	246	}
71	gezelter	1211
72	tim	963	RealType theta = acos(cosTheta);
73	gezelter	1211
74	tim	963	RealType firstDerivative;
75	gezelter	1211
76	gezelter	1309	bendType_->calcForce(theta, potential_, firstDerivative);
77	gezelter	1211
78	tim	963	RealType sinTheta = sqrt(1.0 - cosTheta * cosTheta);
79	gezelter	1211
80	gezelter	246	if (fabs(sinTheta) < 1.0E-12) {
81	gezelter	507	sinTheta = 1.0E-12;
82	gezelter	246	}
83	gezelter	1211
84	tim	963	RealType commonFactor1 = -firstDerivative / sinTheta * d12inv;
85			RealType commonFactor2 = -firstDerivative / sinTheta * d32inv;
86	gezelter	1211
87	gezelter	246	Vector3d force1 = commonFactor1(r12(d12invcosTheta) - r32d32inv);
88			Vector3d force3 = commonFactor2(r32(d32invcosTheta) - r12d12inv);
89			atom1_->addFrc(force1);
90			ghostAtom->addFrc(-force1);
91			/*@todo test correctness /
92	gezelter	1309	ghostAtom->addTrq(cross(r32, force3) );
93
94			atom1_->addParticlePot(potential_);
95			ghostAtom->addParticlePot(potential_);
96
97	tim	749	angle = theta /M_PI * 180.0;
98	gezelter	1211
99			}
100	gezelter	1390	} //end namespace OpenMD
101	gezelter	2