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->getA().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:	1443
Committed:	Thu May 27 14:17:39 2010 UTC (14 years, 11 months ago) by gezelter
Original Path:	*trunk/src/primitives/GhostBend.cpp*
File size:	3760 byte(s)
Log Message:	Fixed a potential bug. If Ghost atoms have no electroFrame (i.e. if they are DirectionalAtoms, but not dipoles), the GhostBend and GhostTorsions would give nans. We should be using getA instead of getElectroFrame.
#	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	1443
58			Vector3d r32 = ghostAtom->getA().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