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, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#include "config.h"
#include <cmath>
#include "primitives/GhostBend.hpp"
#include "primitives/DirectionalAtom.hpp"
namespace OpenMD {

  /**@todo still a lot left to improve*/
  void GhostBend::calcForce(RealType& angle, bool doParticlePot) {
    DirectionalAtom* ghostAtom = static_cast<DirectionalAtom*>(atoms_[1]);
    
    Vector3d pos1 = atoms_[0]->getPos();
    Vector3d pos2 = ghostAtom->getPos();

    Vector3d r21 = pos1 - pos2;   
    RealType d21 = r21.length();
    
    RealType d21inv = 1.0 / d21;
   
    // we need the transpose of A to get the lab fixed vector:
    Vector3d r23 = ghostAtom->getA().transpose().getColumn(2);
    RealType d23 = r23.length();
    
    RealType d23inv = 1.0 / d23;
    
    RealType cosTheta = dot(r21, r23) / (d21 * d23);

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

    RealType dVdTheta;
    
    bendType_->calcForce(theta, potential_, dVdTheta);
    
    RealType sinTheta = sqrt(1.0 - cosTheta * cosTheta);
    
    if (fabs(sinTheta) < 1.0E-6) {
      sinTheta = 1.0E-6;
    }
    
    RealType commonFactor1 = dVdTheta / sinTheta * d21inv;
    RealType commonFactor2 = dVdTheta / sinTheta * d23inv;
    
    Vector3d force1 = commonFactor1 * (r23 * d23inv - r21*d21inv*cosTheta);
    Vector3d force3 = commonFactor2 * (r21 * d21inv - r23*d23inv*cosTheta);

    // Total force in current bend is zero

    atoms_[0]->addFrc(force1);
    ghostAtom->addFrc(-force1);

    ghostAtom->addTrq( cross(r23, force3) );    
    if(doParticlePot) {
      atoms_[0]->addParticlePot(potential_);
      ghostAtom->addParticlePot(potential_);
    }

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

Revision:	1953
Committed:	Thu Dec 5 18:19:26 2013 UTC (11 years, 10 months ago) by gezelter
File size:	3980 byte(s)
Log Message:	Rewrote much of selection module, added a bond correlation function
#	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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1782	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43	gezelter	1782	#include "config.h"
44			#include <cmath>
45	gezelter	246	#include "primitives/GhostBend.hpp"
46			#include "primitives/DirectionalAtom.hpp"
47	gezelter	1390	namespace OpenMD {
48	gezelter	2
49	gezelter	507	/*@todo still a lot left to improve/
50	gezelter	1782	void GhostBend::calcForce(RealType& angle, bool doParticlePot) {
51	gezelter	1953	DirectionalAtom* ghostAtom = static_cast<DirectionalAtom*>(atoms_[1]);
52	gezelter	2
53	gezelter	1953	Vector3d pos1 = atoms_[0]->getPos();
54	gezelter	246	Vector3d pos2 = ghostAtom->getPos();
55	gezelter	1459
56			Vector3d r21 = pos1 - pos2;
57			RealType d21 = r21.length();
58	gezelter	1211
59	gezelter	1459	RealType d21inv = 1.0 / d21;
60	gezelter	1443
61	gezelter	1459	// we need the transpose of A to get the lab fixed vector:
62			Vector3d r23 = ghostAtom->getA().transpose().getColumn(2);
63			RealType d23 = r23.length();
64	gezelter	1211
65	gezelter	1459	RealType d23inv = 1.0 / d23;
66	gezelter	1211
67	gezelter	1459	RealType cosTheta = dot(r21, r23) / (d21 * d23);
68
69	gezelter	246	//check roundoff
70			if (cosTheta > 1.0) {
71	gezelter	507	cosTheta = 1.0;
72	gezelter	246	} else if (cosTheta < -1.0) {
73	gezelter	507	cosTheta = -1.0;
74	gezelter	246	}
75	gezelter	1211
76	tim	963	RealType theta = acos(cosTheta);
77	gezelter	1459
78			RealType dVdTheta;
79	gezelter	1211
80	gezelter	1459	bendType_->calcForce(theta, potential_, dVdTheta);
81	gezelter	1211
82	tim	963	RealType sinTheta = sqrt(1.0 - cosTheta * cosTheta);
83	gezelter	1211
84	gezelter	1459	if (fabs(sinTheta) < 1.0E-6) {
85			sinTheta = 1.0E-6;
86	gezelter	246	}
87	gezelter	1211
88	gezelter	1459	RealType commonFactor1 = dVdTheta / sinTheta * d21inv;
89			RealType commonFactor2 = dVdTheta / sinTheta * d23inv;
90	gezelter	1211
91	gezelter	1459	Vector3d force1 = commonFactor1 * (r23 * d23inv - r21d21invcosTheta);
92			Vector3d force3 = commonFactor2 * (r21 * d21inv - r23d23invcosTheta);
93
94			// Total force in current bend is zero
95
96	gezelter	1953	atoms_[0]->addFrc(force1);
97	gezelter	246	ghostAtom->addFrc(-force1);
98	gezelter	1309
99	gezelter	1459	ghostAtom->addTrq( cross(r23, force3) );
100	gezelter	1782	if(doParticlePot) {
101	gezelter	1953	atoms_[0]->addParticlePot(potential_);
102	gezelter	1782	ghostAtom->addParticlePot(potential_);
103			}
104	gezelter	1459
105	tim	749	angle = theta /M_PI * 180.0;
106	gezelter	1459
107	gezelter	1211	}
108	gezelter	1390	} //end namespace OpenMD
109	gezelter	2