src/primitives/Bend.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/Bend.hpp"

namespace OpenMD {
  
  /**@todo still a lot left to improve*/
  void Bend::calcForce(RealType& angle) {
    Vector3d pos1 = atom1_->getPos();
    Vector3d pos2 = atom2_->getPos();
    Vector3d pos3 = atom3_->getPos();
    
    Vector3d r21 = pos1 - pos2;
    RealType d21 = r21.length();
    
    RealType d21inv = 1.0 / d21;
    
    Vector3d r23 = pos3 - pos2;
    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
    Vector3d force2 = force1 + force3;
    force2 *= -1.0;
    
    atom1_->addFrc(force1);
    atom2_->addFrc(force2);
    atom3_->addFrc(force3);

    atom1_->addParticlePot(potential_);
    atom2_->addParticlePot(potential_);
    atom3_->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/Bend.cpp*
File size:	3703 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	gezelter	2
42	gezelter	246	#include "primitives/Bend.hpp"
43	gezelter	2
44	gezelter	1390	namespace OpenMD {
45	gezelter	1211
46	gezelter	507	/*@todo still a lot left to improve/
47	tim	963	void Bend::calcForce(RealType& angle) {
48	gezelter	246	Vector3d pos1 = atom1_->getPos();
49			Vector3d pos2 = atom2_->getPos();
50			Vector3d pos3 = atom3_->getPos();
51	gezelter	1211
52	gezelter	246	Vector3d r21 = pos1 - pos2;
53	tim	963	RealType d21 = r21.length();
54	gezelter	1211
55	tim	963	RealType d21inv = 1.0 / d21;
56	gezelter	1211
57	gezelter	246	Vector3d r23 = pos3 - pos2;
58	tim	963	RealType d23 = r23.length();
59	gezelter	1211
60	tim	963	RealType d23inv = 1.0 / d23;
61	gezelter	1211
62	tim	963	RealType cosTheta = dot(r21, r23) / (d21 * d23);
63	gezelter	1211
64	gezelter	246	//check roundoff
65			if (cosTheta > 1.0) {
66	gezelter	507	cosTheta = 1.0;
67	gezelter	246	} else if (cosTheta < -1.0) {
68	gezelter	507	cosTheta = -1.0;
69	gezelter	246	}
70	gezelter	1211
71	tim	963	RealType theta = acos(cosTheta);
72	gezelter	1211
73	tim	963	RealType dVdTheta;
74	gezelter	2
75	gezelter	246	bendType_->calcForce(theta, potential_, dVdTheta);
76	gezelter	1211
77	tim	963	RealType sinTheta = sqrt(1.0 - cosTheta * cosTheta);
78	gezelter	1211
79	gezelter	246	if (fabs(sinTheta) < 1.0E-6) {
80	gezelter	507	sinTheta = 1.0E-6;
81	gezelter	246	}
82	gezelter	1211
83	tim	963	RealType commonFactor1 = dVdTheta / sinTheta * d21inv;
84			RealType commonFactor2 = dVdTheta / sinTheta * d23inv;
85	gezelter	1211
86	gezelter	246	Vector3d force1 = commonFactor1 * (r23 * d23inv - r21d21invcosTheta);
87			Vector3d force3 = commonFactor2 * (r21 * d21inv - r23d23invcosTheta);
88	gezelter	2
89	gezelter	1211	// Total force in current bend is zero
90	gezelter	246	Vector3d force2 = force1 + force3;
91			force2 *= -1.0;
92	gezelter	1211
93	gezelter	246	atom1_->addFrc(force1);
94			atom2_->addFrc(force2);
95			atom3_->addFrc(force3);
96	gezelter	1309
97			atom1_->addParticlePot(potential_);
98			atom2_->addParticlePot(potential_);
99			atom3_->addParticlePot(potential_);
100
101	tim	749	angle = theta /M_PI * 180.0;
102	gezelter	507	}
103	gezelter	246
104	gezelter	1390	} //end namespace OpenMD