| 1 |
/* |
| 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. Redistributions of source code must retain the above copyright |
| 10 |
* notice, this list of conditions and the following disclaimer. |
| 11 |
* |
| 12 |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
* 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 |
* |
| 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 |
*/ |
| 41 |
|
| 42 |
#include "primitives/Bend.hpp" |
| 43 |
|
| 44 |
namespace OpenMD { |
| 45 |
|
| 46 |
/**@todo still a lot left to improve*/ |
| 47 |
void Bend::calcForce(RealType& angle) { |
| 48 |
Vector3d pos1 = atom1_->getPos(); |
| 49 |
Vector3d pos2 = atom2_->getPos(); |
| 50 |
Vector3d pos3 = atom3_->getPos(); |
| 51 |
|
| 52 |
Vector3d r21 = pos1 - pos2; |
| 53 |
RealType d21 = r21.length(); |
| 54 |
|
| 55 |
RealType d21inv = 1.0 / d21; |
| 56 |
|
| 57 |
Vector3d r23 = pos3 - pos2; |
| 58 |
RealType d23 = r23.length(); |
| 59 |
|
| 60 |
RealType d23inv = 1.0 / d23; |
| 61 |
|
| 62 |
RealType cosTheta = dot(r21, r23) / (d21 * d23); |
| 63 |
|
| 64 |
//check roundoff |
| 65 |
if (cosTheta > 1.0) { |
| 66 |
cosTheta = 1.0; |
| 67 |
} else if (cosTheta < -1.0) { |
| 68 |
cosTheta = -1.0; |
| 69 |
} |
| 70 |
|
| 71 |
RealType theta = acos(cosTheta); |
| 72 |
|
| 73 |
RealType dVdTheta; |
| 74 |
|
| 75 |
bendType_->calcForce(theta, potential_, dVdTheta); |
| 76 |
|
| 77 |
RealType sinTheta = sqrt(1.0 - cosTheta * cosTheta); |
| 78 |
|
| 79 |
if (fabs(sinTheta) < 1.0E-6) { |
| 80 |
sinTheta = 1.0E-6; |
| 81 |
} |
| 82 |
|
| 83 |
RealType commonFactor1 = dVdTheta / sinTheta * d21inv; |
| 84 |
RealType commonFactor2 = dVdTheta / sinTheta * d23inv; |
| 85 |
|
| 86 |
Vector3d force1 = commonFactor1 * (r23 * d23inv - r21*d21inv*cosTheta); |
| 87 |
Vector3d force3 = commonFactor2 * (r21 * d21inv - r23*d23inv*cosTheta); |
| 88 |
|
| 89 |
// Total force in current bend is zero |
| 90 |
Vector3d force2 = force1 + force3; |
| 91 |
force2 *= -1.0; |
| 92 |
|
| 93 |
atom1_->addFrc(force1); |
| 94 |
atom2_->addFrc(force2); |
| 95 |
atom3_->addFrc(force3); |
| 96 |
|
| 97 |
atom1_->addParticlePot(potential_); |
| 98 |
atom2_->addParticlePot(potential_); |
| 99 |
atom3_->addParticlePot(potential_); |
| 100 |
|
| 101 |
angle = theta /M_PI * 180.0; |
| 102 |
} |
| 103 |
|
| 104 |
} //end namespace OpenMD |
