| 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. Acknowledgement of the program authors must be made in any |
| 10 |
* publication of scientific results based in part on use of the |
| 11 |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
* the article in which the program was described (Matthew |
| 13 |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
* |
| 18 |
* 2. Redistributions of source code must retain the above copyright |
| 19 |
* notice, this list of conditions and the following disclaimer. |
| 20 |
* |
| 21 |
* 3. Redistributions in binary form must reproduce the above copyright |
| 22 |
* notice, this list of conditions and the following disclaimer in the |
| 23 |
* documentation and/or other materials provided with the |
| 24 |
* distribution. |
| 25 |
* |
| 26 |
* This software is provided "AS IS," without a warranty of any |
| 27 |
* kind. All express or implied conditions, representations and |
| 28 |
* warranties, including any implied warranty of merchantability, |
| 29 |
* fitness for a particular purpose or non-infringement, are hereby |
| 30 |
* excluded. The University of Notre Dame and its licensors shall not |
| 31 |
* be liable for any damages suffered by licensee as a result of |
| 32 |
* using, modifying or distributing the software or its |
| 33 |
* derivatives. In no event will the University of Notre Dame or its |
| 34 |
* licensors be liable for any lost revenue, profit or data, or for |
| 35 |
* direct, indirect, special, consequential, incidental or punitive |
| 36 |
* damages, however caused and regardless of the theory of liability, |
| 37 |
* arising out of the use of or inability to use software, even if the |
| 38 |
* University of Notre Dame has been advised of the possibility of |
| 39 |
* such damages. |
| 40 |
*/ |
| 41 |
|
| 42 |
#include "primitives/GhostTorsion.hpp" |
| 43 |
|
| 44 |
namespace oopse { |
| 45 |
|
| 46 |
GhostTorsion::GhostTorsion(Atom *atom1, Atom *atom2, DirectionalAtom* ghostAtom, |
| 47 |
TorsionType *tt) : Torsion(atom1, atom2, ghostAtom, ghostAtom, tt) {} |
| 48 |
|
| 49 |
void GhostTorsion::calcForce() { |
| 50 |
DirectionalAtom* ghostAtom = static_cast<DirectionalAtom*>(atom3_); |
| 51 |
|
| 52 |
Vector3d pos1 = atom1_->getPos(); |
| 53 |
Vector3d pos2 = atom2_->getPos(); |
| 54 |
Vector3d pos3 = ghostAtom->getPos(); |
| 55 |
|
| 56 |
Vector3d r21 = pos1 - pos2; |
| 57 |
Vector3d r32 = pos2 - pos3; |
| 58 |
Vector3d r43 = ghostAtom->getElectroFrame().getColumn(2); |
| 59 |
|
| 60 |
// Calculate the cross products and distances |
| 61 |
Vector3d A = cross(r21, r32); |
| 62 |
double rA = A.length(); |
| 63 |
Vector3d B = cross(r32, r43); |
| 64 |
double rB = B.length(); |
| 65 |
Vector3d C = cross(r32, A); |
| 66 |
double rC = C.length(); |
| 67 |
|
| 68 |
A.normalize(); |
| 69 |
B.normalize(); |
| 70 |
C.normalize(); |
| 71 |
|
| 72 |
// Calculate the sin and cos |
| 73 |
double cos_phi = dot(A, B) ; |
| 74 |
double sin_phi = dot(C, B); |
| 75 |
|
| 76 |
double dVdPhi; |
| 77 |
torsionType_->calcForce(cos_phi, sin_phi, potential_, dVdPhi); |
| 78 |
|
| 79 |
Vector3d dcosdA = (cos_phi * A - B) /rA; |
| 80 |
Vector3d dcosdB = (cos_phi * B - A) /rB; |
| 81 |
|
| 82 |
double dVdcosPhi = -dVdPhi / sin_phi; |
| 83 |
|
| 84 |
Vector3d f1 = dVdcosPhi * cross(r32, dcosdA); |
| 85 |
Vector3d f2 = dVdcosPhi * ( cross(r43, dcosdB) - cross(r21, dcosdA)); |
| 86 |
Vector3d f3 = dVdcosPhi * cross(dcosdB, r32); |
| 87 |
|
| 88 |
atom1_->addFrc(f1); |
| 89 |
atom2_->addFrc(f2 - f1); |
| 90 |
|
| 91 |
ghostAtom->addFrc(-f2); |
| 92 |
|
| 93 |
f3.negate(); |
| 94 |
ghostAtom->addTrq(cross(r43, f3)); |
| 95 |
} |
| 96 |
|
| 97 |
} |
| 98 |
|
