| 6 |
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* 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 |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 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. |
| 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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
#include "primitives/GhostTorsion.hpp" |
| 44 |
|
|
| 45 |
< |
namespace oopse { |
| 46 |
< |
|
| 47 |
< |
GhostTorsion::GhostTorsion(Atom *atom1, Atom *atom2, DirectionalAtom* ghostAtom, |
| 48 |
< |
TorsionType *tt) : Torsion(atom1, atom2, ghostAtom, ghostAtom, tt) {} |
| 49 |
< |
|
| 45 |
> |
namespace OpenMD { |
| 46 |
> |
|
| 47 |
> |
GhostTorsion::GhostTorsion(Atom *atom1, Atom *atom2, |
| 48 |
> |
DirectionalAtom* ghostAtom, TorsionType *tt) |
| 49 |
> |
: Torsion(atom1, atom2, ghostAtom, ghostAtom, tt) {} |
| 50 |
> |
|
| 51 |
|
void GhostTorsion::calcForce(RealType& angle) { |
| 52 |
|
DirectionalAtom* ghostAtom = static_cast<DirectionalAtom*>(atom3_); |
| 53 |
< |
|
| 53 |
> |
|
| 54 |
|
Vector3d pos1 = atom1_->getPos(); |
| 55 |
|
Vector3d pos2 = atom2_->getPos(); |
| 56 |
|
Vector3d pos3 = ghostAtom->getPos(); |
| 57 |
< |
|
| 57 |
> |
|
| 58 |
|
Vector3d r21 = pos1 - pos2; |
| 59 |
|
Vector3d r32 = pos2 - pos3; |
| 60 |
< |
Vector3d r43 = ghostAtom->getElectroFrame().getColumn(2); |
| 61 |
< |
|
| 60 |
> |
Vector3d r43 = ghostAtom->getA().transpose().getColumn(2); |
| 61 |
> |
|
| 62 |
|
// Calculate the cross products and distances |
| 63 |
|
Vector3d A = cross(r21, r32); |
| 64 |
|
RealType rA = A.length(); |
| 65 |
|
Vector3d B = cross(r32, r43); |
| 66 |
|
RealType rB = B.length(); |
| 65 |
– |
Vector3d C = cross(r32, A); |
| 66 |
– |
RealType rC = C.length(); |
| 67 |
|
|
| 68 |
+ |
/* |
| 69 |
+ |
If either of the two cross product vectors is tiny, that means |
| 70 |
+ |
the three atoms involved are colinear, and the torsion angle is |
| 71 |
+ |
going to be undefined. The easiest check for this problem is |
| 72 |
+ |
to use the product of the two lengths. |
| 73 |
+ |
*/ |
| 74 |
+ |
if (rA * rB < OpenMD::epsilon) return; |
| 75 |
+ |
|
| 76 |
|
A.normalize(); |
| 77 |
|
B.normalize(); |
| 70 |
– |
C.normalize(); |
| 78 |
|
|
| 79 |
|
// Calculate the sin and cos |
| 80 |
|
RealType cos_phi = dot(A, B) ; |
| 81 |
< |
|
| 81 |
> |
|
| 82 |
|
RealType dVdcosPhi; |
| 83 |
|
torsionType_->calcForce(cos_phi, potential_, dVdcosPhi); |
| 84 |
< |
|
| 84 |
> |
|
| 85 |
|
Vector3d dcosdA = (cos_phi * A - B) /rA; |
| 86 |
|
Vector3d dcosdB = (cos_phi * B - A) /rB; |
| 87 |
< |
|
| 87 |
> |
|
| 88 |
|
Vector3d f1 = dVdcosPhi * cross(r32, dcosdA); |
| 89 |
|
Vector3d f2 = dVdcosPhi * ( cross(r43, dcosdB) - cross(r21, dcosdA)); |
| 90 |
|
Vector3d f3 = dVdcosPhi * cross(dcosdB, r32); |
| 91 |
< |
|
| 91 |
> |
|
| 92 |
|
atom1_->addFrc(f1); |
| 93 |
|
atom2_->addFrc(f2 - f1); |
| 94 |
< |
|
| 94 |
> |
|
| 95 |
|
ghostAtom->addFrc(-f2); |
| 96 |
< |
|
| 96 |
> |
|
| 97 |
|
f3.negate(); |
| 98 |
|
ghostAtom->addTrq(cross(r43, f3)); |
| 99 |
+ |
|
| 100 |
+ |
atom1_->addParticlePot(potential_); |
| 101 |
+ |
atom2_->addParticlePot(potential_); |
| 102 |
+ |
ghostAtom->addParticlePot(potential_); |
| 103 |
|
|
| 104 |
|
angle = acos(cos_phi) /M_PI * 180.0; |
| 105 |
|
} |
| 95 |
– |
|
| 106 |
|
} |
| 107 |
|
|
