| 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). |
| 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 "config.h" |
| 44 |
+ |
#include <cmath> |
| 45 |
+ |
|
| 46 |
|
#include "primitives/GhostTorsion.hpp" |
| 47 |
|
|
| 48 |
|
namespace OpenMD { |
| 51 |
|
DirectionalAtom* ghostAtom, TorsionType *tt) |
| 52 |
|
: Torsion(atom1, atom2, ghostAtom, ghostAtom, tt) {} |
| 53 |
|
|
| 54 |
< |
void GhostTorsion::calcForce(RealType& angle) { |
| 54 |
> |
void GhostTorsion::calcForce(RealType& angle, bool doParticlePot) { |
| 55 |
|
DirectionalAtom* ghostAtom = static_cast<DirectionalAtom*>(atom3_); |
| 56 |
|
|
| 57 |
|
Vector3d pos1 = atom1_->getPos(); |
| 60 |
|
|
| 61 |
|
Vector3d r21 = pos1 - pos2; |
| 62 |
|
Vector3d r32 = pos2 - pos3; |
| 63 |
< |
Vector3d r43 = ghostAtom->getElectroFrame().getColumn(2); |
| 63 |
> |
Vector3d r43 = ghostAtom->getA().transpose().getColumn(2); |
| 64 |
|
|
| 65 |
|
// Calculate the cross products and distances |
| 66 |
|
Vector3d A = cross(r21, r32); |
| 67 |
|
RealType rA = A.length(); |
| 68 |
|
Vector3d B = cross(r32, r43); |
| 69 |
|
RealType rB = B.length(); |
| 70 |
< |
Vector3d C = cross(r32, A); |
| 71 |
< |
RealType rC = C.length(); |
| 70 |
> |
|
| 71 |
> |
/* |
| 72 |
> |
If either of the two cross product vectors is tiny, that means |
| 73 |
> |
the three atoms involved are colinear, and the torsion angle is |
| 74 |
> |
going to be undefined. The easiest check for this problem is |
| 75 |
> |
to use the product of the two lengths. |
| 76 |
> |
*/ |
| 77 |
> |
if (rA * rB < OpenMD::epsilon) return; |
| 78 |
|
|
| 79 |
|
A.normalize(); |
| 80 |
|
B.normalize(); |
| 71 |
– |
C.normalize(); |
| 81 |
|
|
| 82 |
|
// Calculate the sin and cos |
| 83 |
|
RealType cos_phi = dot(A, B) ; |
| 100 |
|
f3.negate(); |
| 101 |
|
ghostAtom->addTrq(cross(r43, f3)); |
| 102 |
|
|
| 103 |
< |
atom1_->addParticlePot(potential_); |
| 104 |
< |
atom2_->addParticlePot(potential_); |
| 105 |
< |
ghostAtom->addParticlePot(potential_); |
| 103 |
> |
if (doParticlePot) { |
| 104 |
> |
atom1_->addParticlePot(potential_); |
| 105 |
> |
atom2_->addParticlePot(potential_); |
| 106 |
> |
ghostAtom->addParticlePot(potential_); |
| 107 |
> |
} |
| 108 |
|
|
| 109 |
|
angle = acos(cos_phi) /M_PI * 180.0; |
| 110 |
|
} |
