| 36 |
|
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
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* [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 |
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#include "primitives/GhostBend.hpp" |
| 50 |
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|
| 51 |
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Vector3d pos1 = atom1_->getPos(); |
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Vector3d pos2 = ghostAtom->getPos(); |
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+ |
|
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+ |
Vector3d r21 = pos1 - pos2; |
| 55 |
+ |
RealType d21 = r21.length(); |
| 56 |
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|
| 57 |
< |
Vector3d r12 = pos1 - pos2; |
| 58 |
< |
RealType d12 = r12.length(); |
| 57 |
> |
RealType d21inv = 1.0 / d21; |
| 58 |
> |
|
| 59 |
> |
// we need the transpose of A to get the lab fixed vector: |
| 60 |
> |
Vector3d r23 = ghostAtom->getA().transpose().getColumn(2); |
| 61 |
> |
RealType d23 = r23.length(); |
| 62 |
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|
| 63 |
< |
RealType d12inv = 1.0 / d12; |
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> |
RealType d23inv = 1.0 / d23; |
| 64 |
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|
| 65 |
< |
Vector3d r32 = ghostAtom->getElectroFrame().getColumn(2); |
| 66 |
< |
RealType d32 = r32.length(); |
| 60 |
< |
|
| 61 |
< |
RealType d32inv = 1.0 / d32; |
| 62 |
< |
|
| 63 |
< |
RealType cosTheta = dot(r12, r32) / (d12 * d32); |
| 64 |
< |
|
| 65 |
> |
RealType cosTheta = dot(r21, r23) / (d21 * d23); |
| 66 |
> |
|
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//check roundoff |
| 68 |
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if (cosTheta > 1.0) { |
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cosTheta = 1.0; |
| 72 |
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} |
| 73 |
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|
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RealType theta = acos(cosTheta); |
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+ |
|
| 76 |
+ |
RealType dVdTheta; |
| 77 |
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|
| 78 |
< |
RealType firstDerivative; |
| 78 |
> |
bendType_->calcForce(theta, potential_, dVdTheta); |
| 79 |
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|
| 76 |
– |
bendType_->calcForce(theta, potential_, firstDerivative); |
| 77 |
– |
|
| 80 |
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RealType sinTheta = sqrt(1.0 - cosTheta * cosTheta); |
| 81 |
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|
| 82 |
< |
if (fabs(sinTheta) < 1.0E-12) { |
| 83 |
< |
sinTheta = 1.0E-12; |
| 82 |
> |
if (fabs(sinTheta) < 1.0E-6) { |
| 83 |
> |
sinTheta = 1.0E-6; |
| 84 |
|
} |
| 85 |
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|
| 86 |
< |
RealType commonFactor1 = -firstDerivative / sinTheta * d12inv; |
| 87 |
< |
RealType commonFactor2 = -firstDerivative / sinTheta * d32inv; |
| 86 |
> |
RealType commonFactor1 = dVdTheta / sinTheta * d21inv; |
| 87 |
> |
RealType commonFactor2 = dVdTheta / sinTheta * d23inv; |
| 88 |
|
|
| 89 |
< |
Vector3d force1 = commonFactor1*(r12*(d12inv*cosTheta) - r32*d32inv); |
| 90 |
< |
Vector3d force3 = commonFactor2*(r32*(d32inv*cosTheta) - r12*d12inv); |
| 89 |
> |
Vector3d force1 = commonFactor1 * (r23 * d23inv - r21*d21inv*cosTheta); |
| 90 |
> |
Vector3d force3 = commonFactor2 * (r21 * d21inv - r23*d23inv*cosTheta); |
| 91 |
> |
|
| 92 |
> |
// Total force in current bend is zero |
| 93 |
> |
|
| 94 |
|
atom1_->addFrc(force1); |
| 95 |
|
ghostAtom->addFrc(-force1); |
| 91 |
– |
/**@todo test correctness */ |
| 92 |
– |
ghostAtom->addTrq(cross(r32, force3) ); |
| 96 |
|
|
| 97 |
+ |
ghostAtom->addTrq( cross(r23, force3) ); |
| 98 |
+ |
|
| 99 |
|
atom1_->addParticlePot(potential_); |
| 100 |
|
ghostAtom->addParticlePot(potential_); |
| 101 |
|
|
| 102 |
|
angle = theta /M_PI * 180.0; |
| 103 |
< |
|
| 103 |
> |
|
| 104 |
|
} |
| 105 |
|
} //end namespace OpenMD |
| 106 |
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