| 49 |
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| 50 |
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Vector3d pos1 = atom1_->getPos(); |
| 51 |
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Vector3d pos2 = ghostAtom->getPos(); |
| 52 |
< |
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| 52 |
> |
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| 53 |
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Vector3d r12 = pos1 - pos2; |
| 54 |
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RealType d12 = r12.length(); |
| 55 |
< |
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| 55 |
> |
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| 56 |
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RealType d12inv = 1.0 / d12; |
| 57 |
< |
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| 57 |
> |
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| 58 |
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Vector3d r32 = ghostAtom->getElectroFrame().getColumn(2); |
| 59 |
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RealType d32 = r32.length(); |
| 60 |
< |
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| 60 |
> |
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| 61 |
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RealType d32inv = 1.0 / d32; |
| 62 |
< |
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| 62 |
> |
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| 63 |
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RealType cosTheta = dot(r12, r32) / (d12 * d32); |
| 64 |
< |
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| 64 |
> |
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| 65 |
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//check roundoff |
| 66 |
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if (cosTheta > 1.0) { |
| 67 |
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cosTheta = 1.0; |
| 68 |
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} else if (cosTheta < -1.0) { |
| 69 |
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cosTheta = -1.0; |
| 70 |
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} |
| 71 |
< |
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| 71 |
> |
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| 72 |
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RealType theta = acos(cosTheta); |
| 73 |
< |
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| 73 |
> |
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| 74 |
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RealType firstDerivative; |
| 75 |
< |
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| 75 |
> |
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| 76 |
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bendType_->calcForce(theta, firstDerivative, potential_); |
| 77 |
< |
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| 77 |
> |
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| 78 |
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RealType sinTheta = sqrt(1.0 - cosTheta * cosTheta); |
| 79 |
< |
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| 79 |
> |
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| 80 |
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if (fabs(sinTheta) < 1.0E-12) { |
| 81 |
|
sinTheta = 1.0E-12; |
| 82 |
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} |
| 83 |
< |
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| 83 |
> |
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| 84 |
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RealType commonFactor1 = -firstDerivative / sinTheta * d12inv; |
| 85 |
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RealType commonFactor2 = -firstDerivative / sinTheta * d32inv; |
| 86 |
< |
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| 86 |
> |
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| 87 |
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Vector3d force1 = commonFactor1*(r12*(d12inv*cosTheta) - r32*d32inv); |
| 88 |
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Vector3d force3 = commonFactor2*(r32*(d32inv*cosTheta) - r12*d12inv); |
| 89 |
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atom1_->addFrc(force1); |
| 90 |
|
ghostAtom->addFrc(-force1); |
| 91 |
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/**@todo test correctness */ |
| 92 |
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ghostAtom->addTrq(cross(r32, force3) ); |
| 93 |
< |
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| 93 |
> |
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| 94 |
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angle = theta /M_PI * 180.0; |
| 95 |
< |
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| 96 |
< |
} |
| 97 |
< |
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| 95 |
> |
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| 96 |
> |
} |
| 97 |
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} //end namespace oopse |
| 98 |
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