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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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> |
* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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#include "primitives/GhostBend.hpp" |
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#include "primitives/DirectionalAtom.hpp" |
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namespace oopse { |
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namespace OpenMD { |
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|
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/**@todo still a lot left to improve*/ |
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void GhostBend::calcForce() { |
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void GhostBend::calcForce(RealType& angle) { |
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DirectionalAtom* ghostAtom = static_cast<DirectionalAtom*>(atom2_); |
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|
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Vector3d pos1 = atom1_->getPos(); |
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Vector3d pos2 = ghostAtom->getPos(); |
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|
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> |
|
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Vector3d r12 = pos1 - pos2; |
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double d12 = r12.length(); |
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|
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double d12inv = 1.0 / d12; |
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|
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Vector3d r32 = ghostAtom->getElectroFrame().getColumn(2); |
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double d32 = r32.length(); |
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|
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double d32inv = 1.0 / d32; |
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|
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double cosTheta = dot(r12, r32) / (d12 * d32); |
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|
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> |
RealType d12 = r12.length(); |
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> |
|
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> |
RealType d12inv = 1.0 / d12; |
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> |
|
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> |
Vector3d r32 = ghostAtom->getA().getColumn(2); |
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RealType d32 = r32.length(); |
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> |
|
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> |
RealType d32inv = 1.0 / d32; |
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> |
|
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RealType cosTheta = dot(r12, r32) / (d12 * d32); |
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|
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//check roundoff |
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if (cosTheta > 1.0) { |
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cosTheta = 1.0; |
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} else if (cosTheta < -1.0) { |
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cosTheta = -1.0; |
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} |
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|
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double theta = acos(cosTheta); |
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|
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double firstDerivative; |
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|
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bendType_->calcForce(theta, firstDerivative, potential_); |
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|
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double sinTheta = sqrt(1.0 - cosTheta * cosTheta); |
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|
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> |
|
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> |
RealType theta = acos(cosTheta); |
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> |
|
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> |
RealType firstDerivative; |
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> |
|
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> |
bendType_->calcForce(theta, potential_, firstDerivative); |
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> |
|
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> |
RealType sinTheta = sqrt(1.0 - cosTheta * cosTheta); |
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> |
|
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if (fabs(sinTheta) < 1.0E-12) { |
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sinTheta = 1.0E-12; |
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} |
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|
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double commonFactor1 = -firstDerivative / sinTheta * d12inv; |
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double commonFactor2 = -firstDerivative / sinTheta * d32inv; |
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|
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> |
|
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> |
RealType commonFactor1 = -firstDerivative / sinTheta * d12inv; |
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> |
RealType commonFactor2 = -firstDerivative / sinTheta * d32inv; |
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> |
|
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Vector3d force1 = commonFactor1*(r12*(d12inv*cosTheta) - r32*d32inv); |
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Vector3d force3 = commonFactor2*(r32*(d32inv*cosTheta) - r12*d12inv); |
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atom1_->addFrc(force1); |
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ghostAtom->addFrc(-force1); |
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/**@todo test correctness */ |
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ghostAtom->addTrq(cross(r32, force3) ); |
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ghostAtom->addTrq(cross(r32, force3) ); |
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|
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} |
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atom1_->addParticlePot(potential_); |
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> |
ghostAtom->addParticlePot(potential_); |
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|
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< |
} //end namespace oopse |
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angle = theta /M_PI * 180.0; |
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> |
|
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> |
} |
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> |
} //end namespace OpenMD |
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|
