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namespace OpenMD { |
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Inversion::Inversion(Atom *atom1, Atom *atom2, Atom *atom3, |
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< |
Atom *atom4, InversionType *it) : |
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< |
atom1_(atom1), atom2_(atom2), atom3_(atom3), atom4_(atom4), |
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< |
inversionType_(it) { |
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> |
Atom *atom4, InversionType *it) : |
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> |
ShortRangeInteraction(), inversionType_(it) { |
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> |
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> |
atoms_.resize(4); |
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> |
atoms_[0] = atom1; |
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> |
atoms_[1] = atom2; |
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> |
atoms_[2] = atom3; |
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> |
atoms_[3] = atom4; |
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> |
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inversionKey_ = inversionType_->getKey(); |
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} |
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// version of this potential (i.e. Amber-style), the central atom |
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// is treated as atom *3* in a standard torsion form: |
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< |
Vector3d pos1 = atom2_->getPos(); |
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< |
Vector3d pos2 = atom3_->getPos(); |
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< |
Vector3d pos3 = atom1_->getPos(); |
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< |
Vector3d pos4 = atom4_->getPos(); |
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> |
Vector3d pos1 = atoms_[1]->getPos(); |
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> |
Vector3d pos2 = atoms_[2]->getPos(); |
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> |
Vector3d pos3 = atoms_[0]->getPos(); |
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> |
Vector3d pos4 = atoms_[3]->getPos(); |
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Vector3d r31 = pos1 - pos3; |
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Vector3d r23 = pos3 - pos2; |
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RealType rA = A.length(); |
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Vector3d B = cross(r43, r23); |
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RealType rB = B.length(); |
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– |
//Vector3d C = cross(r23, A); |
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//RealType rC = C.length(); |
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A.normalize(); |
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B.normalize(); |
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//C.normalize(); |
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// Calculate the sin and cos |
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RealType cos_phi = dot(A, B) ; |
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// Confusing enough? Good. |
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< |
atom2_->addFrc(f1); |
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< |
atom1_->addFrc(f2 - f1 + f3); |
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< |
atom4_->addFrc(-f2); |
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< |
atom3_->addFrc(-f3); |
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> |
atoms_[1]->addFrc(f1); |
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> |
atoms_[0]->addFrc(f2 - f1 + f3); |
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> |
atoms_[3]->addFrc(-f2); |
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> |
atoms_[2]->addFrc(-f3); |
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if (doParticlePot) { |
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< |
atom1_->addParticlePot(potential_); |
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< |
atom2_->addParticlePot(potential_); |
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< |
atom3_->addParticlePot(potential_); |
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< |
atom4_->addParticlePot(potential_); |
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> |
atoms_[0]->addParticlePot(potential_); |
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> |
atoms_[1]->addParticlePot(potential_); |
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> |
atoms_[2]->addParticlePot(potential_); |
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> |
atoms_[3]->addParticlePot(potential_); |
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} |
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angle = acos(cos_phi) /M_PI * 180.0; |
