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*/ |
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#include "primitives/Inversion.hpp" |
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+ |
#include "fstream" |
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namespace oopse { |
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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 pos2 = atom1_->getPos(); |
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> |
Vector3d pos3 = atom4_->getPos(); |
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> |
Vector3d pos4 = atom3_->getPos(); |
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|
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/*std::ofstream myfile; |
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myfile.open("Inversion", std::ios::app); |
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myfile << atom1_->getType() << " - atom1; " |
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<< atom2_->getType() << " - atom2; " |
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<< atom3_->getType() << " - atom3; " |
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<< atom4_->getType() << " - atom4; " |
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<< std::endl; |
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*/ |
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Vector3d r21 = pos1 - pos2; |
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Vector3d r32 = pos2 - pos3; |
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Vector3d r43 = pos3 - pos4; |
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> |
Vector3d r42 = pos2 - pos4; |
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// Calculate the cross products and distances |
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Vector3d A = cross(r21, r32); |
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RealType rA = A.length(); |
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Vector3d B = cross(r32, r43); |
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Vector3d B = cross(r32, r42); |
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RealType rB = B.length(); |
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Vector3d C = cross(r32, A); |
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RealType rC = C.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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//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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if (cos_phi > 1.0) cos_phi = 1.0; |
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< |
if (cos_phi < -1.0) cos_phi = -1.0; |
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> |
if (cos_phi > 1.0) {cos_phi = 1.0; std::cout << "!!!! cos_phi is bigger than 1.0" |
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> |
<< std::endl;} |
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> |
if (cos_phi < -1.0) {cos_phi = -1.0; std::cout << "!!!! cos_phi is less than -1.0" |
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> |
<< std::endl;} |
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> |
//std::cout << "We actually use this inversion!!!!" << std::endl; |
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RealType dVdcosPhi; |
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//cos_phi = 2.0*cos_phi*cos_phi - 1.0; |
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inversionType_->calcForce(cos_phi, potential_, dVdcosPhi); |
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< |
Vector3d f1; |
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< |
Vector3d f2; |
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< |
Vector3d f3; |
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> |
Vector3d f1 ; |
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> |
Vector3d f2 ; |
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> |
Vector3d f3 ; |
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Vector3d dcosdA = (cos_phi * A - B) /rA; |
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Vector3d dcosdB = (cos_phi * B - A) /rB; |
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f1 = dVdcosPhi * cross(r32, dcosdA); |
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< |
f2 = dVdcosPhi * ( cross(r43, dcosdB) - cross(r21, dcosdA)); |
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> |
f2 = dVdcosPhi * ( cross(r42, dcosdB) - cross(r21, dcosdA)); |
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f3 = dVdcosPhi * cross(dcosdB, r32); |
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// In OOPSE's version of an improper torsion, the central atom |
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// Confusing enough? Good. |
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| 120 |
< |
atom3_->addFrc(f1); |
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< |
atom1_->addFrc(f2 - f1); |
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< |
atom2_->addFrc(f3 - f2); |
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< |
atom4_->addFrc(-f3); |
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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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> |
|
| 125 |
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angle = acos(cos_phi) /M_PI * 180.0; |
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} |
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