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#include "simError.h" |
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#include "MoLocator.hpp" |
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#include "MatVec3.h" |
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MoLocator::MoLocator( MoleculeStamp* theStamp, ForceFields* theFF){ |
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} |
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void MoLocator::placeMol( const Vector3d& offset, const Vector3d& ort, Molecule* mol){ |
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Vector3d newCoor; |
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Vector3d velocity(0.0, 0.0, 0.0); |
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Vector3d angMomentum(0.0, 0.0, 0.0); |
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double quaternion[4]; |
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double newCoor[3]; |
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double curRefCoor[3]; |
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double zeroVector[3]; |
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vector<StuntDouble*> myIntegrableObjects; |
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quaternion[0] = 1.0; |
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quaternion[1] = 0.0; |
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quaternion[2] = 0.0; |
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quaternion[3] = 0.0; |
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double rotMat[3][3]; |
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zeroVector[0] = 0.0; |
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zeroVector[1] = 0.0; |
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zeroVector[2] = 0.0; |
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latVec2RotMat(ort, rotMat); |
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myIntegrableObjects = mol->getIntegrableObjects(); |
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if(myIntegrableObjects.size() != nIntegrableObjects){ |
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for(int i=0; i<nIntegrableObjects; i++) { |
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newCoor = refCoords[i] + offset; |
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myIntegrableObjects[i]->setPos( newCoor.vec); |
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myIntegrableObjects[i]->setVel(velocity.vec); |
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//calculate the reference coordinate for integrable objects after rotation |
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curRefCoor[0] = refCoords[i][0]; |
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curRefCoor[1] = refCoords[i][1]; |
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curRefCoor[2] = refCoords[i][2]; |
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matVecMul3(rotMat, curRefCoor, newCoor); |
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if(myIntegrableObjects[i]->isDirectional()){ |
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myIntegrableObjects[i]->setQ(quaternion); |
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myIntegrableObjects[i]->setJ(angMomentum.vec); |
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} |
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newCoor[0] += offset[0]; |
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newCoor[1] += offset[1]; |
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newCoor[2] += offset[2]; |
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myIntegrableObjects[i]->setPos( newCoor); |
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myIntegrableObjects[i]->setVel(zeroVector); |
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if(myIntegrableObjects[i]->isDirectional()){ |
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myIntegrableObjects[i]->setA(rotMat); |
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myIntegrableObjects[i]->setJ(zeroVector); |
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} |
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} |
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} |
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int nAtomsInRb; |
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double totMassInRb; |
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double currAtomMass; |
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double totMass; |
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double molMass; |
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mass.resize(nIntegrableObjects); |
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nAtoms= myStamp->getNAtoms(); |
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nRigidBodies = myStamp->getNRigidBodies(); |
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// |
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for(size_t i=0; i<nAtoms; i++){ |
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currAtomStamp = myStamp->getAtom(i); |
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refCoords.push_back(coor); |
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} |
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//calculate the reference center of mass |
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molMass = 0; |
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refMolCom.x = 0; |
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refMolCom.y = 0; |
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refMolCom.z = 0; |
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for(int i = 0; i < nIntegrableObjects; i++){ |
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refMolCom += refCoords[i] * mass[i]; |
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totMass += mass[i]; |
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molMass += mass[i]; |
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} |
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refMolCom / = totMass; |
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refMolCom /= molMass; |
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//move the reference center of mass to (0,0,0) and adjust the reference coordinate |
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//of the integrabel objects |
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refCoords[i] -= refMolCom; |
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} |
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void latVec2RotMat(const Vector3d& lv, double rotMat[3][3]){ |
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double theta, phi, psi; |
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theta =acos(lv.z); |
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phi = atan2(lv.y, lv.x); |
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psi = 0; |
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rotMat[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
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rotMat[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
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rotMat[0][2] = sin(theta) * sin(psi); |
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rotMat[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
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rotMat[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
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rotMat[1][2] = sin(theta) * cos(psi); |
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rotMat[2][0] = sin(phi) * sin(theta); |
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rotMat[2][1] = -cos(phi) * sin(theta); |
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rotMat[2][2] = cos(theta); |
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} |
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