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#include "utils/simError.h" |
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#include "applications/simpleBuilder/MoLocator.hpp" |
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#include "math/MatVec3.h" |
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#include "types/AtomType.hpp" |
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namespace oopse { |
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MoLocator::MoLocator( MoleculeStamp* theStamp, ForceField* theFF){ |
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MoLocator::MoLocator( MoleculeStamp* theStamp, ForceFields* theFF){ |
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myStamp = theStamp; |
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myFF = theFF; |
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nIntegrableObjects = myStamp->getNIntegrable(); |
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calcRefCoords(); |
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calcRef(); |
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} |
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void MoLocator::placeMol( const Vector3d& offset, const Vector3d& ort, Molecule* mol){ |
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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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std::vector<StuntDouble*> myIntegrableObjects; |
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double rotMat[3][3]; |
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Vector3d newCoor; |
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Vector3d curRefCoor; |
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RotMat3x3d rotMat = latVec2RotMat(ort); |
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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(mol->getNIntegrableObjects() != nIntegrableObjects){ |
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sprintf( painCave.errMsg, |
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"MoLocator error.\n" |
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" The number of integrable objects of MoleculeStamp is not the same as that of Molecule\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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if(myIntegrableObjects.size() != nIntegrableObjects){ |
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sprintf( painCave.errMsg, |
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"MoLocator error.\n" |
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" The number of integrable objects of MoleculeStamp is not the same as that of Molecule\n"); |
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painCave.isFatal = 1; |
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simError(); |
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Molecule::IntegrableObjectIterator ii; |
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StuntDouble* integrableObject; |
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int i; |
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for (integrableObject = mol->beginIntegrableObject(ii), i = 0; integrableObject != NULL; |
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integrableObject = mol->nextIntegrableObject(ii), ++i) { |
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} |
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for(int i=0; i<nIntegrableObjects; i++) { |
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newCoor = rotMat * refCoords[i]; |
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newCoor += offset; |
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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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integrableObject->setPos( newCoor); |
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integrableObject->setVel(V3Zero); |
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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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if(integrableObject->isDirectional()){ |
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integrableObject->setA(rotMat * integrableObject->getA()); |
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integrableObject->setJ(V3Zero); |
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} |
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} |
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} |
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} |
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void MoLocator::calcRefCoords( void ){ |
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void MoLocator::calcRef( void ){ |
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AtomStamp* currAtomStamp; |
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int nAtoms; |
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int nRigidBodies; |
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continue; |
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//get mass and the reference coordinate |
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else{ |
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currAtomMass = myFF->getAtomTypeMass(currAtomStamp->getType()); |
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mass.push_back(currAtomMass); |
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coor.x() = currAtomStamp->getPosX(); |
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coor.y() = currAtomStamp->getPosY(); |
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for(int j = 0; j < nAtomsInRb; j++){ |
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currAtomMass = myFF->getAtomTypeMass(currAtomStamp->getType()); |
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currAtomMass = getAtomMass(currAtomStamp->getType(), myFF); |
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totMassInRb += currAtomMass; |
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coor.x() += currAtomStamp->getPosX() * currAtomMass; |
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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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double getAtomMass(const std::string& at, ForceField* myFF) { |
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double mass; |
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AtomType* atomType= myFF->getAtomType(at); |
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if (atomType != NULL) { |
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mass = atomType->getMass(); |
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} else { |
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mass = 0.0; |
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std::cerr << "Can not find AtomType: " << at << std::endl; |
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} |
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return mass; |
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} |
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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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double getMolMass(MoleculeStamp *molStamp, ForceField *myFF) { |
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int nAtoms; |
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AtomStamp *currAtomStamp; |
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double totMass; |
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totMass = 0; |
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nAtoms = molStamp->getNAtoms(); |
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for(size_t i = 0; i < nAtoms; i++) { |
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totMass += getAtomMass(currAtomStamp->getType(), myFF); |
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} |
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} |
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RotMat3x3d latVec2RotMat(const Vector3d& lv){ |
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double theta =acos(lv[2]); |
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double phi = atan2(lv[1], lv[0]); |
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double psi = 0; |
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return RotMat3x3d(phi, theta, psi); |
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} |
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} |
