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/* |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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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 curRefCoor; |
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RotMat3x3d rotMat = latVec2RotMat(ort); |
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newCoor = rotMat * refCoords[i]; |
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newCoor += offset; |
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integrableObject->setPos( newCoor); |
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integrableObject->setPos(newCoor); |
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integrableObject->setVel(V3Zero); |
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if(integrableObject->isDirectional()){ |
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RigidBodyStamp* rbStamp; |
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int nAtoms; |
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int nRigidBodies; |
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std::vector<double> mass; |
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std::vector<RealType> mass; |
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Vector3d coor; |
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Vector3d refMolCom; |
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int nAtomsInRb; |
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double totMassInRb; |
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double currAtomMass; |
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double molMass; |
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RealType totMassInRb; |
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RealType currAtomMass; |
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RealType molMass; |
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nAtoms= myStamp->getNAtoms(); |
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nRigidBodies = myStamp->getNRigidBodies(); |
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for(size_t i=0; i<nAtoms; i++){ |
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currAtomStamp = myStamp->getAtom(i); |
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currAtomStamp = myStamp->getAtomStamp(i); |
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if( !currAtomStamp->havePosition() ){ |
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sprintf( painCave.errMsg, |
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"MoLocator error.\n" |
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" Component %s, atom %s does not have a position specified.\n" |
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" This means MoLocator cannot initalize it's position.\n", |
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myStamp->getID(), |
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currAtomStamp->getType() ); |
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myStamp->getName().c_str(), |
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currAtomStamp->getType().c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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for(int i = 0; i < nRigidBodies; i++){ |
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rbStamp = myStamp->getRigidBody(i); |
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rbStamp = myStamp->getRigidBodyStamp(i); |
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nAtomsInRb = rbStamp->getNMembers(); |
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coor.x() = 0.0; |
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for(int j = 0; j < nAtomsInRb; j++){ |
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currAtomStamp = myStamp->getAtom(rbStamp->getMember(j)); |
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currAtomStamp = myStamp->getAtomStamp(rbStamp->getMemberAt(j)); |
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currAtomMass = getAtomMass(currAtomStamp->getType(), myFF); |
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totMassInRb += currAtomMass; |
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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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for(int i = 0; i < nIntegrableObjects; i++) |
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refCoords[i] -= refMolCom; |
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for(int i = 0; i < nIntegrableObjects; i++) |
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refCoords[i] -= refMolCom; |
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} |
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double getAtomMass(const std::string& at, ForceField* myFF) { |
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double mass; |
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RealType getAtomMass(const std::string& at, ForceField* myFF) { |
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RealType 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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return mass; |
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} |
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double getMolMass(MoleculeStamp *molStamp, ForceField *myFF) { |
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RealType getMolMass(MoleculeStamp *molStamp, ForceField *myFF) { |
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int nAtoms; |
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double totMass = 0; |
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RealType 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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AtomStamp *currAtomStamp = molStamp->getAtom(i); |
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AtomStamp *currAtomStamp = molStamp->getAtomStamp(i); |
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totMass += getAtomMass(currAtomStamp->getType(), myFF); |
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} |
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return totMass; |
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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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RealType theta =acos(lv[2]); |
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RealType phi = atan2(lv[1], lv[0]); |
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RealType psi = 0; |
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return RotMat3x3d(phi, theta, psi); |
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