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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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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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#include <iostream> |
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#include "utils/simError.h" |
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#include "utils/MoLocator.hpp" |
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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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|
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myStamp = theStamp; |
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myFF = theFF; |
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nIntegrableObjects = myStamp->getNIntegrable(); |
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calcRef(); |
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} |
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namespace OpenMD { |
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MoLocator::MoLocator( MoleculeStamp* theStamp, ForceField* theFF){ |
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|
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myStamp = theStamp; |
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myFF = theFF; |
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nIntegrableObjects = myStamp->getNIntegrable(); |
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calcRef(); |
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} |
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|
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void MoLocator::placeMol( const Vector3d& offset, const Vector3d& ort, Molecule* mol){ |
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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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|
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|
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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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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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|
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|
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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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newCoor = rotMat * refCoords[i]; |
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newCoor += offset; |
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|
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integrableObject->setPos( newCoor); |
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integrableObject->setVel(V3Zero); |
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|
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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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integrableObject = mol->nextIntegrableObject(ii), ++i) { |
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|
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newCoor = rotMat * refCoords[i]; |
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newCoor += offset; |
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|
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integrableObject->setPos(newCoor); |
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integrableObject->setVel(V3Zero); |
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|
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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::calcRef( void ){ |
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AtomStamp* currAtomStamp; |
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int nAtoms; |
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int nRigidBodies; |
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std::vector<double> 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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} |
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|
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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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|
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currAtomStamp = myStamp->getAtom(i); |
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|
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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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|
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painCave.isFatal = 1; |
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simError(); |
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void MoLocator::calcRef( void ){ |
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AtomStamp* currAtomStamp; |
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RigidBodyStamp* rbStamp; |
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int nAtoms; |
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int nRigidBodies; |
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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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RealType totMassInRb; |
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RealType currAtomMass; |
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RealType molMass; |
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|
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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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|
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currAtomStamp = myStamp->getAtomStamp(i); |
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|
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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->getName().c_str(), |
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currAtomStamp->getType().c_str()); |
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|
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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//if atom belongs to rigidbody, just skip it |
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if(myStamp->isAtomInRigidBody(i)) |
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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 = getAtomMass(currAtomStamp->getType(), myFF); |
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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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coor.z() = currAtomStamp->getPosZ(); |
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refCoords.push_back(coor); |
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|
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} |
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} |
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|
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//if atom belongs to rigidbody, just skip it |
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if(myStamp->isAtomInRigidBody(i)) |
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continue; |
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//get mass and the reference coordinate |
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else{ |
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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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coor.z() = currAtomStamp->getPosZ(); |
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for(int i = 0; i < nRigidBodies; i++){ |
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|
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rbStamp = myStamp->getRigidBodyStamp(i); |
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nAtomsInRb = rbStamp->getNMembers(); |
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|
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coor.x() = 0.0; |
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coor.y() = 0.0; |
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coor.z() = 0.0; |
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totMassInRb = 0.0; |
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|
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for(int j = 0; j < nAtomsInRb; j++){ |
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|
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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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|
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coor.x() += currAtomStamp->getPosX() * currAtomMass; |
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coor.y() += currAtomStamp->getPosY() * currAtomMass; |
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coor.z() += currAtomStamp->getPosZ() * currAtomMass; |
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} |
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|
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mass.push_back(totMassInRb); |
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coor /= totMassInRb; |
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refCoords.push_back(coor); |
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|
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} |
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} |
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|
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for(int i = 0; i < nRigidBodies; i++){ |
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coor.x() = 0; |
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coor.y() = 0; |
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coor.z() = 0; |
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totMassInRb = 0; |
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|
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for(int j = 0; j < nAtomsInRb; j++){ |
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|
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currAtomMass = getAtomMass(currAtomStamp->getType(), myFF); |
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totMassInRb += currAtomMass; |
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|
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coor.x() += currAtomStamp->getPosX() * currAtomMass; |
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coor.y() += currAtomStamp->getPosY() * currAtomMass; |
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coor.z() += currAtomStamp->getPosZ() * currAtomMass; |
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|
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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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|
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for(int i = 0; i < nIntegrableObjects; i++){ |
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refMolCom += refCoords[i] * mass[i]; |
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molMass += mass[i]; |
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} |
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|
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mass.push_back(totMassInRb); |
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coor /= totMassInRb; |
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refCoords.push_back(coor); |
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|
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refMolCom /= molMass; |
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|
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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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} |
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|
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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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|
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for(int i = 0; i < nIntegrableObjects; i++){ |
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refMolCom += refCoords[i] * mass[i]; |
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molMass += mass[i]; |
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} |
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|
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refMolCom /= molMass; |
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|
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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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} |
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|
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|
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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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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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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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|
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double getMolMass(MoleculeStamp *molStamp, ForceField *myFF) { |
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} |
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|
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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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< |
|
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> |
|
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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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< |
totMass += getAtomMass(currAtomStamp->getType(), myFF); |
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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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< |
|
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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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|
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} |
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> |
RotMat3x3d latVec2RotMat(const Vector3d& lv){ |
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> |
|
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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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> |
|
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return RotMat3x3d(phi, theta, psi); |
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< |
|
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> |
|
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> |
} |
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} |
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– |
} |
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|
