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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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* non-exclusive, royalty free, license to use, modify and |
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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. 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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* 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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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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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, 234107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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/** |
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* @file MoleculeCreator.cpp |
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* @author tlin |
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* @date 11/04/2004 |
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* @version 1.0 |
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*/ |
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|
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#include <cassert> |
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#include <typeinfo> |
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#include <set> |
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|
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#include "brains/MoleculeCreator.hpp" |
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#include "primitives/GhostBend.hpp" |
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#include "primitives/GhostTorsion.hpp" |
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#include "types/AtomType.hpp" |
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#include "types/FixedBondType.hpp" |
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#include "utils/simError.h" |
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#include "utils/StringUtils.hpp" |
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|
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namespace OpenMD { |
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|
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Molecule* MoleculeCreator::createMolecule(ForceField* ff, |
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MoleculeStamp *molStamp, |
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int stampId, int globalIndex, |
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LocalIndexManager* localIndexMan) { |
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Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName(), |
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molStamp->getRegion() ); |
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|
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//create atoms |
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Atom* atom; |
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AtomStamp* currentAtomStamp; |
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int nAtom = molStamp->getNAtoms(); |
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for (int i = 0; i < nAtom; ++i) { |
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currentAtomStamp = molStamp->getAtomStamp(i); |
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atom = createAtom(ff, mol, currentAtomStamp, localIndexMan); |
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mol->addAtom(atom); |
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} |
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|
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//create rigidbodies |
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RigidBody* rb; |
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RigidBodyStamp * currentRigidBodyStamp; |
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int nRigidbodies = molStamp->getNRigidBodies(); |
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|
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for (int i = 0; i < nRigidbodies; ++i) { |
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currentRigidBodyStamp = molStamp->getRigidBodyStamp(i); |
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rb = createRigidBody(molStamp, mol, currentRigidBodyStamp, |
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localIndexMan); |
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mol->addRigidBody(rb); |
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} |
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|
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//create bonds |
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Bond* bond; |
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BondStamp* currentBondStamp; |
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int nBonds = molStamp->getNBonds(); |
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|
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for (int i = 0; i < nBonds; ++i) { |
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currentBondStamp = molStamp->getBondStamp(i); |
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bond = createBond(ff, mol, currentBondStamp, localIndexMan); |
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mol->addBond(bond); |
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} |
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|
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//create bends |
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Bend* bend; |
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BendStamp* currentBendStamp; |
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int nBends = molStamp->getNBends(); |
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for (int i = 0; i < nBends; ++i) { |
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currentBendStamp = molStamp->getBendStamp(i); |
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bend = createBend(ff, mol, currentBendStamp, localIndexMan); |
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mol->addBend(bend); |
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} |
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|
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//create torsions |
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Torsion* torsion; |
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TorsionStamp* currentTorsionStamp; |
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int nTorsions = molStamp->getNTorsions(); |
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for (int i = 0; i < nTorsions; ++i) { |
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currentTorsionStamp = molStamp->getTorsionStamp(i); |
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torsion = createTorsion(ff, mol, currentTorsionStamp, localIndexMan); |
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mol->addTorsion(torsion); |
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} |
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|
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//create inversions |
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Inversion* inversion; |
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InversionStamp* currentInversionStamp; |
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int nInversions = molStamp->getNInversions(); |
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for (int i = 0; i < nInversions; ++i) { |
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currentInversionStamp = molStamp->getInversionStamp(i); |
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inversion = createInversion(ff, mol, currentInversionStamp, |
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localIndexMan); |
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if (inversion != NULL ) { |
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mol->addInversion(inversion); |
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} |
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} |
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|
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//create cutoffGroups |
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CutoffGroup* cutoffGroup; |
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CutoffGroupStamp* currentCutoffGroupStamp; |
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int nCutoffGroups = molStamp->getNCutoffGroups(); |
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for (int i = 0; i < nCutoffGroups; ++i) { |
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currentCutoffGroupStamp = molStamp->getCutoffGroupStamp(i); |
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cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp, |
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localIndexMan); |
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mol->addCutoffGroup(cutoffGroup); |
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} |
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|
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//every free atom is a cutoff group |
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std::vector<Atom*> freeAtoms; |
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std::vector<Atom*>::iterator ai; |
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std::vector<Atom*>::iterator fai; |
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|
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//add all atoms into allAtoms set |
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for(atom = mol->beginAtom(fai); atom != NULL; atom = mol->nextAtom(fai)) { |
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freeAtoms.push_back(atom); |
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} |
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|
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Molecule::CutoffGroupIterator ci; |
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CutoffGroup* cg; |
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|
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for (cg = mol->beginCutoffGroup(ci); cg != NULL; |
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cg = mol->nextCutoffGroup(ci)) { |
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|
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for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
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//erase the atoms belong to cutoff groups from freeAtoms vector |
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freeAtoms.erase(std::remove(freeAtoms.begin(), freeAtoms.end(), atom), |
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freeAtoms.end()); |
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} |
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} |
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|
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// loop over the free atoms and then create one cutoff group for |
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// every single free atom |
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|
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for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) { |
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cutoffGroup = createCutoffGroup(mol, *fai, localIndexMan); |
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mol->addCutoffGroup(cutoffGroup); |
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} |
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//create constraints |
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createConstraintPair(mol); |
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createConstraintElem(mol); |
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|
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// Does this molecule stamp define a total constrained charge value? |
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// If so, let the created molecule know about it. |
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|
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if (molStamp->haveConstrainTotalCharge() ) { |
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mol->setConstrainTotalCharge( molStamp->getConstrainTotalCharge() ); |
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} |
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|
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//the construction of this molecule is finished |
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mol->complete(); |
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|
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return mol; |
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} |
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|
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|
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Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol, |
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AtomStamp* stamp, |
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LocalIndexManager* localIndexMan) { |
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AtomType * atomType; |
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Atom* atom; |
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|
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atomType = ff->getAtomType(stamp->getType()); |
203 |
|
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if (atomType == NULL) { |
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sprintf(painCave.errMsg, "Can not find Matching Atom Type for[%s]", |
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stamp->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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//below code still have some kind of hard-coding smell |
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if (atomType->isDirectional()){ |
214 |
|
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DirectionalAtom* dAtom; |
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dAtom = new DirectionalAtom(atomType); |
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atom = dAtom; |
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} |
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else{ |
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atom = new Atom(atomType); |
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} |
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|
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atom->setLocalIndex(localIndexMan->getNextAtomIndex()); |
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|
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return atom; |
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} |
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|
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RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp, |
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Molecule* mol, |
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RigidBodyStamp* rbStamp, |
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LocalIndexManager* localIndexMan){ |
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Atom* atom; |
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int nAtoms; |
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Vector3d refCoor; |
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AtomStamp* atomStamp; |
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|
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RigidBody* rb = new RigidBody(); |
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nAtoms = rbStamp->getNMembers(); |
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for (int i = 0; i < nAtoms; ++i) { |
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//rbStamp->getMember(i) return the local index of current atom |
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//inside the molecule. It is not the same as local index of |
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//atom which is the index of atom at DataStorage class |
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atom = mol->getAtomAt(rbStamp->getMemberAt(i)); |
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atomStamp= molStamp->getAtomStamp(rbStamp->getMemberAt(i)); |
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rb->addAtom(atom, atomStamp); |
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} |
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|
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//after all of the atoms are added, we need to calculate the |
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//reference coordinates |
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rb->calcRefCoords(); |
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|
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//set the local index of this rigid body, global index will be set later |
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rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex()); |
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|
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// The rule for naming a rigidbody is: MoleculeName_RB_Integer |
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// The first part is the name of the molecule |
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// The second part is always fixed as "RB" |
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// The third part is the index of the rigidbody defined in meta-data file |
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// For example, Butane_RB_0 is a valid rigid body name of butane molecule |
260 |
|
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std::string s = OpenMD_itoa(mol->getNRigidBodies(), 10); |
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rb->setType(mol->getType() + "_RB_" + s.c_str()); |
263 |
return rb; |
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} |
265 |
|
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Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, |
267 |
BondStamp* stamp, |
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LocalIndexManager* localIndexMan) { |
269 |
BondType* bondType; |
270 |
Atom* atomA; |
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Atom* atomB; |
272 |
|
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atomA = mol->getAtomAt(stamp->getA()); |
274 |
atomB = mol->getAtomAt(stamp->getB()); |
275 |
|
276 |
assert( atomA && atomB); |
277 |
|
278 |
bondType = ff->getBondType(atomA->getType(), atomB->getType()); |
279 |
|
280 |
if (bondType == NULL) { |
281 |
sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]", |
282 |
atomA->getType().c_str(), |
283 |
atomB->getType().c_str()); |
284 |
|
285 |
painCave.isFatal = 1; |
286 |
simError(); |
287 |
} |
288 |
Bond* bond = new Bond(atomA, atomB, bondType); |
289 |
|
290 |
//set the local index of this bond, the global index will be set later |
291 |
bond->setLocalIndex(localIndexMan->getNextBondIndex()); |
292 |
|
293 |
// The rule for naming a bond is: MoleculeName_Bond_Integer |
294 |
// The first part is the name of the molecule |
295 |
// The second part is always fixed as "Bond" |
296 |
// The third part is the index of the bond defined in meta-data file |
297 |
// For example, Butane_bond_0 is a valid Bond name in a butane molecule |
298 |
|
299 |
std::string s = OpenMD_itoa(mol->getNBonds(), 10); |
300 |
bond->setName(mol->getType() + "_Bond_" + s.c_str()); |
301 |
return bond; |
302 |
} |
303 |
|
304 |
Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, |
305 |
BendStamp* stamp, |
306 |
LocalIndexManager* localIndexMan) { |
307 |
Bend* bend = NULL; |
308 |
std::vector<int> bendAtoms = stamp->getMembers(); |
309 |
if (bendAtoms.size() == 3) { |
310 |
Atom* atomA = mol->getAtomAt(bendAtoms[0]); |
311 |
Atom* atomB = mol->getAtomAt(bendAtoms[1]); |
312 |
Atom* atomC = mol->getAtomAt(bendAtoms[2]); |
313 |
|
314 |
assert( atomA && atomB && atomC); |
315 |
|
316 |
BendType* bendType = ff->getBendType(atomA->getType().c_str(), |
317 |
atomB->getType().c_str(), |
318 |
atomC->getType().c_str()); |
319 |
|
320 |
if (bendType == NULL) { |
321 |
sprintf(painCave.errMsg, |
322 |
"Can not find Matching Bend Type for[%s, %s, %s]", |
323 |
atomA->getType().c_str(), |
324 |
atomB->getType().c_str(), |
325 |
atomC->getType().c_str()); |
326 |
|
327 |
painCave.isFatal = 1; |
328 |
simError(); |
329 |
} |
330 |
|
331 |
bend = new Bend(atomA, atomB, atomC, bendType); |
332 |
} else if ( bendAtoms.size() == 2 && stamp->haveGhostVectorSource()) { |
333 |
int ghostIndex = stamp->getGhostVectorSource(); |
334 |
int normalIndex = ghostIndex != bendAtoms[0] ? bendAtoms[0] : bendAtoms[1]; |
335 |
Atom* normalAtom = mol->getAtomAt(normalIndex) ; |
336 |
DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex)); |
337 |
if (ghostAtom == NULL) { |
338 |
sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom"); |
339 |
painCave.isFatal = 1; |
340 |
simError(); |
341 |
} |
342 |
|
343 |
BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST"); |
344 |
|
345 |
if (bendType == NULL) { |
346 |
sprintf(painCave.errMsg, |
347 |
"Can not find Matching Bend Type for[%s, %s, %s]", |
348 |
normalAtom->getType().c_str(), |
349 |
ghostAtom->getType().c_str(), |
350 |
"GHOST"); |
351 |
|
352 |
painCave.isFatal = 1; |
353 |
simError(); |
354 |
} |
355 |
|
356 |
bend = new GhostBend(normalAtom, ghostAtom, bendType); |
357 |
|
358 |
} |
359 |
|
360 |
//set the local index of this bend, the global index will be set later |
361 |
bend->setLocalIndex(localIndexMan->getNextBendIndex()); |
362 |
|
363 |
// The rule for naming a bend is: MoleculeName_Bend_Integer |
364 |
// The first part is the name of the molecule |
365 |
// The second part is always fixed as "Bend" |
366 |
// The third part is the index of the bend defined in meta-data file |
367 |
// For example, Butane_Bend_0 is a valid Bend name in a butane molecule |
368 |
|
369 |
std::string s = OpenMD_itoa(mol->getNBends(), 10); |
370 |
bend->setName(mol->getType() + "_Bend_" + s.c_str()); |
371 |
return bend; |
372 |
} |
373 |
|
374 |
Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, |
375 |
TorsionStamp* stamp, |
376 |
LocalIndexManager* localIndexMan) { |
377 |
|
378 |
Torsion* torsion = NULL; |
379 |
std::vector<int> torsionAtoms = stamp->getMembers(); |
380 |
if (torsionAtoms.size() < 3) { |
381 |
return torsion; |
382 |
} |
383 |
|
384 |
Atom* atomA = mol->getAtomAt(torsionAtoms[0]); |
385 |
Atom* atomB = mol->getAtomAt(torsionAtoms[1]); |
386 |
Atom* atomC = mol->getAtomAt(torsionAtoms[2]); |
387 |
|
388 |
if (torsionAtoms.size() == 4) { |
389 |
Atom* atomD = mol->getAtomAt(torsionAtoms[3]); |
390 |
|
391 |
assert(atomA && atomB && atomC && atomD); |
392 |
|
393 |
TorsionType* torsionType = ff->getTorsionType(atomA->getType(), |
394 |
atomB->getType(), |
395 |
atomC->getType(), |
396 |
atomD->getType()); |
397 |
if (torsionType == NULL) { |
398 |
sprintf(painCave.errMsg, |
399 |
"Can not find Matching Torsion Type for[%s, %s, %s, %s]", |
400 |
atomA->getType().c_str(), |
401 |
atomB->getType().c_str(), |
402 |
atomC->getType().c_str(), |
403 |
atomD->getType().c_str()); |
404 |
|
405 |
painCave.isFatal = 1; |
406 |
simError(); |
407 |
} |
408 |
|
409 |
torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType); |
410 |
} |
411 |
else { |
412 |
|
413 |
DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(stamp->getGhostVectorSource())); |
414 |
if (dAtom == NULL) { |
415 |
sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom"); |
416 |
painCave.isFatal = 1; |
417 |
simError(); |
418 |
} |
419 |
|
420 |
TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(), |
421 |
atomC->getType(), "GHOST"); |
422 |
|
423 |
if (torsionType == NULL) { |
424 |
sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]", |
425 |
atomA->getType().c_str(), |
426 |
atomB->getType().c_str(), |
427 |
atomC->getType().c_str(), |
428 |
"GHOST"); |
429 |
|
430 |
painCave.isFatal = 1; |
431 |
simError(); |
432 |
} |
433 |
|
434 |
torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType); |
435 |
} |
436 |
|
437 |
//set the local index of this torsion, the global index will be set later |
438 |
torsion->setLocalIndex(localIndexMan->getNextTorsionIndex()); |
439 |
|
440 |
// The rule for naming a torsion is: MoleculeName_Torsion_Integer |
441 |
// The first part is the name of the molecule |
442 |
// The second part is always fixed as "Torsion" |
443 |
// The third part is the index of the torsion defined in meta-data file |
444 |
// For example, Butane_Torsion_0 is a valid Torsion name in a |
445 |
// butane molecule |
446 |
|
447 |
std::string s = OpenMD_itoa(mol->getNTorsions(), 10); |
448 |
torsion->setName(mol->getType() + "_Torsion_" + s.c_str()); |
449 |
return torsion; |
450 |
} |
451 |
|
452 |
Inversion* MoleculeCreator::createInversion(ForceField* ff, Molecule* mol, |
453 |
InversionStamp* stamp, |
454 |
LocalIndexManager* localIndexMan) { |
455 |
|
456 |
Inversion* inversion = NULL; |
457 |
int center = stamp->getCenter(); |
458 |
std::vector<int> satellites = stamp->getSatellites(); |
459 |
if (satellites.size() != 3) { |
460 |
return inversion; |
461 |
} |
462 |
|
463 |
Atom* atomA = mol->getAtomAt(center); |
464 |
Atom* atomB = mol->getAtomAt(satellites[0]); |
465 |
Atom* atomC = mol->getAtomAt(satellites[1]); |
466 |
Atom* atomD = mol->getAtomAt(satellites[2]); |
467 |
|
468 |
assert(atomA && atomB && atomC && atomD); |
469 |
|
470 |
InversionType* inversionType = ff->getInversionType(atomA->getType(), |
471 |
atomB->getType(), |
472 |
atomC->getType(), |
473 |
atomD->getType()); |
474 |
|
475 |
if (inversionType == NULL) { |
476 |
sprintf(painCave.errMsg, "No Matching Inversion Type for[%s, %s, %s, %s]\n" |
477 |
"\t(May not be a problem: not all inversions are parametrized)\n", |
478 |
atomA->getType().c_str(), |
479 |
atomB->getType().c_str(), |
480 |
atomC->getType().c_str(), |
481 |
atomD->getType().c_str()); |
482 |
|
483 |
painCave.isFatal = 0; |
484 |
painCave.severity = OPENMD_INFO; |
485 |
simError(); |
486 |
return NULL; |
487 |
} else { |
488 |
|
489 |
inversion = new Inversion(atomA, atomB, atomC, atomD, inversionType); |
490 |
|
491 |
// set the local index of this inversion, the global index will |
492 |
// be set later |
493 |
inversion->setLocalIndex(localIndexMan->getNextInversionIndex()); |
494 |
|
495 |
// The rule for naming an inversion is: MoleculeName_Inversion_Integer |
496 |
// The first part is the name of the molecule |
497 |
// The second part is always fixed as "Inversion" |
498 |
// The third part is the index of the inversion defined in meta-data file |
499 |
// For example, Benzene_Inversion_0 is a valid Inversion name in a |
500 |
// Benzene molecule |
501 |
|
502 |
std::string s = OpenMD_itoa(mol->getNInversions(), 10); |
503 |
inversion->setName(mol->getType() + "_Inversion_" + s.c_str()); |
504 |
return inversion; |
505 |
} |
506 |
} |
507 |
|
508 |
|
509 |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, |
510 |
CutoffGroupStamp* stamp, |
511 |
LocalIndexManager* localIndexMan) { |
512 |
int nAtoms; |
513 |
CutoffGroup* cg; |
514 |
Atom* atom; |
515 |
cg = new CutoffGroup(); |
516 |
|
517 |
nAtoms = stamp->getNMembers(); |
518 |
for (int i =0; i < nAtoms; ++i) { |
519 |
atom = mol->getAtomAt(stamp->getMemberAt(i)); |
520 |
assert(atom); |
521 |
cg->addAtom(atom); |
522 |
} |
523 |
|
524 |
//set the local index of this cutoffGroup, global index will be set later |
525 |
cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex()); |
526 |
|
527 |
return cg; |
528 |
} |
529 |
|
530 |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom, |
531 |
LocalIndexManager* localIndexMan) { |
532 |
CutoffGroup* cg; |
533 |
cg = new CutoffGroup(); |
534 |
cg->addAtom(atom); |
535 |
|
536 |
//set the local index of this cutoffGroup, global index will be set later |
537 |
cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex()); |
538 |
|
539 |
return cg; |
540 |
} |
541 |
|
542 |
void MoleculeCreator::createConstraintPair(Molecule* mol) { |
543 |
|
544 |
//add bond constraints |
545 |
Molecule::BondIterator bi; |
546 |
Bond* bond; |
547 |
for (bond = mol->beginBond(bi); bond != NULL; bond = mol->nextBond(bi)) { |
548 |
|
549 |
BondType* bt = bond->getBondType(); |
550 |
|
551 |
if (typeid(FixedBondType) == typeid(*bt)) { |
552 |
FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt); |
553 |
|
554 |
ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA()); |
555 |
ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB()); |
556 |
ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength()); |
557 |
mol->addConstraintPair(consPair); |
558 |
} |
559 |
} |
560 |
|
561 |
//rigidbody -- rigidbody constraint is not support yet |
562 |
} |
563 |
|
564 |
void MoleculeCreator::createConstraintElem(Molecule* mol) { |
565 |
|
566 |
ConstraintPair* consPair; |
567 |
Molecule::ConstraintPairIterator cpi; |
568 |
std::set<StuntDouble*> sdSet; |
569 |
for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) { |
570 |
|
571 |
StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble(); |
572 |
if (sdSet.find(sdA) == sdSet.end()){ |
573 |
sdSet.insert(sdA); |
574 |
mol->addConstraintElem(new ConstraintElem(sdA)); |
575 |
} |
576 |
|
577 |
StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble(); |
578 |
if (sdSet.find(sdB) == sdSet.end()){ |
579 |
sdSet.insert(sdB); |
580 |
mol->addConstraintElem(new ConstraintElem(sdB)); |
581 |
} |
582 |
|
583 |
} |
584 |
|
585 |
} |
586 |
|
587 |
} |