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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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* such damages. |
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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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* @time 13:44am |
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* @version 1.0 |
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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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* @time 13:44am |
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* @version 1.0 |
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*/ |
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#include <cassert> |
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#include <set> |
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#include "utils/StringUtils.hpp" |
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namespace oopse { |
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Molecule* MoleculeCreator::createMolecule(ForceField* ff, MoleculeStamp *molStamp, |
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int stampId, int globalIndex, LocalIndexManager* localIndexMan) { |
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|
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Molecule* MoleculeCreator::createMolecule(ForceField* ff, MoleculeStamp *molStamp, |
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int stampId, int globalIndex, LocalIndexManager* localIndexMan) { |
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|
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Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getID()); |
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Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName()); |
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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->getAtom(i); |
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atom = createAtom(ff, mol, currentAtomStamp, localIndexMan); |
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mol->addAtom(atom); |
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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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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->getRigidBody(i); |
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rb = createRigidBody(molStamp, mol, currentRigidBodyStamp, localIndexMan); |
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mol->addRigidBody(rb); |
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currentRigidBodyStamp = molStamp->getRigidBodyStamp(i); |
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rb = createRigidBody(molStamp, mol, currentRigidBodyStamp, 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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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->getBond(i); |
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bond = createBond(ff, mol, currentBondStamp); |
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mol->addBond(bond); |
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currentBondStamp = molStamp->getBondStamp(i); |
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bond = createBond(ff, mol, currentBondStamp); |
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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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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->getBend(i); |
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bend = createBend(ff, mol, currentBendStamp); |
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mol->addBend(bend); |
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currentBendStamp = molStamp->getBendStamp(i); |
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bend = createBend(ff, mol, currentBendStamp); |
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mol->addBend(bend); |
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} |
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//create torsions |
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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->getTorsion(i); |
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torsion = createTorsion(ff, mol, currentTorsionStamp); |
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mol->addTorsion(torsion); |
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currentTorsionStamp = molStamp->getTorsionStamp(i); |
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torsion = createTorsion(ff, mol, currentTorsionStamp); |
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mol->addTorsion(torsion); |
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} |
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|
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//create cutoffGroups |
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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->getCutoffGroup(i); |
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cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp); |
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mol->addCutoffGroup(cutoffGroup); |
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currentCutoffGroupStamp = molStamp->getCutoffGroupStamp(i); |
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cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp); |
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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::set<Atom*> allAtoms; |
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Molecule::AtomIterator ai; |
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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(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
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allAtoms.insert(atom); |
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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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Molecule::CutoffGroupIterator ci; |
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CutoffGroup* cg; |
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std::set<Atom*> cutoffAtoms; |
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|
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//add all of the atoms belong to cutoff groups into cutoffAtoms set |
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for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
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for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
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cutoffAtoms.insert(atom); |
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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), freeAtoms.end()); |
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} |
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|
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} |
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|
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//find all free atoms (which do not belong to cutoff groups) |
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//performs the "difference" operation from set theory, the output range contains a copy of every |
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//element that is contained in [allAtoms.begin(), allAtoms.end()) and not contained in |
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//[cutoffAtoms.begin(), cutoffAtoms.end()). |
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std::vector<Atom*> freeAtoms; |
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std::set_difference(allAtoms.begin(), allAtoms.end(), cutoffAtoms.begin(), cutoffAtoms.end(), |
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std::back_inserter(freeAtoms)); |
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|
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if (freeAtoms.size() != allAtoms.size() - cutoffAtoms.size()) { |
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//Some atoms in rigidAtoms are not in allAtoms, something must be wrong |
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sprintf(painCave.errMsg, "Atoms in cutoff groups are not in the atom list of the same molecule"); |
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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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//loop over the free atoms and then create one cutoff group for every single free atom |
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std::vector<Atom*>::iterator fai; |
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|
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|
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for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) { |
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cutoffGroup = createCutoffGroup(mol, *fai); |
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mol->addCutoffGroup(cutoffGroup); |
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cutoffGroup = createCutoffGroup(mol, *fai); |
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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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mol->complete(); |
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return mol; |
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} |
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} |
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Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol, AtomStamp* stamp, |
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LocalIndexManager* localIndexMan) { |
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Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol, AtomStamp* stamp, |
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LocalIndexManager* localIndexMan) { |
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AtomType * atomType; |
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Atom* atom; |
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atomType = ff->getAtomType(stamp->getType()); |
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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()); |
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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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painCave.isFatal = 1; |
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simError(); |
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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()){ |
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DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType); |
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DirectionalAtomType* dAtomType = dynamic_cast<DirectionalAtomType*>(atomType); |
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|
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if (dAtomType == NULL) { |
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sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType"); |
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if (dAtomType == NULL) { |
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sprintf(painCave.errMsg, "Can not cast AtomType to DirectionalAtomType"); |
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|
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painCave.isFatal = 1; |
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simError(); |
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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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DirectionalAtom* dAtom; |
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dAtom = new DirectionalAtom(dAtomType); |
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atom = dAtom; |
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DirectionalAtom* dAtom; |
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dAtom = new DirectionalAtom(dAtomType); |
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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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atom = new Atom(atomType); |
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} |
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atom->setLocalIndex(localIndexMan->getNextAtomIndex()); |
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return atom; |
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} |
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} |
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RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp, Molecule* mol, |
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RigidBodyStamp* rbStamp, |
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LocalIndexManager* localIndexMan) { |
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RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp, 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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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 inside the molecule. |
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//It is not the same as local index of atom which is the index of atom at DataStorage class |
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atom = mol->getAtomAt(rbStamp->getMember(i)); |
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atomStamp= molStamp->getAtom(rbStamp->getMember(i)); |
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rb->addAtom(atom, atomStamp); |
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//rbStamp->getMember(i) return the local index of current atom inside the molecule. |
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//It is not the same as local index of 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 reference coordinates |
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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 |
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/**@todo replace itoa by lexi_cast */ |
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char buffer [33]; |
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sprintf(buffer, "%d", mol->getNRigidBodies()); |
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//rb->setType(mol->getType() + "_RB_" + toString<int>(mol->getNRigidBodies())); |
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rb->setType(mol->getType() + "_RB_" + buffer); |
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std::string s = OOPSE_itoa(mol->getNRigidBodies(), 10); |
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> |
rb->setType(mol->getType() + "_RB_" + s.c_str()); |
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|
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return rb; |
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} |
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} |
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|
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Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, BondStamp* stamp) { |
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> |
Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, BondStamp* stamp) { |
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BondType* bondType; |
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Atom* atomA; |
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Atom* atomB; |
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bondType = ff->getBondType(atomA->getType(), atomB->getType()); |
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|
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if (bondType == NULL) { |
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sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]", |
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atomA->getType().c_str(), |
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atomB->getType().c_str()); |
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> |
sprintf(painCave.errMsg, "Can not find Matching Bond Type for[%s, %s]", |
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atomA->getType().c_str(), |
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atomB->getType().c_str()); |
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|
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painCave.isFatal = 1; |
263 |
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simError(); |
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> |
painCave.isFatal = 1; |
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> |
simError(); |
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} |
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return new Bond(atomA, atomB, bondType); |
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} |
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} |
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|
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Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) { |
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< |
bool isGhostBend = false; |
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< |
int ghostIndex; |
268 |
> |
Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) { |
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> |
Bend* bend = NULL; |
270 |
> |
std::vector<int> bendAtoms = stamp->getMembers(); |
271 |
> |
if (bendAtoms.size() == 3) { |
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> |
Atom* atomA = mol->getAtomAt(bendAtoms[0]); |
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> |
Atom* atomB = mol->getAtomAt(bendAtoms[1]); |
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> |
Atom* atomC = mol->getAtomAt(bendAtoms[2]); |
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|
276 |
< |
|
292 |
< |
// |
293 |
< |
if (stamp->haveExtras()){ |
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< |
LinkedAssign* extras = stamp->getExtras(); |
295 |
< |
LinkedAssign* currentExtra = extras; |
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> |
assert( atomA && atomB && atomC); |
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|
|
278 |
< |
while (currentExtra != NULL){ |
298 |
< |
if (!strcmp(currentExtra->getlhs(), "ghostVectorSource")){ |
299 |
< |
switch (currentExtra->getType()){ |
300 |
< |
case 0: |
301 |
< |
ghostIndex = currentExtra->getInt(); |
302 |
< |
isGhostBend = true; |
303 |
< |
break; |
278 |
> |
BendType* bendType = ff->getBendType(atomA->getType().c_str(), atomB->getType().c_str(), atomC->getType().c_str()); |
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|
|
280 |
< |
default: |
281 |
< |
sprintf(painCave.errMsg, |
282 |
< |
"SimSetup Error: ghostVectorSource must be an int.\n"); |
283 |
< |
painCave.isFatal = 1; |
284 |
< |
simError(); |
310 |
< |
} |
311 |
< |
} else{ |
312 |
< |
sprintf(painCave.errMsg, |
313 |
< |
"SimSetup Error: unhandled bend assignment:\n"); |
314 |
< |
painCave.isFatal = 1; |
315 |
< |
simError(); |
316 |
< |
} |
317 |
< |
currentExtra = currentExtra->getNext(); |
318 |
< |
} |
319 |
< |
|
320 |
< |
} |
280 |
> |
if (bendType == NULL) { |
281 |
> |
sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]", |
282 |
> |
atomA->getType().c_str(), |
283 |
> |
atomB->getType().c_str(), |
284 |
> |
atomC->getType().c_str()); |
285 |
|
|
286 |
< |
if (isGhostBend) { |
286 |
> |
painCave.isFatal = 1; |
287 |
> |
simError(); |
288 |
> |
} |
289 |
|
|
290 |
< |
int indexA = stamp->getA(); |
291 |
< |
int indexB= stamp->getB(); |
290 |
> |
bend = new Bend(atomA, atomB, atomC, bendType); |
291 |
> |
} else if ( bendAtoms.size() == 2 && stamp->haveGhostVectorSource()) { |
292 |
> |
int ghostIndex = stamp->getGhostVectorSource(); |
293 |
> |
int normalIndex = ghostIndex != bendAtoms[0] ? bendAtoms[0] : bendAtoms[1]; |
294 |
> |
Atom* normalAtom = mol->getAtomAt(normalIndex) ; |
295 |
> |
DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex)); |
296 |
> |
if (ghostAtom == NULL) { |
297 |
> |
sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom"); |
298 |
> |
painCave.isFatal = 1; |
299 |
> |
simError(); |
300 |
> |
} |
301 |
> |
|
302 |
> |
BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST"); |
303 |
|
|
304 |
< |
assert(indexA != indexB); |
305 |
< |
|
306 |
< |
int normalIndex; |
307 |
< |
if (indexA == ghostIndex) { |
308 |
< |
normalIndex = indexB; |
332 |
< |
} else if (indexB == ghostIndex) { |
333 |
< |
normalIndex = indexA; |
334 |
< |
} |
335 |
< |
|
336 |
< |
Atom* normalAtom = mol->getAtomAt(normalIndex) ; |
337 |
< |
DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex)); |
338 |
< |
if (ghostAtom == NULL) { |
339 |
< |
sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom"); |
340 |
< |
painCave.isFatal = 1; |
341 |
< |
simError(); |
342 |
< |
} |
343 |
< |
|
344 |
< |
BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST"); |
304 |
> |
if (bendType == NULL) { |
305 |
> |
sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]", |
306 |
> |
normalAtom->getType().c_str(), |
307 |
> |
ghostAtom->getType().c_str(), |
308 |
> |
"GHOST"); |
309 |
|
|
310 |
< |
if (bendType == NULL) { |
311 |
< |
sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]", |
312 |
< |
normalAtom->getType().c_str(), |
349 |
< |
ghostAtom->getType().c_str(), |
350 |
< |
"GHOST"); |
351 |
< |
|
352 |
< |
painCave.isFatal = 1; |
353 |
< |
simError(); |
354 |
< |
} |
310 |
> |
painCave.isFatal = 1; |
311 |
> |
simError(); |
312 |
> |
} |
313 |
|
|
314 |
< |
return new GhostBend(normalAtom, ghostAtom, bendType); |
314 |
> |
bend = new GhostBend(normalAtom, ghostAtom, bendType); |
315 |
|
|
316 |
< |
} else { |
317 |
< |
|
318 |
< |
Atom* atomA = mol->getAtomAt(stamp->getA()); |
319 |
< |
Atom* atomB = mol->getAtomAt(stamp->getB()); |
362 |
< |
Atom* atomC = mol->getAtomAt(stamp->getC()); |
316 |
> |
} |
317 |
> |
|
318 |
> |
return bend; |
319 |
> |
} |
320 |
|
|
321 |
< |
assert( atomA && atomB && atomC); |
365 |
< |
|
366 |
< |
BendType* bendType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType()); |
321 |
> |
Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) { |
322 |
|
|
323 |
< |
if (bendType == NULL) { |
324 |
< |
sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]", |
325 |
< |
atomA->getType().c_str(), |
326 |
< |
atomB->getType().c_str(), |
372 |
< |
atomC->getType().c_str()); |
373 |
< |
|
374 |
< |
painCave.isFatal = 1; |
375 |
< |
simError(); |
376 |
< |
} |
377 |
< |
|
378 |
< |
return new Bend(atomA, atomB, atomC, bendType); |
323 |
> |
Torsion* torsion = NULL; |
324 |
> |
std::vector<int> torsionAtoms = stamp->getMembers(); |
325 |
> |
if (torsionAtoms.size() < 3) { |
326 |
> |
return torsion; |
327 |
|
} |
380 |
– |
} |
328 |
|
|
329 |
< |
Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) { |
329 |
> |
Atom* atomA = mol->getAtomAt(torsionAtoms[0]); |
330 |
> |
Atom* atomB = mol->getAtomAt(torsionAtoms[1]); |
331 |
> |
Atom* atomC = mol->getAtomAt(torsionAtoms[2]); |
332 |
|
|
333 |
< |
Atom* atomA = mol->getAtomAt(stamp->getA()); |
334 |
< |
Atom* atomB = mol->getAtomAt(stamp->getB()); |
386 |
< |
Atom* atomC = mol->getAtomAt(stamp->getC()); |
387 |
< |
Torsion* torsion; |
333 |
> |
if (torsionAtoms.size() == 4) { |
334 |
> |
Atom* atomD = mol->getAtomAt(torsionAtoms[3]); |
335 |
|
|
336 |
< |
if (stamp->getD() != -1) { |
390 |
< |
Atom* atomD = mol->getAtomAt(stamp->getD()); |
391 |
< |
|
392 |
< |
assert(atomA && atomB && atomC && atomD); |
336 |
> |
assert(atomA && atomB && atomC && atomD); |
337 |
|
|
338 |
< |
TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(), |
339 |
< |
atomC->getType(), atomD->getType()); |
338 |
> |
TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(), |
339 |
> |
atomC->getType(), atomD->getType()); |
340 |
|
|
341 |
< |
if (torsionType == NULL) { |
342 |
< |
sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]", |
343 |
< |
atomA->getType().c_str(), |
344 |
< |
atomB->getType().c_str(), |
345 |
< |
atomC->getType().c_str(), |
346 |
< |
atomD->getType().c_str()); |
341 |
> |
if (torsionType == NULL) { |
342 |
> |
sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]", |
343 |
> |
atomA->getType().c_str(), |
344 |
> |
atomB->getType().c_str(), |
345 |
> |
atomC->getType().c_str(), |
346 |
> |
atomD->getType().c_str()); |
347 |
|
|
348 |
< |
painCave.isFatal = 1; |
349 |
< |
simError(); |
350 |
< |
} |
348 |
> |
painCave.isFatal = 1; |
349 |
> |
simError(); |
350 |
> |
} |
351 |
|
|
352 |
< |
torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType); |
352 |
> |
torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType); |
353 |
|
} |
354 |
|
else { |
355 |
|
|
356 |
< |
DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(atomC); |
357 |
< |
if (dAtom == NULL) { |
358 |
< |
sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom"); |
359 |
< |
painCave.isFatal = 1; |
360 |
< |
simError(); |
361 |
< |
} |
356 |
> |
DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(stamp->getGhostVectorSource())); |
357 |
> |
if (dAtom == NULL) { |
358 |
> |
sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom"); |
359 |
> |
painCave.isFatal = 1; |
360 |
> |
simError(); |
361 |
> |
} |
362 |
|
|
363 |
< |
TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(), |
364 |
< |
atomC->getType(), "GHOST"); |
363 |
> |
TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(), |
364 |
> |
atomC->getType(), "GHOST"); |
365 |
|
|
366 |
< |
if (torsionType == NULL) { |
367 |
< |
sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]", |
368 |
< |
atomA->getType().c_str(), |
369 |
< |
atomB->getType().c_str(), |
370 |
< |
atomC->getType().c_str(), |
371 |
< |
"GHOST"); |
366 |
> |
if (torsionType == NULL) { |
367 |
> |
sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]", |
368 |
> |
atomA->getType().c_str(), |
369 |
> |
atomB->getType().c_str(), |
370 |
> |
atomC->getType().c_str(), |
371 |
> |
"GHOST"); |
372 |
|
|
373 |
< |
painCave.isFatal = 1; |
374 |
< |
simError(); |
375 |
< |
} |
373 |
> |
painCave.isFatal = 1; |
374 |
> |
simError(); |
375 |
> |
} |
376 |
|
|
377 |
< |
torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType); |
377 |
> |
torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType); |
378 |
|
} |
379 |
|
|
380 |
|
return torsion; |
381 |
< |
} |
381 |
> |
} |
382 |
|
|
383 |
< |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) { |
383 |
> |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) { |
384 |
|
int nAtoms; |
385 |
|
CutoffGroup* cg; |
386 |
|
Atom* atom; |
388 |
|
|
389 |
|
nAtoms = stamp->getNMembers(); |
390 |
|
for (int i =0; i < nAtoms; ++i) { |
391 |
< |
atom = mol->getAtomAt(stamp->getMember(i)); |
392 |
< |
assert(atom); |
393 |
< |
cg->addAtom(atom); |
391 |
> |
atom = mol->getAtomAt(stamp->getMemberAt(i)); |
392 |
> |
assert(atom); |
393 |
> |
cg->addAtom(atom); |
394 |
|
} |
395 |
|
|
396 |
|
return cg; |
397 |
< |
} |
397 |
> |
} |
398 |
|
|
399 |
< |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) { |
399 |
> |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) { |
400 |
|
CutoffGroup* cg; |
401 |
|
cg = new CutoffGroup(); |
402 |
|
cg->addAtom(atom); |
403 |
|
return cg; |
404 |
< |
} |
404 |
> |
} |
405 |
|
|
406 |
< |
void MoleculeCreator::createConstraintPair(Molecule* mol) { |
406 |
> |
void MoleculeCreator::createConstraintPair(Molecule* mol) { |
407 |
|
|
408 |
|
//add bond constraints |
409 |
|
Molecule::BondIterator bi; |
410 |
|
Bond* bond; |
411 |
|
for (bond = mol->beginBond(bi); bond != NULL; bond = mol->nextBond(bi)) { |
412 |
|
|
413 |
< |
BondType* bt = bond->getBondType(); |
413 |
> |
BondType* bt = bond->getBondType(); |
414 |
|
|
415 |
< |
//class Parent1 {}; |
416 |
< |
//class Child1 : public Parent {}; |
417 |
< |
//class Child2 : public Parent {}; |
418 |
< |
//Child1* ch1 = new Child1(); |
419 |
< |
//Child2* ch2 = dynamic_cast<Child2*>(ch1); |
420 |
< |
//the dynamic_cast is succeed in above line. A compiler bug? |
415 |
> |
//class Parent1 {}; |
416 |
> |
//class Child1 : public Parent {}; |
417 |
> |
//class Child2 : public Parent {}; |
418 |
> |
//Child1* ch1 = new Child1(); |
419 |
> |
//Child2* ch2 = dynamic_cast<Child2*>(ch1); |
420 |
> |
//the dynamic_cast is succeed in above line. A compiler bug? |
421 |
|
|
422 |
< |
if (typeid(FixedBondType) == typeid(*bt)) { |
423 |
< |
FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt); |
422 |
> |
if (typeid(FixedBondType) == typeid(*bt)) { |
423 |
> |
FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt); |
424 |
|
|
425 |
< |
ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA()); |
426 |
< |
ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB()); |
427 |
< |
ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength()); |
428 |
< |
mol->addConstraintPair(consPair); |
429 |
< |
} |
425 |
> |
ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA()); |
426 |
> |
ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB()); |
427 |
> |
ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength()); |
428 |
> |
mol->addConstraintPair(consPair); |
429 |
> |
} |
430 |
|
} |
431 |
|
|
432 |
|
//rigidbody -- rigidbody constraint is not support yet |
433 |
< |
} |
433 |
> |
} |
434 |
|
|
435 |
< |
void MoleculeCreator::createConstraintElem(Molecule* mol) { |
435 |
> |
void MoleculeCreator::createConstraintElem(Molecule* mol) { |
436 |
|
|
437 |
|
ConstraintPair* consPair; |
438 |
|
Molecule::ConstraintPairIterator cpi; |
439 |
|
std::set<StuntDouble*> sdSet; |
440 |
|
for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) { |
441 |
|
|
442 |
< |
StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble(); |
443 |
< |
if (sdSet.find(sdA) == sdSet.end()){ |
444 |
< |
sdSet.insert(sdA); |
445 |
< |
mol->addConstraintElem(new ConstraintElem(sdA)); |
446 |
< |
} |
442 |
> |
StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble(); |
443 |
> |
if (sdSet.find(sdA) == sdSet.end()){ |
444 |
> |
sdSet.insert(sdA); |
445 |
> |
mol->addConstraintElem(new ConstraintElem(sdA)); |
446 |
> |
} |
447 |
|
|
448 |
< |
StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble(); |
449 |
< |
if (sdSet.find(sdB) == sdSet.end()){ |
450 |
< |
sdSet.insert(sdB); |
451 |
< |
mol->addConstraintElem(new ConstraintElem(sdB)); |
452 |
< |
} |
448 |
> |
StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble(); |
449 |
> |
if (sdSet.find(sdB) == sdSet.end()){ |
450 |
> |
sdSet.insert(sdB); |
451 |
> |
mol->addConstraintElem(new ConstraintElem(sdB)); |
452 |
> |
} |
453 |
|
|
454 |
|
} |
455 |
|
|
456 |
< |
} |
456 |
> |
} |
457 |
|
|
458 |
|
} |