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#include "utils/StringUtils.hpp" |
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namespace oopse { |
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< |
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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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//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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//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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//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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> |
//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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//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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< |
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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< |
painCave.isFatal = 1; |
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simError(); |
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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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> |
//loop over the free atoms and then create one cutoff group for every single free atom |
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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); |
