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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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< |
Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getID()); |
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> |
Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName()); |
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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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> |
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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int nRigidbodies = molStamp->getNRigidBodies(); |
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for (int i = 0; i < nRigidbodies; ++i) { |
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currentRigidBodyStamp = molStamp->getRigidBody(i); |
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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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int nBonds = molStamp->getNBonds(); |
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for (int i = 0; i < nBonds; ++i) { |
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currentBondStamp = molStamp->getBond(i); |
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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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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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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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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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> |
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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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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> |
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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//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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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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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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> |
stamp->getType().c_str()); |
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painCave.isFatal = 1; |
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simError(); |
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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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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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Bend* MoleculeCreator::createBend(ForceField* ff, Molecule* mol, BendStamp* stamp) { |
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bool isGhostBend = false; |
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int ghostIndex; |
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> |
Bend* bend = NULL; |
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> |
std::vector<int> bendAtoms = stamp->getMembers(); |
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> |
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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< |
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< |
// |
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< |
if (stamp->haveExtras()){ |
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< |
LinkedAssign* extras = stamp->getExtras(); |
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< |
LinkedAssign* currentExtra = extras; |
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assert( atomA && atomB && atomC); |
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< |
while (currentExtra != NULL){ |
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< |
if (!strcmp(currentExtra->getlhs(), "ghostVectorSource")){ |
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< |
switch (currentExtra->getType()){ |
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case 0: |
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< |
ghostIndex = currentExtra->getInt(); |
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< |
isGhostBend = true; |
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< |
break; |
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> |
BendType* bendType = ff->getBendType(atomA->getType().c_str(), atomB->getType().c_str(), atomC->getType().c_str()); |
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default: |
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< |
sprintf(painCave.errMsg, |
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"SimSetup Error: ghostVectorSource must be an int.\n"); |
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< |
painCave.isFatal = 1; |
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< |
simError(); |
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} |
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} else{ |
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< |
sprintf(painCave.errMsg, |
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"SimSetup Error: unhandled bend assignment:\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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< |
currentExtra = currentExtra->getNext(); |
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< |
} |
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< |
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} |
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> |
if (bendType == NULL) { |
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> |
sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]", |
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> |
atomA->getType().c_str(), |
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atomB->getType().c_str(), |
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atomC->getType().c_str()); |
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< |
if (isGhostBend) { |
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< |
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< |
int indexA = stamp->getA(); |
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< |
int indexB= stamp->getB(); |
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< |
assert(indexA != indexB); |
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< |
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< |
int normalIndex; |
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< |
if (indexA == ghostIndex) { |
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< |
normalIndex = indexB; |
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< |
} else if (indexB == ghostIndex) { |
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< |
normalIndex = indexA; |
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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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> |
bend = new Bend(atomA, atomB, atomC, bendType); |
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> |
} else if ( bendAtoms.size() == 2 && stamp->haveGhostVectorSource()) { |
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> |
int ghostIndex = stamp->getGhostVectorSource(); |
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> |
int normalIndex = ghostIndex != bendAtoms[0] ? bendAtoms[0] : bendAtoms[1]; |
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Atom* normalAtom = mol->getAtomAt(normalIndex) ; |
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DirectionalAtom* ghostAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(ghostIndex)); |
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if (ghostAtom == NULL) { |
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simError(); |
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} |
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< |
return new GhostBend(normalAtom, ghostAtom, bendType); |
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> |
bend = new GhostBend(normalAtom, ghostAtom, bendType); |
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< |
} else { |
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< |
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< |
Atom* atomA = mol->getAtomAt(stamp->getA()); |
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< |
Atom* atomB = mol->getAtomAt(stamp->getB()); |
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< |
Atom* atomC = mol->getAtomAt(stamp->getC()); |
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< |
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< |
assert( atomA && atomB && atomC); |
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< |
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< |
BendType* bendType = ff->getBendType(atomA->getType(), atomB->getType(), atomC->getType()); |
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< |
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< |
if (bendType == NULL) { |
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< |
sprintf(painCave.errMsg, "Can not find Matching Bend Type for[%s, %s, %s]", |
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< |
atomA->getType().c_str(), |
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< |
atomB->getType().c_str(), |
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< |
atomC->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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< |
return new Bend(atomA, atomB, atomC, bendType); |
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< |
} |
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> |
} |
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> |
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> |
return bend; |
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} |
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Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) { |
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< |
Atom* atomA = mol->getAtomAt(stamp->getA()); |
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< |
Atom* atomB = mol->getAtomAt(stamp->getB()); |
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< |
Atom* atomC = mol->getAtomAt(stamp->getC()); |
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< |
Torsion* torsion; |
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> |
Torsion* torsion = NULL; |
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> |
std::vector<int> torsionAtoms = stamp->getMembers(); |
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> |
if (torsionAtoms.size() < 3) { |
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> |
return torsion; |
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> |
} |
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< |
if (stamp->getD() != -1) { |
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< |
Atom* atomD = mol->getAtomAt(stamp->getD()); |
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> |
Atom* atomA = mol->getAtomAt(torsionAtoms[0]); |
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> |
Atom* atomB = mol->getAtomAt(torsionAtoms[1]); |
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> |
Atom* atomC = mol->getAtomAt(torsionAtoms[2]); |
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+ |
if (torsionAtoms.size() == 4) { |
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+ |
Atom* atomD = mol->getAtomAt(torsionAtoms[3]); |
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+ |
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assert(atomA && atomB && atomC && atomD); |
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TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(), |
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} |
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else { |
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< |
DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(atomC); |
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> |
DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(stamp->getGhostVectorSource())); |
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if (dAtom == NULL) { |
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sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom"); |
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painCave.isFatal = 1; |
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nAtoms = stamp->getNMembers(); |
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for (int i =0; i < nAtoms; ++i) { |
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< |
atom = mol->getAtomAt(stamp->getMember(i)); |
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> |
atom = mol->getAtomAt(stamp->getMemberAt(i)); |
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assert(atom); |
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cg->addAtom(atom); |
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} |
