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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. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* 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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|
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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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#include <cassert> |
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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 "types/DirectionalAtomType.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 oopse { |
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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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|
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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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} |
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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->getRigidBody(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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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->getBond(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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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->getBend(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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|
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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->getTorsion(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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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->getCutoffGroup(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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|
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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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} |
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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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|
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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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|
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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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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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} |
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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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//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, 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()); |
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|
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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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|
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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()){ |
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|
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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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|
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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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} |
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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, 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 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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} |
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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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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 rigidbody MoleculeName_RB_Integer |
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//The first part is the name of the molecule |
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//The second part is alway 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 |
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/**@todo replace itoa by lexi_cast */ |
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rb->setType(mol->getType() + "_RB_" + toString(mol->getNRigidBodies())); |
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|
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return rb; |
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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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BondType* bondType; |
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Atom* atomA; |
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Atom* atomB; |
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|
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atomA = mol->getAtomAt(stamp->getA()); |
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atomB = mol->getAtomAt(stamp->getB()); |
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|
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assert( atomA && atomB); |
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|
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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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|
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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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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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|
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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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|
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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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|
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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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|
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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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|
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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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} |
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|
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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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sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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BendType* bendType = ff->getBendType(normalAtom->getType(), ghostAtom->getType(), "GHOST"); |
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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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normalAtom->getType().c_str(), |
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ghostAtom->getType().c_str(), |
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"GHOST"); |
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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 GhostBend(normalAtom, ghostAtom, bendType); |
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|
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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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Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, TorsionStamp* stamp) { |
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TorsionType* torsionType; |
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Atom* atomA; |
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Atom* atomB; |
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Atom* atomC; |
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Atom* atomD; |
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|
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atomA = mol->getAtomAt(stamp->getA()); |
| 386 |
atomB = mol->getAtomAt(stamp->getB()); |
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atomC = mol->getAtomAt(stamp->getC()); |
| 388 |
atomD = mol->getAtomAt(stamp->getD()); |
| 389 |
|
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assert(atomA && atomB && atomC && atomD); |
| 391 |
|
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torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(), |
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atomC->getType(), atomD->getType()); |
| 394 |
|
| 395 |
if (torsionType == NULL) { |
| 396 |
sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %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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atomD->getType().c_str()); |
| 401 |
|
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painCave.isFatal = 1; |
| 403 |
simError(); |
| 404 |
} |
| 405 |
|
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return new Torsion(atomA, atomB, atomC, atomD, torsionType); |
| 407 |
} |
| 408 |
|
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CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, CutoffGroupStamp* stamp) { |
| 410 |
int nAtoms; |
| 411 |
CutoffGroup* cg; |
| 412 |
Atom* atom; |
| 413 |
cg = new CutoffGroup(); |
| 414 |
|
| 415 |
nAtoms = stamp->getNMembers(); |
| 416 |
for (int i =0; i < nAtoms; ++i) { |
| 417 |
atom = mol->getAtomAt(stamp->getMember(i)); |
| 418 |
assert(atom); |
| 419 |
cg->addAtom(atom); |
| 420 |
} |
| 421 |
|
| 422 |
return cg; |
| 423 |
} |
| 424 |
|
| 425 |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom) { |
| 426 |
CutoffGroup* cg; |
| 427 |
cg = new CutoffGroup(); |
| 428 |
cg->addAtom(atom); |
| 429 |
return cg; |
| 430 |
} |
| 431 |
|
| 432 |
void MoleculeCreator::createConstraintPair(Molecule* mol) { |
| 433 |
|
| 434 |
//add bond constraints |
| 435 |
Molecule::BondIterator bi; |
| 436 |
Bond* bond; |
| 437 |
for (bond = mol->beginBond(bi); bond != NULL; bond = mol->nextBond(bi)) { |
| 438 |
|
| 439 |
BondType* bt = bond->getBondType(); |
| 440 |
|
| 441 |
//class Parent1 {}; |
| 442 |
//class Child1 : public Parent {}; |
| 443 |
//class Child2 : public Parent {}; |
| 444 |
//Child1* ch1 = new Child1(); |
| 445 |
//Child2* ch2 = dynamic_cast<Child2*>(ch1); |
| 446 |
//the dynamic_cast is succeed in above line. A compiler bug? |
| 447 |
|
| 448 |
if (typeid(FixedBondType) == typeid(*bt)) { |
| 449 |
FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt); |
| 450 |
|
| 451 |
ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA()); |
| 452 |
ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB()); |
| 453 |
ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength()); |
| 454 |
mol->addConstraintPair(consPair); |
| 455 |
} |
| 456 |
} |
| 457 |
|
| 458 |
//rigidbody -- rigidbody constraint is not support yet |
| 459 |
} |
| 460 |
|
| 461 |
void MoleculeCreator::createConstraintElem(Molecule* mol) { |
| 462 |
|
| 463 |
ConstraintPair* consPair; |
| 464 |
Molecule::ConstraintPairIterator cpi; |
| 465 |
std::set<StuntDouble*> sdSet; |
| 466 |
for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) { |
| 467 |
|
| 468 |
StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble(); |
| 469 |
if (sdSet.find(sdA) == sdSet.end()){ |
| 470 |
sdSet.insert(sdA); |
| 471 |
mol->addConstraintElem(new ConstraintElem(sdA)); |
| 472 |
} |
| 473 |
|
| 474 |
StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble(); |
| 475 |
if (sdSet.find(sdB) == sdSet.end()){ |
| 476 |
sdSet.insert(sdB); |
| 477 |
mol->addConstraintElem(new ConstraintElem(sdB)); |
| 478 |
} |
| 479 |
|
| 480 |
} |
| 481 |
|
| 482 |
} |
| 483 |
|
| 484 |
} |
