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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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/** |
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* @file MoleculeCreator.cpp |
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* @author tlin |
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* @date 11/04/2004 |
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* @version 1.0 |
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*/ |
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|
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#include <cassert> |
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#include <typeinfo> |
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#include <set> |
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|
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#include "brains/MoleculeCreator.hpp" |
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#include "primitives/GhostBend.hpp" |
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#include "primitives/GhostTorsion.hpp" |
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#include "types/AtomType.hpp" |
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#include "types/FixedBondType.hpp" |
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#include "utils/simError.h" |
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#include "utils/StringUtils.hpp" |
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|
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namespace OpenMD { |
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|
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Molecule* MoleculeCreator::createMolecule(ForceField* ff, |
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MoleculeStamp *molStamp, |
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int stampId, int globalIndex, |
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LocalIndexManager* localIndexMan) { |
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Molecule* mol = new Molecule(stampId, globalIndex, molStamp->getName()); |
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|
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//create atoms |
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Atom* atom; |
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AtomStamp* currentAtomStamp; |
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int nAtom = molStamp->getNAtoms(); |
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for (int i = 0; i < nAtom; ++i) { |
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currentAtomStamp = molStamp->getAtomStamp(i); |
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atom = createAtom(ff, mol, currentAtomStamp, localIndexMan); |
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mol->addAtom(atom); |
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} |
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|
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//create rigidbodies |
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RigidBody* rb; |
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RigidBodyStamp * currentRigidBodyStamp; |
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int nRigidbodies = molStamp->getNRigidBodies(); |
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|
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for (int i = 0; i < nRigidbodies; ++i) { |
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currentRigidBodyStamp = molStamp->getRigidBodyStamp(i); |
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rb = createRigidBody(molStamp, mol, currentRigidBodyStamp, |
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localIndexMan); |
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mol->addRigidBody(rb); |
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} |
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|
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//create bonds |
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Bond* bond; |
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BondStamp* currentBondStamp; |
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int nBonds = molStamp->getNBonds(); |
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|
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for (int i = 0; i < nBonds; ++i) { |
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currentBondStamp = molStamp->getBondStamp(i); |
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bond = createBond(ff, mol, currentBondStamp); |
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mol->addBond(bond); |
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} |
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|
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//create bends |
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Bend* bend; |
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BendStamp* currentBendStamp; |
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int nBends = molStamp->getNBends(); |
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for (int i = 0; i < nBends; ++i) { |
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currentBendStamp = molStamp->getBendStamp(i); |
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bend = createBend(ff, mol, currentBendStamp); |
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mol->addBend(bend); |
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} |
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|
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//create torsions |
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Torsion* torsion; |
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TorsionStamp* currentTorsionStamp; |
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int nTorsions = molStamp->getNTorsions(); |
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for (int i = 0; i < nTorsions; ++i) { |
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currentTorsionStamp = molStamp->getTorsionStamp(i); |
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torsion = createTorsion(ff, mol, currentTorsionStamp); |
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mol->addTorsion(torsion); |
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} |
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|
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//create inversions |
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Inversion* inversion; |
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InversionStamp* currentInversionStamp; |
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int nInversions = molStamp->getNInversions(); |
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for (int i = 0; i < nInversions; ++i) { |
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currentInversionStamp = molStamp->getInversionStamp(i); |
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inversion = createInversion(ff, mol, currentInversionStamp); |
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if (inversion != NULL ) { |
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mol->addInversion(inversion); |
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} |
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} |
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|
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//create cutoffGroups |
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CutoffGroup* cutoffGroup; |
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CutoffGroupStamp* currentCutoffGroupStamp; |
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int nCutoffGroups = molStamp->getNCutoffGroups(); |
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for (int i = 0; i < nCutoffGroups; ++i) { |
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currentCutoffGroupStamp = molStamp->getCutoffGroupStamp(i); |
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cutoffGroup = createCutoffGroup(mol, currentCutoffGroupStamp, localIndexMan); |
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mol->addCutoffGroup(cutoffGroup); |
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} |
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|
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//every free atom is a cutoff group |
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std::vector<Atom*> freeAtoms; |
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std::vector<Atom*>::iterator ai; |
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std::vector<Atom*>::iterator fai; |
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|
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//add all atoms into allAtoms set |
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for(atom = mol->beginAtom(fai); atom != NULL; atom = mol->nextAtom(fai)) { |
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freeAtoms.push_back(atom); |
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} |
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|
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Molecule::CutoffGroupIterator ci; |
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CutoffGroup* cg; |
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|
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for (cg = mol->beginCutoffGroup(ci); cg != NULL; |
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cg = mol->nextCutoffGroup(ci)) { |
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|
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for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
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//erase the atoms belong to cutoff groups from freeAtoms vector |
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freeAtoms.erase(std::remove(freeAtoms.begin(), freeAtoms.end(), atom), |
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freeAtoms.end()); |
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} |
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} |
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|
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// loop over the free atoms and then create one cutoff group for |
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// every single free atom |
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|
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for (fai = freeAtoms.begin(); fai != freeAtoms.end(); ++fai) { |
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cutoffGroup = createCutoffGroup(mol, *fai, localIndexMan); |
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mol->addCutoffGroup(cutoffGroup); |
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} |
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//create constraints |
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createConstraintPair(mol); |
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createConstraintElem(mol); |
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|
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// Does this molecule stamp define a total constrained charge value? |
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// If so, let the created molecule know about it. |
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|
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if (molStamp->haveConstrainTotalCharge() ) { |
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mol->setConstrainTotalCharge( molStamp->getConstrainTotalCharge() ); |
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} |
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|
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//the construction of this molecule is finished |
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mol->complete(); |
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|
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return mol; |
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} |
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|
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|
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Atom* MoleculeCreator::createAtom(ForceField* ff, Molecule* mol, |
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AtomStamp* stamp, |
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LocalIndexManager* localIndexMan) { |
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AtomType * atomType; |
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Atom* atom; |
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|
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atomType = ff->getAtomType(stamp->getType()); |
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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().c_str()); |
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|
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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//below code still have some kind of hard-coding smell |
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if (atomType->isDirectional()){ |
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|
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DirectionalAtom* dAtom; |
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dAtom = new DirectionalAtom(atomType); |
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atom = dAtom; |
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} |
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else{ |
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atom = new Atom(atomType); |
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} |
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|
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atom->setLocalIndex(localIndexMan->getNextAtomIndex()); |
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|
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return atom; |
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} |
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|
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RigidBody* MoleculeCreator::createRigidBody(MoleculeStamp *molStamp, |
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Molecule* mol, |
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RigidBodyStamp* rbStamp, |
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LocalIndexManager* localIndexMan) { |
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Atom* atom; |
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int nAtoms; |
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Vector3d refCoor; |
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AtomStamp* atomStamp; |
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|
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RigidBody* rb = new RigidBody(); |
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nAtoms = rbStamp->getNMembers(); |
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for (int i = 0; i < nAtoms; ++i) { |
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//rbStamp->getMember(i) return the local index of current atom |
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//inside the molecule. It is not the same as local index of |
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//atom which is the index of atom at DataStorage class |
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atom = mol->getAtomAt(rbStamp->getMemberAt(i)); |
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atomStamp= molStamp->getAtomStamp(rbStamp->getMemberAt(i)); |
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rb->addAtom(atom, atomStamp); |
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} |
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|
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//after all of the atoms are added, we need to calculate the |
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//reference coordinates |
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rb->calcRefCoords(); |
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|
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//set the local index of this rigid body, global index will be set later |
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rb->setLocalIndex(localIndexMan->getNextRigidBodyIndex()); |
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|
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//the rule for naming 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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std::string s = OpenMD_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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Bond* MoleculeCreator::createBond(ForceField* ff, Molecule* mol, |
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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, |
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BendStamp* stamp) { |
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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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assert( atomA && atomB && atomC); |
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|
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BendType* bendType = ff->getBendType(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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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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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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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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bend = new GhostBend(normalAtom, ghostAtom, bendType); |
| 338 |
|
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} |
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|
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return bend; |
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} |
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|
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Torsion* MoleculeCreator::createTorsion(ForceField* ff, Molecule* mol, |
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TorsionStamp* stamp) { |
| 346 |
|
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Torsion* torsion = NULL; |
| 348 |
std::vector<int> torsionAtoms = stamp->getMembers(); |
| 349 |
if (torsionAtoms.size() < 3) { |
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return torsion; |
| 351 |
} |
| 352 |
|
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Atom* atomA = mol->getAtomAt(torsionAtoms[0]); |
| 354 |
Atom* atomB = mol->getAtomAt(torsionAtoms[1]); |
| 355 |
Atom* atomC = mol->getAtomAt(torsionAtoms[2]); |
| 356 |
|
| 357 |
if (torsionAtoms.size() == 4) { |
| 358 |
Atom* atomD = mol->getAtomAt(torsionAtoms[3]); |
| 359 |
|
| 360 |
assert(atomA && atomB && atomC && atomD); |
| 361 |
|
| 362 |
TorsionType* torsionType = ff->getTorsionType(atomA->getType(), |
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atomB->getType(), |
| 364 |
atomC->getType(), |
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atomD->getType()); |
| 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 |
atomD->getType().c_str()); |
| 372 |
|
| 373 |
painCave.isFatal = 1; |
| 374 |
simError(); |
| 375 |
} |
| 376 |
|
| 377 |
torsion = new Torsion(atomA, atomB, atomC, atomD, torsionType); |
| 378 |
} |
| 379 |
else { |
| 380 |
|
| 381 |
DirectionalAtom* dAtom = dynamic_cast<DirectionalAtom*>(mol->getAtomAt(stamp->getGhostVectorSource())); |
| 382 |
if (dAtom == NULL) { |
| 383 |
sprintf(painCave.errMsg, "Can not cast Atom to DirectionalAtom"); |
| 384 |
painCave.isFatal = 1; |
| 385 |
simError(); |
| 386 |
} |
| 387 |
|
| 388 |
TorsionType* torsionType = ff->getTorsionType(atomA->getType(), atomB->getType(), |
| 389 |
atomC->getType(), "GHOST"); |
| 390 |
|
| 391 |
if (torsionType == NULL) { |
| 392 |
sprintf(painCave.errMsg, "Can not find Matching Torsion Type for[%s, %s, %s, %s]", |
| 393 |
atomA->getType().c_str(), |
| 394 |
atomB->getType().c_str(), |
| 395 |
atomC->getType().c_str(), |
| 396 |
"GHOST"); |
| 397 |
|
| 398 |
painCave.isFatal = 1; |
| 399 |
simError(); |
| 400 |
} |
| 401 |
|
| 402 |
torsion = new GhostTorsion(atomA, atomB, dAtom, torsionType); |
| 403 |
} |
| 404 |
|
| 405 |
return torsion; |
| 406 |
} |
| 407 |
|
| 408 |
Inversion* MoleculeCreator::createInversion(ForceField* ff, Molecule* mol, |
| 409 |
InversionStamp* stamp) { |
| 410 |
|
| 411 |
Inversion* inversion = NULL; |
| 412 |
int center = stamp->getCenter(); |
| 413 |
std::vector<int> satellites = stamp->getSatellites(); |
| 414 |
if (satellites.size() != 3) { |
| 415 |
return inversion; |
| 416 |
} |
| 417 |
|
| 418 |
Atom* atomA = mol->getAtomAt(center); |
| 419 |
Atom* atomB = mol->getAtomAt(satellites[0]); |
| 420 |
Atom* atomC = mol->getAtomAt(satellites[1]); |
| 421 |
Atom* atomD = mol->getAtomAt(satellites[2]); |
| 422 |
|
| 423 |
assert(atomA && atomB && atomC && atomD); |
| 424 |
|
| 425 |
InversionType* inversionType = ff->getInversionType(atomA->getType(), |
| 426 |
atomB->getType(), |
| 427 |
atomC->getType(), |
| 428 |
atomD->getType()); |
| 429 |
|
| 430 |
if (inversionType == NULL) { |
| 431 |
sprintf(painCave.errMsg, "No Matching Inversion Type for[%s, %s, %s, %s]\n" |
| 432 |
"\t(May not be a problem: not all inversions are parametrized)\n", |
| 433 |
atomA->getType().c_str(), |
| 434 |
atomB->getType().c_str(), |
| 435 |
atomC->getType().c_str(), |
| 436 |
atomD->getType().c_str()); |
| 437 |
|
| 438 |
painCave.isFatal = 0; |
| 439 |
painCave.severity = OPENMD_INFO; |
| 440 |
simError(); |
| 441 |
return NULL; |
| 442 |
} else { |
| 443 |
|
| 444 |
inversion = new Inversion(atomA, atomB, atomC, atomD, inversionType); |
| 445 |
return inversion; |
| 446 |
} |
| 447 |
} |
| 448 |
|
| 449 |
|
| 450 |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule* mol, |
| 451 |
CutoffGroupStamp* stamp, |
| 452 |
LocalIndexManager* localIndexMan) { |
| 453 |
int nAtoms; |
| 454 |
CutoffGroup* cg; |
| 455 |
Atom* atom; |
| 456 |
cg = new CutoffGroup(); |
| 457 |
|
| 458 |
nAtoms = stamp->getNMembers(); |
| 459 |
for (int i =0; i < nAtoms; ++i) { |
| 460 |
atom = mol->getAtomAt(stamp->getMemberAt(i)); |
| 461 |
assert(atom); |
| 462 |
cg->addAtom(atom); |
| 463 |
} |
| 464 |
|
| 465 |
//set the local index of this cutoffGroup, global index will be set later |
| 466 |
cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex()); |
| 467 |
|
| 468 |
return cg; |
| 469 |
} |
| 470 |
|
| 471 |
CutoffGroup* MoleculeCreator::createCutoffGroup(Molecule * mol, Atom* atom, |
| 472 |
LocalIndexManager* localIndexMan) { |
| 473 |
CutoffGroup* cg; |
| 474 |
cg = new CutoffGroup(); |
| 475 |
cg->addAtom(atom); |
| 476 |
|
| 477 |
//set the local index of this cutoffGroup, global index will be set later |
| 478 |
cg->setLocalIndex(localIndexMan->getNextCutoffGroupIndex()); |
| 479 |
|
| 480 |
return cg; |
| 481 |
} |
| 482 |
|
| 483 |
void MoleculeCreator::createConstraintPair(Molecule* mol) { |
| 484 |
|
| 485 |
//add bond constraints |
| 486 |
Molecule::BondIterator bi; |
| 487 |
Bond* bond; |
| 488 |
for (bond = mol->beginBond(bi); bond != NULL; bond = mol->nextBond(bi)) { |
| 489 |
|
| 490 |
BondType* bt = bond->getBondType(); |
| 491 |
|
| 492 |
//class Parent1 {}; |
| 493 |
//class Child1 : public Parent {}; |
| 494 |
//class Child2 : public Parent {}; |
| 495 |
//Child1* ch1 = new Child1(); |
| 496 |
//Child2* ch2 = dynamic_cast<Child2*>(ch1); |
| 497 |
//the dynamic_cast is succeed in above line. A compiler bug? |
| 498 |
|
| 499 |
if (typeid(FixedBondType) == typeid(*bt)) { |
| 500 |
FixedBondType* fbt = dynamic_cast<FixedBondType*>(bt); |
| 501 |
|
| 502 |
ConstraintElem* consElemA = new ConstraintElem(bond->getAtomA()); |
| 503 |
ConstraintElem* consElemB = new ConstraintElem(bond->getAtomB()); |
| 504 |
ConstraintPair* consPair = new ConstraintPair(consElemA, consElemB, fbt->getEquilibriumBondLength()); |
| 505 |
mol->addConstraintPair(consPair); |
| 506 |
} |
| 507 |
} |
| 508 |
|
| 509 |
//rigidbody -- rigidbody constraint is not support yet |
| 510 |
} |
| 511 |
|
| 512 |
void MoleculeCreator::createConstraintElem(Molecule* mol) { |
| 513 |
|
| 514 |
ConstraintPair* consPair; |
| 515 |
Molecule::ConstraintPairIterator cpi; |
| 516 |
std::set<StuntDouble*> sdSet; |
| 517 |
for (consPair = mol->beginConstraintPair(cpi); consPair != NULL; consPair = mol->nextConstraintPair(cpi)) { |
| 518 |
|
| 519 |
StuntDouble* sdA = consPair->getConsElem1()->getStuntDouble(); |
| 520 |
if (sdSet.find(sdA) == sdSet.end()){ |
| 521 |
sdSet.insert(sdA); |
| 522 |
mol->addConstraintElem(new ConstraintElem(sdA)); |
| 523 |
} |
| 524 |
|
| 525 |
StuntDouble* sdB = consPair->getConsElem2()->getStuntDouble(); |
| 526 |
if (sdSet.find(sdB) == sdSet.end()){ |
| 527 |
sdSet.insert(sdB); |
| 528 |
mol->addConstraintElem(new ConstraintElem(sdB)); |
| 529 |
} |
| 530 |
|
| 531 |
} |
| 532 |
|
| 533 |
} |
| 534 |
|
| 535 |
} |
