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/* |
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* copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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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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* @date 11/03/2004 |
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* @version 1.0 |
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*/ |
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#ifdef IS_MPI |
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#include "mpi.h" |
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#include "math/ParallelRandNumGen.hpp" |
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#endif |
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#include <exception> |
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#include <iostream> |
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#include <sstream> |
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#include "types/FixedChargeAdapter.hpp" |
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#include "types/FluctuatingChargeAdapter.hpp" |
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#ifdef IS_MPI |
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#include "mpi.h" |
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#include "math/ParallelRandNumGen.hpp" |
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#endif |
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namespace OpenMD { |
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MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode); |
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#endif |
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SimplePreprocessor preprocessor; |
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preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, |
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ppStream); |
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preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream); |
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#ifdef IS_MPI |
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//brocasting the stream size |
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Molecule::AtomIterator ai; |
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Molecule::RigidBodyIterator ri; |
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Molecule::CutoffGroupIterator ci; |
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Molecule::BondIterator boi; |
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Molecule::BendIterator bei; |
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Molecule::TorsionIterator ti; |
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Molecule::InversionIterator ii; |
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Molecule::IntegrableObjectIterator ioi; |
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Molecule * mol; |
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Atom * atom; |
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RigidBody * rb; |
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CutoffGroup * cg; |
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Molecule* mol; |
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Atom* atom; |
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RigidBody* rb; |
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CutoffGroup* cg; |
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Bond* bond; |
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Bend* bend; |
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Torsion* torsion; |
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Inversion* inversion; |
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int beginAtomIndex; |
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int beginRigidBodyIndex; |
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int beginCutoffGroupIndex; |
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int beginBondIndex; |
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int beginBendIndex; |
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int beginTorsionIndex; |
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int beginInversionIndex; |
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int nGlobalAtoms = info->getNGlobalAtoms(); |
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int nGlobalRigidBodies = info->getNGlobalRigidBodies(); |
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beginAtomIndex = 0; |
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//rigidbody's index begins right after atom's |
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// The rigid body indices begin immediately after the atom indices: |
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beginRigidBodyIndex = info->getNGlobalAtoms(); |
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beginCutoffGroupIndex = 0; |
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beginBondIndex = 0; |
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beginBendIndex = 0; |
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beginTorsionIndex = 0; |
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beginInversionIndex = 0; |
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for(int i = 0; i < info->getNGlobalMolecules(); i++) { |
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#ifdef IS_MPI |
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// stuff to do if I own this molecule |
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mol = info->getMoleculeByGlobalIndex(i); |
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//local index(index in DataStorge) of atom is important |
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for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
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// The local index(index in DataStorge) of the atom is important: |
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for(atom = mol->beginAtom(ai); atom != NULL; |
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atom = mol->nextAtom(ai)) { |
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atom->setGlobalIndex(beginAtomIndex++); |
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} |
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rb->setGlobalIndex(beginRigidBodyIndex++); |
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} |
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//local index of cutoff group is trivial, it only depends on |
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//the order of travesing |
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// The local index of other objects only depends on the order |
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// of traversal: |
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for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
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cg = mol->nextCutoffGroup(ci)) { |
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cg->setGlobalIndex(beginCutoffGroupIndex++); |
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} |
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for(bond = mol->beginBond(boi); bond != NULL; |
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bond = mol->nextBond(boi)) { |
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bond->setGlobalIndex(beginBondIndex++); |
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} |
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for(bend = mol->beginBend(bei); bend != NULL; |
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bend = mol->nextBend(bei)) { |
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bend->setGlobalIndex(beginBendIndex++); |
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} |
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for(torsion = mol->beginTorsion(ti); torsion != NULL; |
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torsion = mol->nextTorsion(ti)) { |
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torsion->setGlobalIndex(beginTorsionIndex++); |
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} |
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for(inversion = mol->beginInversion(ii); inversion != NULL; |
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inversion = mol->nextInversion(ii)) { |
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inversion->setGlobalIndex(beginInversionIndex++); |
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} |
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#ifdef IS_MPI |
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} else { |
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beginAtomIndex += stamp->getNAtoms(); |
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beginRigidBodyIndex += stamp->getNRigidBodies(); |
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beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms(); |
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beginBondIndex += stamp->getNBonds(); |
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beginBendIndex += stamp->getNBends(); |
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beginTorsionIndex += stamp->getNTorsions(); |
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beginInversionIndex += stamp->getNInversions(); |
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} |
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#endif |
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//fill globalGroupMembership |
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std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0); |
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for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
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for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
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for(mol = info->beginMolecule(mi); mol != NULL; |
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mol = info->nextMolecule(mi)) { |
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for (cg = mol->beginCutoffGroup(ci); cg != NULL; |
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cg = mol->nextCutoffGroup(ci)) { |
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for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
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globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex(); |
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} |
