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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 SimCreator.cpp |
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* @author tlin |
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* @date 11/03/2004 |
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* @time 13:51am |
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* @version 1.0 |
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*/ |
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|
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#include "brains/MoleculeCreator.hpp" |
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#include "brains/SimCreator.hpp" |
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#include "brains/SimSnapshotManager.hpp" |
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#include "io/DumpReader.hpp" |
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#include "io/parse_me.h" |
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#include "UseTheForce/ForceFieldFactory.hpp" |
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#include "utils/simError.h" |
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#include "utils/StringUtils.hpp" |
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#include "math/SeqRandNumGen.hpp" |
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#ifdef IS_MPI |
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#include "io/mpiBASS.h" |
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#include "math/ParallelRandNumGen.hpp" |
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#endif |
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|
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namespace oopse { |
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|
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void SimCreator::parseFile(const std::string mdFileName, MakeStamps* stamps, Globals* simParams){ |
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|
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#ifdef IS_MPI |
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|
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if (worldRank == 0) { |
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#endif // is_mpi |
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|
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simParams->initalize(); |
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set_interface_stamps(stamps, simParams); |
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|
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#ifdef IS_MPI |
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|
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mpiEventInit(); |
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|
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#endif |
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|
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yacc_BASS(mdFileName.c_str()); |
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|
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#ifdef IS_MPI |
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|
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throwMPIEvent(NULL); |
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} else { |
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set_interface_stamps(stamps, simParams); |
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mpiEventInit(); |
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MPIcheckPoint(); |
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mpiEventLoop(); |
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} |
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|
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#endif |
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|
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} |
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|
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SimInfo* SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) { |
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|
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MakeStamps * stamps = new MakeStamps(); |
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|
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Globals * simParams = new Globals(); |
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|
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//parse meta-data file |
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parseFile(mdFileName, stamps, simParams); |
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|
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//create the force field |
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ForceField * ff = ForceFieldFactory::getInstance()->createForceField( |
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simParams->getForceField()); |
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|
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if (ff == NULL) { |
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sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n", |
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simParams->getForceField()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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if (simParams->haveForceFieldFileName()) { |
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ff->setForceFieldFileName(simParams->getForceFieldFileName()); |
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} |
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|
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std::string forcefieldFileName; |
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forcefieldFileName = ff->getForceFieldFileName(); |
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|
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if (simParams->haveForceFieldVariant()) { |
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//If the force field has variant, the variant force field name will be |
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//Base.variant.frc. For exampel EAM.u6.frc |
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|
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std::string variant = simParams->getForceFieldVariant(); |
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|
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std::string::size_type pos = forcefieldFileName.rfind(".frc"); |
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variant = "." + variant; |
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if (pos != std::string::npos) { |
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forcefieldFileName.insert(pos, variant); |
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} else { |
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//If the default force field file name does not containt .frc suffix, just append the .variant |
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forcefieldFileName.append(variant); |
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} |
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} |
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|
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ff->parse(forcefieldFileName); |
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|
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//extract the molecule stamps |
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std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs; |
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compList(stamps, simParams, moleculeStampPairs); |
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|
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//create SimInfo |
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SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams); |
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|
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//gather parameters (SimCreator only retrieves part of the parameters) |
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gatherParameters(info, mdFileName); |
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|
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//divide the molecules and determine the global index of molecules |
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#ifdef IS_MPI |
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divideMolecules(info); |
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#endif |
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|
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//create the molecules |
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createMolecules(info); |
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|
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|
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//allocate memory for DataStorage(circular reference, need to break it) |
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info->setSnapshotManager(new SimSnapshotManager(info)); |
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|
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//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the |
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//global index will never change again). Local indices of atoms and rigidbodies are already set by |
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//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager. |
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setGlobalIndex(info); |
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|
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//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point |
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//atoms don't have the global index yet (their global index are all initialized to -1). |
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//Therefore we have to call addExcludePairs explicitly here. A way to work around is that |
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//we can determine the beginning global indices of atoms before they get created. |
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SimInfo::MoleculeIterator mi; |
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Molecule* mol; |
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for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
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info->addExcludePairs(mol); |
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} |
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|
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|
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//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as |
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//eta, chi for NPT integrator) |
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if (loadInitCoords) |
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loadCoordinates(info); |
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|
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return info; |
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} |
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|
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void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) { |
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|
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//figure out the ouput file names |
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std::string prefix; |
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|
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#ifdef IS_MPI |
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|
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if (worldRank == 0) { |
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#endif // is_mpi |
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Globals * simParams = info->getSimParams(); |
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if (simParams->haveFinalConfig()) { |
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prefix = getPrefix(simParams->getFinalConfig()); |
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} else { |
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prefix = getPrefix(mdfile); |
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} |
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|
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info->setFinalConfigFileName(prefix + ".eor"); |
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info->setDumpFileName(prefix + ".dump"); |
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info->setStatFileName(prefix + ".stat"); |
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|
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#ifdef IS_MPI |
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|
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} |
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|
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#endif |
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|
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} |
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|
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#ifdef IS_MPI |
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void SimCreator::divideMolecules(SimInfo *info) { |
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double numerator; |
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double denominator; |
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double precast; |
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double x; |
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double y; |
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double a; |
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int old_atoms; |
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int add_atoms; |
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int new_atoms; |
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int nTarget; |
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int done; |
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int i; |
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int j; |
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int loops; |
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int which_proc; |
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int nProcessors; |
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std::vector<int> atomsPerProc; |
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int nGlobalMols = info->getNGlobalMolecules(); |
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std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition: |
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|
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MPI_Comm_size(MPI_COMM_WORLD, &nProcessors); |
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|
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if (nProcessors > nGlobalMols) { |
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sprintf(painCave.errMsg, |
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"nProcessors (%d) > nMol (%d)\n" |
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"\tThe number of processors is larger than\n" |
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"\tthe number of molecules. This will not result in a \n" |
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"\tusable division of atoms for force decomposition.\n" |
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"\tEither try a smaller number of processors, or run the\n" |
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"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols); |
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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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int seedValue; |
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Globals * simParams = info->getSimParams(); |
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SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator |
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if (simParams->haveSeed()) { |
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seedValue = simParams->getSeed(); |
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myRandom = new SeqRandNumGen(seedValue); |
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}else { |
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myRandom = new SeqRandNumGen(); |
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} |
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|
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|
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a = 3.0 * nGlobalMols / info->getNGlobalAtoms(); |
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|
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//initialize atomsPerProc |
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atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0); |
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|
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if (worldRank == 0) { |
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numerator = info->getNGlobalAtoms(); |
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denominator = nProcessors; |
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precast = numerator / denominator; |
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nTarget = (int)(precast + 0.5); |
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|
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for(i = 0; i < nGlobalMols; i++) { |
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done = 0; |
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loops = 0; |
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|
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while (!done) { |
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loops++; |
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|
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// Pick a processor at random |
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|
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which_proc = (int) (myRandom->rand() * nProcessors); |
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|
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//get the molecule stamp first |
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int stampId = info->getMoleculeStampId(i); |
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MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId); |
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|
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// How many atoms does this processor have so far? |
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old_atoms = atomsPerProc[which_proc]; |
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add_atoms = moleculeStamp->getNAtoms(); |
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new_atoms = old_atoms + add_atoms; |
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|
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// If we've been through this loop too many times, we need |
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// to just give up and assign the molecule to this processor |
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// and be done with it. |
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|
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if (loops > 100) { |
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sprintf(painCave.errMsg, |
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"I've tried 100 times to assign molecule %d to a " |
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" processor, but can't find a good spot.\n" |
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"I'm assigning it at random to processor %d.\n", |
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i, which_proc); |
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|
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painCave.isFatal = 0; |
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simError(); |
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|
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molToProcMap[i] = which_proc; |
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atomsPerProc[which_proc] += add_atoms; |
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|
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done = 1; |
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continue; |
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} |
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|
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// If we can add this molecule to this processor without sending |
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// it above nTarget, then go ahead and do it: |
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|
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if (new_atoms <= nTarget) { |
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molToProcMap[i] = which_proc; |
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atomsPerProc[which_proc] += add_atoms; |
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|
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done = 1; |
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continue; |
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} |
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|
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// The only situation left is when new_atoms > nTarget. We |
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// want to accept this with some probability that dies off the |
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// farther we are from nTarget |
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|
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// roughly: x = new_atoms - nTarget |
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// Pacc(x) = exp(- a * x) |
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// where a = penalty / (average atoms per molecule) |
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|
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x = (double)(new_atoms - nTarget); |
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y = myRandom->rand(); |
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|
| 339 |
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if (y < exp(- a * x)) { |
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molToProcMap[i] = which_proc; |
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atomsPerProc[which_proc] += add_atoms; |
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|
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done = 1; |
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continue; |
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} else { |
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continue; |
| 347 |
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} |
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} |
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} |
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|
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delete myRandom; |
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|
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// Spray out this nonsense to all other processors: |
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|
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MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
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} else { |
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|
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// Listen to your marching orders from processor 0: |
| 359 |
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|
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MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
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} |
| 362 |
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|
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info->setMolToProcMap(molToProcMap); |
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sprintf(checkPointMsg, |
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"Successfully divided the molecules among the processors.\n"); |
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MPIcheckPoint(); |
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} |
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|
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#endif |
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|
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void SimCreator::createMolecules(SimInfo *info) { |
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MoleculeCreator molCreator; |
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int stampId; |
| 374 |
< |
|
| 375 |
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for(int i = 0; i < info->getNGlobalMolecules(); i++) { |
| 376 |
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|
| 377 |
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#ifdef IS_MPI |
| 378 |
< |
|
| 379 |
< |
if (info->getMolToProc(i) == worldRank) { |
| 380 |
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#endif |
| 381 |
< |
|
| 382 |
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stampId = info->getMoleculeStampId(i); |
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Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId), |
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stampId, i, info->getLocalIndexManager()); |
| 385 |
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|
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info->addMolecule(mol); |
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|
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#ifdef IS_MPI |
| 389 |
< |
|
| 390 |
< |
} |
| 391 |
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|
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#endif |
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|
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< |
} //end for(int i=0) |
| 395 |
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} |
| 396 |
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|
| 397 |
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void SimCreator::compList(MakeStamps *stamps, Globals* simParams, |
| 398 |
< |
std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) { |
| 399 |
< |
int i; |
| 400 |
< |
char * id; |
| 401 |
< |
MoleculeStamp * currentStamp; |
| 402 |
< |
Component** the_components = simParams->getComponents(); |
| 403 |
< |
int n_components = simParams->getNComponents(); |
| 404 |
< |
|
| 405 |
< |
if (!simParams->haveNMol()) { |
| 406 |
< |
// we don't have the total number of molecules, so we assume it is |
| 407 |
< |
// given in each component |
| 408 |
< |
|
| 409 |
< |
for(i = 0; i < n_components; i++) { |
| 410 |
< |
if (!the_components[i]->haveNMol()) { |
| 411 |
< |
// we have a problem |
| 412 |
< |
sprintf(painCave.errMsg, |
| 413 |
< |
"SimCreator Error. No global NMol or component NMol given.\n" |
| 414 |
< |
"\tCannot calculate the number of atoms.\n"); |
| 415 |
< |
|
| 416 |
< |
painCave.isFatal = 1; |
| 417 |
< |
simError(); |
| 418 |
< |
} |
| 419 |
< |
|
| 420 |
< |
id = the_components[i]->getType(); |
| 421 |
< |
currentStamp = (stamps->extractMolStamp(id))->getStamp(); |
| 422 |
< |
|
| 423 |
< |
if (currentStamp == NULL) { |
| 424 |
< |
sprintf(painCave.errMsg, |
| 425 |
< |
"SimCreator error: Component \"%s\" was not found in the " |
| 426 |
< |
"list of declared molecules\n", id); |
| 427 |
< |
|
| 428 |
< |
painCave.isFatal = 1; |
| 429 |
< |
simError(); |
| 430 |
< |
} |
| 431 |
< |
|
| 432 |
< |
moleculeStampPairs.push_back( |
| 433 |
< |
std::make_pair(currentStamp, the_components[i]->getNMol())); |
| 434 |
< |
} //end for (i = 0; i < n_components; i++) |
| 435 |
< |
} else { |
| 436 |
< |
sprintf(painCave.errMsg, "SimSetup error.\n" |
| 437 |
< |
"\tSorry, the ability to specify total" |
| 438 |
< |
" nMols and then give molfractions in the components\n" |
| 439 |
< |
"\tis not currently supported." |
| 440 |
< |
" Please give nMol in the components.\n"); |
| 441 |
< |
|
| 442 |
< |
painCave.isFatal = 1; |
| 443 |
< |
simError(); |
| 444 |
< |
} |
| 445 |
< |
|
| 446 |
< |
#ifdef IS_MPI |
| 447 |
< |
|
| 448 |
< |
strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
| 449 |
< |
MPIcheckPoint(); |
| 450 |
< |
|
| 451 |
< |
#endif // is_mpi |
| 452 |
< |
|
| 453 |
< |
} |
| 454 |
< |
|
| 455 |
< |
void SimCreator::setGlobalIndex(SimInfo *info) { |
| 456 |
< |
SimInfo::MoleculeIterator mi; |
| 457 |
< |
Molecule::AtomIterator ai; |
| 458 |
< |
Molecule::RigidBodyIterator ri; |
| 459 |
< |
Molecule::CutoffGroupIterator ci; |
| 460 |
< |
Molecule * mol; |
| 461 |
< |
Atom * atom; |
| 462 |
< |
RigidBody * rb; |
| 463 |
< |
CutoffGroup * cg; |
| 464 |
< |
int beginAtomIndex; |
| 465 |
< |
int beginRigidBodyIndex; |
| 466 |
< |
int beginCutoffGroupIndex; |
| 467 |
< |
int nGlobalAtoms = info->getNGlobalAtoms(); |
| 468 |
< |
|
| 469 |
< |
#ifndef IS_MPI |
| 470 |
< |
|
| 471 |
< |
beginAtomIndex = 0; |
| 472 |
< |
beginRigidBodyIndex = 0; |
| 473 |
< |
beginCutoffGroupIndex = 0; |
| 474 |
< |
|
| 475 |
< |
#else |
| 476 |
< |
|
| 477 |
< |
int nproc; |
| 478 |
< |
int myNode; |
| 479 |
< |
|
| 480 |
< |
myNode = worldRank; |
| 481 |
< |
MPI_Comm_size(MPI_COMM_WORLD, &nproc); |
| 482 |
< |
|
| 483 |
< |
std::vector < int > tmpAtomsInProc(nproc, 0); |
| 484 |
< |
std::vector < int > tmpRigidBodiesInProc(nproc, 0); |
| 485 |
< |
std::vector < int > tmpCutoffGroupsInProc(nproc, 0); |
| 486 |
< |
std::vector < int > NumAtomsInProc(nproc, 0); |
| 487 |
< |
std::vector < int > NumRigidBodiesInProc(nproc, 0); |
| 488 |
< |
std::vector < int > NumCutoffGroupsInProc(nproc, 0); |
| 489 |
< |
|
| 490 |
< |
tmpAtomsInProc[myNode] = info->getNAtoms(); |
| 491 |
< |
tmpRigidBodiesInProc[myNode] = info->getNRigidBodies(); |
| 492 |
< |
tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups(); |
| 493 |
< |
|
| 494 |
< |
//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups |
| 495 |
< |
MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT, |
| 496 |
< |
MPI_SUM, MPI_COMM_WORLD); |
| 497 |
< |
MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc, |
| 498 |
< |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 499 |
< |
MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc, |
| 500 |
< |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 501 |
< |
|
| 502 |
< |
beginAtomIndex = 0; |
| 503 |
< |
beginRigidBodyIndex = 0; |
| 504 |
< |
beginCutoffGroupIndex = 0; |
| 505 |
< |
|
| 506 |
< |
for(int i = 0; i < myNode; i++) { |
| 507 |
< |
beginAtomIndex += NumAtomsInProc[i]; |
| 508 |
< |
beginRigidBodyIndex += NumRigidBodiesInProc[i]; |
| 509 |
< |
beginCutoffGroupIndex += NumCutoffGroupsInProc[i]; |
| 510 |
< |
} |
| 511 |
< |
|
| 512 |
< |
#endif |
| 513 |
< |
|
| 514 |
< |
//rigidbody's index begins right after atom's |
| 515 |
< |
beginRigidBodyIndex += info->getNGlobalAtoms(); |
| 516 |
< |
|
| 517 |
< |
for(mol = info->beginMolecule(mi); mol != NULL; |
| 518 |
< |
mol = info->nextMolecule(mi)) { |
| 519 |
< |
|
| 520 |
< |
//local index(index in DataStorge) of atom is important |
| 521 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 522 |
< |
atom->setGlobalIndex(beginAtomIndex++); |
| 523 |
< |
} |
| 524 |
< |
|
| 525 |
< |
for(rb = mol->beginRigidBody(ri); rb != NULL; |
| 526 |
< |
rb = mol->nextRigidBody(ri)) { |
| 527 |
< |
rb->setGlobalIndex(beginRigidBodyIndex++); |
| 528 |
< |
} |
| 529 |
< |
|
| 530 |
< |
//local index of cutoff group is trivial, it only depends on the order of travesing |
| 531 |
< |
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 532 |
< |
cg = mol->nextCutoffGroup(ci)) { |
| 533 |
< |
cg->setGlobalIndex(beginCutoffGroupIndex++); |
| 534 |
< |
} |
| 535 |
< |
} |
| 536 |
< |
|
| 537 |
< |
//fill globalGroupMembership |
| 538 |
< |
std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0); |
| 539 |
< |
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 540 |
< |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
| 541 |
< |
|
| 542 |
< |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
| 543 |
< |
globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex(); |
| 544 |
< |
} |
| 545 |
< |
|
| 546 |
< |
} |
| 547 |
< |
} |
| 548 |
< |
|
| 549 |
< |
#ifdef IS_MPI |
| 550 |
< |
// Since the globalGroupMembership has been zero filled and we've only |
| 551 |
< |
// poked values into the atoms we know, we can do an Allreduce |
| 552 |
< |
// to get the full globalGroupMembership array (We think). |
| 553 |
< |
// This would be prettier if we could use MPI_IN_PLACE like the MPI-2 |
| 554 |
< |
// docs said we could. |
| 555 |
< |
std::vector<int> tmpGroupMembership(nGlobalAtoms, 0); |
| 556 |
< |
MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms, |
| 557 |
< |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 558 |
< |
info->setGlobalGroupMembership(tmpGroupMembership); |
| 559 |
< |
#else |
| 560 |
< |
info->setGlobalGroupMembership(globalGroupMembership); |
| 561 |
< |
#endif |
| 562 |
< |
|
| 563 |
< |
//fill molMembership |
| 564 |
< |
std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0); |
| 565 |
< |
|
| 566 |
< |
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 567 |
< |
|
| 568 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 569 |
< |
globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex(); |
| 570 |
< |
} |
| 571 |
< |
} |
| 572 |
< |
|
| 573 |
< |
#ifdef IS_MPI |
| 574 |
< |
std::vector<int> tmpMolMembership(nGlobalAtoms, 0); |
| 575 |
< |
|
| 576 |
< |
MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms, |
| 577 |
< |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 578 |
< |
|
| 579 |
< |
info->setGlobalMolMembership(tmpMolMembership); |
| 580 |
< |
#else |
| 581 |
< |
info->setGlobalMolMembership(globalMolMembership); |
| 582 |
< |
#endif |
| 583 |
< |
|
| 584 |
< |
} |
| 585 |
< |
|
| 586 |
< |
void SimCreator::loadCoordinates(SimInfo* info) { |
| 587 |
< |
Globals* simParams; |
| 588 |
< |
simParams = info->getSimParams(); |
| 589 |
< |
|
| 590 |
< |
if (!simParams->haveInitialConfig()) { |
| 591 |
< |
sprintf(painCave.errMsg, |
| 592 |
< |
"Cannot intialize a simulation without an initial configuration file.\n"); |
| 593 |
< |
painCave.isFatal = 1;; |
| 594 |
< |
simError(); |
| 595 |
< |
} |
| 596 |
< |
|
| 597 |
< |
DumpReader reader(info, simParams->getInitialConfig()); |
| 598 |
< |
int nframes = reader.getNFrames(); |
| 599 |
< |
|
| 600 |
< |
if (nframes > 0) { |
| 601 |
< |
reader.readFrame(nframes - 1); |
| 602 |
< |
} else { |
| 603 |
< |
//invalid initial coordinate file |
| 604 |
< |
sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n", |
| 605 |
< |
simParams->getInitialConfig()); |
| 606 |
< |
painCave.isFatal = 1; |
| 607 |
< |
simError(); |
| 608 |
< |
} |
| 609 |
< |
|
| 610 |
< |
//copy the current snapshot to previous snapshot |
| 611 |
< |
info->getSnapshotManager()->advance(); |
| 612 |
< |
} |
| 613 |
< |
|
| 614 |
< |
} //end namespace oopse |
| 615 |
< |
|
| 616 |
< |
|
| 1 |
> |
/* |
| 2 |
> |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
| 3 |
> |
* |
| 4 |
> |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
> |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
> |
* redistribute this software in source and binary code form, provided |
| 7 |
> |
* that the following conditions are met: |
| 8 |
> |
* |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
> |
* notice, this list of conditions and the following disclaimer. |
| 11 |
> |
* |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
> |
* notice, this list of conditions and the following disclaimer in the |
| 14 |
> |
* documentation and/or other materials provided with the |
| 15 |
> |
* distribution. |
| 16 |
> |
* |
| 17 |
> |
* This software is provided "AS IS," without a warranty of any |
| 18 |
> |
* kind. All express or implied conditions, representations and |
| 19 |
> |
* warranties, including any implied warranty of merchantability, |
| 20 |
> |
* fitness for a particular purpose or non-infringement, are hereby |
| 21 |
> |
* excluded. The University of Notre Dame and its licensors shall not |
| 22 |
> |
* be liable for any damages suffered by licensee as a result of |
| 23 |
> |
* using, modifying or distributing the software or its |
| 24 |
> |
* derivatives. In no event will the University of Notre Dame or its |
| 25 |
> |
* licensors be liable for any lost revenue, profit or data, or for |
| 26 |
> |
* direct, indirect, special, consequential, incidental or punitive |
| 27 |
> |
* damages, however caused and regardless of the theory of liability, |
| 28 |
> |
* arising out of the use of or inability to use software, even if the |
| 29 |
> |
* University of Notre Dame has been advised of the possibility of |
| 30 |
> |
* such damages. |
| 31 |
> |
* |
| 32 |
> |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
> |
* research, please cite the appropriate papers when you publish your |
| 34 |
> |
* work. Good starting points are: |
| 35 |
> |
* |
| 36 |
> |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
> |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
> |
*/ |
| 42 |
> |
|
| 43 |
> |
/** |
| 44 |
> |
* @file SimCreator.cpp |
| 45 |
> |
* @author tlin |
| 46 |
> |
* @date 11/03/2004 |
| 47 |
> |
* @time 13:51am |
| 48 |
> |
* @version 1.0 |
| 49 |
> |
*/ |
| 50 |
> |
#include <exception> |
| 51 |
> |
#include <iostream> |
| 52 |
> |
#include <sstream> |
| 53 |
> |
#include <string> |
| 54 |
> |
|
| 55 |
> |
#include "brains/MoleculeCreator.hpp" |
| 56 |
> |
#include "brains/SimCreator.hpp" |
| 57 |
> |
#include "brains/SimSnapshotManager.hpp" |
| 58 |
> |
#include "io/DumpReader.hpp" |
| 59 |
> |
#include "UseTheForce/ForceFieldFactory.hpp" |
| 60 |
> |
#include "utils/simError.h" |
| 61 |
> |
#include "utils/StringUtils.hpp" |
| 62 |
> |
#include "math/SeqRandNumGen.hpp" |
| 63 |
> |
#include "mdParser/MDLexer.hpp" |
| 64 |
> |
#include "mdParser/MDParser.hpp" |
| 65 |
> |
#include "mdParser/MDTreeParser.hpp" |
| 66 |
> |
#include "mdParser/SimplePreprocessor.hpp" |
| 67 |
> |
#include "antlr/ANTLRException.hpp" |
| 68 |
> |
#include "antlr/TokenStreamRecognitionException.hpp" |
| 69 |
> |
#include "antlr/TokenStreamIOException.hpp" |
| 70 |
> |
#include "antlr/TokenStreamException.hpp" |
| 71 |
> |
#include "antlr/RecognitionException.hpp" |
| 72 |
> |
#include "antlr/CharStreamException.hpp" |
| 73 |
> |
|
| 74 |
> |
#include "antlr/MismatchedCharException.hpp" |
| 75 |
> |
#include "antlr/MismatchedTokenException.hpp" |
| 76 |
> |
#include "antlr/NoViableAltForCharException.hpp" |
| 77 |
> |
#include "antlr/NoViableAltException.hpp" |
| 78 |
> |
|
| 79 |
> |
#ifdef IS_MPI |
| 80 |
> |
#include "mpi.h" |
| 81 |
> |
#include "math/ParallelRandNumGen.hpp" |
| 82 |
> |
#endif |
| 83 |
> |
|
| 84 |
> |
namespace OpenMD { |
| 85 |
> |
|
| 86 |
> |
Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){ |
| 87 |
> |
Globals* simParams = NULL; |
| 88 |
> |
try { |
| 89 |
> |
|
| 90 |
> |
// Create a preprocessor that preprocesses md file into an ostringstream |
| 91 |
> |
std::stringstream ppStream; |
| 92 |
> |
#ifdef IS_MPI |
| 93 |
> |
int streamSize; |
| 94 |
> |
const int masterNode = 0; |
| 95 |
> |
int commStatus; |
| 96 |
> |
if (worldRank == masterNode) { |
| 97 |
> |
commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
| 98 |
> |
#endif |
| 99 |
> |
SimplePreprocessor preprocessor; |
| 100 |
> |
preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream); |
| 101 |
> |
|
| 102 |
> |
#ifdef IS_MPI |
| 103 |
> |
//brocasting the stream size |
| 104 |
> |
streamSize = ppStream.str().size() +1; |
| 105 |
> |
commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD); |
| 106 |
> |
|
| 107 |
> |
commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
| 108 |
> |
|
| 109 |
> |
|
| 110 |
> |
} else { |
| 111 |
> |
|
| 112 |
> |
commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD); |
| 113 |
> |
|
| 114 |
> |
//get stream size |
| 115 |
> |
commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD); |
| 116 |
> |
|
| 117 |
> |
char* buf = new char[streamSize]; |
| 118 |
> |
assert(buf); |
| 119 |
> |
|
| 120 |
> |
//receive file content |
| 121 |
> |
commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); |
| 122 |
> |
|
| 123 |
> |
ppStream.str(buf); |
| 124 |
> |
delete [] buf; |
| 125 |
> |
|
| 126 |
> |
} |
| 127 |
> |
#endif |
| 128 |
> |
// Create a scanner that reads from the input stream |
| 129 |
> |
MDLexer lexer(ppStream); |
| 130 |
> |
lexer.setFilename(filename); |
| 131 |
> |
lexer.initDeferredLineCount(); |
| 132 |
> |
|
| 133 |
> |
// Create a parser that reads from the scanner |
| 134 |
> |
MDParser parser(lexer); |
| 135 |
> |
parser.setFilename(filename); |
| 136 |
> |
|
| 137 |
> |
// Create an observer that synchorizes file name change |
| 138 |
> |
FilenameObserver observer; |
| 139 |
> |
observer.setLexer(&lexer); |
| 140 |
> |
observer.setParser(&parser); |
| 141 |
> |
lexer.setObserver(&observer); |
| 142 |
> |
|
| 143 |
> |
antlr::ASTFactory factory; |
| 144 |
> |
parser.initializeASTFactory(factory); |
| 145 |
> |
parser.setASTFactory(&factory); |
| 146 |
> |
parser.mdfile(); |
| 147 |
> |
|
| 148 |
> |
// Create a tree parser that reads information into Globals |
| 149 |
> |
MDTreeParser treeParser; |
| 150 |
> |
treeParser.initializeASTFactory(factory); |
| 151 |
> |
treeParser.setASTFactory(&factory); |
| 152 |
> |
simParams = treeParser.walkTree(parser.getAST()); |
| 153 |
> |
} |
| 154 |
> |
|
| 155 |
> |
|
| 156 |
> |
catch(antlr::MismatchedCharException& e) { |
| 157 |
> |
sprintf(painCave.errMsg, |
| 158 |
> |
"parser exception: %s %s:%d:%d\n", |
| 159 |
> |
e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn()); |
| 160 |
> |
painCave.isFatal = 1; |
| 161 |
> |
simError(); |
| 162 |
> |
} |
| 163 |
> |
catch(antlr::MismatchedTokenException &e) { |
| 164 |
> |
sprintf(painCave.errMsg, |
| 165 |
> |
"parser exception: %s %s:%d:%d\n", |
| 166 |
> |
e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn()); |
| 167 |
> |
painCave.isFatal = 1; |
| 168 |
> |
simError(); |
| 169 |
> |
} |
| 170 |
> |
catch(antlr::NoViableAltForCharException &e) { |
| 171 |
> |
sprintf(painCave.errMsg, |
| 172 |
> |
"parser exception: %s %s:%d:%d\n", |
| 173 |
> |
e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn()); |
| 174 |
> |
painCave.isFatal = 1; |
| 175 |
> |
simError(); |
| 176 |
> |
} |
| 177 |
> |
catch(antlr::NoViableAltException &e) { |
| 178 |
> |
sprintf(painCave.errMsg, |
| 179 |
> |
"parser exception: %s %s:%d:%d\n", |
| 180 |
> |
e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn()); |
| 181 |
> |
painCave.isFatal = 1; |
| 182 |
> |
simError(); |
| 183 |
> |
} |
| 184 |
> |
|
| 185 |
> |
catch(antlr::TokenStreamRecognitionException& e) { |
| 186 |
> |
sprintf(painCave.errMsg, |
| 187 |
> |
"parser exception: %s %s:%d:%d\n", |
| 188 |
> |
e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn()); |
| 189 |
> |
painCave.isFatal = 1; |
| 190 |
> |
simError(); |
| 191 |
> |
} |
| 192 |
> |
|
| 193 |
> |
catch(antlr::TokenStreamIOException& e) { |
| 194 |
> |
sprintf(painCave.errMsg, |
| 195 |
> |
"parser exception: %s\n", |
| 196 |
> |
e.getMessage().c_str()); |
| 197 |
> |
painCave.isFatal = 1; |
| 198 |
> |
simError(); |
| 199 |
> |
} |
| 200 |
> |
|
| 201 |
> |
catch(antlr::TokenStreamException& e) { |
| 202 |
> |
sprintf(painCave.errMsg, |
| 203 |
> |
"parser exception: %s\n", |
| 204 |
> |
e.getMessage().c_str()); |
| 205 |
> |
painCave.isFatal = 1; |
| 206 |
> |
simError(); |
| 207 |
> |
} |
| 208 |
> |
catch (antlr::RecognitionException& e) { |
| 209 |
> |
sprintf(painCave.errMsg, |
| 210 |
> |
"parser exception: %s %s:%d:%d\n", |
| 211 |
> |
e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn()); |
| 212 |
> |
painCave.isFatal = 1; |
| 213 |
> |
simError(); |
| 214 |
> |
} |
| 215 |
> |
catch (antlr::CharStreamException& e) { |
| 216 |
> |
sprintf(painCave.errMsg, |
| 217 |
> |
"parser exception: %s\n", |
| 218 |
> |
e.getMessage().c_str()); |
| 219 |
> |
painCave.isFatal = 1; |
| 220 |
> |
simError(); |
| 221 |
> |
} |
| 222 |
> |
catch (OpenMDException& e) { |
| 223 |
> |
sprintf(painCave.errMsg, |
| 224 |
> |
"%s\n", |
| 225 |
> |
e.getMessage().c_str()); |
| 226 |
> |
painCave.isFatal = 1; |
| 227 |
> |
simError(); |
| 228 |
> |
} |
| 229 |
> |
catch (std::exception& e) { |
| 230 |
> |
sprintf(painCave.errMsg, |
| 231 |
> |
"parser exception: %s\n", |
| 232 |
> |
e.what()); |
| 233 |
> |
painCave.isFatal = 1; |
| 234 |
> |
simError(); |
| 235 |
> |
} |
| 236 |
> |
|
| 237 |
> |
simParams->setMDfileVersion(mdFileVersion); |
| 238 |
> |
return simParams; |
| 239 |
> |
} |
| 240 |
> |
|
| 241 |
> |
SimInfo* SimCreator::createSim(const std::string & mdFileName, |
| 242 |
> |
bool loadInitCoords) { |
| 243 |
> |
|
| 244 |
> |
const int bufferSize = 65535; |
| 245 |
> |
char buffer[bufferSize]; |
| 246 |
> |
int lineNo = 0; |
| 247 |
> |
std::string mdRawData; |
| 248 |
> |
int metaDataBlockStart = -1; |
| 249 |
> |
int metaDataBlockEnd = -1; |
| 250 |
> |
int i; |
| 251 |
> |
int mdOffset; |
| 252 |
> |
int mdFileVersion; |
| 253 |
> |
|
| 254 |
> |
#ifdef IS_MPI |
| 255 |
> |
const int masterNode = 0; |
| 256 |
> |
if (worldRank == masterNode) { |
| 257 |
> |
#endif |
| 258 |
> |
|
| 259 |
> |
std::ifstream mdFile_(mdFileName.c_str()); |
| 260 |
> |
|
| 261 |
> |
if (mdFile_.fail()) { |
| 262 |
> |
sprintf(painCave.errMsg, |
| 263 |
> |
"SimCreator: Cannot open file: %s\n", |
| 264 |
> |
mdFileName.c_str()); |
| 265 |
> |
painCave.isFatal = 1; |
| 266 |
> |
simError(); |
| 267 |
> |
} |
| 268 |
> |
|
| 269 |
> |
mdFile_.getline(buffer, bufferSize); |
| 270 |
> |
++lineNo; |
| 271 |
> |
std::string line = trimLeftCopy(buffer); |
| 272 |
> |
i = CaseInsensitiveFind(line, "<OpenMD"); |
| 273 |
> |
if (static_cast<size_t>(i) == string::npos) { |
| 274 |
> |
// try the older file strings to see if that works: |
| 275 |
> |
i = CaseInsensitiveFind(line, "<OOPSE"); |
| 276 |
> |
} |
| 277 |
> |
|
| 278 |
> |
if (static_cast<size_t>(i) == string::npos) { |
| 279 |
> |
// still no luck! |
| 280 |
> |
sprintf(painCave.errMsg, |
| 281 |
> |
"SimCreator: File: %s is not a valid OpenMD file!\n", |
| 282 |
> |
mdFileName.c_str()); |
| 283 |
> |
painCave.isFatal = 1; |
| 284 |
> |
simError(); |
| 285 |
> |
} |
| 286 |
> |
|
| 287 |
> |
// found the correct opening string, now try to get the file |
| 288 |
> |
// format version number. |
| 289 |
> |
|
| 290 |
> |
StringTokenizer tokenizer(line, "=<> \t\n\r"); |
| 291 |
> |
std::string fileType = tokenizer.nextToken(); |
| 292 |
> |
toUpper(fileType); |
| 293 |
> |
|
| 294 |
> |
mdFileVersion = 0; |
| 295 |
> |
|
| 296 |
> |
if (fileType == "OPENMD") { |
| 297 |
> |
while (tokenizer.hasMoreTokens()) { |
| 298 |
> |
std::string token(tokenizer.nextToken()); |
| 299 |
> |
toUpper(token); |
| 300 |
> |
if (token == "VERSION") { |
| 301 |
> |
mdFileVersion = tokenizer.nextTokenAsInt(); |
| 302 |
> |
break; |
| 303 |
> |
} |
| 304 |
> |
} |
| 305 |
> |
} |
| 306 |
> |
|
| 307 |
> |
//scan through the input stream and find MetaData tag |
| 308 |
> |
while(mdFile_.getline(buffer, bufferSize)) { |
| 309 |
> |
++lineNo; |
| 310 |
> |
|
| 311 |
> |
std::string line = trimLeftCopy(buffer); |
| 312 |
> |
if (metaDataBlockStart == -1) { |
| 313 |
> |
i = CaseInsensitiveFind(line, "<MetaData>"); |
| 314 |
> |
if (i != string::npos) { |
| 315 |
> |
metaDataBlockStart = lineNo; |
| 316 |
> |
mdOffset = mdFile_.tellg(); |
| 317 |
> |
} |
| 318 |
> |
} else { |
| 319 |
> |
i = CaseInsensitiveFind(line, "</MetaData>"); |
| 320 |
> |
if (i != string::npos) { |
| 321 |
> |
metaDataBlockEnd = lineNo; |
| 322 |
> |
} |
| 323 |
> |
} |
| 324 |
> |
} |
| 325 |
> |
|
| 326 |
> |
if (metaDataBlockStart == -1) { |
| 327 |
> |
sprintf(painCave.errMsg, |
| 328 |
> |
"SimCreator: File: %s did not contain a <MetaData> tag!\n", |
| 329 |
> |
mdFileName.c_str()); |
| 330 |
> |
painCave.isFatal = 1; |
| 331 |
> |
simError(); |
| 332 |
> |
} |
| 333 |
> |
if (metaDataBlockEnd == -1) { |
| 334 |
> |
sprintf(painCave.errMsg, |
| 335 |
> |
"SimCreator: File: %s did not contain a closed MetaData block!\n", |
| 336 |
> |
mdFileName.c_str()); |
| 337 |
> |
painCave.isFatal = 1; |
| 338 |
> |
simError(); |
| 339 |
> |
} |
| 340 |
> |
|
| 341 |
> |
mdFile_.clear(); |
| 342 |
> |
mdFile_.seekg(0); |
| 343 |
> |
mdFile_.seekg(mdOffset); |
| 344 |
> |
|
| 345 |
> |
mdRawData.clear(); |
| 346 |
> |
|
| 347 |
> |
for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) { |
| 348 |
> |
mdFile_.getline(buffer, bufferSize); |
| 349 |
> |
mdRawData += buffer; |
| 350 |
> |
mdRawData += "\n"; |
| 351 |
> |
} |
| 352 |
> |
|
| 353 |
> |
mdFile_.close(); |
| 354 |
> |
|
| 355 |
> |
#ifdef IS_MPI |
| 356 |
> |
} |
| 357 |
> |
#endif |
| 358 |
> |
|
| 359 |
> |
std::stringstream rawMetaDataStream(mdRawData); |
| 360 |
> |
|
| 361 |
> |
//parse meta-data file |
| 362 |
> |
Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion, |
| 363 |
> |
metaDataBlockStart + 1); |
| 364 |
> |
|
| 365 |
> |
//create the force field |
| 366 |
> |
ForceField * ff = ForceFieldFactory::getInstance()->createForceField(simParams->getForceField()); |
| 367 |
> |
|
| 368 |
> |
if (ff == NULL) { |
| 369 |
> |
sprintf(painCave.errMsg, |
| 370 |
> |
"ForceField Factory can not create %s force field\n", |
| 371 |
> |
simParams->getForceField().c_str()); |
| 372 |
> |
painCave.isFatal = 1; |
| 373 |
> |
simError(); |
| 374 |
> |
} |
| 375 |
> |
|
| 376 |
> |
if (simParams->haveForceFieldFileName()) { |
| 377 |
> |
ff->setForceFieldFileName(simParams->getForceFieldFileName()); |
| 378 |
> |
} |
| 379 |
> |
|
| 380 |
> |
std::string forcefieldFileName; |
| 381 |
> |
forcefieldFileName = ff->getForceFieldFileName(); |
| 382 |
> |
|
| 383 |
> |
if (simParams->haveForceFieldVariant()) { |
| 384 |
> |
//If the force field has variant, the variant force field name will be |
| 385 |
> |
//Base.variant.frc. For exampel EAM.u6.frc |
| 386 |
> |
|
| 387 |
> |
std::string variant = simParams->getForceFieldVariant(); |
| 388 |
> |
|
| 389 |
> |
std::string::size_type pos = forcefieldFileName.rfind(".frc"); |
| 390 |
> |
variant = "." + variant; |
| 391 |
> |
if (pos != std::string::npos) { |
| 392 |
> |
forcefieldFileName.insert(pos, variant); |
| 393 |
> |
} else { |
| 394 |
> |
//If the default force field file name does not containt .frc suffix, just append the .variant |
| 395 |
> |
forcefieldFileName.append(variant); |
| 396 |
> |
} |
| 397 |
> |
} |
| 398 |
> |
|
| 399 |
> |
ff->parse(forcefieldFileName); |
| 400 |
> |
//create SimInfo |
| 401 |
> |
SimInfo * info = new SimInfo(ff, simParams); |
| 402 |
> |
|
| 403 |
> |
info->setRawMetaData(mdRawData); |
| 404 |
> |
|
| 405 |
> |
//gather parameters (SimCreator only retrieves part of the |
| 406 |
> |
//parameters) |
| 407 |
> |
gatherParameters(info, mdFileName); |
| 408 |
> |
|
| 409 |
> |
//divide the molecules and determine the global index of molecules |
| 410 |
> |
#ifdef IS_MPI |
| 411 |
> |
divideMolecules(info); |
| 412 |
> |
#endif |
| 413 |
> |
|
| 414 |
> |
//create the molecules |
| 415 |
> |
createMolecules(info); |
| 416 |
> |
|
| 417 |
> |
//allocate memory for DataStorage(circular reference, need to |
| 418 |
> |
//break it) |
| 419 |
> |
info->setSnapshotManager(new SimSnapshotManager(info)); |
| 420 |
> |
|
| 421 |
> |
//set the global index of atoms, rigidbodies and cutoffgroups |
| 422 |
> |
//(only need to be set once, the global index will never change |
| 423 |
> |
//again). Local indices of atoms and rigidbodies are already set |
| 424 |
> |
//by MoleculeCreator class which actually delegates the |
| 425 |
> |
//responsibility to LocalIndexManager. |
| 426 |
> |
setGlobalIndex(info); |
| 427 |
> |
|
| 428 |
> |
//Although addInteractionPairs is called inside SimInfo's addMolecule |
| 429 |
> |
//method, at that point atoms don't have the global index yet |
| 430 |
> |
//(their global index are all initialized to -1). Therefore we |
| 431 |
> |
//have to call addInteractionPairs explicitly here. A way to work |
| 432 |
> |
//around is that we can determine the beginning global indices of |
| 433 |
> |
//atoms before they get created. |
| 434 |
> |
SimInfo::MoleculeIterator mi; |
| 435 |
> |
Molecule* mol; |
| 436 |
> |
for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 437 |
> |
info->addInteractionPairs(mol); |
| 438 |
> |
} |
| 439 |
> |
|
| 440 |
> |
if (loadInitCoords) |
| 441 |
> |
loadCoordinates(info, mdFileName); |
| 442 |
> |
return info; |
| 443 |
> |
} |
| 444 |
> |
|
| 445 |
> |
void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) { |
| 446 |
> |
|
| 447 |
> |
//figure out the output file names |
| 448 |
> |
std::string prefix; |
| 449 |
> |
|
| 450 |
> |
#ifdef IS_MPI |
| 451 |
> |
|
| 452 |
> |
if (worldRank == 0) { |
| 453 |
> |
#endif // is_mpi |
| 454 |
> |
Globals * simParams = info->getSimParams(); |
| 455 |
> |
if (simParams->haveFinalConfig()) { |
| 456 |
> |
prefix = getPrefix(simParams->getFinalConfig()); |
| 457 |
> |
} else { |
| 458 |
> |
prefix = getPrefix(mdfile); |
| 459 |
> |
} |
| 460 |
> |
|
| 461 |
> |
info->setFinalConfigFileName(prefix + ".eor"); |
| 462 |
> |
info->setDumpFileName(prefix + ".dump"); |
| 463 |
> |
info->setStatFileName(prefix + ".stat"); |
| 464 |
> |
info->setRestFileName(prefix + ".zang"); |
| 465 |
> |
|
| 466 |
> |
#ifdef IS_MPI |
| 467 |
> |
|
| 468 |
> |
} |
| 469 |
> |
|
| 470 |
> |
#endif |
| 471 |
> |
|
| 472 |
> |
} |
| 473 |
> |
|
| 474 |
> |
#ifdef IS_MPI |
| 475 |
> |
void SimCreator::divideMolecules(SimInfo *info) { |
| 476 |
> |
RealType numerator; |
| 477 |
> |
RealType denominator; |
| 478 |
> |
RealType precast; |
| 479 |
> |
RealType x; |
| 480 |
> |
RealType y; |
| 481 |
> |
RealType a; |
| 482 |
> |
int old_atoms; |
| 483 |
> |
int add_atoms; |
| 484 |
> |
int new_atoms; |
| 485 |
> |
int nTarget; |
| 486 |
> |
int done; |
| 487 |
> |
int i; |
| 488 |
> |
int j; |
| 489 |
> |
int loops; |
| 490 |
> |
int which_proc; |
| 491 |
> |
int nProcessors; |
| 492 |
> |
std::vector<int> atomsPerProc; |
| 493 |
> |
int nGlobalMols = info->getNGlobalMolecules(); |
| 494 |
> |
std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition: |
| 495 |
> |
|
| 496 |
> |
MPI_Comm_size(MPI_COMM_WORLD, &nProcessors); |
| 497 |
> |
|
| 498 |
> |
if (nProcessors > nGlobalMols) { |
| 499 |
> |
sprintf(painCave.errMsg, |
| 500 |
> |
"nProcessors (%d) > nMol (%d)\n" |
| 501 |
> |
"\tThe number of processors is larger than\n" |
| 502 |
> |
"\tthe number of molecules. This will not result in a \n" |
| 503 |
> |
"\tusable division of atoms for force decomposition.\n" |
| 504 |
> |
"\tEither try a smaller number of processors, or run the\n" |
| 505 |
> |
"\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols); |
| 506 |
> |
|
| 507 |
> |
painCave.isFatal = 1; |
| 508 |
> |
simError(); |
| 509 |
> |
} |
| 510 |
> |
|
| 511 |
> |
int seedValue; |
| 512 |
> |
Globals * simParams = info->getSimParams(); |
| 513 |
> |
SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator |
| 514 |
> |
if (simParams->haveSeed()) { |
| 515 |
> |
seedValue = simParams->getSeed(); |
| 516 |
> |
myRandom = new SeqRandNumGen(seedValue); |
| 517 |
> |
}else { |
| 518 |
> |
myRandom = new SeqRandNumGen(); |
| 519 |
> |
} |
| 520 |
> |
|
| 521 |
> |
|
| 522 |
> |
a = 3.0 * nGlobalMols / info->getNGlobalAtoms(); |
| 523 |
> |
|
| 524 |
> |
//initialize atomsPerProc |
| 525 |
> |
atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0); |
| 526 |
> |
|
| 527 |
> |
if (worldRank == 0) { |
| 528 |
> |
numerator = info->getNGlobalAtoms(); |
| 529 |
> |
denominator = nProcessors; |
| 530 |
> |
precast = numerator / denominator; |
| 531 |
> |
nTarget = (int)(precast + 0.5); |
| 532 |
> |
|
| 533 |
> |
for(i = 0; i < nGlobalMols; i++) { |
| 534 |
> |
done = 0; |
| 535 |
> |
loops = 0; |
| 536 |
> |
|
| 537 |
> |
while (!done) { |
| 538 |
> |
loops++; |
| 539 |
> |
|
| 540 |
> |
// Pick a processor at random |
| 541 |
> |
|
| 542 |
> |
which_proc = (int) (myRandom->rand() * nProcessors); |
| 543 |
> |
|
| 544 |
> |
//get the molecule stamp first |
| 545 |
> |
int stampId = info->getMoleculeStampId(i); |
| 546 |
> |
MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId); |
| 547 |
> |
|
| 548 |
> |
// How many atoms does this processor have so far? |
| 549 |
> |
old_atoms = atomsPerProc[which_proc]; |
| 550 |
> |
add_atoms = moleculeStamp->getNAtoms(); |
| 551 |
> |
new_atoms = old_atoms + add_atoms; |
| 552 |
> |
|
| 553 |
> |
// If we've been through this loop too many times, we need |
| 554 |
> |
// to just give up and assign the molecule to this processor |
| 555 |
> |
// and be done with it. |
| 556 |
> |
|
| 557 |
> |
if (loops > 100) { |
| 558 |
> |
sprintf(painCave.errMsg, |
| 559 |
> |
"I've tried 100 times to assign molecule %d to a " |
| 560 |
> |
" processor, but can't find a good spot.\n" |
| 561 |
> |
"I'm assigning it at random to processor %d.\n", |
| 562 |
> |
i, which_proc); |
| 563 |
> |
|
| 564 |
> |
painCave.isFatal = 0; |
| 565 |
> |
simError(); |
| 566 |
> |
|
| 567 |
> |
molToProcMap[i] = which_proc; |
| 568 |
> |
atomsPerProc[which_proc] += add_atoms; |
| 569 |
> |
|
| 570 |
> |
done = 1; |
| 571 |
> |
continue; |
| 572 |
> |
} |
| 573 |
> |
|
| 574 |
> |
// If we can add this molecule to this processor without sending |
| 575 |
> |
// it above nTarget, then go ahead and do it: |
| 576 |
> |
|
| 577 |
> |
if (new_atoms <= nTarget) { |
| 578 |
> |
molToProcMap[i] = which_proc; |
| 579 |
> |
atomsPerProc[which_proc] += add_atoms; |
| 580 |
> |
|
| 581 |
> |
done = 1; |
| 582 |
> |
continue; |
| 583 |
> |
} |
| 584 |
> |
|
| 585 |
> |
// The only situation left is when new_atoms > nTarget. We |
| 586 |
> |
// want to accept this with some probability that dies off the |
| 587 |
> |
// farther we are from nTarget |
| 588 |
> |
|
| 589 |
> |
// roughly: x = new_atoms - nTarget |
| 590 |
> |
// Pacc(x) = exp(- a * x) |
| 591 |
> |
// where a = penalty / (average atoms per molecule) |
| 592 |
> |
|
| 593 |
> |
x = (RealType)(new_atoms - nTarget); |
| 594 |
> |
y = myRandom->rand(); |
| 595 |
> |
|
| 596 |
> |
if (y < exp(- a * x)) { |
| 597 |
> |
molToProcMap[i] = which_proc; |
| 598 |
> |
atomsPerProc[which_proc] += add_atoms; |
| 599 |
> |
|
| 600 |
> |
done = 1; |
| 601 |
> |
continue; |
| 602 |
> |
} else { |
| 603 |
> |
continue; |
| 604 |
> |
} |
| 605 |
> |
} |
| 606 |
> |
} |
| 607 |
> |
|
| 608 |
> |
delete myRandom; |
| 609 |
> |
|
| 610 |
> |
// Spray out this nonsense to all other processors: |
| 611 |
> |
|
| 612 |
> |
MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
| 613 |
> |
} else { |
| 614 |
> |
|
| 615 |
> |
// Listen to your marching orders from processor 0: |
| 616 |
> |
|
| 617 |
> |
MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
| 618 |
> |
} |
| 619 |
> |
|
| 620 |
> |
info->setMolToProcMap(molToProcMap); |
| 621 |
> |
sprintf(checkPointMsg, |
| 622 |
> |
"Successfully divided the molecules among the processors.\n"); |
| 623 |
> |
errorCheckPoint(); |
| 624 |
> |
} |
| 625 |
> |
|
| 626 |
> |
#endif |
| 627 |
> |
|
| 628 |
> |
void SimCreator::createMolecules(SimInfo *info) { |
| 629 |
> |
MoleculeCreator molCreator; |
| 630 |
> |
int stampId; |
| 631 |
> |
|
| 632 |
> |
for(int i = 0; i < info->getNGlobalMolecules(); i++) { |
| 633 |
> |
|
| 634 |
> |
#ifdef IS_MPI |
| 635 |
> |
|
| 636 |
> |
if (info->getMolToProc(i) == worldRank) { |
| 637 |
> |
#endif |
| 638 |
> |
|
| 639 |
> |
stampId = info->getMoleculeStampId(i); |
| 640 |
> |
Molecule * mol = molCreator.createMolecule(info->getForceField(), |
| 641 |
> |
info->getMoleculeStamp(stampId), |
| 642 |
> |
stampId, i, |
| 643 |
> |
info->getLocalIndexManager()); |
| 644 |
> |
|
| 645 |
> |
info->addMolecule(mol); |
| 646 |
> |
|
| 647 |
> |
#ifdef IS_MPI |
| 648 |
> |
|
| 649 |
> |
} |
| 650 |
> |
|
| 651 |
> |
#endif |
| 652 |
> |
|
| 653 |
> |
} //end for(int i=0) |
| 654 |
> |
} |
| 655 |
> |
|
| 656 |
> |
void SimCreator::setGlobalIndex(SimInfo *info) { |
| 657 |
> |
SimInfo::MoleculeIterator mi; |
| 658 |
> |
Molecule::AtomIterator ai; |
| 659 |
> |
Molecule::RigidBodyIterator ri; |
| 660 |
> |
Molecule::CutoffGroupIterator ci; |
| 661 |
> |
Molecule::IntegrableObjectIterator ioi; |
| 662 |
> |
Molecule * mol; |
| 663 |
> |
Atom * atom; |
| 664 |
> |
RigidBody * rb; |
| 665 |
> |
CutoffGroup * cg; |
| 666 |
> |
int beginAtomIndex; |
| 667 |
> |
int beginRigidBodyIndex; |
| 668 |
> |
int beginCutoffGroupIndex; |
| 669 |
> |
int nGlobalAtoms = info->getNGlobalAtoms(); |
| 670 |
> |
|
| 671 |
> |
beginAtomIndex = 0; |
| 672 |
> |
beginRigidBodyIndex = 0; |
| 673 |
> |
beginCutoffGroupIndex = 0; |
| 674 |
> |
|
| 675 |
> |
for(int i = 0; i < info->getNGlobalMolecules(); i++) { |
| 676 |
> |
|
| 677 |
> |
#ifdef IS_MPI |
| 678 |
> |
if (info->getMolToProc(i) == worldRank) { |
| 679 |
> |
#endif |
| 680 |
> |
// stuff to do if I own this molecule |
| 681 |
> |
mol = info->getMoleculeByGlobalIndex(i); |
| 682 |
> |
|
| 683 |
> |
//local index(index in DataStorge) of atom is important |
| 684 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 685 |
> |
atom->setGlobalIndex(beginAtomIndex++); |
| 686 |
> |
} |
| 687 |
> |
|
| 688 |
> |
for(rb = mol->beginRigidBody(ri); rb != NULL; |
| 689 |
> |
rb = mol->nextRigidBody(ri)) { |
| 690 |
> |
rb->setGlobalIndex(beginRigidBodyIndex++); |
| 691 |
> |
} |
| 692 |
> |
|
| 693 |
> |
//local index of cutoff group is trivial, it only depends on |
| 694 |
> |
//the order of travesing |
| 695 |
> |
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 696 |
> |
cg = mol->nextCutoffGroup(ci)) { |
| 697 |
> |
cg->setGlobalIndex(beginCutoffGroupIndex++); |
| 698 |
> |
} |
| 699 |
> |
|
| 700 |
> |
#ifdef IS_MPI |
| 701 |
> |
} else { |
| 702 |
> |
|
| 703 |
> |
// stuff to do if I don't own this molecule |
| 704 |
> |
|
| 705 |
> |
int stampId = info->getMoleculeStampId(i); |
| 706 |
> |
MoleculeStamp* stamp = info->getMoleculeStamp(stampId); |
| 707 |
> |
|
| 708 |
> |
beginAtomIndex += stamp->getNAtoms(); |
| 709 |
> |
beginRigidBodyIndex += stamp->getNRigidBodies(); |
| 710 |
> |
beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms(); |
| 711 |
> |
} |
| 712 |
> |
#endif |
| 713 |
> |
|
| 714 |
> |
} //end for(int i=0) |
| 715 |
> |
|
| 716 |
> |
//fill globalGroupMembership |
| 717 |
> |
std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0); |
| 718 |
> |
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 719 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
| 720 |
> |
|
| 721 |
> |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
| 722 |
> |
globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex(); |
| 723 |
> |
} |
| 724 |
> |
|
| 725 |
> |
} |
| 726 |
> |
} |
| 727 |
> |
|
| 728 |
> |
#ifdef IS_MPI |
| 729 |
> |
// Since the globalGroupMembership has been zero filled and we've only |
| 730 |
> |
// poked values into the atoms we know, we can do an Allreduce |
| 731 |
> |
// to get the full globalGroupMembership array (We think). |
| 732 |
> |
// This would be prettier if we could use MPI_IN_PLACE like the MPI-2 |
| 733 |
> |
// docs said we could. |
| 734 |
> |
std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0); |
| 735 |
> |
MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms, |
| 736 |
> |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 737 |
> |
info->setGlobalGroupMembership(tmpGroupMembership); |
| 738 |
> |
#else |
| 739 |
> |
info->setGlobalGroupMembership(globalGroupMembership); |
| 740 |
> |
#endif |
| 741 |
> |
|
| 742 |
> |
//fill molMembership |
| 743 |
> |
std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0); |
| 744 |
> |
|
| 745 |
> |
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 746 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 747 |
> |
globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex(); |
| 748 |
> |
} |
| 749 |
> |
} |
| 750 |
> |
|
| 751 |
> |
#ifdef IS_MPI |
| 752 |
> |
std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0); |
| 753 |
> |
|
| 754 |
> |
MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms, |
| 755 |
> |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 756 |
> |
|
| 757 |
> |
info->setGlobalMolMembership(tmpMolMembership); |
| 758 |
> |
#else |
| 759 |
> |
info->setGlobalMolMembership(globalMolMembership); |
| 760 |
> |
#endif |
| 761 |
> |
|
| 762 |
> |
// nIOPerMol holds the number of integrable objects per molecule |
| 763 |
> |
// here the molecules are listed by their global indices. |
| 764 |
> |
|
| 765 |
> |
std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0); |
| 766 |
> |
for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 767 |
> |
nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects(); |
| 768 |
> |
} |
| 769 |
> |
|
| 770 |
> |
#ifdef IS_MPI |
| 771 |
> |
std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0); |
| 772 |
> |
MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0], |
| 773 |
> |
info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 774 |
> |
#else |
| 775 |
> |
std::vector<int> numIntegrableObjectsPerMol = nIOPerMol; |
| 776 |
> |
#endif |
| 777 |
> |
|
| 778 |
> |
std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules()); |
| 779 |
> |
|
| 780 |
> |
int startingIndex = 0; |
| 781 |
> |
for (int i = 0; i < info->getNGlobalMolecules(); i++) { |
| 782 |
> |
startingIOIndexForMol[i] = startingIndex; |
| 783 |
> |
startingIndex += numIntegrableObjectsPerMol[i]; |
| 784 |
> |
} |
| 785 |
> |
|
| 786 |
> |
std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL); |
| 787 |
> |
for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 788 |
> |
int myGlobalIndex = mol->getGlobalIndex(); |
| 789 |
> |
int globalIO = startingIOIndexForMol[myGlobalIndex]; |
| 790 |
> |
for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL; |
| 791 |
> |
integrableObject = mol->nextIntegrableObject(ioi)) { |
| 792 |
> |
integrableObject->setGlobalIntegrableObjectIndex(globalIO); |
| 793 |
> |
IOIndexToIntegrableObject[globalIO] = integrableObject; |
| 794 |
> |
globalIO++; |
| 795 |
> |
} |
| 796 |
> |
} |
| 797 |
> |
|
| 798 |
> |
info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject); |
| 799 |
> |
|
| 800 |
> |
} |
| 801 |
> |
|
| 802 |
> |
void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) { |
| 803 |
> |
Globals* simParams; |
| 804 |
> |
|
| 805 |
> |
simParams = info->getSimParams(); |
| 806 |
> |
|
| 807 |
> |
DumpReader reader(info, mdFileName); |
| 808 |
> |
int nframes = reader.getNFrames(); |
| 809 |
> |
|
| 810 |
> |
if (nframes > 0) { |
| 811 |
> |
reader.readFrame(nframes - 1); |
| 812 |
> |
} else { |
| 813 |
> |
//invalid initial coordinate file |
| 814 |
> |
sprintf(painCave.errMsg, |
| 815 |
> |
"Initial configuration file %s should at least contain one frame\n", |
| 816 |
> |
mdFileName.c_str()); |
| 817 |
> |
painCave.isFatal = 1; |
| 818 |
> |
simError(); |
| 819 |
> |
} |
| 820 |
> |
//copy the current snapshot to previous snapshot |
| 821 |
> |
info->getSnapshotManager()->advance(); |
| 822 |
> |
} |
| 823 |
> |
|
| 824 |
> |
} //end namespace OpenMD |
| 825 |
> |
|
| 826 |
> |
|
