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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, |
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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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info->setRestFileName(prefix + ".zang"); |
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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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|
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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; |
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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: |
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|
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MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
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} |
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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; |
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|
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for(int i = 0; i < info->getNGlobalMolecules(); i++) { |
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|
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#ifdef IS_MPI |
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|
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if (info->getMolToProc(i) == worldRank) { |
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#endif |
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|
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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()); |
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|
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info->addMolecule(mol); |
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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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} //end for(int i=0) |
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} |
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|
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void SimCreator::compList(MakeStamps *stamps, Globals* simParams, |
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std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) { |
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int i; |
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char * id; |
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LinkedMolStamp* extractedStamp = NULL; |
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MoleculeStamp * currentStamp; |
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Component** the_components = simParams->getComponents(); |
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int n_components = simParams->getNComponents(); |
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|
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if (!simParams->haveNMol()) { |
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// we don't have the total number of molecules, so we assume it is |
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// given in each component |
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|
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for(i = 0; i < n_components; i++) { |
| 413 |
if (!the_components[i]->haveNMol()) { |
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// we have a problem |
| 415 |
sprintf(painCave.errMsg, |
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"SimCreator Error. No global NMol or component NMol given.\n" |
| 417 |
"\tCannot calculate the number of atoms.\n"); |
| 418 |
|
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painCave.isFatal = 1; |
| 420 |
simError(); |
| 421 |
} |
| 422 |
|
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id = the_components[i]->getType(); |
| 424 |
|
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extractedStamp = stamps->extractMolStamp(id); |
| 426 |
if (extractedStamp == NULL) { |
| 427 |
sprintf(painCave.errMsg, |
| 428 |
"SimCreator error: Component \"%s\" was not found in the " |
| 429 |
"list of declared molecules\n", id); |
| 430 |
|
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painCave.isFatal = 1; |
| 432 |
simError(); |
| 433 |
} |
| 434 |
|
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currentStamp = extractedStamp->getStamp(); |
| 436 |
|
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|
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moleculeStampPairs.push_back( |
| 439 |
std::make_pair(currentStamp, the_components[i]->getNMol())); |
| 440 |
} //end for (i = 0; i < n_components; i++) |
| 441 |
} else { |
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sprintf(painCave.errMsg, "SimSetup error.\n" |
| 443 |
"\tSorry, the ability to specify total" |
| 444 |
" nMols and then give molfractions in the components\n" |
| 445 |
"\tis not currently supported." |
| 446 |
" Please give nMol in the components.\n"); |
| 447 |
|
| 448 |
painCave.isFatal = 1; |
| 449 |
simError(); |
| 450 |
} |
| 451 |
|
| 452 |
#ifdef IS_MPI |
| 453 |
|
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strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
| 455 |
MPIcheckPoint(); |
| 456 |
|
| 457 |
#endif // is_mpi |
| 458 |
|
| 459 |
} |
| 460 |
|
| 461 |
void SimCreator::setGlobalIndex(SimInfo *info) { |
| 462 |
SimInfo::MoleculeIterator mi; |
| 463 |
Molecule::AtomIterator ai; |
| 464 |
Molecule::RigidBodyIterator ri; |
| 465 |
Molecule::CutoffGroupIterator ci; |
| 466 |
Molecule * mol; |
| 467 |
Atom * atom; |
| 468 |
RigidBody * rb; |
| 469 |
CutoffGroup * cg; |
| 470 |
int beginAtomIndex; |
| 471 |
int beginRigidBodyIndex; |
| 472 |
int beginCutoffGroupIndex; |
| 473 |
int nGlobalAtoms = info->getNGlobalAtoms(); |
| 474 |
|
| 475 |
#ifndef IS_MPI |
| 476 |
|
| 477 |
beginAtomIndex = 0; |
| 478 |
beginRigidBodyIndex = 0; |
| 479 |
beginCutoffGroupIndex = 0; |
| 480 |
|
| 481 |
#else |
| 482 |
|
| 483 |
int nproc; |
| 484 |
int myNode; |
| 485 |
|
| 486 |
myNode = worldRank; |
| 487 |
MPI_Comm_size(MPI_COMM_WORLD, &nproc); |
| 488 |
|
| 489 |
std::vector < int > tmpAtomsInProc(nproc, 0); |
| 490 |
std::vector < int > tmpRigidBodiesInProc(nproc, 0); |
| 491 |
std::vector < int > tmpCutoffGroupsInProc(nproc, 0); |
| 492 |
std::vector < int > NumAtomsInProc(nproc, 0); |
| 493 |
std::vector < int > NumRigidBodiesInProc(nproc, 0); |
| 494 |
std::vector < int > NumCutoffGroupsInProc(nproc, 0); |
| 495 |
|
| 496 |
tmpAtomsInProc[myNode] = info->getNAtoms(); |
| 497 |
tmpRigidBodiesInProc[myNode] = info->getNRigidBodies(); |
| 498 |
tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups(); |
| 499 |
|
| 500 |
//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups |
| 501 |
MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT, |
| 502 |
MPI_SUM, MPI_COMM_WORLD); |
| 503 |
MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc, |
| 504 |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 505 |
MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc, |
| 506 |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 507 |
|
| 508 |
beginAtomIndex = 0; |
| 509 |
beginRigidBodyIndex = 0; |
| 510 |
beginCutoffGroupIndex = 0; |
| 511 |
|
| 512 |
for(int i = 0; i < myNode; i++) { |
| 513 |
beginAtomIndex += NumAtomsInProc[i]; |
| 514 |
beginRigidBodyIndex += NumRigidBodiesInProc[i]; |
| 515 |
beginCutoffGroupIndex += NumCutoffGroupsInProc[i]; |
| 516 |
} |
| 517 |
|
| 518 |
#endif |
| 519 |
|
| 520 |
//rigidbody's index begins right after atom's |
| 521 |
beginRigidBodyIndex += info->getNGlobalAtoms(); |
| 522 |
|
| 523 |
for(mol = info->beginMolecule(mi); mol != NULL; |
| 524 |
mol = info->nextMolecule(mi)) { |
| 525 |
|
| 526 |
//local index(index in DataStorge) of atom is important |
| 527 |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 528 |
atom->setGlobalIndex(beginAtomIndex++); |
| 529 |
} |
| 530 |
|
| 531 |
for(rb = mol->beginRigidBody(ri); rb != NULL; |
| 532 |
rb = mol->nextRigidBody(ri)) { |
| 533 |
rb->setGlobalIndex(beginRigidBodyIndex++); |
| 534 |
} |
| 535 |
|
| 536 |
//local index of cutoff group is trivial, it only depends on the order of travesing |
| 537 |
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 538 |
cg = mol->nextCutoffGroup(ci)) { |
| 539 |
cg->setGlobalIndex(beginCutoffGroupIndex++); |
| 540 |
} |
| 541 |
} |
| 542 |
|
| 543 |
//fill globalGroupMembership |
| 544 |
std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0); |
| 545 |
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 546 |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
| 547 |
|
| 548 |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
| 549 |
globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex(); |
| 550 |
} |
| 551 |
|
| 552 |
} |
| 553 |
} |
| 554 |
|
| 555 |
#ifdef IS_MPI |
| 556 |
// Since the globalGroupMembership has been zero filled and we've only |
| 557 |
// poked values into the atoms we know, we can do an Allreduce |
| 558 |
// to get the full globalGroupMembership array (We think). |
| 559 |
// This would be prettier if we could use MPI_IN_PLACE like the MPI-2 |
| 560 |
// docs said we could. |
| 561 |
std::vector<int> tmpGroupMembership(nGlobalAtoms, 0); |
| 562 |
MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms, |
| 563 |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 564 |
info->setGlobalGroupMembership(tmpGroupMembership); |
| 565 |
#else |
| 566 |
info->setGlobalGroupMembership(globalGroupMembership); |
| 567 |
#endif |
| 568 |
|
| 569 |
//fill molMembership |
| 570 |
std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0); |
| 571 |
|
| 572 |
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
| 573 |
|
| 574 |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 575 |
globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex(); |
| 576 |
} |
| 577 |
} |
| 578 |
|
| 579 |
#ifdef IS_MPI |
| 580 |
std::vector<int> tmpMolMembership(nGlobalAtoms, 0); |
| 581 |
|
| 582 |
MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms, |
| 583 |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
| 584 |
|
| 585 |
info->setGlobalMolMembership(tmpMolMembership); |
| 586 |
#else |
| 587 |
info->setGlobalMolMembership(globalMolMembership); |
| 588 |
#endif |
| 589 |
|
| 590 |
} |
| 591 |
|
| 592 |
void SimCreator::loadCoordinates(SimInfo* info) { |
| 593 |
Globals* simParams; |
| 594 |
simParams = info->getSimParams(); |
| 595 |
|
| 596 |
if (!simParams->haveInitialConfig()) { |
| 597 |
sprintf(painCave.errMsg, |
| 598 |
"Cannot intialize a simulation without an initial configuration file.\n"); |
| 599 |
painCave.isFatal = 1;; |
| 600 |
simError(); |
| 601 |
} |
| 602 |
|
| 603 |
DumpReader reader(info, simParams->getInitialConfig()); |
| 604 |
int nframes = reader.getNFrames(); |
| 605 |
|
| 606 |
if (nframes > 0) { |
| 607 |
reader.readFrame(nframes - 1); |
| 608 |
} else { |
| 609 |
//invalid initial coordinate file |
| 610 |
sprintf(painCave.errMsg, |
| 611 |
"Initial configuration file %s should at least contain one frame\n", |
| 612 |
simParams->getInitialConfig()); |
| 613 |
painCave.isFatal = 1; |
| 614 |
simError(); |
| 615 |
} |
| 616 |
|
| 617 |
//copy the current snapshot to previous snapshot |
| 618 |
info->getSnapshotManager()->advance(); |
| 619 |
} |
| 620 |
|
| 621 |
} //end namespace oopse |
| 622 |
|
| 623 |
|
