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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); |
306 |
|
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painCave.isFatal = 0; |
308 |
simError(); |
309 |
|
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molToProcMap[i] = which_proc; |
311 |
atomsPerProc[which_proc] += add_atoms; |
312 |
|
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done = 1; |
314 |
continue; |
315 |
} |
316 |
|
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// If we can add this molecule to this processor without sending |
318 |
// it above nTarget, then go ahead and do it: |
319 |
|
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if (new_atoms <= nTarget) { |
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molToProcMap[i] = which_proc; |
322 |
atomsPerProc[which_proc] += add_atoms; |
323 |
|
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done = 1; |
325 |
continue; |
326 |
} |
327 |
|
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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; |
342 |
|
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done = 1; |
344 |
continue; |
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} else { |
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continue; |
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} |
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} |
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} |
350 |
|
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delete myRandom; |
352 |
|
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// Spray out this nonsense to all other processors: |
354 |
|
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MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
356 |
} else { |
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|
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// Listen to your marching orders from processor 0: |
359 |
|
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MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
361 |
} |
362 |
|
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info->setMolToProcMap(molToProcMap); |
364 |
sprintf(checkPointMsg, |
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"Successfully divided the molecules among the processors.\n"); |
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MPIcheckPoint(); |
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} |
368 |
|
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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 |
|
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for(int i = 0; i < info->getNGlobalMolecules(); i++) { |
376 |
|
377 |
#ifdef IS_MPI |
378 |
|
379 |
if (info->getMolToProc(i) == worldRank) { |
380 |
#endif |
381 |
|
382 |
stampId = info->getMoleculeStampId(i); |
383 |
Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId), |
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stampId, i, info->getLocalIndexManager()); |
385 |
|
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info->addMolecule(mol); |
387 |
|
388 |
#ifdef IS_MPI |
389 |
|
390 |
} |
391 |
|
392 |
#endif |
393 |
|
394 |
} //end for(int i=0) |
395 |
} |
396 |
|
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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 |
LinkedMolStamp* extractedStamp = NULL; |
402 |
MoleculeStamp * currentStamp; |
403 |
Component** the_components = simParams->getComponents(); |
404 |
int n_components = simParams->getNComponents(); |
405 |
|
406 |
if (!simParams->haveNMol()) { |
407 |
// we don't have the total number of molecules, so we assume it is |
408 |
// given in each component |
409 |
|
410 |
for(i = 0; i < n_components; i++) { |
411 |
if (!the_components[i]->haveNMol()) { |
412 |
// we have a problem |
413 |
sprintf(painCave.errMsg, |
414 |
"SimCreator Error. No global NMol or component NMol given.\n" |
415 |
"\tCannot calculate the number of atoms.\n"); |
416 |
|
417 |
painCave.isFatal = 1; |
418 |
simError(); |
419 |
} |
420 |
|
421 |
id = the_components[i]->getType(); |
422 |
|
423 |
extractedStamp = stamps->extractMolStamp(id); |
424 |
if (extractedStamp == NULL) { |
425 |
sprintf(painCave.errMsg, |
426 |
"SimCreator error: Component \"%s\" was not found in the " |
427 |
"list of declared molecules\n", id); |
428 |
|
429 |
painCave.isFatal = 1; |
430 |
simError(); |
431 |
} |
432 |
|
433 |
currentStamp = extractedStamp->getStamp(); |
434 |
|
435 |
|
436 |
moleculeStampPairs.push_back( |
437 |
std::make_pair(currentStamp, the_components[i]->getNMol())); |
438 |
} //end for (i = 0; i < n_components; i++) |
439 |
} else { |
440 |
sprintf(painCave.errMsg, "SimSetup error.\n" |
441 |
"\tSorry, the ability to specify total" |
442 |
" nMols and then give molfractions in the components\n" |
443 |
"\tis not currently supported." |
444 |
" Please give nMol in the components.\n"); |
445 |
|
446 |
painCave.isFatal = 1; |
447 |
simError(); |
448 |
} |
449 |
|
450 |
#ifdef IS_MPI |
451 |
|
452 |
strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
453 |
MPIcheckPoint(); |
454 |
|
455 |
#endif // is_mpi |
456 |
|
457 |
} |
458 |
|
459 |
void SimCreator::setGlobalIndex(SimInfo *info) { |
460 |
SimInfo::MoleculeIterator mi; |
461 |
Molecule::AtomIterator ai; |
462 |
Molecule::RigidBodyIterator ri; |
463 |
Molecule::CutoffGroupIterator ci; |
464 |
Molecule * mol; |
465 |
Atom * atom; |
466 |
RigidBody * rb; |
467 |
CutoffGroup * cg; |
468 |
int beginAtomIndex; |
469 |
int beginRigidBodyIndex; |
470 |
int beginCutoffGroupIndex; |
471 |
int nGlobalAtoms = info->getNGlobalAtoms(); |
472 |
|
473 |
#ifndef IS_MPI |
474 |
|
475 |
beginAtomIndex = 0; |
476 |
beginRigidBodyIndex = 0; |
477 |
beginCutoffGroupIndex = 0; |
478 |
|
479 |
#else |
480 |
|
481 |
int nproc; |
482 |
int myNode; |
483 |
|
484 |
myNode = worldRank; |
485 |
MPI_Comm_size(MPI_COMM_WORLD, &nproc); |
486 |
|
487 |
std::vector < int > tmpAtomsInProc(nproc, 0); |
488 |
std::vector < int > tmpRigidBodiesInProc(nproc, 0); |
489 |
std::vector < int > tmpCutoffGroupsInProc(nproc, 0); |
490 |
std::vector < int > NumAtomsInProc(nproc, 0); |
491 |
std::vector < int > NumRigidBodiesInProc(nproc, 0); |
492 |
std::vector < int > NumCutoffGroupsInProc(nproc, 0); |
493 |
|
494 |
tmpAtomsInProc[myNode] = info->getNAtoms(); |
495 |
tmpRigidBodiesInProc[myNode] = info->getNRigidBodies(); |
496 |
tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups(); |
497 |
|
498 |
//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups |
499 |
MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT, |
500 |
MPI_SUM, MPI_COMM_WORLD); |
501 |
MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc, |
502 |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
503 |
MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc, |
504 |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
505 |
|
506 |
beginAtomIndex = 0; |
507 |
beginRigidBodyIndex = 0; |
508 |
beginCutoffGroupIndex = 0; |
509 |
|
510 |
for(int i = 0; i < myNode; i++) { |
511 |
beginAtomIndex += NumAtomsInProc[i]; |
512 |
beginRigidBodyIndex += NumRigidBodiesInProc[i]; |
513 |
beginCutoffGroupIndex += NumCutoffGroupsInProc[i]; |
514 |
} |
515 |
|
516 |
#endif |
517 |
|
518 |
//rigidbody's index begins right after atom's |
519 |
beginRigidBodyIndex += info->getNGlobalAtoms(); |
520 |
|
521 |
for(mol = info->beginMolecule(mi); mol != NULL; |
522 |
mol = info->nextMolecule(mi)) { |
523 |
|
524 |
//local index(index in DataStorge) of atom is important |
525 |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
526 |
atom->setGlobalIndex(beginAtomIndex++); |
527 |
} |
528 |
|
529 |
for(rb = mol->beginRigidBody(ri); rb != NULL; |
530 |
rb = mol->nextRigidBody(ri)) { |
531 |
rb->setGlobalIndex(beginRigidBodyIndex++); |
532 |
} |
533 |
|
534 |
//local index of cutoff group is trivial, it only depends on the order of travesing |
535 |
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
536 |
cg = mol->nextCutoffGroup(ci)) { |
537 |
cg->setGlobalIndex(beginCutoffGroupIndex++); |
538 |
} |
539 |
} |
540 |
|
541 |
//fill globalGroupMembership |
542 |
std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0); |
543 |
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
544 |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
545 |
|
546 |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
547 |
globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex(); |
548 |
} |
549 |
|
550 |
} |
551 |
} |
552 |
|
553 |
#ifdef IS_MPI |
554 |
// Since the globalGroupMembership has been zero filled and we've only |
555 |
// poked values into the atoms we know, we can do an Allreduce |
556 |
// to get the full globalGroupMembership array (We think). |
557 |
// This would be prettier if we could use MPI_IN_PLACE like the MPI-2 |
558 |
// docs said we could. |
559 |
std::vector<int> tmpGroupMembership(nGlobalAtoms, 0); |
560 |
MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms, |
561 |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
562 |
info->setGlobalGroupMembership(tmpGroupMembership); |
563 |
#else |
564 |
info->setGlobalGroupMembership(globalGroupMembership); |
565 |
#endif |
566 |
|
567 |
//fill molMembership |
568 |
std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0); |
569 |
|
570 |
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
571 |
|
572 |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
573 |
globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex(); |
574 |
} |
575 |
} |
576 |
|
577 |
#ifdef IS_MPI |
578 |
std::vector<int> tmpMolMembership(nGlobalAtoms, 0); |
579 |
|
580 |
MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms, |
581 |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
582 |
|
583 |
info->setGlobalMolMembership(tmpMolMembership); |
584 |
#else |
585 |
info->setGlobalMolMembership(globalMolMembership); |
586 |
#endif |
587 |
|
588 |
} |
589 |
|
590 |
void SimCreator::loadCoordinates(SimInfo* info) { |
591 |
Globals* simParams; |
592 |
simParams = info->getSimParams(); |
593 |
|
594 |
if (!simParams->haveInitialConfig()) { |
595 |
sprintf(painCave.errMsg, |
596 |
"Cannot intialize a simulation without an initial configuration file.\n"); |
597 |
painCave.isFatal = 1;; |
598 |
simError(); |
599 |
} |
600 |
|
601 |
DumpReader reader(info, simParams->getInitialConfig()); |
602 |
int nframes = reader.getNFrames(); |
603 |
|
604 |
if (nframes > 0) { |
605 |
reader.readFrame(nframes - 1); |
606 |
} else { |
607 |
//invalid initial coordinate file |
608 |
sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n", |
609 |
simParams->getInitialConfig()); |
610 |
painCave.isFatal = 1; |
611 |
simError(); |
612 |
} |
613 |
|
614 |
//copy the current snapshot to previous snapshot |
615 |
info->getSnapshotManager()->advance(); |
616 |
} |
617 |
|
618 |
} //end namespace oopse |
619 |
|
620 |
|