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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 <sprng.h> |
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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++; |
284 |
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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; |
297 |
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|
298 |
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// If we've been through this loop too many times, we need |
299 |
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// to just give up and assign the molecule to this processor |
300 |
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// and be done with it. |
301 |
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|
302 |
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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 " |
305 |
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" processor, but can't find a good spot.\n" |
306 |
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"I'm assigning it at random to processor %d.\n", |
307 |
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i, which_proc); |
308 |
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|
309 |
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painCave.isFatal = 0; |
310 |
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simError(); |
311 |
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|
312 |
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molToProcMap[i] = which_proc; |
313 |
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atomsPerProc[which_proc] += add_atoms; |
314 |
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|
315 |
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done = 1; |
316 |
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continue; |
317 |
< |
} |
318 |
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|
319 |
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// If we can add this molecule to this processor without sending |
320 |
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// it above nTarget, then go ahead and do it: |
321 |
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|
322 |
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if (new_atoms <= nTarget) { |
323 |
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molToProcMap[i] = which_proc; |
324 |
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atomsPerProc[which_proc] += add_atoms; |
325 |
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|
326 |
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done = 1; |
327 |
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continue; |
328 |
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} |
329 |
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|
330 |
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// The only situation left is when new_atoms > nTarget. We |
331 |
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// want to accept this with some probability that dies off the |
332 |
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// farther we are from nTarget |
333 |
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|
334 |
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// roughly: x = new_atoms - nTarget |
335 |
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// Pacc(x) = exp(- a * x) |
336 |
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// where a = penalty / (average atoms per molecule) |
337 |
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|
338 |
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x = (double)(new_atoms - nTarget); |
339 |
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y = myRandom->rand(); |
340 |
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|
341 |
< |
if (y < exp(- a * x)) { |
342 |
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molToProcMap[i] = which_proc; |
343 |
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atomsPerProc[which_proc] += add_atoms; |
344 |
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|
345 |
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done = 1; |
346 |
< |
continue; |
347 |
< |
} else { |
348 |
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continue; |
349 |
< |
} |
350 |
< |
} |
351 |
< |
} |
352 |
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|
353 |
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delete myRandom; |
354 |
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|
355 |
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// Spray out this nonsense to all other processors: |
356 |
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|
357 |
< |
MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
358 |
< |
} else { |
359 |
< |
|
360 |
< |
// Listen to your marching orders from processor 0: |
361 |
< |
|
362 |
< |
MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
363 |
< |
} |
364 |
< |
|
365 |
< |
info->setMolToProcMap(molToProcMap); |
366 |
< |
sprintf(checkPointMsg, |
367 |
< |
"Successfully divided the molecules among the processors.\n"); |
368 |
< |
MPIcheckPoint(); |
369 |
< |
} |
370 |
< |
|
371 |
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#endif |
372 |
< |
|
373 |
< |
void SimCreator::createMolecules(SimInfo *info) { |
374 |
< |
MoleculeCreator molCreator; |
375 |
< |
int stampId; |
376 |
< |
|
377 |
< |
for(int i = 0; i < info->getNGlobalMolecules(); i++) { |
378 |
< |
|
379 |
< |
#ifdef IS_MPI |
380 |
< |
|
381 |
< |
if (info->getMolToProc(i) == worldRank) { |
382 |
< |
#endif |
383 |
< |
|
384 |
< |
stampId = info->getMoleculeStampId(i); |
385 |
< |
Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId), |
386 |
< |
stampId, i, info->getLocalIndexManager()); |
387 |
< |
|
388 |
< |
info->addMolecule(mol); |
389 |
< |
|
390 |
< |
#ifdef IS_MPI |
391 |
< |
|
392 |
< |
} |
393 |
< |
|
394 |
< |
#endif |
395 |
< |
|
396 |
< |
} //end for(int i=0) |
397 |
< |
} |
398 |
< |
|
399 |
< |
void SimCreator::compList(MakeStamps *stamps, Globals* simParams, |
400 |
< |
std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) { |
401 |
< |
int i; |
402 |
< |
char * id; |
403 |
< |
MoleculeStamp * currentStamp; |
404 |
< |
Component** the_components = simParams->getComponents(); |
405 |
< |
int n_components = simParams->getNComponents(); |
406 |
< |
|
407 |
< |
if (!simParams->haveNMol()) { |
408 |
< |
// we don't have the total number of molecules, so we assume it is |
409 |
< |
// given in each component |
410 |
< |
|
411 |
< |
for(i = 0; i < n_components; i++) { |
412 |
< |
if (!the_components[i]->haveNMol()) { |
413 |
< |
// we have a problem |
414 |
< |
sprintf(painCave.errMsg, |
415 |
< |
"SimCreator Error. No global NMol or component NMol given.\n" |
416 |
< |
"\tCannot calculate the number of atoms.\n"); |
417 |
< |
|
418 |
< |
painCave.isFatal = 1; |
419 |
< |
simError(); |
420 |
< |
} |
421 |
< |
|
422 |
< |
id = the_components[i]->getType(); |
423 |
< |
currentStamp = (stamps->extractMolStamp(id))->getStamp(); |
424 |
< |
|
425 |
< |
if (currentStamp == NULL) { |
426 |
< |
sprintf(painCave.errMsg, |
427 |
< |
"SimCreator error: Component \"%s\" was not found in the " |
428 |
< |
"list of declared molecules\n", id); |
429 |
< |
|
430 |
< |
painCave.isFatal = 1; |
431 |
< |
simError(); |
432 |
< |
} |
433 |
< |
|
434 |
< |
moleculeStampPairs.push_back( |
435 |
< |
std::make_pair(currentStamp, the_components[i]->getNMol())); |
436 |
< |
} //end for (i = 0; i < n_components; i++) |
437 |
< |
} else { |
438 |
< |
sprintf(painCave.errMsg, "SimSetup error.\n" |
439 |
< |
"\tSorry, the ability to specify total" |
440 |
< |
" nMols and then give molfractions in the components\n" |
441 |
< |
"\tis not currently supported." |
442 |
< |
" Please give nMol in the components.\n"); |
443 |
< |
|
444 |
< |
painCave.isFatal = 1; |
445 |
< |
simError(); |
446 |
< |
} |
447 |
< |
|
448 |
< |
#ifdef IS_MPI |
449 |
< |
|
450 |
< |
strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
451 |
< |
MPIcheckPoint(); |
452 |
< |
|
453 |
< |
#endif // is_mpi |
454 |
< |
|
455 |
< |
} |
456 |
< |
|
457 |
< |
void SimCreator::setGlobalIndex(SimInfo *info) { |
458 |
< |
SimInfo::MoleculeIterator mi; |
459 |
< |
Molecule::AtomIterator ai; |
460 |
< |
Molecule::RigidBodyIterator ri; |
461 |
< |
Molecule::CutoffGroupIterator ci; |
462 |
< |
Molecule * mol; |
463 |
< |
Atom * atom; |
464 |
< |
RigidBody * rb; |
465 |
< |
CutoffGroup * cg; |
466 |
< |
int beginAtomIndex; |
467 |
< |
int beginRigidBodyIndex; |
468 |
< |
int beginCutoffGroupIndex; |
469 |
< |
int nGlobalAtoms = info->getNGlobalAtoms(); |
470 |
< |
|
471 |
< |
#ifndef IS_MPI |
472 |
< |
|
473 |
< |
beginAtomIndex = 0; |
474 |
< |
beginRigidBodyIndex = 0; |
475 |
< |
beginCutoffGroupIndex = 0; |
476 |
< |
|
477 |
< |
#else |
478 |
< |
|
479 |
< |
int nproc; |
480 |
< |
int myNode; |
481 |
< |
|
482 |
< |
myNode = worldRank; |
483 |
< |
MPI_Comm_size(MPI_COMM_WORLD, &nproc); |
484 |
< |
|
485 |
< |
std::vector < int > tmpAtomsInProc(nproc, 0); |
486 |
< |
std::vector < int > tmpRigidBodiesInProc(nproc, 0); |
487 |
< |
std::vector < int > tmpCutoffGroupsInProc(nproc, 0); |
488 |
< |
std::vector < int > NumAtomsInProc(nproc, 0); |
489 |
< |
std::vector < int > NumRigidBodiesInProc(nproc, 0); |
490 |
< |
std::vector < int > NumCutoffGroupsInProc(nproc, 0); |
491 |
< |
|
492 |
< |
tmpAtomsInProc[myNode] = info->getNAtoms(); |
493 |
< |
tmpRigidBodiesInProc[myNode] = info->getNRigidBodies(); |
494 |
< |
tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups(); |
495 |
< |
|
496 |
< |
//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups |
497 |
< |
MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT, |
498 |
< |
MPI_SUM, MPI_COMM_WORLD); |
499 |
< |
MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc, |
500 |
< |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
501 |
< |
MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc, |
502 |
< |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
503 |
< |
|
504 |
< |
beginAtomIndex = 0; |
505 |
< |
beginRigidBodyIndex = 0; |
506 |
< |
beginCutoffGroupIndex = 0; |
507 |
< |
|
508 |
< |
for(int i = 0; i < myNode; i++) { |
509 |
< |
beginAtomIndex += NumAtomsInProc[i]; |
510 |
< |
beginRigidBodyIndex += NumRigidBodiesInProc[i]; |
511 |
< |
beginCutoffGroupIndex += NumCutoffGroupsInProc[i]; |
512 |
< |
} |
513 |
< |
|
514 |
< |
#endif |
515 |
< |
|
516 |
< |
//rigidbody's index begins right after atom's |
517 |
< |
beginRigidBodyIndex += info->getNGlobalAtoms(); |
518 |
< |
|
519 |
< |
for(mol = info->beginMolecule(mi); mol != NULL; |
520 |
< |
mol = info->nextMolecule(mi)) { |
521 |
< |
|
522 |
< |
//local index(index in DataStorge) of atom is important |
523 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
524 |
< |
atom->setGlobalIndex(beginAtomIndex++); |
525 |
< |
} |
526 |
< |
|
527 |
< |
for(rb = mol->beginRigidBody(ri); rb != NULL; |
528 |
< |
rb = mol->nextRigidBody(ri)) { |
529 |
< |
rb->setGlobalIndex(beginRigidBodyIndex++); |
530 |
< |
} |
531 |
< |
|
532 |
< |
//local index of cutoff group is trivial, it only depends on the order of travesing |
533 |
< |
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
534 |
< |
cg = mol->nextCutoffGroup(ci)) { |
535 |
< |
cg->setGlobalIndex(beginCutoffGroupIndex++); |
536 |
< |
} |
537 |
< |
} |
538 |
< |
|
539 |
< |
//fill globalGroupMembership |
540 |
< |
std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0); |
541 |
< |
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
542 |
< |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
543 |
< |
|
544 |
< |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
545 |
< |
globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex(); |
546 |
< |
} |
547 |
< |
|
548 |
< |
} |
549 |
< |
} |
550 |
< |
|
551 |
< |
#ifdef IS_MPI |
552 |
< |
// Since the globalGroupMembership has been zero filled and we've only |
553 |
< |
// poked values into the atoms we know, we can do an Allreduce |
554 |
< |
// to get the full globalGroupMembership array (We think). |
555 |
< |
// This would be prettier if we could use MPI_IN_PLACE like the MPI-2 |
556 |
< |
// docs said we could. |
557 |
< |
std::vector<int> tmpGroupMembership(nGlobalAtoms, 0); |
558 |
< |
MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms, |
559 |
< |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
560 |
< |
info->setGlobalGroupMembership(tmpGroupMembership); |
561 |
< |
#else |
562 |
< |
info->setGlobalGroupMembership(globalGroupMembership); |
563 |
< |
#endif |
564 |
< |
|
565 |
< |
//fill molMembership |
566 |
< |
std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0); |
567 |
< |
|
568 |
< |
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
569 |
< |
|
570 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
571 |
< |
globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex(); |
572 |
< |
} |
573 |
< |
} |
574 |
< |
|
575 |
< |
#ifdef IS_MPI |
576 |
< |
std::vector<int> tmpMolMembership(nGlobalAtoms, 0); |
577 |
< |
|
578 |
< |
MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms, |
579 |
< |
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
580 |
< |
|
581 |
< |
info->setGlobalMolMembership(tmpMolMembership); |
582 |
< |
#else |
583 |
< |
info->setGlobalMolMembership(globalMolMembership); |
584 |
< |
#endif |
585 |
< |
|
586 |
< |
} |
587 |
< |
|
588 |
< |
void SimCreator::loadCoordinates(SimInfo* info) { |
589 |
< |
Globals* simParams; |
590 |
< |
simParams = info->getSimParams(); |
591 |
< |
|
592 |
< |
if (!simParams->haveInitialConfig()) { |
593 |
< |
sprintf(painCave.errMsg, |
594 |
< |
"Cannot intialize a simulation without an initial configuration file.\n"); |
595 |
< |
painCave.isFatal = 1;; |
596 |
< |
simError(); |
597 |
< |
} |
598 |
< |
|
599 |
< |
DumpReader reader(info, simParams->getInitialConfig()); |
600 |
< |
int nframes = reader.getNFrames(); |
601 |
< |
|
602 |
< |
if (nframes > 0) { |
603 |
< |
reader.readFrame(nframes - 1); |
604 |
< |
} else { |
605 |
< |
//invalid initial coordinate file |
606 |
< |
sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n", |
607 |
< |
simParams->getInitialConfig()); |
608 |
< |
painCave.isFatal = 1; |
609 |
< |
simError(); |
610 |
< |
} |
611 |
< |
|
612 |
< |
//copy the current snapshot to previous snapshot |
613 |
< |
info->getSnapshotManager()->advance(); |
614 |
< |
} |
615 |
< |
|
616 |
< |
} //end namespace oopse |
617 |
< |
|
618 |
< |
|
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. Acknowledgement of the program authors must be made in any |
10 |
> |
* publication of scientific results based in part on use of the |
11 |
> |
* program. An acceptable form of acknowledgement is citation of |
12 |
> |
* the article in which the program was described (Matthew |
13 |
> |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
14 |
> |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
15 |
> |
* Parallel Simulation Engine for Molecular Dynamics," |
16 |
> |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
17 |
> |
* |
18 |
> |
* 2. Redistributions of source code must retain the above copyright |
19 |
> |
* notice, this list of conditions and the following disclaimer. |
20 |
> |
* |
21 |
> |
* 3. Redistributions in binary form must reproduce the above copyright |
22 |
> |
* notice, this list of conditions and the following disclaimer in the |
23 |
> |
* documentation and/or other materials provided with the |
24 |
> |
* distribution. |
25 |
> |
* |
26 |
> |
* This software is provided "AS IS," without a warranty of any |
27 |
> |
* kind. All express or implied conditions, representations and |
28 |
> |
* warranties, including any implied warranty of merchantability, |
29 |
> |
* fitness for a particular purpose or non-infringement, are hereby |
30 |
> |
* excluded. The University of Notre Dame and its licensors shall not |
31 |
> |
* be liable for any damages suffered by licensee as a result of |
32 |
> |
* using, modifying or distributing the software or its |
33 |
> |
* derivatives. In no event will the University of Notre Dame or its |
34 |
> |
* licensors be liable for any lost revenue, profit or data, or for |
35 |
> |
* direct, indirect, special, consequential, incidental or punitive |
36 |
> |
* damages, however caused and regardless of the theory of liability, |
37 |
> |
* arising out of the use of or inability to use software, even if the |
38 |
> |
* University of Notre Dame has been advised of the possibility of |
39 |
> |
* such damages. |
40 |
> |
*/ |
41 |
> |
|
42 |
> |
/** |
43 |
> |
* @file SimCreator.cpp |
44 |
> |
* @author tlin |
45 |
> |
* @date 11/03/2004 |
46 |
> |
* @time 13:51am |
47 |
> |
* @version 1.0 |
48 |
> |
*/ |
49 |
> |
|
50 |
> |
#include "brains/MoleculeCreator.hpp" |
51 |
> |
#include "brains/SimCreator.hpp" |
52 |
> |
#include "brains/SimSnapshotManager.hpp" |
53 |
> |
#include "io/DumpReader.hpp" |
54 |
> |
#include "io/parse_me.h" |
55 |
> |
#include "UseTheForce/ForceFieldFactory.hpp" |
56 |
> |
#include "utils/simError.h" |
57 |
> |
#include "utils/StringUtils.hpp" |
58 |
> |
#include "math/SeqRandNumGen.hpp" |
59 |
> |
#ifdef IS_MPI |
60 |
> |
#include "io/mpiBASS.h" |
61 |
> |
#include "math/ParallelRandNumGen.hpp" |
62 |
> |
#endif |
63 |
> |
|
64 |
> |
namespace oopse { |
65 |
> |
|
66 |
> |
void SimCreator::parseFile(const std::string mdFileName, MakeStamps* stamps, Globals* simParams){ |
67 |
> |
|
68 |
> |
#ifdef IS_MPI |
69 |
> |
|
70 |
> |
if (worldRank == 0) { |
71 |
> |
#endif // is_mpi |
72 |
> |
|
73 |
> |
simParams->initalize(); |
74 |
> |
set_interface_stamps(stamps, simParams); |
75 |
> |
|
76 |
> |
#ifdef IS_MPI |
77 |
> |
|
78 |
> |
mpiEventInit(); |
79 |
> |
|
80 |
> |
#endif |
81 |
> |
|
82 |
> |
yacc_BASS(mdFileName.c_str()); |
83 |
> |
|
84 |
> |
#ifdef IS_MPI |
85 |
> |
|
86 |
> |
throwMPIEvent(NULL); |
87 |
> |
} else { |
88 |
> |
set_interface_stamps(stamps, simParams); |
89 |
> |
mpiEventInit(); |
90 |
> |
MPIcheckPoint(); |
91 |
> |
mpiEventLoop(); |
92 |
> |
} |
93 |
> |
|
94 |
> |
#endif |
95 |
> |
|
96 |
> |
} |
97 |
> |
|
98 |
> |
SimInfo* SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) { |
99 |
> |
|
100 |
> |
MakeStamps * stamps = new MakeStamps(); |
101 |
> |
|
102 |
> |
Globals * simParams = new Globals(); |
103 |
> |
|
104 |
> |
//parse meta-data file |
105 |
> |
parseFile(mdFileName, stamps, simParams); |
106 |
> |
|
107 |
> |
//create the force field |
108 |
> |
ForceField * ff = ForceFieldFactory::getInstance()->createForceField( |
109 |
> |
simParams->getForceField()); |
110 |
> |
|
111 |
> |
if (ff == NULL) { |
112 |
> |
sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n", |
113 |
> |
simParams->getForceField()); |
114 |
> |
painCave.isFatal = 1; |
115 |
> |
simError(); |
116 |
> |
} |
117 |
> |
|
118 |
> |
if (simParams->haveForceFieldFileName()) { |
119 |
> |
ff->setForceFieldFileName(simParams->getForceFieldFileName()); |
120 |
> |
} |
121 |
> |
|
122 |
> |
std::string forcefieldFileName; |
123 |
> |
forcefieldFileName = ff->getForceFieldFileName(); |
124 |
> |
|
125 |
> |
if (simParams->haveForceFieldVariant()) { |
126 |
> |
//If the force field has variant, the variant force field name will be |
127 |
> |
//Base.variant.frc. For exampel EAM.u6.frc |
128 |
> |
|
129 |
> |
std::string variant = simParams->getForceFieldVariant(); |
130 |
> |
|
131 |
> |
std::string::size_type pos = forcefieldFileName.rfind(".frc"); |
132 |
> |
variant = "." + variant; |
133 |
> |
if (pos != std::string::npos) { |
134 |
> |
forcefieldFileName.insert(pos, variant); |
135 |
> |
} else { |
136 |
> |
//If the default force field file name does not containt .frc suffix, just append the .variant |
137 |
> |
forcefieldFileName.append(variant); |
138 |
> |
} |
139 |
> |
} |
140 |
> |
|
141 |
> |
ff->parse(forcefieldFileName); |
142 |
> |
|
143 |
> |
//extract the molecule stamps |
144 |
> |
std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs; |
145 |
> |
compList(stamps, simParams, moleculeStampPairs); |
146 |
> |
|
147 |
> |
//create SimInfo |
148 |
> |
SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams); |
149 |
> |
|
150 |
> |
//gather parameters (SimCreator only retrieves part of the parameters) |
151 |
> |
gatherParameters(info, mdFileName); |
152 |
> |
|
153 |
> |
//divide the molecules and determine the global index of molecules |
154 |
> |
#ifdef IS_MPI |
155 |
> |
divideMolecules(info); |
156 |
> |
#endif |
157 |
> |
|
158 |
> |
//create the molecules |
159 |
> |
createMolecules(info); |
160 |
> |
|
161 |
> |
|
162 |
> |
//allocate memory for DataStorage(circular reference, need to break it) |
163 |
> |
info->setSnapshotManager(new SimSnapshotManager(info)); |
164 |
> |
|
165 |
> |
//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the |
166 |
> |
//global index will never change again). Local indices of atoms and rigidbodies are already set by |
167 |
> |
//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager. |
168 |
> |
setGlobalIndex(info); |
169 |
> |
|
170 |
> |
//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point |
171 |
> |
//atoms don't have the global index yet (their global index are all initialized to -1). |
172 |
> |
//Therefore we have to call addExcludePairs explicitly here. A way to work around is that |
173 |
> |
//we can determine the beginning global indices of atoms before they get created. |
174 |
> |
SimInfo::MoleculeIterator mi; |
175 |
> |
Molecule* mol; |
176 |
> |
for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
177 |
> |
info->addExcludePairs(mol); |
178 |
> |
} |
179 |
> |
|
180 |
> |
|
181 |
> |
//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as |
182 |
> |
//eta, chi for NPT integrator) |
183 |
> |
if (loadInitCoords) |
184 |
> |
loadCoordinates(info); |
185 |
> |
|
186 |
> |
return info; |
187 |
> |
} |
188 |
> |
|
189 |
> |
void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) { |
190 |
> |
|
191 |
> |
//figure out the ouput file names |
192 |
> |
std::string prefix; |
193 |
> |
|
194 |
> |
#ifdef IS_MPI |
195 |
> |
|
196 |
> |
if (worldRank == 0) { |
197 |
> |
#endif // is_mpi |
198 |
> |
Globals * simParams = info->getSimParams(); |
199 |
> |
if (simParams->haveFinalConfig()) { |
200 |
> |
prefix = getPrefix(simParams->getFinalConfig()); |
201 |
> |
} else { |
202 |
> |
prefix = getPrefix(mdfile); |
203 |
> |
} |
204 |
> |
|
205 |
> |
info->setFinalConfigFileName(prefix + ".eor"); |
206 |
> |
info->setDumpFileName(prefix + ".dump"); |
207 |
> |
info->setStatFileName(prefix + ".stat"); |
208 |
> |
|
209 |
> |
#ifdef IS_MPI |
210 |
> |
|
211 |
> |
} |
212 |
> |
|
213 |
> |
#endif |
214 |
> |
|
215 |
> |
} |
216 |
> |
|
217 |
> |
#ifdef IS_MPI |
218 |
> |
void SimCreator::divideMolecules(SimInfo *info) { |
219 |
> |
double numerator; |
220 |
> |
double denominator; |
221 |
> |
double precast; |
222 |
> |
double x; |
223 |
> |
double y; |
224 |
> |
double a; |
225 |
> |
int old_atoms; |
226 |
> |
int add_atoms; |
227 |
> |
int new_atoms; |
228 |
> |
int nTarget; |
229 |
> |
int done; |
230 |
> |
int i; |
231 |
> |
int j; |
232 |
> |
int loops; |
233 |
> |
int which_proc; |
234 |
> |
int nProcessors; |
235 |
> |
std::vector<int> atomsPerProc; |
236 |
> |
int nGlobalMols = info->getNGlobalMolecules(); |
237 |
> |
std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition: |
238 |
> |
|
239 |
> |
MPI_Comm_size(MPI_COMM_WORLD, &nProcessors); |
240 |
> |
|
241 |
> |
if (nProcessors > nGlobalMols) { |
242 |
> |
sprintf(painCave.errMsg, |
243 |
> |
"nProcessors (%d) > nMol (%d)\n" |
244 |
> |
"\tThe number of processors is larger than\n" |
245 |
> |
"\tthe number of molecules. This will not result in a \n" |
246 |
> |
"\tusable division of atoms for force decomposition.\n" |
247 |
> |
"\tEither try a smaller number of processors, or run the\n" |
248 |
> |
"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols); |
249 |
> |
|
250 |
> |
painCave.isFatal = 1; |
251 |
> |
simError(); |
252 |
> |
} |
253 |
> |
|
254 |
> |
int seedValue; |
255 |
> |
Globals * simParams = info->getSimParams(); |
256 |
> |
SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator |
257 |
> |
if (simParams->haveSeed()) { |
258 |
> |
seedValue = simParams->getSeed(); |
259 |
> |
myRandom = new SeqRandNumGen(seedValue); |
260 |
> |
}else { |
261 |
> |
myRandom = new SeqRandNumGen(); |
262 |
> |
} |
263 |
> |
|
264 |
> |
|
265 |
> |
a = 3.0 * nGlobalMols / info->getNGlobalAtoms(); |
266 |
> |
|
267 |
> |
//initialize atomsPerProc |
268 |
> |
atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0); |
269 |
> |
|
270 |
> |
if (worldRank == 0) { |
271 |
> |
numerator = info->getNGlobalAtoms(); |
272 |
> |
denominator = nProcessors; |
273 |
> |
precast = numerator / denominator; |
274 |
> |
nTarget = (int)(precast + 0.5); |
275 |
> |
|
276 |
> |
for(i = 0; i < nGlobalMols; i++) { |
277 |
> |
done = 0; |
278 |
> |
loops = 0; |
279 |
> |
|
280 |
> |
while (!done) { |
281 |
> |
loops++; |
282 |
> |
|
283 |
> |
// Pick a processor at random |
284 |
> |
|
285 |
> |
which_proc = (int) (myRandom->rand() * nProcessors); |
286 |
> |
|
287 |
> |
//get the molecule stamp first |
288 |
> |
int stampId = info->getMoleculeStampId(i); |
289 |
> |
MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId); |
290 |
> |
|
291 |
> |
// How many atoms does this processor have so far? |
292 |
> |
old_atoms = atomsPerProc[which_proc]; |
293 |
> |
add_atoms = moleculeStamp->getNAtoms(); |
294 |
> |
new_atoms = old_atoms + add_atoms; |
295 |
> |
|
296 |
> |
// If we've been through this loop too many times, we need |
297 |
> |
// to just give up and assign the molecule to this processor |
298 |
> |
// and be done with it. |
299 |
> |
|
300 |
> |
if (loops > 100) { |
301 |
> |
sprintf(painCave.errMsg, |
302 |
> |
"I've tried 100 times to assign molecule %d to a " |
303 |
> |
" processor, but can't find a good spot.\n" |
304 |
> |
"I'm assigning it at random to processor %d.\n", |
305 |
> |
i, which_proc); |
306 |
> |
|
307 |
> |
painCave.isFatal = 0; |
308 |
> |
simError(); |
309 |
> |
|
310 |
> |
molToProcMap[i] = which_proc; |
311 |
> |
atomsPerProc[which_proc] += add_atoms; |
312 |
> |
|
313 |
> |
done = 1; |
314 |
> |
continue; |
315 |
> |
} |
316 |
> |
|
317 |
> |
// If we can add this molecule to this processor without sending |
318 |
> |
// it above nTarget, then go ahead and do it: |
319 |
> |
|
320 |
> |
if (new_atoms <= nTarget) { |
321 |
> |
molToProcMap[i] = which_proc; |
322 |
> |
atomsPerProc[which_proc] += add_atoms; |
323 |
> |
|
324 |
> |
done = 1; |
325 |
> |
continue; |
326 |
> |
} |
327 |
> |
|
328 |
> |
// The only situation left is when new_atoms > nTarget. We |
329 |
> |
// want to accept this with some probability that dies off the |
330 |
> |
// farther we are from nTarget |
331 |
> |
|
332 |
> |
// roughly: x = new_atoms - nTarget |
333 |
> |
// Pacc(x) = exp(- a * x) |
334 |
> |
// where a = penalty / (average atoms per molecule) |
335 |
> |
|
336 |
> |
x = (double)(new_atoms - nTarget); |
337 |
> |
y = myRandom->rand(); |
338 |
> |
|
339 |
> |
if (y < exp(- a * x)) { |
340 |
> |
molToProcMap[i] = which_proc; |
341 |
> |
atomsPerProc[which_proc] += add_atoms; |
342 |
> |
|
343 |
> |
done = 1; |
344 |
> |
continue; |
345 |
> |
} else { |
346 |
> |
continue; |
347 |
> |
} |
348 |
> |
} |
349 |
> |
} |
350 |
> |
|
351 |
> |
delete myRandom; |
352 |
> |
|
353 |
> |
// Spray out this nonsense to all other processors: |
354 |
> |
|
355 |
> |
MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
356 |
> |
} else { |
357 |
> |
|
358 |
> |
// Listen to your marching orders from processor 0: |
359 |
> |
|
360 |
> |
MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
361 |
> |
} |
362 |
> |
|
363 |
> |
info->setMolToProcMap(molToProcMap); |
364 |
> |
sprintf(checkPointMsg, |
365 |
> |
"Successfully divided the molecules among the processors.\n"); |
366 |
> |
MPIcheckPoint(); |
367 |
> |
} |
368 |
> |
|
369 |
> |
#endif |
370 |
> |
|
371 |
> |
void SimCreator::createMolecules(SimInfo *info) { |
372 |
> |
MoleculeCreator molCreator; |
373 |
> |
int stampId; |
374 |
> |
|
375 |
> |
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), |
384 |
> |
stampId, i, info->getLocalIndexManager()); |
385 |
> |
|
386 |
> |
info->addMolecule(mol); |
387 |
> |
|
388 |
> |
#ifdef IS_MPI |
389 |
> |
|
390 |
> |
} |
391 |
> |
|
392 |
> |
#endif |
393 |
> |
|
394 |
> |
} //end for(int i=0) |
395 |
> |
} |
396 |
> |
|
397 |
> |
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 |
> |
|