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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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* @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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#include <sprng.h>
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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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#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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namespace oopse {
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void SimCreator::parseFile(const std::string mdFileName, MakeStamps* stamps, Globals* simParams){
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#ifdef IS_MPI
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if (worldRank == 0) {
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#endif // is_mpi
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simParams->initalize();
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set_interface_stamps(stamps, simParams);
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#ifdef IS_MPI
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mpiEventInit();
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#endif
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yacc_BASS(mdFileName.c_str());
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#ifdef IS_MPI
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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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#endif
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}
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SimInfo* SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
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MakeStamps * stamps = new MakeStamps();
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Globals * simParams = new Globals();
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//parse meta-data file
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parseFile(mdFileName, stamps, simParams);
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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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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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if (simParams->haveForceFieldFileName()) {
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ff->setForceFieldFileName(simParams->getForceFieldFileName());
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}
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std::string forcefieldFileName;
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forcefieldFileName = ff->getForceFieldFileName();
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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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std::string variant = simParams->getForceFieldVariant();
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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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ff->parse(forcefieldFileName);
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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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//create SimInfo
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SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
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//gather parameters (SimCreator only retrieves part of the parameters)
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gatherParameters(info, mdFileName);
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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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//create the molecules
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createMolecules(info);
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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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//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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//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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//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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return info;
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}
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void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
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//figure out the ouput file names
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std::string prefix;
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#ifdef IS_MPI
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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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info->setFinalConfigFileName(prefix + ".eor");
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info->setDumpFileName(prefix + ".dump");
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info->setStatFileName(prefix + ".stat");
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#ifdef IS_MPI
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}
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#endif
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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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MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
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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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painCave.isFatal = 1;
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simError();
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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 MTRand(seedValue);
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}else {
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myRandom = new MTRand();
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}
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a = 3.0 * nGlobalMols / info->getNGlobalAtoms();
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//initialize atomsPerProc
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atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0);
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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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for(i = 0; i < nGlobalMols; i++) {
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done = 0;
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loops = 0;
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while (!done) {
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loops++;
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// Pick a processor at random
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which_proc = (int) (myRandom->rand() * nProcessors);
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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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// 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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// 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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if (loops > 100) {
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sprintf(painCave.errMsg,
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"I've tried 100 times to assign molecule %d to a "
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" processor, but can't find a good spot.\n"
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"I'm assigning it at random to processor %d.\n",
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i, which_proc);
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painCave.isFatal = 0;
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simError();
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molToProcMap[i] = which_proc;
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atomsPerProc[which_proc] += add_atoms;
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done = 1;
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continue;
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}
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// If we can add this molecule to this processor without sending
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// it above nTarget, then go ahead and do it:
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if (new_atoms <= nTarget) {
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molToProcMap[i] = which_proc;
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atomsPerProc[which_proc] += add_atoms;
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done = 1;
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continue;
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}
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// The only situation left is when new_atoms > nTarget. We
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// want to accept this with some probability that dies off the
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// farther we are from nTarget
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// 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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x = (double)(new_atoms - nTarget);
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y = myRandom->rand();
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if (y < exp(- a * x)) {
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molToProcMap[i] = which_proc;
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atomsPerProc[which_proc] += add_atoms;
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done = 1;
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continue;
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} else {
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continue;
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}
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}
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}
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delete myRandom;
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// Spray out this nonsense to all other processors:
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MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
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} else {
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// Listen to your marching orders from processor 0:
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MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
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}
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info->setMolToProcMap(molToProcMap);
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sprintf(checkPointMsg,
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"Successfully divided the molecules among the processors.\n");
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MPIcheckPoint();
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}
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#endif
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void SimCreator::createMolecules(SimInfo *info) {
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MoleculeCreator molCreator;
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int stampId;
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for(int i = 0; i < info->getNGlobalMolecules(); i++) {
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#ifdef IS_MPI
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if (info->getMolToProc(i) == worldRank) {
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#endif
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stampId = info->getMoleculeStampId(i);
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Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId),
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stampId, i, info->getLocalIndexManager());
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info->addMolecule(mol);
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#ifdef IS_MPI
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| 391 |
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}
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#endif
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} //end for(int i=0)
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}
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void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
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std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
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int i;
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char * id;
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MoleculeStamp * currentStamp;
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Component** the_components = simParams->getComponents();
|
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int n_components = simParams->getNComponents();
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if (!simParams->haveNMol()) {
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// we don't have the total number of molecules, so we assume it is
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// given in each component
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| 410 |
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for(i = 0; i < n_components; i++) {
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if (!the_components[i]->haveNMol()) {
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// we have a problem
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sprintf(painCave.errMsg,
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"SimCreator Error. No global NMol or component NMol given.\n"
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| 416 |
"\tCannot calculate the number of atoms.\n");
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| 417 |
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| 418 |
painCave.isFatal = 1;
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simError();
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}
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id = the_components[i]->getType();
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currentStamp = (stamps->extractMolStamp(id))->getStamp();
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| 424 |
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| 425 |
if (currentStamp == NULL) {
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| 426 |
sprintf(painCave.errMsg,
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"SimCreator error: Component \"%s\" was not found in the "
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"list of declared molecules\n", id);
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| 429 |
|
| 430 |
painCave.isFatal = 1;
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| 431 |
simError();
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| 432 |
}
|
| 433 |
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| 434 |
moleculeStampPairs.push_back(
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std::make_pair(currentStamp, the_components[i]->getNMol()));
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} //end for (i = 0; i < n_components; i++)
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| 437 |
} else {
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| 438 |
sprintf(painCave.errMsg, "SimSetup error.\n"
|
| 439 |
"\tSorry, the ability to specify total"
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| 440 |
" nMols and then give molfractions in the components\n"
|
| 441 |
"\tis not currently supported."
|
| 442 |
" Please give nMol in the components.\n");
|
| 443 |
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| 444 |
painCave.isFatal = 1;
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simError();
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}
|
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#ifdef IS_MPI
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| 449 |
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strcpy(checkPointMsg, "Component stamps successfully extracted\n");
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MPIcheckPoint();
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| 453 |
#endif // is_mpi
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|
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}
|
| 456 |
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void SimCreator::setGlobalIndex(SimInfo *info) {
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| 458 |
SimInfo::MoleculeIterator mi;
|
| 459 |
Molecule::AtomIterator ai;
|
| 460 |
Molecule::RigidBodyIterator ri;
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| 461 |
Molecule::CutoffGroupIterator ci;
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| 462 |
Molecule * mol;
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Atom * atom;
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| 464 |
RigidBody * rb;
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| 465 |
CutoffGroup * cg;
|
| 466 |
int beginAtomIndex;
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| 467 |
int beginRigidBodyIndex;
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int beginCutoffGroupIndex;
|
| 469 |
int nGlobalAtoms = info->getNGlobalAtoms();
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| 470 |
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| 471 |
#ifndef IS_MPI
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| 472 |
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| 473 |
beginAtomIndex = 0;
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| 474 |
beginRigidBodyIndex = 0;
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beginCutoffGroupIndex = 0;
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| 476 |
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#else
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| 478 |
|
| 479 |
int nproc;
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| 480 |
int myNode;
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| 481 |
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| 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 |
|
