--- trunk/src/brains/SimCreator.cpp 2005/02/04 05:26:30 285 +++ trunk/src/brains/SimCreator.cpp 2005/12/16 18:26:41 816 @@ -1,4 +1,4 @@ - /* +/* * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. * * The University of Notre Dame grants you ("Licensee") a @@ -47,119 +47,199 @@ * @version 1.0 */ -#include +#include +#include +#include #include "brains/MoleculeCreator.hpp" #include "brains/SimCreator.hpp" #include "brains/SimSnapshotManager.hpp" #include "io/DumpReader.hpp" -#include "io/parse_me.h" #include "UseTheForce/ForceFieldFactory.hpp" #include "utils/simError.h" #include "utils/StringUtils.hpp" -#ifdef IS_MPI -#include "io/mpiBASS.h" -#include "math/randomSPRNG.hpp" -#endif +#include "math/SeqRandNumGen.hpp" +#include "mdParser/MDLexer.hpp" +#include "mdParser/MDParser.hpp" +#include "mdParser/MDTreeParser.hpp" +#include "mdParser/SimplePreprocessor.hpp" +#include "antlr/ANTLRException.hpp" +#include "antlr/TokenStreamRecognitionException.hpp" +#include "antlr/TokenStreamIOException.hpp" +#include "antlr/TokenStreamException.hpp" +#include "antlr/RecognitionException.hpp" +#include "antlr/CharStreamException.hpp" -namespace oopse { +#include "antlr/MismatchedCharException.hpp" +#include "antlr/MismatchedTokenException.hpp" +#include "antlr/NoViableAltForCharException.hpp" +#include "antlr/NoViableAltException.hpp" -void SimCreator::parseFile(const std::string mdFileName, MakeStamps* stamps, Globals* simParams){ - #ifdef IS_MPI - - if (worldRank == 0) { -#endif // is_mpi - - simParams->initalize(); - set_interface_stamps(stamps, simParams); - -#ifdef IS_MPI - - mpiEventInit(); - +#include "math/ParallelRandNumGen.hpp" #endif - yacc_BASS(mdFileName.c_str()); +namespace oopse { + +Globals* SimCreator::parseFile(const std::string mdFileName){ + Globals* simParams = NULL; + try { -#ifdef IS_MPI + // Create a preprocessor that preprocesses md file into an ostringstream + std::stringstream ppStream; +#ifdef IS_MPI + int streamSize; + const int masterNode = 0; + int commStatus; + if (worldRank == masterNode) { +#endif + + SimplePreprocessor preprocessor; + preprocessor.preprocess(mdFileName, ppStream); + +#ifdef IS_MPI + //brocasting the stream size + streamSize = ppStream.str().size() +1; + commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD); - throwMPIEvent(NULL); - } else { - set_interface_stamps(stamps, simParams); - mpiEventInit(); - MPIcheckPoint(); - mpiEventLoop(); - } + commStatus = MPI_Bcast(ppStream.str().c_str(), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); + + + } else { + //get stream size + commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD); + + char* buf = new char[streamSize]; + assert(buf); + + //receive file content + commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); + + ppStream.str(buf); + delete buf; -#endif + } +#endif + // Create a scanner that reads from the input stream + MDLexer lexer(ppStream); + lexer.setFilename(mdFileName); + lexer.initDeferredLineCount(); + + // Create a parser that reads from the scanner + MDParser parser(lexer); + parser.setFilename(mdFileName); -} - -SimInfo* SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) { + // Create an observer that synchorizes file name change + FilenameObserver observer; + observer.setLexer(&lexer); + observer.setParser(&parser); + lexer.setObserver(&observer); - MakeStamps * stamps = new MakeStamps(); + antlr::ASTFactory factory; + parser.initializeASTFactory(factory); + parser.setASTFactory(&factory); + parser.mdfile(); - Globals * simParams = new Globals(); + // Create a tree parser that reads information into Globals + MDTreeParser treeParser; + treeParser.initializeASTFactory(factory); + treeParser.setASTFactory(&factory); + simParams = treeParser.walkTree(parser.getAST()); - //parse meta-data file - parseFile(mdFileName, stamps, simParams); + } + + catch(antlr::MismatchedCharException& e) { + cerr<< "parser exception: " << e.getMessage() << " " << e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl; + } + catch(antlr::MismatchedTokenException &e) { + cerr<< "parser exception: " << e.getMessage() << " " << e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl; + } + catch(antlr::NoViableAltForCharException &e) { + cerr<< "parser exception: " << e.getMessage() << " " << e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl; + } + catch(antlr::NoViableAltException &e) { + cerr<< "parser exception: " << e.getMessage() << " " << e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl; + } + catch(antlr::TokenStreamRecognitionException& e) { + cerr<< "parser exception: " << e.getMessage() << " " << e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl; + } + catch(antlr::TokenStreamIOException& e) { + cerr<< "parser exception: " << e.getMessage() << endl; + } + catch(antlr::TokenStreamException& e) { + cerr<< "parser exception: " << e.getMessage() << endl; + } + catch (antlr::RecognitionException& e) { + cerr<< "parser exception: " << e.getMessage() << " " << e.getFilename() << ":" << e.getLine() << " " << e.getColumn() << endl; + } + catch (antlr::CharStreamException& e) { + cerr << "parser exception: " << e.getMessage() << endl; + } + catch (exception& e) { + cerr << "parser exception: " << e.what() << endl; + } + return simParams; + } + + SimInfo* SimCreator::createSim(const std::string & mdFileName, + bool loadInitCoords) { + + //parse meta-data file + Globals* simParams = parseFile(mdFileName); + //create the force field - ForceField * ff = ForceFieldFactory::getInstance()->createForceField( - simParams->getForceField()); + ForceField * ff = ForceFieldFactory::getInstance() + ->createForceField(simParams->getForceField()); if (ff == NULL) { - sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n", - simParams->getForceField()); - painCave.isFatal = 1; - simError(); + sprintf(painCave.errMsg, + "ForceField Factory can not create %s force field\n", + simParams->getForceField().c_str()); + painCave.isFatal = 1; + simError(); } - + if (simParams->haveForceFieldFileName()) { - ff->setForceFieldFileName(simParams->getForceFieldFileName()); + ff->setForceFieldFileName(simParams->getForceFieldFileName()); } std::string forcefieldFileName; forcefieldFileName = ff->getForceFieldFileName(); - + if (simParams->haveForceFieldVariant()) { - //If the force field has variant, the variant force field name will be - //Base.variant.frc. For exampel EAM.u6.frc - - std::string variant = simParams->getForceFieldVariant(); - - std::string::size_type pos = forcefieldFileName.rfind(".frc"); - variant = "." + variant; - if (pos != std::string::npos) { - forcefieldFileName.insert(pos, variant); - } else { - //If the default force field file name does not containt .frc suffix, just append the .variant - forcefieldFileName.append(variant); - } + //If the force field has variant, the variant force field name will be + //Base.variant.frc. For exampel EAM.u6.frc + + std::string variant = simParams->getForceFieldVariant(); + + std::string::size_type pos = forcefieldFileName.rfind(".frc"); + variant = "." + variant; + if (pos != std::string::npos) { + forcefieldFileName.insert(pos, variant); + } else { + //If the default force field file name does not containt .frc suffix, just append the .variant + forcefieldFileName.append(variant); + } } ff->parse(forcefieldFileName); - - //extract the molecule stamps - std::vector < std::pair > moleculeStampPairs; - compList(stamps, simParams, moleculeStampPairs); - + //create SimInfo - SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams); - + SimInfo * info = new SimInfo(ff, simParams); + //gather parameters (SimCreator only retrieves part of the parameters) gatherParameters(info, mdFileName); - + //divide the molecules and determine the global index of molecules #ifdef IS_MPI divideMolecules(info); #endif - + //create the molecules createMolecules(info); - - + + //allocate memory for DataStorage(circular reference, need to break it) info->setSnapshotManager(new SimSnapshotManager(info)); @@ -167,7 +247,7 @@ SimInfo* SimCreator::createSim(const std::string & md //global index will never change again). Local indices of atoms and rigidbodies are already set by //MoleculeCreator class which actually delegates the responsibility to LocalIndexManager. setGlobalIndex(info); - + //Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point //atoms don't have the global index yet (their global index are all initialized to -1). //Therefore we have to call addExcludePairs explicitly here. A way to work around is that @@ -175,101 +255,46 @@ SimInfo* SimCreator::createSim(const std::string & md SimInfo::MoleculeIterator mi; Molecule* mol; for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { - info->addExcludePairs(mol); + info->addExcludePairs(mol); } - - //load initial coordinates, some extra information are pushed into SimInfo's property map ( such as - //eta, chi for NPT integrator) if (loadInitCoords) - loadCoordinates(info); + loadCoordinates(info); return info; -} - -void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) { - - //setup seed for random number generator - int seedValue; - Globals * simParams = info->getSimParams(); - - if (simParams->haveSeed()) { - seedValue = simParams->getSeed(); - - if (seedValue < 100000000 ) { - sprintf(painCave.errMsg, - "Seed for sprng library should contain at least 9 digits\n" - "OOPSE will generate a seed for user\n"); - - painCave.isFatal = 0; - simError(); - - //using seed generated by system instead of invalid seed set by user - -#ifndef IS_MPI - - seedValue = make_sprng_seed(); - -#else - - if (worldRank == 0) { - seedValue = make_sprng_seed(); - } - - MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); - -#endif - - } //end if (seedValue /1000000000 == 0) - } else { - -#ifndef IS_MPI - - seedValue = make_sprng_seed(); - -#else - - if (worldRank == 0) { - seedValue = make_sprng_seed(); - } - - MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); - -#endif - - } //end of simParams->haveSeed() - - info->setSeed(seedValue); - - - //figure out the ouput file names + } + + void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) { + + //figure out the output file names std::string prefix; - + #ifdef IS_MPI - + if (worldRank == 0) { #endif // is_mpi - - if (simParams->haveFinalConfig()) { - prefix = getPrefix(simParams->getFinalConfig()); - } else { - prefix = getPrefix(mdfile); - } - - info->setFinalConfigFileName(prefix + ".eor"); - info->setDumpFileName(prefix + ".dump"); - info->setStatFileName(prefix + ".stat"); - + Globals * simParams = info->getSimParams(); + if (simParams->haveFinalConfig()) { + prefix = getPrefix(simParams->getFinalConfig()); + } else { + prefix = getPrefix(mdfile); + } + + info->setFinalConfigFileName(prefix + ".eor"); + info->setDumpFileName(prefix + ".dump"); + info->setStatFileName(prefix + ".stat"); + info->setRestFileName(prefix + ".zang"); + #ifdef IS_MPI - + } - + #endif - -} - + + } + #ifdef IS_MPI -void SimCreator::divideMolecules(SimInfo *info) { + void SimCreator::divideMolecules(SimInfo *info) { double numerator; double denominator; double precast; @@ -287,214 +312,168 @@ void SimCreator::divideMolecules(SimInfo *info) { int which_proc; int nProcessors; std::vector atomsPerProc; - randomSPRNG myRandom(info->getSeed()); int nGlobalMols = info->getNGlobalMolecules(); std::vector molToProcMap(nGlobalMols, -1); // default to an error condition: MPI_Comm_size(MPI_COMM_WORLD, &nProcessors); - + if (nProcessors > nGlobalMols) { - sprintf(painCave.errMsg, - "nProcessors (%d) > nMol (%d)\n" - "\tThe number of processors is larger than\n" - "\tthe number of molecules. This will not result in a \n" - "\tusable division of atoms for force decomposition.\n" - "\tEither try a smaller number of processors, or run the\n" - "\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols); - - painCave.isFatal = 1; - simError(); + sprintf(painCave.errMsg, + "nProcessors (%d) > nMol (%d)\n" + "\tThe number of processors is larger than\n" + "\tthe number of molecules. This will not result in a \n" + "\tusable division of atoms for force decomposition.\n" + "\tEither try a smaller number of processors, or run the\n" + "\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols); + + painCave.isFatal = 1; + simError(); } - + + int seedValue; + Globals * simParams = info->getSimParams(); + SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator + if (simParams->haveSeed()) { + seedValue = simParams->getSeed(); + myRandom = new SeqRandNumGen(seedValue); + }else { + myRandom = new SeqRandNumGen(); + } + + a = 3.0 * nGlobalMols / info->getNGlobalAtoms(); - + //initialize atomsPerProc atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0); - + if (worldRank == 0) { - numerator = info->getNGlobalAtoms(); - denominator = nProcessors; - precast = numerator / denominator; - nTarget = (int)(precast + 0.5); - - for(i = 0; i < nGlobalMols; i++) { - done = 0; - loops = 0; - - while (!done) { - loops++; - - // Pick a processor at random - - which_proc = (int) (myRandom.getRandom() * nProcessors); - - //get the molecule stamp first - int stampId = info->getMoleculeStampId(i); - MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId); - - // How many atoms does this processor have so far? - old_atoms = atomsPerProc[which_proc]; - add_atoms = moleculeStamp->getNAtoms(); - new_atoms = old_atoms + add_atoms; - - // If we've been through this loop too many times, we need - // to just give up and assign the molecule to this processor - // and be done with it. - - if (loops > 100) { - sprintf(painCave.errMsg, - "I've tried 100 times to assign molecule %d to a " - " processor, but can't find a good spot.\n" - "I'm assigning it at random to processor %d.\n", - i, which_proc); - - painCave.isFatal = 0; - simError(); - - molToProcMap[i] = which_proc; - atomsPerProc[which_proc] += add_atoms; - - done = 1; - continue; - } - - // If we can add this molecule to this processor without sending - // it above nTarget, then go ahead and do it: - - if (new_atoms <= nTarget) { - molToProcMap[i] = which_proc; - atomsPerProc[which_proc] += add_atoms; - - done = 1; - continue; - } - - // The only situation left is when new_atoms > nTarget. We - // want to accept this with some probability that dies off the - // farther we are from nTarget - - // roughly: x = new_atoms - nTarget - // Pacc(x) = exp(- a * x) - // where a = penalty / (average atoms per molecule) - - x = (double)(new_atoms - nTarget); - y = myRandom.getRandom(); - - if (y < exp(- a * x)) { - molToProcMap[i] = which_proc; - atomsPerProc[which_proc] += add_atoms; - - done = 1; - continue; - } else { - continue; - } - } + numerator = info->getNGlobalAtoms(); + denominator = nProcessors; + precast = numerator / denominator; + nTarget = (int)(precast + 0.5); + + for(i = 0; i < nGlobalMols; i++) { + done = 0; + loops = 0; + + while (!done) { + loops++; + + // Pick a processor at random + + which_proc = (int) (myRandom->rand() * nProcessors); + + //get the molecule stamp first + int stampId = info->getMoleculeStampId(i); + MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId); + + // How many atoms does this processor have so far? + old_atoms = atomsPerProc[which_proc]; + add_atoms = moleculeStamp->getNAtoms(); + new_atoms = old_atoms + add_atoms; + + // If we've been through this loop too many times, we need + // to just give up and assign the molecule to this processor + // and be done with it. + + if (loops > 100) { + sprintf(painCave.errMsg, + "I've tried 100 times to assign molecule %d to a " + " processor, but can't find a good spot.\n" + "I'm assigning it at random to processor %d.\n", + i, which_proc); + + painCave.isFatal = 0; + simError(); + + molToProcMap[i] = which_proc; + atomsPerProc[which_proc] += add_atoms; + + done = 1; + continue; + } + + // If we can add this molecule to this processor without sending + // it above nTarget, then go ahead and do it: + + if (new_atoms <= nTarget) { + molToProcMap[i] = which_proc; + atomsPerProc[which_proc] += add_atoms; + + done = 1; + continue; + } + + // The only situation left is when new_atoms > nTarget. We + // want to accept this with some probability that dies off the + // farther we are from nTarget + + // roughly: x = new_atoms - nTarget + // Pacc(x) = exp(- a * x) + // where a = penalty / (average atoms per molecule) + + x = (double)(new_atoms - nTarget); + y = myRandom->rand(); + + if (y < exp(- a * x)) { + molToProcMap[i] = which_proc; + atomsPerProc[which_proc] += add_atoms; + + done = 1; + continue; + } else { + continue; + } } - - // Spray out this nonsense to all other processors: - - MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); + } + + delete myRandom; + + // Spray out this nonsense to all other processors: + + MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); } else { - - // Listen to your marching orders from processor 0: - - MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); + + // Listen to your marching orders from processor 0: + + MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); } - + info->setMolToProcMap(molToProcMap); sprintf(checkPointMsg, "Successfully divided the molecules among the processors.\n"); MPIcheckPoint(); -} - + } + #endif - -void SimCreator::createMolecules(SimInfo *info) { + + void SimCreator::createMolecules(SimInfo *info) { MoleculeCreator molCreator; int stampId; - + for(int i = 0; i < info->getNGlobalMolecules(); i++) { - + #ifdef IS_MPI - - if (info->getMolToProc(i) == worldRank) { + + if (info->getMolToProc(i) == worldRank) { #endif - - stampId = info->getMoleculeStampId(i); - Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId), - stampId, i, info->getLocalIndexManager()); - - info->addMolecule(mol); - + + stampId = info->getMoleculeStampId(i); + Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId), + stampId, i, info->getLocalIndexManager()); + + info->addMolecule(mol); + #ifdef IS_MPI - - } - + + } + #endif - + } //end for(int i=0) -} - -void SimCreator::compList(MakeStamps *stamps, Globals* simParams, - std::vector < std::pair > &moleculeStampPairs) { - int i; - char * id; - MoleculeStamp * currentStamp; - Component** the_components = simParams->getComponents(); - int n_components = simParams->getNComponents(); - - if (!simParams->haveNMol()) { - // we don't have the total number of molecules, so we assume it is - // given in each component - - for(i = 0; i < n_components; i++) { - if (!the_components[i]->haveNMol()) { - // we have a problem - sprintf(painCave.errMsg, - "SimCreator Error. No global NMol or component NMol given.\n" - "\tCannot calculate the number of atoms.\n"); - - painCave.isFatal = 1; - simError(); - } - - id = the_components[i]->getType(); - currentStamp = (stamps->extractMolStamp(id))->getStamp(); - - if (currentStamp == NULL) { - sprintf(painCave.errMsg, - "SimCreator error: Component \"%s\" was not found in the " - "list of declared molecules\n", id); - - painCave.isFatal = 1; - simError(); - } - - moleculeStampPairs.push_back( - std::make_pair(currentStamp, the_components[i]->getNMol())); - } //end for (i = 0; i < n_components; i++) - } else { - sprintf(painCave.errMsg, "SimSetup error.\n" - "\tSorry, the ability to specify total" - " nMols and then give molfractions in the components\n" - "\tis not currently supported." - " Please give nMol in the components.\n"); - - painCave.isFatal = 1; - simError(); - } - -#ifdef IS_MPI - - strcpy(checkPointMsg, "Component stamps successfully extracted\n"); - MPIcheckPoint(); - -#endif // is_mpi - -} - -void SimCreator::setGlobalIndex(SimInfo *info) { + } + + void SimCreator::setGlobalIndex(SimInfo *info) { SimInfo::MoleculeIterator mi; Molecule::AtomIterator ai; Molecule::RigidBodyIterator ri; @@ -509,30 +488,30 @@ void SimCreator::setGlobalIndex(SimInfo *info) { int nGlobalAtoms = info->getNGlobalAtoms(); #ifndef IS_MPI - + beginAtomIndex = 0; beginRigidBodyIndex = 0; beginCutoffGroupIndex = 0; - + #else - + int nproc; int myNode; - + myNode = worldRank; MPI_Comm_size(MPI_COMM_WORLD, &nproc); - + std::vector < int > tmpAtomsInProc(nproc, 0); std::vector < int > tmpRigidBodiesInProc(nproc, 0); std::vector < int > tmpCutoffGroupsInProc(nproc, 0); std::vector < int > NumAtomsInProc(nproc, 0); std::vector < int > NumRigidBodiesInProc(nproc, 0); std::vector < int > NumCutoffGroupsInProc(nproc, 0); - + tmpAtomsInProc[myNode] = info->getNAtoms(); tmpRigidBodiesInProc[myNode] = info->getNRigidBodies(); tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroups(); - + //do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT, MPI_SUM, MPI_COMM_WORLD); @@ -540,53 +519,54 @@ void SimCreator::setGlobalIndex(SimInfo *info) { MPI_INT, MPI_SUM, MPI_COMM_WORLD); MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc, MPI_INT, MPI_SUM, MPI_COMM_WORLD); - + beginAtomIndex = 0; beginRigidBodyIndex = 0; beginCutoffGroupIndex = 0; - + for(int i = 0; i < myNode; i++) { - beginAtomIndex += NumAtomsInProc[i]; - beginRigidBodyIndex += NumRigidBodiesInProc[i]; - beginCutoffGroupIndex += NumCutoffGroupsInProc[i]; + beginAtomIndex += NumAtomsInProc[i]; + beginRigidBodyIndex += NumRigidBodiesInProc[i]; + beginCutoffGroupIndex += NumCutoffGroupsInProc[i]; } - + +#endif + //rigidbody's index begins right after atom's beginRigidBodyIndex += info->getNGlobalAtoms(); -#endif - + for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { - - //local index(index in DataStorge) of atom is important - for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { - atom->setGlobalIndex(beginAtomIndex++); - } - - for(rb = mol->beginRigidBody(ri); rb != NULL; - rb = mol->nextRigidBody(ri)) { - rb->setGlobalIndex(beginRigidBodyIndex++); - } - - //local index of cutoff group is trivial, it only depends on the order of travesing - for(cg = mol->beginCutoffGroup(ci); cg != NULL; - cg = mol->nextCutoffGroup(ci)) { - cg->setGlobalIndex(beginCutoffGroupIndex++); - } + + //local index(index in DataStorge) of atom is important + for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { + atom->setGlobalIndex(beginAtomIndex++); + } + + for(rb = mol->beginRigidBody(ri); rb != NULL; + rb = mol->nextRigidBody(ri)) { + rb->setGlobalIndex(beginRigidBodyIndex++); + } + + //local index of cutoff group is trivial, it only depends on the order of travesing + for(cg = mol->beginCutoffGroup(ci); cg != NULL; + cg = mol->nextCutoffGroup(ci)) { + cg->setGlobalIndex(beginCutoffGroupIndex++); + } } - + //fill globalGroupMembership std::vector globalGroupMembership(info->getNGlobalAtoms(), 0); for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { - for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { - - for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { - globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex(); - } - - } + for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { + + for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { + globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex(); + } + + } } - + #ifdef IS_MPI // Since the globalGroupMembership has been zero filled and we've only // poked values into the atoms we know, we can do an Allreduce @@ -596,24 +576,24 @@ void SimCreator::setGlobalIndex(SimInfo *info) { std::vector tmpGroupMembership(nGlobalAtoms, 0); MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms, MPI_INT, MPI_SUM, MPI_COMM_WORLD); - info->setGlobalGroupMembership(tmpGroupMembership); + info->setGlobalGroupMembership(tmpGroupMembership); #else info->setGlobalGroupMembership(globalGroupMembership); #endif - + //fill molMembership std::vector globalMolMembership(info->getNGlobalAtoms(), 0); for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { - - for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { - globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex(); - } + + for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { + globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex(); + } } - + #ifdef IS_MPI std::vector tmpMolMembership(nGlobalAtoms, 0); - + MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms, MPI_INT, MPI_SUM, MPI_COMM_WORLD); @@ -621,37 +601,38 @@ void SimCreator::setGlobalIndex(SimInfo *info) { #else info->setGlobalMolMembership(globalMolMembership); #endif - -} - -void SimCreator::loadCoordinates(SimInfo* info) { + + } + + void SimCreator::loadCoordinates(SimInfo* info) { Globals* simParams; simParams = info->getSimParams(); if (!simParams->haveInitialConfig()) { - sprintf(painCave.errMsg, - "Cannot intialize a simulation without an initial configuration file.\n"); - painCave.isFatal = 1;; - simError(); + sprintf(painCave.errMsg, + "Cannot intialize a simulation without an initial configuration file.\n"); + painCave.isFatal = 1;; + simError(); } - + DumpReader reader(info, simParams->getInitialConfig()); int nframes = reader.getNFrames(); - + if (nframes > 0) { - reader.readFrame(nframes - 1); + reader.readFrame(nframes - 1); } else { - //invalid initial coordinate file - sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n", - simParams->getInitialConfig()); - painCave.isFatal = 1; - simError(); + //invalid initial coordinate file + sprintf(painCave.errMsg, + "Initial configuration file %s should at least contain one frame\n", + simParams->getInitialConfig().c_str()); + painCave.isFatal = 1; + simError(); } - + //copy the current snapshot to previous snapshot info->getSnapshotManager()->advance(); -} - + } + } //end namespace oopse