--- trunk/src/brains/SimCreator.cpp 2005/03/08 21:06:49 403 +++ trunk/src/brains/SimCreator.cpp 2006/05/17 21:51:42 963 @@ -46,88 +46,224 @@ * @time 13:51am * @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" #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" + +#include "antlr/MismatchedCharException.hpp" +#include "antlr/MismatchedTokenException.hpp" +#include "antlr/NoViableAltForCharException.hpp" +#include "antlr/NoViableAltException.hpp" + #ifdef IS_MPI -#include "io/mpiBASS.h" #include "math/ParallelRandNumGen.hpp" #endif namespace oopse { + +Globals* SimCreator::parseFile(const std::string mdFileName){ + Globals* simParams = NULL; + try { - void SimCreator::parseFile(const std::string mdFileName, MakeStamps* stamps, Globals* simParams){ + // 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); -#ifdef IS_MPI + commStatus = MPI_Bcast(static_cast(const_cast(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; - if (worldRank == 0) { -#endif // is_mpi + } +#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); - simParams->initalize(); - set_interface_stamps(stamps, simParams); + // Create an observer that synchorizes file name change + FilenameObserver observer; + observer.setLexer(&lexer); + observer.setParser(&parser); + lexer.setObserver(&observer); + + antlr::ASTFactory factory; + parser.initializeASTFactory(factory); + parser.setASTFactory(&factory); + parser.mdfile(); -#ifdef IS_MPI + // Create a tree parser that reads information into Globals + MDTreeParser treeParser; + treeParser.initializeASTFactory(factory); + treeParser.setASTFactory(&factory); + simParams = treeParser.walkTree(parser.getAST()); - mpiEventInit(); + } -#endif - - yacc_BASS(mdFileName.c_str()); - -#ifdef IS_MPI - - throwMPIEvent(NULL); - } else { - set_interface_stamps(stamps, simParams); - mpiEventInit(); - MPIcheckPoint(); - mpiEventLoop(); - } - -#endif - - } - - SimInfo* SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) { - - MakeStamps * stamps = new MakeStamps(); - - Globals * simParams = new Globals(); + + catch(antlr::MismatchedCharException& e) { + sprintf(painCave.errMsg, + "parser exception: %s %s:%d:%d\n", + e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn()); + painCave.isFatal = 1; + simError(); + } + catch(antlr::MismatchedTokenException &e) { + sprintf(painCave.errMsg, + "parser exception: %s %s:%d:%d\n", + e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn()); + painCave.isFatal = 1; + simError(); + } + catch(antlr::NoViableAltForCharException &e) { + sprintf(painCave.errMsg, + "parser exception: %s %s:%d:%d\n", + e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn()); + painCave.isFatal = 1; + simError(); + } + catch(antlr::NoViableAltException &e) { + sprintf(painCave.errMsg, + "parser exception: %s %s:%d:%d\n", + e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn()); + painCave.isFatal = 1; + simError(); + } + + catch(antlr::TokenStreamRecognitionException& e) { + sprintf(painCave.errMsg, + "parser exception: %s %s:%d:%d\n", + e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn()); + painCave.isFatal = 1; + simError(); + } + + catch(antlr::TokenStreamIOException& e) { + sprintf(painCave.errMsg, + "parser exception: %s\n", + e.getMessage().c_str()); + painCave.isFatal = 1; + simError(); + } + + catch(antlr::TokenStreamException& e) { + sprintf(painCave.errMsg, + "parser exception: %s\n", + e.getMessage().c_str()); + painCave.isFatal = 1; + simError(); + } + catch (antlr::RecognitionException& e) { + sprintf(painCave.errMsg, + "parser exception: %s %s:%d:%d\n", + e.getMessage().c_str(),e.getFilename().c_str(), e.getLine(), e.getColumn()); + painCave.isFatal = 1; + simError(); + } + catch (antlr::CharStreamException& e) { + sprintf(painCave.errMsg, + "parser exception: %s\n", + e.getMessage().c_str()); + painCave.isFatal = 1; + simError(); + } + catch (OOPSEException& e) { + sprintf(painCave.errMsg, + "%s\n", + e.getMessage().c_str()); + painCave.isFatal = 1; + simError(); + } + catch (std::exception& e) { + sprintf(painCave.errMsg, + "parser exception: %s\n", + e.what()); + painCave.isFatal = 1; + simError(); + } - //parse meta-data file - parseFile(mdFileName, stamps, simParams); + 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()); + 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()); } 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) { @@ -139,60 +275,59 @@ namespace oopse { } ff->parse(forcefieldFileName); - - //extract the molecule stamps - std::vector < std::pair > moleculeStampPairs; - compList(stamps, simParams, moleculeStampPairs); - + ff->setFortranForceOptions(); //create SimInfo - SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams); - - //gather parameters (SimCreator only retrieves part of the parameters) + 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) + + + //allocate memory for DataStorage(circular reference, need to + //break it) info->setSnapshotManager(new SimSnapshotManager(info)); - //set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the - //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. + //set the global index of atoms, rigidbodies and cutoffgroups + //(only need to be set once, the 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 - //we can determine the beginning global indices of atoms before they get created. + + //Although addExcludePairs 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 we can determine the beginning global indices of + //atoms before they get created. SimInfo::MoleculeIterator mi; Molecule* mol; for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { 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); return info; } - + void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) { - - //figure out the ouput file names + + //figure out the output file names std::string prefix; - + #ifdef IS_MPI - + if (worldRank == 0) { #endif // is_mpi Globals * simParams = info->getSimParams(); @@ -201,27 +336,28 @@ namespace oopse { } 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) { - double numerator; - double denominator; - double precast; - double x; - double y; - double a; + RealType numerator; + RealType denominator; + RealType precast; + RealType x; + RealType y; + RealType a; int old_atoms; int add_atoms; int new_atoms; @@ -237,7 +373,7 @@ namespace oopse { 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" @@ -246,11 +382,11 @@ namespace oopse { "\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 @@ -260,86 +396,86 @@ namespace oopse { }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->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); + + x = (RealType)(new_atoms - nTarget); y = myRandom->rand(); - + if (y < exp(- a * x)) { molToProcMap[i] = which_proc; atomsPerProc[which_proc] += add_atoms; - + done = 1; continue; } else { @@ -347,115 +483,53 @@ namespace oopse { } } } - + 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); } - + info->setMolToProcMap(molToProcMap); sprintf(checkPointMsg, "Successfully divided the molecules among the processors.\n"); MPIcheckPoint(); } - + #endif - + 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) { #endif - + 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; - LinkedMolStamp* extractedStamp = NULL; - 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(); - - extractedStamp = stamps->extractMolStamp(id); - if (extractedStamp == NULL) { - sprintf(painCave.errMsg, - "SimCreator error: Component \"%s\" was not found in the " - "list of declared molecules\n", id); - - painCave.isFatal = 1; - simError(); - } - - currentStamp = extractedStamp->getStamp(); - - - 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) { SimInfo::MoleculeIterator mi; Molecule::AtomIterator ai; @@ -471,30 +545,30 @@ namespace oopse { 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); @@ -502,54 +576,54 @@ namespace oopse { 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]; } - + #endif - + //rigidbody's index begins right after atom's beginRigidBodyIndex += info->getNGlobalAtoms(); - + 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++); } } - + //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(); } - + } } - + #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 @@ -563,20 +637,20 @@ namespace oopse { #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(); } } - + #ifdef IS_MPI std::vector tmpMolMembership(nGlobalAtoms, 0); - + MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms, MPI_INT, MPI_SUM, MPI_COMM_WORLD); @@ -584,9 +658,9 @@ namespace oopse { #else info->setGlobalMolMembership(globalMolMembership); #endif - + } - + void SimCreator::loadCoordinates(SimInfo* info) { Globals* simParams; simParams = info->getSimParams(); @@ -597,24 +671,25 @@ namespace oopse { painCave.isFatal = 1;; simError(); } - + DumpReader reader(info, simParams->getInitialConfig()); int nframes = reader.getNFrames(); - + if (nframes > 0) { 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()); + 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