--- trunk/src/brains/SimCreator.cpp 2006/05/17 21:51:42 963 +++ trunk/src/brains/SimCreator.cpp 2012/10/01 18:21:15 1801 @@ -1,24 +1,15 @@ /* - * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. + * copyright (c) 2005 The University of Notre Dame. All Rights Reserved. * * The University of Notre Dame grants you ("Licensee") a * non-exclusive, royalty free, license to use, modify and * redistribute this software in source and binary code form, provided * that the following conditions are met: * - * 1. Acknowledgement of the program authors must be made in any - * publication of scientific results based in part on use of the - * program. An acceptable form of acknowledgement is citation of - * the article in which the program was described (Matthew - * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher - * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented - * Parallel Simulation Engine for Molecular Dynamics," - * J. Comput. Chem. 26, pp. 252-271 (2005)) - * - * 2. Redistributions of source code must retain the above copyright + * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * - * 3. Redistributions in binary form must reproduce the above copyright + * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the * distribution. @@ -37,6 +28,16 @@ * arising out of the use of or inability to use software, even if the * University of Notre Dame has been advised of the possibility of * such damages. + * + * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your + * research, please cite the appropriate papers when you publish your + * work. Good starting points are: + * + * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). + * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ /** @@ -55,7 +56,7 @@ #include "brains/SimCreator.hpp" #include "brains/SimSnapshotManager.hpp" #include "io/DumpReader.hpp" -#include "UseTheForce/ForceFieldFactory.hpp" +#include "brains/ForceField.hpp" #include "utils/simError.h" #include "utils/StringUtils.hpp" #include "math/SeqRandNumGen.hpp" @@ -75,174 +76,305 @@ #include "antlr/NoViableAltForCharException.hpp" #include "antlr/NoViableAltException.hpp" +#include "types/DirectionalAdapter.hpp" +#include "types/MultipoleAdapter.hpp" +#include "types/EAMAdapter.hpp" +#include "types/SuttonChenAdapter.hpp" +#include "types/PolarizableAdapter.hpp" +#include "types/FixedChargeAdapter.hpp" +#include "types/FluctuatingChargeAdapter.hpp" + #ifdef IS_MPI +#include "mpi.h" #include "math/ParallelRandNumGen.hpp" #endif -namespace oopse { +namespace OpenMD { -Globals* SimCreator::parseFile(const std::string mdFileName){ - Globals* simParams = NULL; - try { + Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){ + Globals* simParams = NULL; + try { - // Create a preprocessor that preprocesses md file into an ostringstream - std::stringstream ppStream; + // 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 + int streamSize; + const int masterNode = 0; + + if (worldRank == masterNode) { + MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode); +#endif + SimplePreprocessor preprocessor; + preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, + ppStream); - 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); + //brocasting the stream size + streamSize = ppStream.str().size() +1; + MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode); + MPI::COMM_WORLD.Bcast(static_cast(const_cast(ppStream.str().c_str())), + streamSize, MPI::CHAR, masterNode); + + } else { - commStatus = MPI_Bcast(static_cast(const_cast(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); - + MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode); + + //get stream size + MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode); + + char* buf = new char[streamSize]; + assert(buf); - } else { - //get stream size - commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD); + //receive file content + MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode); - 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; + ppStream.str(buf); + delete [] buf; - } + } #endif - // Create a scanner that reads from the input stream - MDLexer lexer(ppStream); - lexer.setFilename(mdFileName); - lexer.initDeferredLineCount(); + // Create a scanner that reads from the input stream + MDLexer lexer(ppStream); + lexer.setFilename(filename); + lexer.initDeferredLineCount(); - // Create a parser that reads from the scanner - MDParser parser(lexer); - parser.setFilename(mdFileName); + // Create a parser that reads from the scanner + MDParser parser(lexer); + parser.setFilename(filename); - // Create an observer that synchorizes file name change - FilenameObserver observer; - observer.setLexer(&lexer); - observer.setParser(&parser); - lexer.setObserver(&observer); + // 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(); + antlr::ASTFactory factory; + parser.initializeASTFactory(factory); + parser.setASTFactory(&factory); + parser.mdfile(); - // Create a tree parser that reads information into Globals - MDTreeParser treeParser; - treeParser.initializeASTFactory(factory); - treeParser.setASTFactory(&factory); - simParams = treeParser.walkTree(parser.getAST()); + // Create a tree parser that reads information into Globals + MDTreeParser treeParser; + treeParser.initializeASTFactory(factory); + treeParser.setASTFactory(&factory); + simParams = treeParser.walkTree(parser.getAST()); + } - } - - 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::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::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(); - } + 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 (OpenMDException& 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(); + } - return simParams; + simParams->setMDfileVersion(mdFileVersion); + return simParams; } SimInfo* SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) { + + const int bufferSize = 65535; + char buffer[bufferSize]; + int lineNo = 0; + std::string mdRawData; + int metaDataBlockStart = -1; + int metaDataBlockEnd = -1; + int i; + streamoff mdOffset(0); + int mdFileVersion; + + +#ifdef IS_MPI + const int masterNode = 0; + if (worldRank == masterNode) { +#endif + + std::ifstream mdFile_; + mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary); + + if (mdFile_.fail()) { + sprintf(painCave.errMsg, + "SimCreator: Cannot open file: %s\n", + mdFileName.c_str()); + painCave.isFatal = 1; + simError(); + } + + mdFile_.getline(buffer, bufferSize); + ++lineNo; + std::string line = trimLeftCopy(buffer); + i = CaseInsensitiveFind(line, "(i) == string::npos) { + // try the older file strings to see if that works: + i = CaseInsensitiveFind(line, "(i) == string::npos) { + // still no luck! + sprintf(painCave.errMsg, + "SimCreator: File: %s is not a valid OpenMD file!\n", + mdFileName.c_str()); + painCave.isFatal = 1; + simError(); + } + + // found the correct opening string, now try to get the file + // format version number. + + StringTokenizer tokenizer(line, "=<> \t\n\r"); + std::string fileType = tokenizer.nextToken(); + toUpper(fileType); + + mdFileVersion = 0; + + if (fileType == "OPENMD") { + while (tokenizer.hasMoreTokens()) { + std::string token(tokenizer.nextToken()); + toUpper(token); + if (token == "VERSION") { + mdFileVersion = tokenizer.nextTokenAsInt(); + break; + } + } + } + + //scan through the input stream and find MetaData tag + while(mdFile_.getline(buffer, bufferSize)) { + ++lineNo; + + std::string line = trimLeftCopy(buffer); + if (metaDataBlockStart == -1) { + i = CaseInsensitiveFind(line, ""); + if (i != string::npos) { + metaDataBlockStart = lineNo; + mdOffset = mdFile_.tellg(); + } + } else { + i = CaseInsensitiveFind(line, ""); + if (i != string::npos) { + metaDataBlockEnd = lineNo; + } + } + } + + if (metaDataBlockStart == -1) { + sprintf(painCave.errMsg, + "SimCreator: File: %s did not contain a tag!\n", + mdFileName.c_str()); + painCave.isFatal = 1; + simError(); + } + if (metaDataBlockEnd == -1) { + sprintf(painCave.errMsg, + "SimCreator: File: %s did not contain a closed MetaData block!\n", + mdFileName.c_str()); + painCave.isFatal = 1; + simError(); + } + + mdFile_.clear(); + mdFile_.seekg(0); + mdFile_.seekg(mdOffset); + mdRawData.clear(); + + for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) { + mdFile_.getline(buffer, bufferSize); + mdRawData += buffer; + mdRawData += "\n"; + } + + mdFile_.close(); + +#ifdef IS_MPI + } +#endif + + std::stringstream rawMetaDataStream(mdRawData); + //parse meta-data file - Globals* simParams = parseFile(mdFileName); + Globals* simParams = parseFile(rawMetaDataStream, mdFileName, mdFileVersion, + metaDataBlockStart + 1); //create the force field - ForceField * ff = ForceFieldFactory::getInstance() - ->createForceField(simParams->getForceField()); - + ForceField * ff = new ForceField(simParams->getForceField()); + if (ff == NULL) { sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n", @@ -275,9 +407,10 @@ Globals* SimCreator::parseFile(const std::string mdFil } ff->parse(forcefieldFileName); - ff->setFortranForceOptions(); //create SimInfo SimInfo * info = new SimInfo(ff, simParams); + + info->setRawMetaData(mdRawData); //gather parameters (SimCreator only retrieves part of the //parameters) @@ -291,10 +424,13 @@ Globals* SimCreator::parseFile(const std::string mdFil //create the molecules createMolecules(info); - + //find the storage layout + + int storageLayout = computeStorageLayout(info); + //allocate memory for DataStorage(circular reference, need to //break it) - info->setSnapshotManager(new SimSnapshotManager(info)); + info->setSnapshotManager(new SimSnapshotManager(info, storageLayout)); //set the global index of atoms, rigidbodies and cutoffgroups //(only need to be set once, the global index will never change @@ -303,21 +439,20 @@ Globals* SimCreator::parseFile(const std::string mdFil //responsibility to LocalIndexManager. setGlobalIndex(info); - //Although addExcludePairs is called inside SimInfo's addMolecule + //Although addInteractionPairs 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 + //have to call addInteractionPairs 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); + info->addInteractionPairs(mol); } if (loadInitCoords) - loadCoordinates(info); - + loadCoordinates(info, mdFileName); return info; } @@ -364,7 +499,6 @@ Globals* SimCreator::parseFile(const std::string mdFil int nTarget; int done; int i; - int j; int loops; int which_proc; int nProcessors; @@ -372,7 +506,7 @@ Globals* SimCreator::parseFile(const std::string mdFil int nGlobalMols = info->getNGlobalMolecules(); std::vector molToProcMap(nGlobalMols, -1); // default to an error condition: - MPI_Comm_size(MPI_COMM_WORLD, &nProcessors); + nProcessors = MPI::COMM_WORLD.Get_size(); if (nProcessors > nGlobalMols) { sprintf(painCave.errMsg, @@ -381,7 +515,7 @@ Globals* SimCreator::parseFile(const std::string mdFil "\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); + "\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols); painCave.isFatal = 1; simError(); @@ -410,6 +544,7 @@ Globals* SimCreator::parseFile(const std::string mdFil nTarget = (int)(precast + 0.5); for(i = 0; i < nGlobalMols; i++) { + done = 0; loops = 0; @@ -434,13 +569,15 @@ Globals* SimCreator::parseFile(const std::string mdFil // 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", + "There have been 100 attempts to assign molecule %d to an\n" + "\tunderworked processor, but there's no good place to\n" + "\tleave it. OpenMD is assigning it at random to processor %d.\n", i, which_proc); - + painCave.isFatal = 0; + painCave.severity = OPENMD_INFO; simError(); molToProcMap[i] = which_proc; @@ -485,21 +622,20 @@ Globals* SimCreator::parseFile(const std::string mdFil } delete myRandom; - + // Spray out this nonsense to all other processors: - - MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); + MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0); } else { // Listen to your marching orders from processor 0: - - MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); + MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0); + } info->setMolToProcMap(molToProcMap); sprintf(checkPointMsg, "Successfully divided the molecules among the processors.\n"); - MPIcheckPoint(); + errorCheckPoint(); } #endif @@ -516,8 +652,10 @@ Globals* SimCreator::parseFile(const std::string mdFil #endif stampId = info->getMoleculeStampId(i); - Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId), - stampId, i, info->getLocalIndexManager()); + Molecule * mol = molCreator.createMolecule(info->getForceField(), + info->getMoleculeStamp(stampId), + stampId, i, + info->getLocalIndexManager()); info->addMolecule(mol); @@ -530,11 +668,117 @@ Globals* SimCreator::parseFile(const std::string mdFil } //end for(int i=0) } + int SimCreator::computeStorageLayout(SimInfo* info) { + + Globals* simParams = info->getSimParams(); + int nRigidBodies = info->getNGlobalRigidBodies(); + set atomTypes = info->getSimulatedAtomTypes(); + set::iterator i; + bool hasDirectionalAtoms = false; + bool hasFixedCharge = false; + bool hasMultipoles = false; + bool hasPolarizable = false; + bool hasFluctuatingCharge = false; + bool hasMetallic = false; + int storageLayout = 0; + storageLayout |= DataStorage::dslPosition; + storageLayout |= DataStorage::dslVelocity; + storageLayout |= DataStorage::dslForce; + + for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { + + DirectionalAdapter da = DirectionalAdapter( (*i) ); + MultipoleAdapter ma = MultipoleAdapter( (*i) ); + EAMAdapter ea = EAMAdapter( (*i) ); + SuttonChenAdapter sca = SuttonChenAdapter( (*i) ); + PolarizableAdapter pa = PolarizableAdapter( (*i) ); + FixedChargeAdapter fca = FixedChargeAdapter( (*i) ); + FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter( (*i) ); + + if (da.isDirectional()){ + hasDirectionalAtoms = true; + } + if (ma.isMultipole()){ + hasMultipoles = true; + } + if (ea.isEAM() || sca.isSuttonChen()){ + hasMetallic = true; + } + if ( fca.isFixedCharge() ){ + hasFixedCharge = true; + } + if ( fqa.isFluctuatingCharge() ){ + hasFluctuatingCharge = true; + } + if ( pa.isPolarizable() ){ + hasPolarizable = true; + } + } + + if (nRigidBodies > 0 || hasDirectionalAtoms) { + storageLayout |= DataStorage::dslAmat; + if(storageLayout & DataStorage::dslVelocity) { + storageLayout |= DataStorage::dslAngularMomentum; + } + if (storageLayout & DataStorage::dslForce) { + storageLayout |= DataStorage::dslTorque; + } + } + if (hasMultipoles) { + storageLayout |= DataStorage::dslElectroFrame; + } + if (hasFixedCharge || hasFluctuatingCharge) { + storageLayout |= DataStorage::dslSkippedCharge; + } + if (hasMetallic) { + storageLayout |= DataStorage::dslDensity; + storageLayout |= DataStorage::dslFunctional; + storageLayout |= DataStorage::dslFunctionalDerivative; + } + if (hasPolarizable) { + storageLayout |= DataStorage::dslElectricField; + } + if (hasFluctuatingCharge){ + storageLayout |= DataStorage::dslFlucQPosition; + if(storageLayout & DataStorage::dslVelocity) { + storageLayout |= DataStorage::dslFlucQVelocity; + } + if (storageLayout & DataStorage::dslForce) { + storageLayout |= DataStorage::dslFlucQForce; + } + } + + // if the user has asked for them, make sure we've got the memory for the + // objects defined. + + if (simParams->getOutputParticlePotential()) { + storageLayout |= DataStorage::dslParticlePot; + } + + if (simParams->havePrintHeatFlux()) { + if (simParams->getPrintHeatFlux()) { + storageLayout |= DataStorage::dslParticlePot; + } + } + + if (simParams->getOutputElectricField()) { + storageLayout |= DataStorage::dslElectricField; + } + if (simParams->getOutputFluctuatingCharges()) { + storageLayout |= DataStorage::dslFlucQPosition; + storageLayout |= DataStorage::dslFlucQVelocity; + storageLayout |= DataStorage::dslFlucQForce; + } + + return storageLayout; + } + void SimCreator::setGlobalIndex(SimInfo *info) { SimInfo::MoleculeIterator mi; Molecule::AtomIterator ai; Molecule::RigidBodyIterator ri; Molecule::CutoffGroupIterator ci; + Molecule::IntegrableObjectIterator ioi; Molecule * mol; Atom * atom; RigidBody * rb; @@ -544,74 +788,52 @@ Globals* SimCreator::parseFile(const std::string mdFil int beginCutoffGroupIndex; 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); - MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc, - 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)) { + beginRigidBodyIndex = info->getNGlobalAtoms(); + beginCutoffGroupIndex = 0; + + for(int i = 0; i < info->getNGlobalMolecules(); i++) { - //local index(index in DataStorge) of atom is important - for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { - atom->setGlobalIndex(beginAtomIndex++); +#ifdef IS_MPI + if (info->getMolToProc(i) == worldRank) { +#endif + // stuff to do if I own this molecule + mol = info->getMoleculeByGlobalIndex(i); + + //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++); + } + +#ifdef IS_MPI + } else { + + // stuff to do if I don't own this molecule + + int stampId = info->getMoleculeStampId(i); + MoleculeStamp* stamp = info->getMoleculeStamp(stampId); + + beginAtomIndex += stamp->getNAtoms(); + beginRigidBodyIndex += stamp->getNRigidBodies(); + beginCutoffGroupIndex += stamp->getNCutoffGroups() + stamp->getNFreeAtoms(); } - - 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++); - } - } - +#endif + + } //end for(int i=0) + //fill globalGroupMembership std::vector globalGroupMembership(info->getNGlobalAtoms(), 0); for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { @@ -623,16 +845,17 @@ Globals* SimCreator::parseFile(const std::string mdFil } } - + #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 // to get the full globalGroupMembership array (We think). // This would be prettier if we could use MPI_IN_PLACE like the MPI-2 // docs said we could. - std::vector tmpGroupMembership(nGlobalAtoms, 0); - MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms, - MPI_INT, MPI_SUM, MPI_COMM_WORLD); + std::vector tmpGroupMembership(info->getNGlobalAtoms(), 0); + MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0], + &tmpGroupMembership[0], nGlobalAtoms, + MPI::INT, MPI::SUM); info->setGlobalGroupMembership(tmpGroupMembership); #else info->setGlobalGroupMembership(globalGroupMembership); @@ -642,54 +865,81 @@ Globals* SimCreator::parseFile(const std::string mdFil 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); + std::vector tmpMolMembership(info->getNGlobalAtoms(), 0); + MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0], + nGlobalAtoms, + MPI::INT, MPI::SUM); - MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms, - MPI_INT, MPI_SUM, MPI_COMM_WORLD); - info->setGlobalMolMembership(tmpMolMembership); #else info->setGlobalMolMembership(globalMolMembership); #endif + + // nIOPerMol holds the number of integrable objects per molecule + // here the molecules are listed by their global indices. + + std::vector nIOPerMol(info->getNGlobalMolecules(), 0); + for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { + nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects(); + } - } - - void SimCreator::loadCoordinates(SimInfo* info) { - Globals* simParams; - simParams = info->getSimParams(); +#ifdef IS_MPI + std::vector numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0); + MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0], + info->getNGlobalMolecules(), MPI::INT, MPI::SUM); +#else + std::vector numIntegrableObjectsPerMol = nIOPerMol; +#endif + + std::vector startingIOIndexForMol(info->getNGlobalMolecules()); - if (!simParams->haveInitialConfig()) { - sprintf(painCave.errMsg, - "Cannot intialize a simulation without an initial configuration file.\n"); - painCave.isFatal = 1;; - simError(); + int startingIndex = 0; + for (int i = 0; i < info->getNGlobalMolecules(); i++) { + startingIOIndexForMol[i] = startingIndex; + startingIndex += numIntegrableObjectsPerMol[i]; } - DumpReader reader(info, simParams->getInitialConfig()); - int nframes = reader.getNFrames(); + std::vector IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL); + for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { + int myGlobalIndex = mol->getGlobalIndex(); + int globalIO = startingIOIndexForMol[myGlobalIndex]; + for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL; + sd = mol->nextIntegrableObject(ioi)) { + sd->setGlobalIntegrableObjectIndex(globalIO); + IOIndexToIntegrableObject[globalIO] = sd; + globalIO++; + } + } + + info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject); + } + + void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) { + + DumpReader reader(info, mdFileName); + 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().c_str()); + mdFileName.c_str()); painCave.isFatal = 1; simError(); } - //copy the current snapshot to previous snapshot info->getSnapshotManager()->advance(); } -} //end namespace oopse +} //end namespace OpenMD