--- trunk/src/brains/SimCreator.cpp 2009/11/25 20:02:06 1390 +++ trunk/src/brains/SimCreator.cpp 2012/10/03 14:07:28 1802 @@ -1,5 +1,5 @@ /* - * 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 @@ -36,7 +36,8 @@ * [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] Vardeman & Gezelter, in progress (2009). + * [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" @@ -75,13 +76,22 @@ #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 OpenMD { - Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int startOfMetaDataBlock ){ + Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int mdFileVersion, int startOfMetaDataBlock ){ Globals* simParams = NULL; try { @@ -90,30 +100,33 @@ namespace OpenMD { #ifdef IS_MPI int streamSize; const int masterNode = 0; - int commStatus; + if (worldRank == masterNode) { -#endif - + MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode); +#endif SimplePreprocessor preprocessor; - preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream); + preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, + ppStream); #ifdef IS_MPI //brocasting the stream size streamSize = ppStream.str().size() +1; - commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD); - - commStatus = MPI_Bcast(static_cast(const_cast(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); - + 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 { + + MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode); + //get stream size - commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD); + MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode); char* buf = new char[streamSize]; assert(buf); //receive file content - commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); + MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode); ppStream.str(buf); delete [] buf; @@ -229,12 +242,13 @@ namespace OpenMD { simError(); } + simParams->setMDfileVersion(mdFileVersion); return simParams; } SimInfo* SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) { - + const int bufferSize = 65535; char buffer[bufferSize]; int lineNo = 0; @@ -242,14 +256,17 @@ namespace OpenMD { int metaDataBlockStart = -1; int metaDataBlockEnd = -1; int i; - int mdOffset; + streamoff mdOffset(0); + int mdFileVersion; + #ifdef IS_MPI const int masterNode = 0; if (worldRank == masterNode) { #endif - std::ifstream mdFile_(mdFileName.c_str()); + std::ifstream mdFile_; + mdFile_.open(mdFileName.c_str(), ifstream::in | ifstream::binary); if (mdFile_.fail()) { sprintf(painCave.errMsg, @@ -276,7 +293,27 @@ namespace OpenMD { 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; @@ -332,10 +369,11 @@ namespace OpenMD { std::stringstream rawMetaDataStream(mdRawData); //parse meta-data file - Globals* simParams = parseFile(rawMetaDataStream, mdFileName, metaDataBlockStart+1); + 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, @@ -369,7 +407,6 @@ namespace OpenMD { } ff->parse(forcefieldFileName); - ff->setFortranForceOptions(); //create SimInfo SimInfo * info = new SimInfo(ff, simParams); @@ -387,10 +424,13 @@ namespace OpenMD { //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 @@ -413,7 +453,6 @@ namespace OpenMD { if (loadInitCoords) loadCoordinates(info, mdFileName); - return info; } @@ -460,7 +499,6 @@ namespace OpenMD { int nTarget; int done; int i; - int j; int loops; int which_proc; int nProcessors; @@ -468,7 +506,7 @@ namespace OpenMD { 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, @@ -506,6 +544,7 @@ namespace OpenMD { nTarget = (int)(precast + 0.5); for(i = 0; i < nGlobalMols; i++) { + done = 0; loops = 0; @@ -530,13 +569,15 @@ namespace OpenMD { // 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; @@ -581,15 +622,14 @@ namespace OpenMD { } 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); @@ -612,8 +652,10 @@ namespace OpenMD { #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); @@ -626,6 +668,111 @@ namespace OpenMD { } //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; @@ -640,76 +787,54 @@ namespace OpenMD { int beginRigidBodyIndex; int beginCutoffGroupIndex; int nGlobalAtoms = info->getNGlobalAtoms(); - - /**@todo fixme */ -#ifndef IS_MPI + int nGlobalRigidBodies = info->getNGlobalRigidBodies(); 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)) { @@ -721,7 +846,7 @@ namespace OpenMD { } } - + #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 @@ -729,28 +854,36 @@ namespace OpenMD { // This would be prettier if we could use MPI_IN_PLACE like the MPI-2 // docs said we could. std::vector tmpGroupMembership(info->getNGlobalAtoms(), 0); - MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms, - MPI_INT, MPI_SUM, MPI_COMM_WORLD); + MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0], + &tmpGroupMembership[0], nGlobalAtoms, + MPI::INT, MPI::SUM); info->setGlobalGroupMembership(tmpGroupMembership); #else info->setGlobalGroupMembership(globalGroupMembership); #endif //fill molMembership - std::vector globalMolMembership(info->getNGlobalAtoms(), 0); + std::vector globalMolMembership(info->getNGlobalAtoms() + + info->getNGlobalRigidBodies(), 0); - for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { + 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 (rb = mol->beginRigidBody(ri); rb != NULL; + rb = mol->nextRigidBody(ri)) { + globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex(); + } } #ifdef IS_MPI - std::vector tmpMolMembership(info->getNGlobalAtoms(), 0); + std::vector tmpMolMembership(info->getNGlobalAtoms() + + info->getNGlobalRigidBodies(), 0); + MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0], + nGlobalAtoms + nGlobalRigidBodies, + 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); @@ -760,14 +893,15 @@ namespace OpenMD { // 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)) { + for (mol = info->beginMolecule(mi); mol != NULL; + mol = info->nextMolecule(mi)) { nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects(); } #ifdef IS_MPI std::vector numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0); - MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0], - info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD); + MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0], + info->getNGlobalMolecules(), MPI::INT, MPI::SUM); #else std::vector numIntegrableObjectsPerMol = nIOPerMol; #endif @@ -781,29 +915,27 @@ namespace OpenMD { } std::vector IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL); - for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { + for (mol = info->beginMolecule(mi); mol != NULL; + mol = info->nextMolecule(mi)) { int myGlobalIndex = mol->getGlobalIndex(); int globalIO = startingIOIndexForMol[myGlobalIndex]; - for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL; - integrableObject = mol->nextIntegrableObject(ioi)) { - integrableObject->setGlobalIntegrableObjectIndex(globalIO); - IOIndexToIntegrableObject[globalIO] = integrableObject; + 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) { - Globals* simParams; - simParams = info->getSimParams(); - - + DumpReader reader(info, mdFileName); int nframes = reader.getNFrames(); - + if (nframes > 0) { reader.readFrame(nframes - 1); } else { @@ -814,7 +946,6 @@ namespace OpenMD { painCave.isFatal = 1; simError(); } - //copy the current snapshot to previous snapshot info->getSnapshotManager()->advance(); }