--- trunk/src/brains/SimCreator.cpp 2006/08/30 20:33:44 1025 +++ trunk/src/brains/SimCreator.cpp 2012/09/10 18:38:44 1796 @@ -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" @@ -75,13 +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 oopse { +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 { @@ -90,33 +100,36 @@ namespace oopse { #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; + delete [] buf; } #endif @@ -145,7 +158,6 @@ namespace oopse { treeParser.initializeASTFactory(factory); treeParser.setASTFactory(&factory); simParams = treeParser.walkTree(parser.getAST()); - } @@ -215,7 +227,7 @@ namespace oopse { painCave.isFatal = 1; simError(); } - catch (OOPSEException& e) { + catch (OpenMDException& e) { sprintf(painCave.errMsg, "%s\n", e.getMessage().c_str()); @@ -230,12 +242,13 @@ namespace oopse { 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; @@ -243,14 +256,17 @@ namespace oopse { 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, @@ -263,15 +279,41 @@ namespace oopse { 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 an OOPSE file!\n", + "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; @@ -327,12 +369,12 @@ namespace oopse { 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, "ForceField Factory can not create %s force field\n", @@ -365,7 +407,6 @@ namespace oopse { } ff->parse(forcefieldFileName); - ff->setFortranForceOptions(); //create SimInfo SimInfo * info = new SimInfo(ff, simParams); @@ -383,10 +424,13 @@ namespace oopse { //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 @@ -395,21 +439,20 @@ namespace oopse { //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, mdFileName); - return info; } @@ -456,7 +499,6 @@ namespace oopse { int nTarget; int done; int i; - int j; int loops; int which_proc; int nProcessors; @@ -464,7 +506,7 @@ namespace oopse { 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, @@ -473,7 +515,7 @@ namespace oopse { "\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(); @@ -579,19 +621,17 @@ namespace oopse { 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 @@ -608,8 +648,10 @@ namespace oopse { #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); @@ -621,7 +663,112 @@ namespace oopse { } //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; @@ -636,76 +783,53 @@ namespace oopse { int beginRigidBodyIndex; int beginCutoffGroupIndex; int nGlobalAtoms = info->getNGlobalAtoms(); - - /**@todo fixme */ -#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)) { @@ -717,16 +841,17 @@ namespace oopse { } } - + #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); @@ -736,18 +861,17 @@ namespace oopse { 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); @@ -763,44 +887,41 @@ namespace oopse { #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 - std::vector startingIOIndexForMol(info->getNGlobalMolecules()); - -int startingIndex = 0; - for (int i = 0; i < info->getNGlobalMolecules(); i++) { - startingIOIndexForMol[i] = startingIndex; - startingIndex += numIntegrableObjectsPerMol[i]; - } - - std::vector IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL); - for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { + std::vector startingIOIndexForMol(info->getNGlobalMolecules()); + + int startingIndex = 0; + for (int i = 0; i < info->getNGlobalMolecules(); i++) { + startingIOIndexForMol[i] = startingIndex; + startingIndex += numIntegrableObjectsPerMol[i]; + } + + 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* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL; - integrableObject = mol->nextIntegrableObject(ioi)) { - integrableObject->setGlobalIntegrableObjectIndex(globalIO); - IOIndexToIntegrableObject[globalIO] = integrableObject; - globalIO++; + for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL; + sd = mol->nextIntegrableObject(ioi)) { + sd->setGlobalIntegrableObjectIndex(globalIO); + IOIndexToIntegrableObject[globalIO] = sd; + globalIO++; } } - - info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject); - + + 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 { @@ -811,11 +932,10 @@ int startingIndex = 0; painCave.isFatal = 1; simError(); } - //copy the current snapshot to previous snapshot info->getSnapshotManager()->advance(); } -} //end namespace oopse +} //end namespace OpenMD