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/* |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* @version 1.0 |
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*/ |
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|
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#include <sprng.h> |
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|
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#include "brains/MoleculeCreator.hpp" |
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#include "brains/SimCreator.hpp" |
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#include "brains/SimSnapshotManager.hpp" |
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#include "UseTheForce/ForceFieldFactory.hpp" |
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#include "utils/simError.h" |
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#include "utils/StringUtils.hpp" |
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#include "math/SeqRandNumGen.hpp" |
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#ifdef IS_MPI |
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#include "io/mpiBASS.h" |
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#include "math/randomSPRNG.hpp" |
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#include "math/ParallelRandNumGen.hpp" |
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#endif |
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namespace oopse { |
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void SimCreator::parseFile(const std::string mdFileName, MakeStamps* stamps, Globals* simParams){ |
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void SimCreator::parseFile(const std::string mdFileName, MakeStamps* stamps, Globals* simParams){ |
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#ifdef IS_MPI |
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if (worldRank == 0) { |
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#endif // is_mpi |
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|
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simParams->initalize(); |
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set_interface_stamps(stamps, simParams); |
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simParams->initalize(); |
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set_interface_stamps(stamps, simParams); |
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#ifdef IS_MPI |
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mpiEventInit(); |
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mpiEventInit(); |
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#endif |
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|
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yacc_BASS(mdFileName.c_str()); |
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yacc_BASS(mdFileName.c_str()); |
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|
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#ifdef IS_MPI |
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|
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throwMPIEvent(NULL); |
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throwMPIEvent(NULL); |
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} else { |
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set_interface_stamps(stamps, simParams); |
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mpiEventInit(); |
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MPIcheckPoint(); |
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mpiEventLoop(); |
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set_interface_stamps(stamps, simParams); |
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mpiEventInit(); |
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MPIcheckPoint(); |
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mpiEventLoop(); |
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} |
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#endif |
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} |
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} |
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SimInfo* SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) { |
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SimInfo* SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) { |
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|
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MakeStamps * stamps = new MakeStamps(); |
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//create the force field |
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ForceField * ff = ForceFieldFactory::getInstance()->createForceField( |
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simParams->getForceField()); |
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simParams->getForceField()); |
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|
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if (ff == NULL) { |
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sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n", |
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simParams->getForceField()); |
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painCave.isFatal = 1; |
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simError(); |
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sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n", |
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simParams->getForceField()); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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if (simParams->haveForceFieldFileName()) { |
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ff->setForceFieldFileName(simParams->getForceFieldFileName()); |
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ff->setForceFieldFileName(simParams->getForceFieldFileName()); |
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} |
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std::string forcefieldFileName; |
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forcefieldFileName = ff->getForceFieldFileName(); |
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|
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if (simParams->haveForceFieldVariant()) { |
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//If the force field has variant, the variant force field name will be |
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//Base.variant.frc. For exampel EAM.u6.frc |
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//If the force field has variant, the variant force field name will be |
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//Base.variant.frc. For exampel EAM.u6.frc |
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std::string variant = simParams->getForceFieldVariant(); |
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std::string variant = simParams->getForceFieldVariant(); |
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std::string::size_type pos = forcefieldFileName.rfind(".frc"); |
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variant = "." + variant; |
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if (pos != std::string::npos) { |
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forcefieldFileName.insert(pos, variant); |
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} else { |
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//If the default force field file name does not containt .frc suffix, just append the .variant |
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forcefieldFileName.append(variant); |
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} |
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std::string::size_type pos = forcefieldFileName.rfind(".frc"); |
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variant = "." + variant; |
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if (pos != std::string::npos) { |
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forcefieldFileName.insert(pos, variant); |
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} else { |
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//If the default force field file name does not containt .frc suffix, just append the .variant |
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forcefieldFileName.append(variant); |
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} |
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} |
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ff->parse(forcefieldFileName); |
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SimInfo::MoleculeIterator mi; |
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Molecule* mol; |
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for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
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info->addExcludePairs(mol); |
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info->addExcludePairs(mol); |
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} |
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//load initial coordinates, some extra information are pushed into SimInfo's property map ( such as |
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//eta, chi for NPT integrator) |
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if (loadInitCoords) |
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loadCoordinates(info); |
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loadCoordinates(info); |
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|
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return info; |
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} |
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} |
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void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) { |
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void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) { |
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|
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//setup seed for random number generator |
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int seedValue; |
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Globals * simParams = info->getSimParams(); |
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|
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if (simParams->haveSeed()) { |
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seedValue = simParams->getSeed(); |
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|
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if (seedValue < 100000000 ) { |
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sprintf(painCave.errMsg, |
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"Seed for sprng library should contain at least 9 digits\n" |
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"OOPSE will generate a seed for user\n"); |
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|
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painCave.isFatal = 0; |
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simError(); |
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|
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//using seed generated by system instead of invalid seed set by user |
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|
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#ifndef IS_MPI |
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seedValue = make_sprng_seed(); |
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#else |
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if (worldRank == 0) { |
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seedValue = make_sprng_seed(); |
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} |
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|
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MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
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#endif |
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|
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} //end if (seedValue /1000000000 == 0) |
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} else { |
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|
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#ifndef IS_MPI |
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|
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seedValue = make_sprng_seed(); |
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|
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#else |
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|
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if (worldRank == 0) { |
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seedValue = make_sprng_seed(); |
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} |
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|
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MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
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|
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#endif |
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|
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} //end of simParams->haveSeed() |
241 |
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|
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info->setSeed(seedValue); |
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|
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|
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//figure out the ouput file names |
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std::string prefix; |
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|
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|
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if (worldRank == 0) { |
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#endif // is_mpi |
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Globals * simParams = info->getSimParams(); |
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if (simParams->haveFinalConfig()) { |
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prefix = getPrefix(simParams->getFinalConfig()); |
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} else { |
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prefix = getPrefix(mdfile); |
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} |
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if (simParams->haveFinalConfig()) { |
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prefix = getPrefix(simParams->getFinalConfig()); |
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} else { |
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prefix = getPrefix(mdfile); |
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} |
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info->setFinalConfigFileName(prefix + ".eor"); |
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info->setDumpFileName(prefix + ".dump"); |
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info->setStatFileName(prefix + ".stat"); |
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|
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info->setFinalConfigFileName(prefix + ".eor"); |
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info->setDumpFileName(prefix + ".dump"); |
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info->setStatFileName(prefix + ".stat"); |
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|
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#ifdef IS_MPI |
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} |
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#endif |
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} |
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} |
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#ifdef IS_MPI |
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void SimCreator::divideMolecules(SimInfo *info) { |
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void SimCreator::divideMolecules(SimInfo *info) { |
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double numerator; |
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double denominator; |
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double precast; |
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int which_proc; |
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int nProcessors; |
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std::vector<int> atomsPerProc; |
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randomSPRNG myRandom(info->getSeed()); |
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int nGlobalMols = info->getNGlobalMolecules(); |
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std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition: |
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MPI_Comm_size(MPI_COMM_WORLD, &nProcessors); |
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|
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if (nProcessors > nGlobalMols) { |
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sprintf(painCave.errMsg, |
243 |
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"nProcessors (%d) > nMol (%d)\n" |
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"\tThe number of processors is larger than\n" |
245 |
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"\tthe number of molecules. This will not result in a \n" |
246 |
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"\tusable division of atoms for force decomposition.\n" |
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"\tEither try a smaller number of processors, or run the\n" |
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"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols); |
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sprintf(painCave.errMsg, |
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"nProcessors (%d) > nMol (%d)\n" |
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"\tThe number of processors is larger than\n" |
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"\tthe number of molecules. This will not result in a \n" |
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"\tusable division of atoms for force decomposition.\n" |
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"\tEither try a smaller number of processors, or run the\n" |
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"\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols); |
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|
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< |
painCave.isFatal = 1; |
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simError(); |
250 |
> |
painCave.isFatal = 1; |
251 |
> |
simError(); |
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} |
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|
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+ |
int seedValue; |
255 |
+ |
Globals * simParams = info->getSimParams(); |
256 |
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SeqRandNumGen* myRandom; //divide labor does not need Parallel random number generator |
257 |
+ |
if (simParams->haveSeed()) { |
258 |
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seedValue = simParams->getSeed(); |
259 |
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myRandom = new SeqRandNumGen(seedValue); |
260 |
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}else { |
261 |
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myRandom = new SeqRandNumGen(); |
262 |
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} |
263 |
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|
264 |
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|
265 |
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a = 3.0 * nGlobalMols / info->getNGlobalAtoms(); |
266 |
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|
267 |
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//initialize atomsPerProc |
268 |
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atomsPerProc.insert(atomsPerProc.end(), nProcessors, 0); |
269 |
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|
270 |
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if (worldRank == 0) { |
271 |
< |
numerator = info->getNGlobalAtoms(); |
272 |
< |
denominator = nProcessors; |
273 |
< |
precast = numerator / denominator; |
274 |
< |
nTarget = (int)(precast + 0.5); |
271 |
> |
numerator = info->getNGlobalAtoms(); |
272 |
> |
denominator = nProcessors; |
273 |
> |
precast = numerator / denominator; |
274 |
> |
nTarget = (int)(precast + 0.5); |
275 |
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|
276 |
< |
for(i = 0; i < nGlobalMols; i++) { |
277 |
< |
done = 0; |
278 |
< |
loops = 0; |
276 |
> |
for(i = 0; i < nGlobalMols; i++) { |
277 |
> |
done = 0; |
278 |
> |
loops = 0; |
279 |
|
|
280 |
< |
while (!done) { |
281 |
< |
loops++; |
280 |
> |
while (!done) { |
281 |
> |
loops++; |
282 |
|
|
283 |
< |
// Pick a processor at random |
283 |
> |
// Pick a processor at random |
284 |
|
|
285 |
< |
which_proc = (int) (myRandom.getRandom() * nProcessors); |
285 |
> |
which_proc = (int) (myRandom->rand() * nProcessors); |
286 |
|
|
287 |
< |
//get the molecule stamp first |
288 |
< |
int stampId = info->getMoleculeStampId(i); |
289 |
< |
MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId); |
287 |
> |
//get the molecule stamp first |
288 |
> |
int stampId = info->getMoleculeStampId(i); |
289 |
> |
MoleculeStamp * moleculeStamp = info->getMoleculeStamp(stampId); |
290 |
|
|
291 |
< |
// How many atoms does this processor have so far? |
292 |
< |
old_atoms = atomsPerProc[which_proc]; |
293 |
< |
add_atoms = moleculeStamp->getNAtoms(); |
294 |
< |
new_atoms = old_atoms + add_atoms; |
291 |
> |
// How many atoms does this processor have so far? |
292 |
> |
old_atoms = atomsPerProc[which_proc]; |
293 |
> |
add_atoms = moleculeStamp->getNAtoms(); |
294 |
> |
new_atoms = old_atoms + add_atoms; |
295 |
|
|
296 |
< |
// If we've been through this loop too many times, we need |
297 |
< |
// to just give up and assign the molecule to this processor |
298 |
< |
// and be done with it. |
296 |
> |
// If we've been through this loop too many times, we need |
297 |
> |
// to just give up and assign the molecule to this processor |
298 |
> |
// and be done with it. |
299 |
|
|
300 |
< |
if (loops > 100) { |
301 |
< |
sprintf(painCave.errMsg, |
302 |
< |
"I've tried 100 times to assign molecule %d to a " |
303 |
< |
" processor, but can't find a good spot.\n" |
304 |
< |
"I'm assigning it at random to processor %d.\n", |
305 |
< |
i, which_proc); |
300 |
> |
if (loops > 100) { |
301 |
> |
sprintf(painCave.errMsg, |
302 |
> |
"I've tried 100 times to assign molecule %d to a " |
303 |
> |
" processor, but can't find a good spot.\n" |
304 |
> |
"I'm assigning it at random to processor %d.\n", |
305 |
> |
i, which_proc); |
306 |
|
|
307 |
< |
painCave.isFatal = 0; |
308 |
< |
simError(); |
307 |
> |
painCave.isFatal = 0; |
308 |
> |
simError(); |
309 |
|
|
310 |
< |
molToProcMap[i] = which_proc; |
311 |
< |
atomsPerProc[which_proc] += add_atoms; |
310 |
> |
molToProcMap[i] = which_proc; |
311 |
> |
atomsPerProc[which_proc] += add_atoms; |
312 |
|
|
313 |
< |
done = 1; |
314 |
< |
continue; |
315 |
< |
} |
313 |
> |
done = 1; |
314 |
> |
continue; |
315 |
> |
} |
316 |
|
|
317 |
< |
// If we can add this molecule to this processor without sending |
318 |
< |
// it above nTarget, then go ahead and do it: |
317 |
> |
// If we can add this molecule to this processor without sending |
318 |
> |
// it above nTarget, then go ahead and do it: |
319 |
|
|
320 |
< |
if (new_atoms <= nTarget) { |
321 |
< |
molToProcMap[i] = which_proc; |
322 |
< |
atomsPerProc[which_proc] += add_atoms; |
320 |
> |
if (new_atoms <= nTarget) { |
321 |
> |
molToProcMap[i] = which_proc; |
322 |
> |
atomsPerProc[which_proc] += add_atoms; |
323 |
|
|
324 |
< |
done = 1; |
325 |
< |
continue; |
326 |
< |
} |
371 |
< |
|
372 |
< |
// The only situation left is when new_atoms > nTarget. We |
373 |
< |
// want to accept this with some probability that dies off the |
374 |
< |
// farther we are from nTarget |
324 |
> |
done = 1; |
325 |
> |
continue; |
326 |
> |
} |
327 |
|
|
328 |
< |
// roughly: x = new_atoms - nTarget |
329 |
< |
// Pacc(x) = exp(- a * x) |
330 |
< |
// where a = penalty / (average atoms per molecule) |
328 |
> |
// The only situation left is when new_atoms > nTarget. We |
329 |
> |
// want to accept this with some probability that dies off the |
330 |
> |
// farther we are from nTarget |
331 |
|
|
332 |
< |
x = (double)(new_atoms - nTarget); |
333 |
< |
y = myRandom.getRandom(); |
332 |
> |
// roughly: x = new_atoms - nTarget |
333 |
> |
// Pacc(x) = exp(- a * x) |
334 |
> |
// where a = penalty / (average atoms per molecule) |
335 |
|
|
336 |
< |
if (y < exp(- a * x)) { |
337 |
< |
molToProcMap[i] = which_proc; |
385 |
< |
atomsPerProc[which_proc] += add_atoms; |
336 |
> |
x = (double)(new_atoms - nTarget); |
337 |
> |
y = myRandom->rand(); |
338 |
|
|
339 |
< |
done = 1; |
340 |
< |
continue; |
341 |
< |
} else { |
342 |
< |
continue; |
343 |
< |
} |
344 |
< |
} |
339 |
> |
if (y < exp(- a * x)) { |
340 |
> |
molToProcMap[i] = which_proc; |
341 |
> |
atomsPerProc[which_proc] += add_atoms; |
342 |
> |
|
343 |
> |
done = 1; |
344 |
> |
continue; |
345 |
> |
} else { |
346 |
> |
continue; |
347 |
> |
} |
348 |
|
} |
349 |
+ |
} |
350 |
|
|
351 |
< |
// Spray out this nonsense to all other processors: |
351 |
> |
delete myRandom; |
352 |
> |
|
353 |
> |
// Spray out this nonsense to all other processors: |
354 |
|
|
355 |
< |
MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
355 |
> |
MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
356 |
|
} else { |
357 |
|
|
358 |
< |
// Listen to your marching orders from processor 0: |
358 |
> |
// Listen to your marching orders from processor 0: |
359 |
|
|
360 |
< |
MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
360 |
> |
MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD); |
361 |
|
} |
362 |
|
|
363 |
|
info->setMolToProcMap(molToProcMap); |
364 |
|
sprintf(checkPointMsg, |
365 |
|
"Successfully divided the molecules among the processors.\n"); |
366 |
|
MPIcheckPoint(); |
367 |
< |
} |
367 |
> |
} |
368 |
|
|
369 |
|
#endif |
370 |
|
|
371 |
< |
void SimCreator::createMolecules(SimInfo *info) { |
371 |
> |
void SimCreator::createMolecules(SimInfo *info) { |
372 |
|
MoleculeCreator molCreator; |
373 |
|
int stampId; |
374 |
|
|
376 |
|
|
377 |
|
#ifdef IS_MPI |
378 |
|
|
379 |
< |
if (info->getMolToProc(i) == worldRank) { |
379 |
> |
if (info->getMolToProc(i) == worldRank) { |
380 |
|
#endif |
381 |
|
|
382 |
< |
stampId = info->getMoleculeStampId(i); |
383 |
< |
Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId), |
384 |
< |
stampId, i, info->getLocalIndexManager()); |
382 |
> |
stampId = info->getMoleculeStampId(i); |
383 |
> |
Molecule * mol = molCreator.createMolecule(info->getForceField(), info->getMoleculeStamp(stampId), |
384 |
> |
stampId, i, info->getLocalIndexManager()); |
385 |
|
|
386 |
< |
info->addMolecule(mol); |
386 |
> |
info->addMolecule(mol); |
387 |
|
|
388 |
|
#ifdef IS_MPI |
389 |
|
|
390 |
< |
} |
390 |
> |
} |
391 |
|
|
392 |
|
#endif |
393 |
|
|
394 |
|
} //end for(int i=0) |
395 |
< |
} |
395 |
> |
} |
396 |
|
|
397 |
< |
void SimCreator::compList(MakeStamps *stamps, Globals* simParams, |
398 |
< |
std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) { |
397 |
> |
void SimCreator::compList(MakeStamps *stamps, Globals* simParams, |
398 |
> |
std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) { |
399 |
|
int i; |
400 |
|
char * id; |
401 |
+ |
LinkedMolStamp* extractedStamp = NULL; |
402 |
|
MoleculeStamp * currentStamp; |
403 |
|
Component** the_components = simParams->getComponents(); |
404 |
|
int n_components = simParams->getNComponents(); |
405 |
|
|
406 |
|
if (!simParams->haveNMol()) { |
407 |
< |
// we don't have the total number of molecules, so we assume it is |
408 |
< |
// given in each component |
407 |
> |
// we don't have the total number of molecules, so we assume it is |
408 |
> |
// given in each component |
409 |
|
|
410 |
< |
for(i = 0; i < n_components; i++) { |
411 |
< |
if (!the_components[i]->haveNMol()) { |
412 |
< |
// we have a problem |
413 |
< |
sprintf(painCave.errMsg, |
414 |
< |
"SimCreator Error. No global NMol or component NMol given.\n" |
415 |
< |
"\tCannot calculate the number of atoms.\n"); |
410 |
> |
for(i = 0; i < n_components; i++) { |
411 |
> |
if (!the_components[i]->haveNMol()) { |
412 |
> |
// we have a problem |
413 |
> |
sprintf(painCave.errMsg, |
414 |
> |
"SimCreator Error. No global NMol or component NMol given.\n" |
415 |
> |
"\tCannot calculate the number of atoms.\n"); |
416 |
|
|
417 |
< |
painCave.isFatal = 1; |
418 |
< |
simError(); |
419 |
< |
} |
417 |
> |
painCave.isFatal = 1; |
418 |
> |
simError(); |
419 |
> |
} |
420 |
> |
|
421 |
> |
id = the_components[i]->getType(); |
422 |
|
|
423 |
< |
id = the_components[i]->getType(); |
424 |
< |
currentStamp = (stamps->extractMolStamp(id))->getStamp(); |
423 |
> |
extractedStamp = stamps->extractMolStamp(id); |
424 |
> |
if (extractedStamp == NULL) { |
425 |
> |
sprintf(painCave.errMsg, |
426 |
> |
"SimCreator error: Component \"%s\" was not found in the " |
427 |
> |
"list of declared molecules\n", id); |
428 |
|
|
429 |
< |
if (currentStamp == NULL) { |
430 |
< |
sprintf(painCave.errMsg, |
431 |
< |
"SimCreator error: Component \"%s\" was not found in the " |
468 |
< |
"list of declared molecules\n", id); |
429 |
> |
painCave.isFatal = 1; |
430 |
> |
simError(); |
431 |
> |
} |
432 |
|
|
433 |
< |
painCave.isFatal = 1; |
471 |
< |
simError(); |
472 |
< |
} |
433 |
> |
currentStamp = extractedStamp->getStamp(); |
434 |
|
|
435 |
< |
moleculeStampPairs.push_back( |
436 |
< |
std::make_pair(currentStamp, the_components[i]->getNMol())); |
437 |
< |
} //end for (i = 0; i < n_components; i++) |
435 |
> |
|
436 |
> |
moleculeStampPairs.push_back( |
437 |
> |
std::make_pair(currentStamp, the_components[i]->getNMol())); |
438 |
> |
} //end for (i = 0; i < n_components; i++) |
439 |
|
} else { |
440 |
< |
sprintf(painCave.errMsg, "SimSetup error.\n" |
441 |
< |
"\tSorry, the ability to specify total" |
442 |
< |
" nMols and then give molfractions in the components\n" |
443 |
< |
"\tis not currently supported." |
444 |
< |
" Please give nMol in the components.\n"); |
440 |
> |
sprintf(painCave.errMsg, "SimSetup error.\n" |
441 |
> |
"\tSorry, the ability to specify total" |
442 |
> |
" nMols and then give molfractions in the components\n" |
443 |
> |
"\tis not currently supported." |
444 |
> |
" Please give nMol in the components.\n"); |
445 |
|
|
446 |
< |
painCave.isFatal = 1; |
447 |
< |
simError(); |
446 |
> |
painCave.isFatal = 1; |
447 |
> |
simError(); |
448 |
|
} |
449 |
|
|
450 |
|
#ifdef IS_MPI |
454 |
|
|
455 |
|
#endif // is_mpi |
456 |
|
|
457 |
< |
} |
457 |
> |
} |
458 |
|
|
459 |
< |
void SimCreator::setGlobalIndex(SimInfo *info) { |
459 |
> |
void SimCreator::setGlobalIndex(SimInfo *info) { |
460 |
|
SimInfo::MoleculeIterator mi; |
461 |
|
Molecule::AtomIterator ai; |
462 |
|
Molecule::RigidBodyIterator ri; |
508 |
|
beginCutoffGroupIndex = 0; |
509 |
|
|
510 |
|
for(int i = 0; i < myNode; i++) { |
511 |
< |
beginAtomIndex += NumAtomsInProc[i]; |
512 |
< |
beginRigidBodyIndex += NumRigidBodiesInProc[i]; |
513 |
< |
beginCutoffGroupIndex += NumCutoffGroupsInProc[i]; |
511 |
> |
beginAtomIndex += NumAtomsInProc[i]; |
512 |
> |
beginRigidBodyIndex += NumRigidBodiesInProc[i]; |
513 |
> |
beginCutoffGroupIndex += NumCutoffGroupsInProc[i]; |
514 |
|
} |
515 |
|
|
516 |
|
#endif |
517 |
|
|
518 |
+ |
//rigidbody's index begins right after atom's |
519 |
+ |
beginRigidBodyIndex += info->getNGlobalAtoms(); |
520 |
+ |
|
521 |
|
for(mol = info->beginMolecule(mi); mol != NULL; |
522 |
|
mol = info->nextMolecule(mi)) { |
523 |
|
|
524 |
< |
//local index(index in DataStorge) of atom is important |
525 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
526 |
< |
atom->setGlobalIndex(beginAtomIndex++); |
527 |
< |
} |
524 |
> |
//local index(index in DataStorge) of atom is important |
525 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
526 |
> |
atom->setGlobalIndex(beginAtomIndex++); |
527 |
> |
} |
528 |
|
|
529 |
< |
for(rb = mol->beginRigidBody(ri); rb != NULL; |
530 |
< |
rb = mol->nextRigidBody(ri)) { |
531 |
< |
rb->setGlobalIndex(beginRigidBodyIndex++); |
532 |
< |
} |
529 |
> |
for(rb = mol->beginRigidBody(ri); rb != NULL; |
530 |
> |
rb = mol->nextRigidBody(ri)) { |
531 |
> |
rb->setGlobalIndex(beginRigidBodyIndex++); |
532 |
> |
} |
533 |
|
|
534 |
< |
//local index of cutoff group is trivial, it only depends on the order of travesing |
535 |
< |
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
536 |
< |
cg = mol->nextCutoffGroup(ci)) { |
537 |
< |
cg->setGlobalIndex(beginCutoffGroupIndex++); |
538 |
< |
} |
534 |
> |
//local index of cutoff group is trivial, it only depends on the order of travesing |
535 |
> |
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
536 |
> |
cg = mol->nextCutoffGroup(ci)) { |
537 |
> |
cg->setGlobalIndex(beginCutoffGroupIndex++); |
538 |
> |
} |
539 |
|
} |
540 |
|
|
541 |
|
//fill globalGroupMembership |
542 |
|
std::vector<int> globalGroupMembership(info->getNGlobalAtoms(), 0); |
543 |
|
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
544 |
< |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
544 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
545 |
|
|
546 |
< |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
547 |
< |
globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex(); |
548 |
< |
} |
546 |
> |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
547 |
> |
globalGroupMembership[atom->getGlobalIndex()] = cg->getGlobalIndex(); |
548 |
> |
} |
549 |
|
|
550 |
< |
} |
550 |
> |
} |
551 |
|
} |
552 |
|
|
553 |
|
#ifdef IS_MPI |
559 |
|
std::vector<int> tmpGroupMembership(nGlobalAtoms, 0); |
560 |
|
MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms, |
561 |
|
MPI_INT, MPI_SUM, MPI_COMM_WORLD); |
562 |
< |
info->setGlobalGroupMembership(tmpGroupMembership); |
562 |
> |
info->setGlobalGroupMembership(tmpGroupMembership); |
563 |
|
#else |
564 |
|
info->setGlobalGroupMembership(globalGroupMembership); |
565 |
|
#endif |
569 |
|
|
570 |
|
for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
571 |
|
|
572 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
573 |
< |
globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex(); |
574 |
< |
} |
572 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
573 |
> |
globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex(); |
574 |
> |
} |
575 |
|
} |
576 |
|
|
577 |
|
#ifdef IS_MPI |
585 |
|
info->setGlobalMolMembership(globalMolMembership); |
586 |
|
#endif |
587 |
|
|
588 |
< |
} |
588 |
> |
} |
589 |
|
|
590 |
< |
void SimCreator::loadCoordinates(SimInfo* info) { |
590 |
> |
void SimCreator::loadCoordinates(SimInfo* info) { |
591 |
|
Globals* simParams; |
592 |
|
simParams = info->getSimParams(); |
593 |
|
|
594 |
|
if (!simParams->haveInitialConfig()) { |
595 |
< |
sprintf(painCave.errMsg, |
596 |
< |
"Cannot intialize a simulation without an initial configuration file.\n"); |
597 |
< |
painCave.isFatal = 1;; |
598 |
< |
simError(); |
595 |
> |
sprintf(painCave.errMsg, |
596 |
> |
"Cannot intialize a simulation without an initial configuration file.\n"); |
597 |
> |
painCave.isFatal = 1;; |
598 |
> |
simError(); |
599 |
|
} |
600 |
|
|
601 |
|
DumpReader reader(info, simParams->getInitialConfig()); |
602 |
|
int nframes = reader.getNFrames(); |
603 |
|
|
604 |
|
if (nframes > 0) { |
605 |
< |
reader.readFrame(nframes - 1); |
605 |
> |
reader.readFrame(nframes - 1); |
606 |
|
} else { |
607 |
< |
//invalid initial coordinate file |
608 |
< |
sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n", |
609 |
< |
simParams->getInitialConfig()); |
610 |
< |
painCave.isFatal = 1; |
611 |
< |
simError(); |
607 |
> |
//invalid initial coordinate file |
608 |
> |
sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n", |
609 |
> |
simParams->getInitialConfig()); |
610 |
> |
painCave.isFatal = 1; |
611 |
> |
simError(); |
612 |
|
} |
613 |
|
|
614 |
|
//copy the current snapshot to previous snapshot |
615 |
|
info->getSnapshotManager()->advance(); |
616 |
< |
} |
616 |
> |
} |
617 |
|
|
618 |
|
} //end namespace oopse |
619 |
|
|