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/* |
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* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project |
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* |
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* Contact: oopse@oopse.org |
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* |
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* This program is free software; you can redistribute it and/or |
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* modify it under the terms of the GNU Lesser General Public License |
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* as published by the Free Software Foundation; either version 2.1 |
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* of the License, or (at your option) any later version. |
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* All we ask is that proper credit is given for our work, which includes |
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* - but is not limited to - adding the above copyright notice to the beginning |
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* of your source code files, and to any copyright notice that you may distribute |
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* with programs based on this work. |
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* |
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* This program is distributed in the hope that it will be useful, |
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* but WITHOUT ANY WARRANTY; without even the implied warranty of |
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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* GNU Lesser General Public License for more details. |
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* |
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* You should have received a copy of the GNU Lesser General Public License |
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* along with this program; if not, write to the Free Software |
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. |
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* |
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*/ |
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tim |
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/** |
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* @file SimCreator.cpp |
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* @author tlin |
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* @date 11/03/2004 |
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* @time 13:51am |
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* @version 1.0 |
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*/ |
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#include "brains/SimCreator.hpp" |
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namespace oopse { |
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void SimSetup::parseFile(char* mdfile, MakeStamps* stamps, Globals* globals){ |
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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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globals->initalize(); |
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set_interface_stamps(stamps, globals); |
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#ifdef IS_MPI |
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mpiEventInit(); |
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#endif |
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yacc_BASS(mdfile); |
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#ifdef IS_MPI |
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throwMPIEvent(NULL); |
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} |
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else{ |
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set_interface_stamps(stamps, globals); |
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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& mdfile) { |
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MakeStamps* stamps = new MakeStamps(); |
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Globals* globals = new Globals(); |
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//parse meta-data file |
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parseFile(mdfile, stamps, globals); |
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//create the force field |
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ForceFiled* ff = ForceFieldFactory::getInstance()->createObject(globals->getForceField()); |
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|
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//create SimInfo |
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SimInfo* info = new SimInfo(); |
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info->setGlobals(globals); |
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info->setForceField(ff); |
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//extract the molecule stamps and add them into SimInfo |
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compList(stamps, info); |
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|
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//gather parameters (SimCreator only retrieves the parameters which will be used to create |
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// the simulation) |
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gatherParameters(info); |
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|
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//divide the molecules and determine the global index of molecules |
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|
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//create the molecules |
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createMolecules(info); |
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|
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//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the |
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//global index will never change again). Local indices of atoms and rigidbodies are already set by |
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//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager. |
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setGlobalIndices(info); |
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//allocate memory for DataStorage(circular reference, need to break it) |
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info->setSnapshotManager(new SimSnapshotManager(info); |
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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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DumpReader reader(info->getInitFilename()); |
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int nframes = reader->getNframes(); |
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if (nframes > 0) { |
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reader.readFrame(info, nframes - 1); |
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} else { |
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//invalid initial coordinate file |
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} |
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//initialize fortran |
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return info; |
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} |
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void SimCreator::gatherParameters(SimInfo* info) { |
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//model->addProperty(new StringGenericData("Ensemble", globals->getForceFiled())); |
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//model->addProperty(new DoubleGenericData("dt"), globals->getDt()); |
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//setup seed for random number generator |
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int seedValue; |
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Globals* globals = info->getGlobals(); |
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if (globals->haveSeed()){ |
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seedValue = globals->getSeed(); |
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if(seedValue / 1000000000 == 0){ |
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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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painCave.isFatal = 0; |
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simError(); |
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//using seed generated by system instead of invalid seed set by user |
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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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MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
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#endif |
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} //end if (seedValue /1000000000 == 0) |
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} else{ |
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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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MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
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#endif |
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}//end of globals->haveSeed() |
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info->setSeed(seedValue); |
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// |
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std::string prefix; |
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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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if(globals->haveFinalConfig()) { |
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prefix = getPrefix(globals->getFinalConfig()); |
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} else { |
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prefix = getPrefix(mdfile_); |
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} |
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info->setFinalConfFileName(prefix + ".eor"); |
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info->setDumpFileName(prefix + ".dump"); |
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info->setStatFileName(prefix + ".stat"); |
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#ifdef IS_MPI |
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} |
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#endif |
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} |
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#ifdef IS_MPI |
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void SimCreator::divideMolecules(SimInfo* info){ |
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int nComponents; |
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MoleculeStamp ** compStamps; |
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randomSPRNG * myRandom; |
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int * componentsNmol; |
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int * AtomsPerProc; |
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double numerator; |
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double denominator; |
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double precast; |
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double x; |
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double y; |
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double a; |
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int old_atoms; |
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int add_atoms; |
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int new_atoms; |
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int nTarget; |
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int molIndex; |
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int atomIndex; |
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int done; |
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int i; |
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int j; |
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int loops; |
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int which_proc; |
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int nmol_global, |
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nmol_local; |
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int natoms_global, |
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int baseSeed = info->getSeed(); |
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CutoffGroupStamp * cg; |
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nComponents = info->nComponents; |
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compStamps = info->compStamps; |
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componentsNmol = info->componentsNmol; |
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AtomsPerProc = new int[parallelData->nProcessors]; |
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parallelData->nMolGlobal = info->n_mol; |
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if (parallelData->nProcessors > parallelData->nMolGlobal) { |
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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", |
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parallelData->nProcessors, |
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parallelData->nMolGlobal); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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myRandom = new randomSPRNG(baseSeed); |
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a = 3.0 * parallelData->nMolGlobal / parallelData->nAtomsGlobal; |
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// Initialize things that we'll send out later: |
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for( i = 0; i < parallelData->nProcessors; i++ ) { |
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AtomsPerProc[i] = 0; |
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} |
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for( i = 0; i < parallelData->nMolGlobal; i++ ) { |
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// default to an error condition: |
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MolToProcMap[i] = -1; |
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} |
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if (parallelData->myNode == 0) { |
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numerator = info->n_atoms; |
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denominator = parallelData->nProcessors; |
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precast = numerator / denominator; |
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nTarget = (int)(precast + 0.5); |
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// Build the array of molecule component types first |
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molIndex = 0; |
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for( i = 0; i < nComponents; i++ ) { |
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for( j = 0; j < componentsNmol[i]; j++ ) { |
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molIndex++; |
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} |
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} |
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for( i = 0; i < molIndex; i++ ) { |
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done = 0; |
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loops = 0; |
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while (!done) { |
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loops++; |
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// Pick a processor at random |
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which_proc |
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= (int) (myRandom->getRandom() * parallelData->nProcessors); |
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// How many atoms does this processor have? |
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old_atoms = AtomsPerProc[which_proc]; |
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add_atoms = compStamps[MolComponentType[i]]->getNAtoms(); |
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new_atoms = old_atoms + add_atoms; |
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// If we've been through this loop too many times, we need |
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// to just give up and assign the molecule to this processor |
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// and be done with it. |
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if (loops > 100) { |
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sprintf( |
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painCave.errMsg, |
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"I've tried 100 times to assign molecule %d to a " |
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" processor, but can't find a good spot.\n" |
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"I'm assigning it at random to processor %d.\n", |
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i, |
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which_proc); |
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painCave.isFatal = 0; |
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simError(); |
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MolToProcMap[i] = which_proc; |
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AtomsPerProc[which_proc] += add_atoms; |
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done = 1; |
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continue; |
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} |
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// If we can add this molecule to this processor without sending |
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// it above nTarget, then go ahead and do it: |
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if (new_atoms <= nTarget) { |
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MolToProcMap[i] = which_proc; |
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AtomsPerProc[which_proc] += add_atoms; |
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done = 1; |
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continue; |
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} |
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// The only situation left is when new_atoms > nTarget. We |
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// want to accept this with some probability that dies off the |
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// farther we are from nTarget |
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// roughly: x = new_atoms - nTarget |
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// Pacc(x) = exp(- a * x) |
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// where a = penalty / (average atoms per molecule) |
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x = (double)(new_atoms - nTarget); |
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y = myRandom->getRandom(); |
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if (y < exp(- a * x)) { |
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MolToProcMap[i] = which_proc; |
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AtomsPerProc[which_proc] += add_atoms; |
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done = 1; |
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continue; |
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} else { continue; } |
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} |
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} |
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// Spray out this nonsense to all other processors: |
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MPI_Bcast(MolToProcMap, parallelData->nMolGlobal, MPI_INT, 0, |
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MPI_COMM_WORLD); |
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} else { |
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// Listen to your marching orders from processor 0: |
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MPI_Bcast(MolToProcMap, parallelData->nMolGlobal, MPI_INT, 0, |
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MPI_COMM_WORLD); } |
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// Let's all check for sanity: |
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nmol_local = 0; |
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for( i = 0; i < parallelData->nMolGlobal; i++ ) { |
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if (MolToProcMap[i] == parallelData->myNode) { |
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nmol_local++; |
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} |
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} |
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MPI_Allreduce(&nmol_local, &nmol_global, 1, MPI_INT, MPI_SUM, |
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MPI_COMM_WORLD); |
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if (nmol_global != info->n_mol) { |
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sprintf(painCave.errMsg, |
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"The sum of all nmol_local, %d, did not equal the " |
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"total number of molecules, %d.\n", |
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nmol_global, |
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info->n_mol); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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sprintf(checkPointMsg, |
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"Successfully divided the molecules among the processors.\n"); |
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MPIcheckPoint(); |
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} |
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#endif |
384 |
tim |
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|
385 |
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1719 |
Molecule* SimCreator::createMolecules(SimInfo* info) { |
386 |
tim |
1725 |
MoleculeCreator molCreator; |
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int stampId; |
388 |
tim |
1713 |
|
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390 |
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for (int i = 0; i < info->getNGlobalMolecules(); i++){ |
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if (info->getMolToProc(i) == worldRank){ |
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stampId = info->getMoleculeStampId(i); |
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Molecule* mol = molCreator.createMolecule(info->getForceField(), |
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info->getMoleculeStamp(stampId), stampId, i); |
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info->addMolecule(mol); |
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} |
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} |
400 |
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tim |
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} |
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|
403 |
tim |
1719 |
void SimSetup::compList(MakeStamps* stamps,SimInfo* info) { |
404 |
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int i; |
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char* id; |
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MoleculeStamp* currentStamp; |
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|
Component* the_components = info->getGlobals()->getComponents(); |
408 |
|
|
int n_components = info->getGlobals()->getNComponents(); |
409 |
|
|
|
410 |
|
|
if (!globals->haveNMol()){ |
411 |
|
|
// we don't have the total number of molecules, so we assume it is |
412 |
|
|
// given in each component |
413 |
|
|
|
414 |
|
|
for (i = 0; i < n_components; i++){ |
415 |
|
|
if (!the_components[i]->haveNMol()){ |
416 |
|
|
// we have a problem |
417 |
|
|
sprintf(painCave.errMsg, |
418 |
|
|
"SimSetup Error. No global NMol or component NMol given.\n" |
419 |
|
|
"\tCannot calculate the number of atoms.\n"); |
420 |
|
|
painCave.isFatal = 1; |
421 |
|
|
simError(); |
422 |
|
|
} |
423 |
|
|
|
424 |
|
|
id = the_components[i]->getType(); |
425 |
|
|
currentStamp = stamps->extractMolStamp(id); |
426 |
|
|
if (currentStamp == NULL){ |
427 |
|
|
sprintf(painCave.errMsg, |
428 |
|
|
"SimSetup error: Component \"%s\" was not found in the " |
429 |
|
|
"list of declared molecules\n", |
430 |
|
|
id); |
431 |
|
|
painCave.isFatal = 1; |
432 |
|
|
simError(); |
433 |
|
|
} |
434 |
|
|
|
435 |
tim |
1725 |
info->addMoleculeStamp(currentStamp, the_components[i]->getNMol); |
436 |
tim |
1719 |
|
437 |
|
|
} //end for (i = 0; i < n_components; i++) |
438 |
|
|
|
439 |
|
|
} else{ |
440 |
|
|
sprintf(painCave.errMsg, |
441 |
|
|
"SimSetup error.\n" |
442 |
|
|
"\tSorry, the ability to specify total" |
443 |
|
|
" nMols and then give molfractions in the components\n" |
444 |
|
|
"\tis not currently supported." |
445 |
|
|
" Please give nMol in the components.\n"); |
446 |
|
|
painCave.isFatal = 1; |
447 |
|
|
simError(); |
448 |
|
|
} |
449 |
|
|
|
450 |
|
|
#ifdef IS_MPI |
451 |
|
|
strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
452 |
|
|
MPIcheckPoint(); |
453 |
|
|
#endif // is_mpi |
454 |
|
|
} |
455 |
|
|
|
456 |
tim |
1725 |
void SimCreator::setGlobalIndices(SimInfo* info) { |
457 |
|
|
typename SimInfo::MoleculeIterator mi; |
458 |
|
|
typename Molecule::AtomIterator ai; |
459 |
|
|
typename Molecule::RigidBodyIterator ri; |
460 |
|
|
typename Molecule::CutoffGroupIterator ci; |
461 |
|
|
Molecule* mol; |
462 |
|
|
Atom* atom; |
463 |
|
|
RigidBody* rb; |
464 |
|
|
CutoffGroup* cg; |
465 |
|
|
int beginAtomIndex; |
466 |
|
|
int beginRigidBodyIndex; |
467 |
|
|
int beginCutoffGroupIndex; |
468 |
tim |
1719 |
|
469 |
tim |
1725 |
#ifdef IS_MPI |
470 |
|
|
beginAtomIndex = 0; |
471 |
|
|
beginRigidBodyIndex = 0; |
472 |
|
|
beginCutoffGroupIndex = 0; |
473 |
|
|
#else |
474 |
|
|
int nproc; |
475 |
|
|
int myNode; |
476 |
|
|
|
477 |
|
|
myNode = worldRank; |
478 |
|
|
MPI_Comm_size(MPI_COMM_WORLD, &nproc); |
479 |
|
|
|
480 |
|
|
std::vector<int> tmpAtomsInProc(nproc, 0); |
481 |
|
|
std::vector<int> tmpRigidBodiesInProc(nproc, 0); |
482 |
|
|
std::vector<int> tmpCutoffGroupsInProc(nproc, 0); |
483 |
|
|
std::vector<int> NumAtomsInProc(nproc, 0); |
484 |
|
|
std::vector<int> NumRigidBodiesInProc(nproc, 0); |
485 |
|
|
std::vector<int> NumCutoffGroupsInProc(nproc, 0); |
486 |
|
|
|
487 |
|
|
tmpAtomInProc[myNode] = info->getNAtoms(); |
488 |
|
|
tmpRigidBodiesInProc[myNode] = info->getNRigidBodiess(); |
489 |
|
|
tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroupss(); |
490 |
|
|
|
491 |
|
|
//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups |
492 |
|
|
MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
493 |
|
|
MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
494 |
|
|
MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
495 |
|
|
|
496 |
|
|
beginAtomIndex = 0; |
497 |
|
|
beginRigidBodyIndex = 0; |
498 |
|
|
beginCutoffGroupIndex = 0; |
499 |
|
|
|
500 |
|
|
for (int i = 0; i < nproc; i++) { |
501 |
|
|
beginAtomIndex += NumAtomsInProc[i]; |
502 |
|
|
beginRigidBodyIndex += NumRigidBodiesInProc[i]; |
503 |
|
|
beginCutoffGroupIndex += NumCutoffGroupsInProc[i]; |
504 |
|
|
} |
505 |
|
|
|
506 |
|
|
#endif |
507 |
|
|
|
508 |
|
|
for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
509 |
|
|
|
510 |
|
|
//local index(index in DataStorge) of atom is important |
511 |
|
|
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
512 |
|
|
atom->setGlobalIndex(beginAtomIndex++); |
513 |
|
|
} |
514 |
|
|
|
515 |
|
|
for (rb = mol->beginRigidBody(ri); rb != NULL; rb = mol->nextRigidBody(ri)) { |
516 |
|
|
rb->setGlobalIndex(beginRigidBodyIndex++); |
517 |
|
|
} |
518 |
|
|
|
519 |
|
|
//local index of cutoff group is trivial, it only depends on the order of travesing |
520 |
|
|
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
521 |
|
|
cg->setGlobalIndex(beginCutoffGroupIndex++); |
522 |
|
|
} |
523 |
|
|
|
524 |
|
|
} |
525 |
|
|
} |
526 |
|
|
|
527 |
tim |
1703 |
} //end namespace oopse |