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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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/** |
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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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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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//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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//create the molecules |
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createMolecules(info); |
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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::mpiMolDivide(){ |
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mpiSim = new mpiSimulation(info); |
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mpiSim->divideLabor(); |
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} |
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#endif |
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Molecule* SimCreator::createMolecules(SimInfo* info) { |
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MoleculeCreator molCreator; |
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int stampId; |
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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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} |
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} |
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void SimSetup::compList(MakeStamps* stamps,SimInfo* info) { |
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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(); |
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int n_components = info->getGlobals()->getNComponents(); |
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if (!globals->haveNMol()){ |
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// we don't have the total number of molecules, so we assume it is |
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// given in each component |
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for (i = 0; i < n_components; i++){ |
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if (!the_components[i]->haveNMol()){ |
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// we have a problem |
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sprintf(painCave.errMsg, |
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"SimSetup Error. No global NMol or component NMol given.\n" |
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"\tCannot calculate the number of atoms.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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id = the_components[i]->getType(); |
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currentStamp = stamps->extractMolStamp(id); |
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if (currentStamp == NULL){ |
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sprintf(painCave.errMsg, |
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"SimSetup error: Component \"%s\" was not found in the " |
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"list of declared molecules\n", |
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id); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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info->addMoleculeStamp(currentStamp, the_components[i]->getNMol); |
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} //end for (i = 0; i < n_components; i++) |
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} else{ |
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sprintf(painCave.errMsg, |
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"SimSetup error.\n" |
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"\tSorry, the ability to specify total" |
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" nMols and then give molfractions in the components\n" |
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"\tis not currently supported." |
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" Please give nMol in the components.\n"); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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#ifdef IS_MPI |
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strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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} |
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void SimCreator::setGlobalIndices(SimInfo* info) { |
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typename SimInfo::MoleculeIterator mi; |
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typename Molecule::AtomIterator ai; |
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typename Molecule::RigidBodyIterator ri; |
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typename Molecule::CutoffGroupIterator ci; |
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Molecule* mol; |
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Atom* atom; |
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RigidBody* rb; |
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CutoffGroup* cg; |
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int beginAtomIndex; |
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int beginRigidBodyIndex; |
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int beginCutoffGroupIndex; |
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#ifdef IS_MPI |
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beginAtomIndex = 0; |
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beginRigidBodyIndex = 0; |
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beginCutoffGroupIndex = 0; |
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#else |
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int nproc; |
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int myNode; |
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myNode = worldRank; |
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MPI_Comm_size(MPI_COMM_WORLD, &nproc); |
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std::vector<int> tmpAtomsInProc(nproc, 0); |
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std::vector<int> tmpRigidBodiesInProc(nproc, 0); |
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std::vector<int> tmpCutoffGroupsInProc(nproc, 0); |
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std::vector<int> NumAtomsInProc(nproc, 0); |
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std::vector<int> NumRigidBodiesInProc(nproc, 0); |
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std::vector<int> NumCutoffGroupsInProc(nproc, 0); |
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tmpAtomInProc[myNode] = info->getNAtoms(); |
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tmpRigidBodiesInProc[myNode] = info->getNRigidBodiess(); |
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tmpCutoffGroupsInProc[myNode] = info->getNCutoffGroupss(); |
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//do MPI_ALLREDUCE to exchange the total number of atoms, rigidbodies and cutoff groups |
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MPI_Allreduce(&tmpAtomsInProc[0], &NumAtomsInProc[0], nproc, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
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MPI_Allreduce(&tmpRigidBodiesInProc[0], &NumRigidBodiesInProc[0], nproc, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
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MPI_Allreduce(&tmpCutoffGroupsInProc[0], &NumCutoffGroupsInProc[0], nproc, MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
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beginAtomIndex = 0; |
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beginRigidBodyIndex = 0; |
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beginCutoffGroupIndex = 0; |
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for (int i = 0; i < nproc; i++) { |
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beginAtomIndex += NumAtomsInProc[i]; |
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beginRigidBodyIndex += NumRigidBodiesInProc[i]; |
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beginCutoffGroupIndex += NumCutoffGroupsInProc[i]; |
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} |
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#endif |
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for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
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//local index(index in DataStorge) of atom is important |
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for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
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atom->setGlobalIndex(beginAtomIndex++); |
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} |
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for (rb = mol->beginRigidBody(ri); rb != NULL; rb = mol->nextRigidBody(ri)) { |
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rb->setGlobalIndex(beginRigidBodyIndex++); |
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} |
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//local index of cutoff group is trivial, it only depends on the order of travesing |
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for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
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cg->setGlobalIndex(beginCutoffGroupIndex++); |
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} |
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} |
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} |
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} //end namespace oopse |