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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()->createForceField(globals->getForceField()); |
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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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//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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//allocate memory for DataStorage(circular reference, need to break it) |
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info->setSnapshotManager(new SimSnapshotManager(info); |
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//load initial coordinates |
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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(SimModel* model) { |
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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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} |
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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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strcpy(checkPointMsg, "Passed nlocal consistency check."); |
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MPIcheckPoint(); |
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} |
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#endif |
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Molecule* SimCreator::createMolecules(SimInfo* info) { |
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for (i = 0; i < mpiSim->getNMolGlobal(); i++){ |
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if (mol2proc[i] == worldRank){ |
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Molecule* mol = MoleculeCreator.createMolecule(molStamp, stampID, globalIndex); |
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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.moleculeStamps.push_back(make_pair(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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} //end namespace oopse |