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root/OpenMD/trunk/src/brains/SimCreator.cpp
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Comparing trunk/src/brains/SimCreator.cpp (file contents):
Revision 417 by chrisfen, Thu Mar 10 15:10:24 2005 UTC vs.
Revision 749 by tim, Wed Nov 16 23:10:02 2005 UTC

# Line 71 | Line 71 | namespace oopse {
71      if (worldRank == 0) {
72   #endif // is_mpi
73        
74 –      simParams->initalize();
74        set_interface_stamps(stamps, simParams);
75        
76   #ifdef IS_MPI
# Line 96 | Line 95 | namespace oopse {
95      
96    }
97    
98 <  SimInfo*  SimCreator::createSim(const std::string & mdFileName, bool loadInitCoords) {
98 >  SimInfo*  SimCreator::createSim(const std::string & mdFileName,
99 >                                  bool loadInitCoords) {
100      
101      MakeStamps * stamps = new MakeStamps();
102      
# Line 106 | Line 106 | namespace oopse {
106      parseFile(mdFileName, stamps, simParams);
107      
108      //create the force field
109 <    ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
110 <                                                                         simParams->getForceField());
109 >    ForceField * ff = ForceFieldFactory::getInstance()
110 >      ->createForceField(simParams->getForceField());
111      
112      if (ff == NULL) {
113 <      sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
114 <              simParams->getForceField());
113 >      sprintf(painCave.errMsg,
114 >              "ForceField Factory can not create %s force field\n",
115 >              simParams->getForceField().c_str());
116        painCave.isFatal = 1;
117        simError();
118      }
# Line 146 | Line 147 | namespace oopse {
147      compList(stamps, simParams, moleculeStampPairs);
148      
149      //create SimInfo
150 <    SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
151 <    
150 >    SimInfo * info = new SimInfo(stamps, moleculeStampPairs, ff, simParams);
151 >    
152      //gather parameters (SimCreator only retrieves part of the parameters)
153      gatherParameters(info, mdFileName);
154      
# Line 178 | Line 179 | namespace oopse {
179        info->addExcludePairs(mol);
180      }
181      
181 –    
182 –    //load initial coordinates, some extra information are pushed into SimInfo's property map ( such as
183 –    //eta, chi for NPT integrator)
182      if (loadInitCoords)
183        loadCoordinates(info);    
184      
# Line 189 | Line 187 | namespace oopse {
187    
188    void SimCreator::gatherParameters(SimInfo *info, const std::string& mdfile) {
189      
190 <    //figure out the ouput file names
190 >    //figure out the output file names
191      std::string prefix;
192      
193   #ifdef IS_MPI
# Line 400 | Line 398 | namespace oopse {
398                              std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
399      int i;
400      char * id;
403 –    LinkedMolStamp* extractedStamp = NULL;
401      MoleculeStamp * currentStamp;
402      Component** the_components = simParams->getComponents();
403      int n_components = simParams->getNComponents();
# Line 421 | Line 418 | namespace oopse {
418          }
419          
420          id = the_components[i]->getType();
421 <        
422 <        extractedStamp = stamps->extractMolStamp(id);
423 <        if (extractedStamp == NULL) {
421 >
422 >        currentStamp = stamps->getMolStamp(id);
423 >        if (currentStamp == NULL) {
424            sprintf(painCave.errMsg,
425                    "SimCreator error: Component \"%s\" was not found in the "
426                    "list of declared molecules\n", id);
# Line 432 | Line 429 | namespace oopse {
429            simError();
430          }
431          
435 –        currentStamp = extractedStamp->getStamp();
436 –        
437 –        
432          moleculeStampPairs.push_back(
433                                       std::make_pair(currentStamp, the_components[i]->getNMol()));
434        } //end for (i = 0; i < n_components; i++)
# Line 609 | Line 603 | namespace oopse {
603        //invalid initial coordinate file
604        sprintf(painCave.errMsg,
605                "Initial configuration file %s should at least contain one frame\n",
606 <              simParams->getInitialConfig());
606 >              simParams->getInitialConfig().c_str());
607        painCave.isFatal = 1;
608        simError();
609      }

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