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Comparing branches/new_design/OOPSE-2.0/src/brains/SimCreator.cpp (file contents):
Revision 1840 by tim, Thu Dec 2 16:04:19 2004 UTC vs.
Revision 1841 by tim, Fri Dec 3 17:59:45 2004 UTC

# Line 47 | Line 47 | void SimCreator::parseFile(const std::string mdFileNam
47  
48   namespace oopse {
49  
50 < void SimCreator::parseFile(const std::string mdFileName,  MakeStamps* stamps, Globals* globals){
50 > void SimCreator::parseFile(const std::string mdFileName,  MakeStamps* stamps, Globals* simParams){
51  
52   #ifdef IS_MPI
53  
54      if (worldRank == 0) {
55   #endif // is_mpi
56  
57 <        globals->initalize();
58 <        set_interface_stamps(stamps, globals);
57 >        simParams->initalize();
58 >        set_interface_stamps(stamps, simParams);
59  
60   #ifdef IS_MPI
61  
# Line 69 | Line 69 | void SimCreator::parseFile(const std::string mdFileNam
69  
70          throwMPIEvent(NULL);
71      } else {
72 <        set_interface_stamps(stamps, globals);
72 >        set_interface_stamps(stamps, simParams);
73          mpiEventInit();
74          MPIcheckPoint();
75          mpiEventLoop();
# Line 83 | Line 83 | SimInfo*  SimCreator::createSim(const std::string & md
83      
84      MakeStamps * stamps = new MakeStamps();
85  
86 <    Globals * globals = new Globals();
86 >    Globals * simParams = new Globals();
87  
88      //parse meta-data file
89 <    parseFile(mdFileName, stamps, globals);
89 >    parseFile(mdFileName, stamps, simParams);
90  
91      //create the force field
92      ForceField * ff = ForceFieldFactory::getInstance()->createForceField(
93 <                          globals->getForceField());
93 >                          simParams->getForceField());
94      
95      if (ff == NULL) {
96          sprintf(painCave.errMsg, "ForceField Factory can not create %s force field\n",
97 <                globals->getForceField());
97 >                simParams->getForceField());
98          painCave.isFatal = 1;
99          simError();
100      }
# Line 102 | Line 102 | SimInfo*  SimCreator::createSim(const std::string & md
102      std::string forcefieldFileName;
103      forcefieldFileName = ff->getForceFieldFileName();
104  
105 <    if (globals->haveForceFieldVariant()) {
105 >    if (simParams->haveForceFieldVariant()) {
106          //If the force field has variant, the variant force field name will be
107          //Base.variant.frc. For exampel EAM.u6.frc
108          
109 <        std::string variant = globals->getForceFieldVariant();
109 >        std::string variant = simParams->getForceFieldVariant();
110  
111          std::string::size_type pos = forcefieldFileName.rfind(".frc");
112          variant = "." + variant;
# Line 122 | Line 122 | SimInfo*  SimCreator::createSim(const std::string & md
122      
123      //extract the molecule stamps
124      std::vector < std::pair<MoleculeStamp *, int> > moleculeStampPairs;
125 <    compList(stamps, globals, moleculeStampPairs);
125 >    compList(stamps, simParams, moleculeStampPairs);
126  
127      //create SimInfo
128 <    SimInfo * info = new SimInfo(moleculeStampPairs, ff, globals);
128 >    SimInfo * info = new SimInfo(moleculeStampPairs, ff, simParams);
129  
130      //gather parameters (SimCreator only retrieves part of the parameters)
131      gatherParameters(info, mdFileName);
# Line 159 | Line 159 | void SimCreator::gatherParameters(SimInfo *info, const
159  
160      //setup seed for random number generator
161      int seedValue;
162 <    Globals * globals = info->getGlobals();
162 >    Globals * simParams = info->getSimParams();
163  
164 <    if (globals->haveSeed()) {
165 <        seedValue = globals->getSeed();
164 >    if (simParams->haveSeed()) {
165 >        seedValue = simParams->getSeed();
166  
167          if (seedValue / 1000000000 == 0) {
168              sprintf(painCave.errMsg,
# Line 205 | Line 205 | void SimCreator::gatherParameters(SimInfo *info, const
205  
206   #endif
207  
208 <    } //end of globals->haveSeed()
208 >    } //end of simParams->haveSeed()
209  
210      info->setSeed(seedValue);
211  
# Line 218 | Line 218 | void SimCreator::gatherParameters(SimInfo *info, const
218      if (worldRank == 0) {
219   #endif // is_mpi
220  
221 <        if (globals->haveFinalConfig()) {
222 <            prefix = getPrefix(globals->getFinalConfig());
221 >        if (simParams->haveFinalConfig()) {
222 >            prefix = getPrefix(simParams->getFinalConfig());
223          } else {
224              prefix = getPrefix(mdfile);
225          }
# Line 409 | Line 409 | void SimCreator::compList(MakeStamps *stamps, Globals*
409      } //end for(int i=0)  
410   }
411  
412 < void SimCreator::compList(MakeStamps *stamps, Globals* globals,
412 > void SimCreator::compList(MakeStamps *stamps, Globals* simParams,
413                          std::vector < std::pair<MoleculeStamp *, int> > &moleculeStampPairs) {
414      int i;
415      char * id;
416      MoleculeStamp * currentStamp;
417 <    Component** the_components = globals->getComponents();
418 <    int n_components = globals->getNComponents();
417 >    Component** the_components = simParams->getComponents();
418 >    int n_components = simParams->getNComponents();
419  
420 <    if (!globals->haveNMol()) {
420 >    if (!simParams->haveNMol()) {
421          // we don't have the total number of molecules, so we assume it is
422          // given in each component
423  
# Line 596 | Line 596 | void SimCreator::loadCoordinates(SimInfo* info) {
596   }
597  
598   void SimCreator::loadCoordinates(SimInfo* info) {
599 <    Globals* globals;
600 <    globals = info->getGlobals();
599 >    Globals* simParams;
600 >    simParams = info->getSimParams();
601      
602 <    if (!globals->haveInitialConfig()) {
602 >    if (!simParams->haveInitialConfig()) {
603          sprintf(painCave.errMsg,
604                  "Cannot intialize a simulation without an initial configuration file.\n");
605          painCave.isFatal = 1;;
606          simError();
607      }
608          
609 <    DumpReader reader(info, globals->getInitialConfig());
609 >    DumpReader reader(info, simParams->getInitialConfig());
610      int nframes = reader.getNFrames();
611  
612      if (nframes > 0) {
# Line 614 | Line 614 | void SimCreator::loadCoordinates(SimInfo* info) {
614      } else {
615          //invalid initial coordinate file
616          sprintf(painCave.errMsg, "Initial configuration file %s should at least contain one frame\n",
617 <                globals->getInitialConfig());
617 >                simParams->getInitialConfig());
618          painCave.isFatal = 1;
619          simError();
620      }

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