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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 780 by mmeineke, Mon Sep 22 21:23:25 2003 UTC vs.
Revision 811 by mmeineke, Tue Oct 21 19:33:19 2003 UTC

# Line 90 | Line 90 | void SimSetup::createSim(void){
90   #endif // is_mpi
91  
92   void SimSetup::createSim(void){
93 –  int i, j, k, globalAtomIndex;
93  
94    // gather all of the information from the Bass file
95  
# Line 108 | Line 107 | void SimSetup::createSim(void){
107  
108    if (!isInfoArray){
109      initSystemCoords();
110 +
111 +    if( !(globals->getUseInitTime()) )
112 +      info[0].currentTime = 0.0;
113    }  
114  
115    // make the output filenames
# Line 129 | Line 131 | void SimSetup::makeMolecules(void){
131  
132  
133   void SimSetup::makeMolecules(void){
134 <  int k, l;
134 >  int k;
135    int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
136    molInit molInfo;
137    DirectionalAtom* dAtom;
# Line 551 | Line 553 | void SimSetup::gatherInfo(void){
553  
554  
555   void SimSetup::gatherInfo(void){
556 <  int i, j, k;
556 >  int i;
557  
558    ensembleCase = -1;
559    ffCase = -1;
# Line 914 | Line 916 | void SimSetup::initSystemCoords(void){
916      if (worldRank == 0){
917   #endif //is_mpi
918        inName = globals->getInitialConfig();
917 –      double* tempDouble = new double[1000000];
919        fileInit = new InitializeFromFile(inName);
920   #ifdef IS_MPI
921      }
# Line 932 | Line 933 | void SimSetup::initSystemCoords(void){
933  
934      sprintf(painCave.errMsg,
935              "Cannot intialize a parallel simulation without an initial configuration file.\n");
936 <    painCave.isFatal;
936 >    painCave.isFatal = 1;;
937      simError();
938  
939   #else
# Line 1158 | Line 1159 | void SimSetup::calcSysValues(void){
1159   }
1160  
1161   void SimSetup::calcSysValues(void){
1162 <  int i, j, k;
1162 >  int i;
1163  
1164    int* molMembershipArray;
1165  
# Line 1257 | Line 1258 | void SimSetup::makeSysArrays(void){
1258  
1259  
1260   void SimSetup::makeSysArrays(void){
1261 <  int i, j, k, l;
1261 >
1262 > #ifndef IS_MPI
1263 >  int k, j;
1264 > #endif // is_mpi
1265 >  int i, l;
1266  
1267    Atom** the_atoms;
1268    Molecule* the_molecules;
# Line 1340 | Line 1345 | void SimSetup::makeIntegrator(void){
1345   void SimSetup::makeIntegrator(void){
1346    int k;
1347  
1348 +  NVE<RealIntegrator>* myNVE = NULL;
1349    NVT<RealIntegrator>* myNVT = NULL;
1350    NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1351    NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
# Line 1349 | Line 1355 | void SimSetup::makeIntegrator(void){
1355        case NVE_ENS:
1356          if (globals->haveZconstraints()){
1357            setupZConstraint(info[k]);
1358 <          new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1358 >          myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1359          }
1360 <        else
1361 <          new NVE<RealIntegrator>(&(info[k]), the_ff);
1360 >        else{
1361 >          myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1362 >        }
1363 >        
1364 >        info->the_integrator = myNVE;
1365          break;
1366  
1367        case NVT_ENS:
# Line 1374 | Line 1383 | void SimSetup::makeIntegrator(void){
1383            painCave.isFatal = 1;
1384            simError();
1385          }
1386 +
1387 +        info->the_integrator = myNVT;
1388          break;
1389  
1390        case NPTi_ENS:
# Line 1415 | Line 1426 | void SimSetup::makeIntegrator(void){
1426            painCave.isFatal = 1;
1427            simError();
1428          }
1429 +
1430 +        info->the_integrator = myNPTi;
1431          break;
1432  
1433        case NPTf_ENS:
# Line 1456 | Line 1469 | void SimSetup::makeIntegrator(void){
1469            painCave.isFatal = 1;
1470            simError();
1471          }
1472 +
1473 +        info->the_integrator = myNPTf;
1474          break;
1475  
1476        default:

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