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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 787 by mmeineke, Thu Sep 25 19:27:15 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 129 | Line 128 | void SimSetup::makeMolecules(void){
128  
129  
130   void SimSetup::makeMolecules(void){
131 <  int k, l;
131 >  int k;
132    int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
133    molInit molInfo;
134    DirectionalAtom* dAtom;
# Line 551 | Line 550 | void SimSetup::gatherInfo(void){
550  
551  
552   void SimSetup::gatherInfo(void){
553 <  int i, j, k;
553 >  int i;
554  
555    ensembleCase = -1;
556    ffCase = -1;
# Line 914 | Line 913 | void SimSetup::initSystemCoords(void){
913      if (worldRank == 0){
914   #endif //is_mpi
915        inName = globals->getInitialConfig();
917 –      double* tempDouble = new double[1000000];
916        fileInit = new InitializeFromFile(inName);
917   #ifdef IS_MPI
918      }
# Line 932 | Line 930 | void SimSetup::initSystemCoords(void){
930  
931      sprintf(painCave.errMsg,
932              "Cannot intialize a parallel simulation without an initial configuration file.\n");
933 <    painCave.isFatal;
933 >    painCave.isFatal = 1;;
934      simError();
935  
936   #else
# Line 1158 | Line 1156 | void SimSetup::calcSysValues(void){
1156   }
1157  
1158   void SimSetup::calcSysValues(void){
1159 <  int i, j, k;
1159 >  int i;
1160  
1161    int* molMembershipArray;
1162  
# Line 1257 | Line 1255 | void SimSetup::makeSysArrays(void){
1255  
1256  
1257   void SimSetup::makeSysArrays(void){
1258 <  int i, j, k, l;
1258 >
1259 > #ifndef IS_MPI
1260 >  int k, j;
1261 > #endif // is_mpi
1262 >  int i, l;
1263  
1264    Atom** the_atoms;
1265    Molecule* the_molecules;
# Line 1340 | Line 1342 | void SimSetup::makeIntegrator(void){
1342   void SimSetup::makeIntegrator(void){
1343    int k;
1344  
1345 +  NVE<RealIntegrator>* myNVE = NULL;
1346    NVT<RealIntegrator>* myNVT = NULL;
1347    NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1348    NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
# Line 1349 | Line 1352 | void SimSetup::makeIntegrator(void){
1352        case NVE_ENS:
1353          if (globals->haveZconstraints()){
1354            setupZConstraint(info[k]);
1355 <          new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1355 >          myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1356          }
1357 <        else
1358 <          new NVE<RealIntegrator>(&(info[k]), the_ff);
1357 >        else{
1358 >          myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1359 >        }
1360 >        
1361 >        info->the_integrator = myNVE;
1362          break;
1363  
1364        case NVT_ENS:
# Line 1374 | Line 1380 | void SimSetup::makeIntegrator(void){
1380            painCave.isFatal = 1;
1381            simError();
1382          }
1383 +
1384 +        info->the_integrator = myNVT;
1385          break;
1386  
1387        case NPTi_ENS:
# Line 1415 | Line 1423 | void SimSetup::makeIntegrator(void){
1423            painCave.isFatal = 1;
1424            simError();
1425          }
1426 +
1427 +        info->the_integrator = myNPTi;
1428          break;
1429  
1430        case NPTf_ENS:
# Line 1456 | Line 1466 | void SimSetup::makeIntegrator(void){
1466            painCave.isFatal = 1;
1467            simError();
1468          }
1469 +
1470 +        info->the_integrator = myNPTf;
1471          break;
1472  
1473        default:

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