--- trunk/OOPSE/libmdtools/SimSetup.cpp	2003/08/26 20:02:29	722
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2003/09/23 20:34:31	782
@@ -22,8 +22,6 @@
 #define NVT_ENS        1
 #define NPTi_ENS       2
 #define NPTf_ENS       3
-#define NPTim_ENS      4
-#define NPTfm_ENS      5
 
 #define FF_DUFF 0
 #define FF_LJ   1
@@ -604,12 +602,6 @@ void SimSetup::gatherInfo(void){
   else if (!strcasecmp(ensemble, "NPTf")){
     ensembleCase = NPTf_ENS;
   }
-  else if (!strcasecmp(ensemble, "NPTim")){
-    ensembleCase = NPTim_ENS;
-  }
-  else if (!strcasecmp(ensemble, "NPTfm")){
-    ensembleCase = NPTfm_ENS;
-  }
   else{
     sprintf(painCave.errMsg,
             "SimSetup Warning. Unrecognized Ensemble -> %s, "
@@ -688,6 +680,12 @@ void SimSetup::gatherInfo(void){
       info[i].thermalTime = globals->getThermalTime();
     }
 
+    info[i].resetIntegrator = 0;
+    if( globals->haveResetTime() ){
+      info[i].resetTime = globals->getResetTime();
+      info[i].resetIntegrator = 1;
+    }
+
     // check for the temperature set flag
 
     if (globals->haveTempSet())
@@ -1342,21 +1340,23 @@ void SimSetup::makeIntegrator(void){
 void SimSetup::makeIntegrator(void){
   int k;
 
+  NVE<RealIntegrator>* myNVE = NULL;
   NVT<RealIntegrator>* myNVT = NULL;
-  NPTi<RealIntegrator>* myNPTi = NULL;
-  NPTf<RealIntegrator>* myNPTf = NULL;
-  NPTim<RealIntegrator>* myNPTim = NULL;
-  NPTfm<RealIntegrator>* myNPTfm = NULL;
-
+  NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
+  NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
+  
   for (k = 0; k < nInfo; k++){
     switch (ensembleCase){
       case NVE_ENS:
         if (globals->haveZconstraints()){
           setupZConstraint(info[k]);
-          new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
+          myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
         }
-        else
-          new NVE<RealIntegrator>(&(info[k]), the_ff);
+        else{
+          myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
+	}
+	
+	info->the_integrator = myNVE;
         break;
 
       case NVT_ENS:
@@ -1378,15 +1378,17 @@ void SimSetup::makeIntegrator(void){
           painCave.isFatal = 1;
           simError();
         }
+
+	info->the_integrator = myNVT;
         break;
 
       case NPTi_ENS:
         if (globals->haveZconstraints()){
           setupZConstraint(info[k]);
-          myNPTi = new ZConstraint<NPTi<RealIntegrator> >(&(info[k]), the_ff);
+          myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
         }
         else
-          myNPTi = new NPTi<RealIntegrator>(&(info[k]), the_ff);
+          myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
 
         myNPTi->setTargetTemp(globals->getTargetTemp());
 
@@ -1419,15 +1421,17 @@ void SimSetup::makeIntegrator(void){
           painCave.isFatal = 1;
           simError();
         }
+
+	info->the_integrator = myNPTi;
         break;
 
       case NPTf_ENS:
         if (globals->haveZconstraints()){
           setupZConstraint(info[k]);
-          myNPTf = new ZConstraint<NPTf<RealIntegrator> >(&(info[k]), the_ff);
+          myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
         }
         else
-          myNPTf = new NPTf<RealIntegrator>(&(info[k]), the_ff);
+          myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
 
         myNPTf->setTargetTemp(globals->getTargetTemp());
 
@@ -1453,95 +1457,15 @@ void SimSetup::makeIntegrator(void){
 
         if (globals->haveTauBarostat())
           myNPTf->setTauBarostat(globals->getTauBarostat());
-        else{
-          sprintf(painCave.errMsg,
-                  "SimSetup error: If you use an NPT\n"
-                  "    ensemble, you must set tauBarostat.\n");
-          painCave.isFatal = 1;
-          simError();
-        }
-        break;
-
-      case NPTim_ENS:
-        if (globals->haveZconstraints()){
-          setupZConstraint(info[k]);
-          myNPTim = new ZConstraint<NPTim<RealIntegrator> >(&(info[k]), the_ff);
-        }
-        else
-          myNPTim = new NPTim<RealIntegrator>(&(info[k]), the_ff);
-
-        myNPTim->setTargetTemp(globals->getTargetTemp());
-
-        if (globals->haveTargetPressure())
-          myNPTim->setTargetPressure(globals->getTargetPressure());
-        else{
-          sprintf(painCave.errMsg,
-                  "SimSetup error: If you use a constant pressure\n"
-                  "    ensemble, you must set targetPressure in the BASS file.\n");
-          painCave.isFatal = 1;
-          simError();
-        }
-
-        if (globals->haveTauThermostat())
-          myNPTim->setTauThermostat(globals->getTauThermostat());
         else{
           sprintf(painCave.errMsg,
                   "SimSetup error: If you use an NPT\n"
-                  "    ensemble, you must set tauThermostat.\n");
-          painCave.isFatal = 1;
-          simError();
-        }
-
-        if (globals->haveTauBarostat())
-          myNPTim->setTauBarostat(globals->getTauBarostat());
-        else{
-          sprintf(painCave.errMsg,
-                  "SimSetup error: If you use an NPT\n"
                   "    ensemble, you must set tauBarostat.\n");
           painCave.isFatal = 1;
           simError();
         }
-        break;
 
-      case NPTfm_ENS:
-        if (globals->haveZconstraints()){
-          setupZConstraint(info[k]);
-          myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >(&(info[k]), the_ff);
-        }
-        else
-          myNPTfm = new NPTfm<RealIntegrator>(&(info[k]), the_ff);
-
-        myNPTfm->setTargetTemp(globals->getTargetTemp());
-
-        if (globals->haveTargetPressure())
-          myNPTfm->setTargetPressure(globals->getTargetPressure());
-        else{
-          sprintf(painCave.errMsg,
-                  "SimSetup error: If you use a constant pressure\n"
-                  "    ensemble, you must set targetPressure in the BASS file.\n");
-          painCave.isFatal = 1;
-          simError();
-        }
-
-        if (globals->haveTauThermostat())
-          myNPTfm->setTauThermostat(globals->getTauThermostat());
-        else{
-          sprintf(painCave.errMsg,
-                  "SimSetup error: If you use an NPT\n"
-                  "    ensemble, you must set tauThermostat.\n");
-          painCave.isFatal = 1;
-          simError();
-        }
-
-        if (globals->haveTauBarostat())
-          myNPTfm->setTauBarostat(globals->getTauBarostat());
-        else{
-          sprintf(painCave.errMsg,
-                  "SimSetup error: If you use an NPT\n"
-                  "    ensemble, you must set tauBarostat.\n");
-          painCave.isFatal = 1;
-          simError();
-        }
+	info->the_integrator = myNPTf;
         break;
 
       default:
@@ -1615,7 +1539,7 @@ void SimSetup::setupZConstraint(SimInfo& theInfo){
   }
   theInfo.addProperty(zconsTol);
 
-  //set Force Substraction Policy
+  //set Force Subtraction Policy
   StringData* zconsForcePolicy = new StringData();
   zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
 
@@ -1624,11 +1548,11 @@ void SimSetup::setupZConstraint(SimInfo& theInfo){
   }
   else{
     sprintf(painCave.errMsg,
-            "ZConstraint Warning: User does not set force substraction policy, "
-            "average force substraction policy is used\n");
+            "ZConstraint Warning: User does not set force Subtraction policy, "
+            "PolicyByMass is used\n");
     painCave.isFatal = 0;
     simError(); 
-    zconsForcePolicy->setData("BYNUMBER");
+    zconsForcePolicy->setData("BYMASS");
   }
 
   theInfo.addProperty(zconsForcePolicy);
@@ -1666,9 +1590,17 @@ void SimSetup::setupZConstraint(SimInfo& theInfo){
     zconsParaData->addItem(tempParaItem);
   }
 
+  //check the uniqueness of index  
+  if(!zconsParaData->isIndexUnique()){
+    sprintf(painCave.errMsg,
+            "ZConstraint Error: molIndex is not unique\n");
+    painCave.isFatal = 1;
+    simError(); 
+  }
+
   //sort the parameters by index of molecules
   zconsParaData->sortByIndex();
-
+  
   //push data into siminfo, therefore, we can retrieve later
   theInfo.addProperty(zconsParaData);
 }