--- branches/new-templateless/OOPSE/libmdtools/SimSetup.cpp	2003/10/31 21:06:47	849
+++ branches/new-templateless/OOPSE/libmdtools/SimSetup.cpp	2003/11/05 19:18:17	851
@@ -1,9 +1,9 @@
-#include <algorithm>
 #include <stdlib.h>
 #include <iostream>
 #include <math.h>
-#include <string>
+#include <string.h>
 #include <sprng.h> 
+
 #include "SimSetup.hpp"
 #include "ReadWrite.hpp"
 #include "parse_me.h"
@@ -1324,175 +1324,184 @@ void SimSetup::makeIntegrator(void){
 	// 	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
       }
       
-//       else{
-	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
-//       }
-	
-	info->the_integrator = myNVE;
-        break;
-	
+      //       else{
+      myNVE = new NVE(&(info[k]), the_ff);
+      //       }
+      
+      info->the_integrator = myNVE;
+      break;
+      
     case NVT_ENS:
+      if (globals->haveZconstraints()){
+	
+	std::cerr << "ZConstraint is temporarily disabled\n";
+	
+	// 	setupZConstraint(info[k]);
+	// 	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
+      }
+      // else
+      myNVT = new NVT(&(info[k]), the_ff);
+      
+      myNVT->setTargetTemp(globals->getTargetTemp());
+      
+      if (globals->haveTauThermostat())
+	myNVT->setTauThermostat(globals->getTauThermostat());
+      else{
+	sprintf(painCave.errMsg,
+		"SimSetup error: If you use the NVT\n"
+		"    ensemble, you must set tauThermostat.\n");
+	painCave.isFatal = 1;
+	simError();
+      }
+      
+      info->the_integrator = myNVT;
+      break;
+      
+    case NPTi_ENS:
       if (globals->haveZconstraints()){
+	
+	std::cerr << "ZConstraint is temporarily disabled\n";
+	
+	// 	  setupZConstraint(info[k]);
+	//           myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
+      }
+      // else
+      myNPTi = new NPTi(&(info[k]), the_ff);
+      
+      myNPTi->setTargetTemp(globals->getTargetTemp());
+      
+      if (globals->haveTargetPressure())
+	myNPTi->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())
+	myNPTi->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())
+	myNPTi->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 = myNPTi;
+      break;
+      
+    case NPTf_ENS:
+      if (globals->haveZconstraints()){
 
 	std::cerr << "ZConstraint is temporarily disabled\n";
 
 // 	setupZConstraint(info[k]);
-// 	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
+// 	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
       }
-        else
-          myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
-
-        myNVT->setTargetTemp(globals->getTargetTemp());
-
-        if (globals->haveTauThermostat())
-          myNVT->setTauThermostat(globals->getTauThermostat());
-        else{
-          sprintf(painCave.errMsg,
-                  "SimSetup error: If you use the NVT\n"
-                  "    ensemble, you must set tauThermostat.\n");
-          painCave.isFatal = 1;
-          simError();
-        }
-
-	info->the_integrator = myNVT;
-        break;
-
-      case NPTi_ENS:
-        if (globals->haveZconstraints()){
-          setupZConstraint(info[k]);
-          myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
-        }
-        else
-          myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
-
-        myNPTi->setTargetTemp(globals->getTargetTemp());
-
-        if (globals->haveTargetPressure())
-          myNPTi->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())
-          myNPTi->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())
-          myNPTi->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 = myNPTi;
-        break;
-
-      case NPTf_ENS:
-        if (globals->haveZconstraints()){
-          setupZConstraint(info[k]);
-          myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
-        }
-        else
-          myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
-
-        myNPTf->setTargetTemp(globals->getTargetTemp());
-
-        if (globals->haveTargetPressure())
-          myNPTf->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())
-          myNPTf->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())
-          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();
-        }
-
-	info->the_integrator = myNPTf;
-        break;
-
-      case NPTxyz_ENS:
-        if (globals->haveZconstraints()){
-          setupZConstraint(info[k]);
-          myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
-        }
-        else
-          myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
-
-        myNPTxyz->setTargetTemp(globals->getTargetTemp());
-
-        if (globals->haveTargetPressure())
-          myNPTxyz->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())
-          myNPTxyz->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())
-          myNPTxyz->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 = myNPTxyz;
-        break;
+//       else
+      myNPTf = new NPTf(&(info[k]), the_ff);
+      
+      myNPTf->setTargetTemp(globals->getTargetTemp());
+      
+      if (globals->haveTargetPressure())
+	myNPTf->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())
+	myNPTf->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())
+	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();
+      }
+      
+      info->the_integrator = myNPTf;
+      break;
+      
+    case NPTxyz_ENS:
+      if (globals->haveZconstraints()){
+	
+	std::cerr << "ZConstraint is temporarily disabled\n";
+	
+	// 	setupZConstraint(info[k]);
+	// 	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
+      }
+//       else
+      myNPTxyz = new NPTxyz(&(info[k]), the_ff);
 
-      default:
-        sprintf(painCave.errMsg,
-                "SimSetup Error. Unrecognized ensemble in case statement.\n");
-        painCave.isFatal = 1;
-        simError();
+      myNPTxyz->setTargetTemp(globals->getTargetTemp());
+      
+      if (globals->haveTargetPressure())
+	myNPTxyz->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())
+	myNPTxyz->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())
+	myNPTxyz->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 = myNPTxyz;
+      break;
+      
+    default:
+      sprintf(painCave.errMsg,
+	      "SimSetup Error. Unrecognized ensemble in case statement.\n");
+      painCave.isFatal = 1;
+      simError();
     }
   }
 }
@@ -1520,107 +1529,107 @@ void SimSetup::initFortran(void){
 #endif // is_mpi
 }
 
-void SimSetup::setupZConstraint(SimInfo& theInfo){
-  int nZConstraints;
-  ZconStamp** zconStamp;
+// void SimSetup::setupZConstraint(SimInfo& theInfo){
+//   int nZConstraints;
+//   ZconStamp** zconStamp;
 
-  if (globals->haveZconstraintTime()){
-    //add sample time of z-constraint  into SimInfo's property list                    
-    DoubleData* zconsTimeProp = new DoubleData();
-    zconsTimeProp->setID(ZCONSTIME_ID);
-    zconsTimeProp->setData(globals->getZconsTime());
-    theInfo.addProperty(zconsTimeProp);
-  }
-  else{
-    sprintf(painCave.errMsg,
-            "ZConstraint error: If you use an ZConstraint\n"
-            " , you must set sample time.\n");
-    painCave.isFatal = 1;
-    simError();
-  }
+//   if (globals->haveZconstraintTime()){
+//     //add sample time of z-constraint  into SimInfo's property list                    
+//     DoubleData* zconsTimeProp = new DoubleData();
+//     zconsTimeProp->setID(ZCONSTIME_ID);
+//     zconsTimeProp->setData(globals->getZconsTime());
+//     theInfo.addProperty(zconsTimeProp);
+//   }
+//   else{
+//     sprintf(painCave.errMsg,
+//             "ZConstraint error: If you use an ZConstraint\n"
+//             " , you must set sample time.\n");
+//     painCave.isFatal = 1;
+//     simError();
+//   }
 
-  //push zconsTol into siminfo, if user does not specify
-  //value for zconsTol, a default value will be used
-  DoubleData* zconsTol = new DoubleData();
-  zconsTol->setID(ZCONSTOL_ID);
-  if (globals->haveZconsTol()){
-    zconsTol->setData(globals->getZconsTol());
-  }
-  else{
-    double defaultZConsTol = 0.01;
-    sprintf(painCave.errMsg,
-            "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
-            " , default value %f is used.\n",
-            defaultZConsTol);
-    painCave.isFatal = 0;
-    simError();      
+//   //push zconsTol into siminfo, if user does not specify
+//   //value for zconsTol, a default value will be used
+//   DoubleData* zconsTol = new DoubleData();
+//   zconsTol->setID(ZCONSTOL_ID);
+//   if (globals->haveZconsTol()){
+//     zconsTol->setData(globals->getZconsTol());
+//   }
+//   else{
+//     double defaultZConsTol = 0.01;
+//     sprintf(painCave.errMsg,
+//             "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
+//             " , default value %f is used.\n",
+//             defaultZConsTol);
+//     painCave.isFatal = 0;
+//     simError();      
 
-    zconsTol->setData(defaultZConsTol);
-  }
-  theInfo.addProperty(zconsTol);
+//     zconsTol->setData(defaultZConsTol);
+//   }
+//   theInfo.addProperty(zconsTol);
 
-  //set Force Subtraction Policy
-  StringData* zconsForcePolicy = new StringData();
-  zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
+//   //set Force Subtraction Policy
+//   StringData* zconsForcePolicy = new StringData();
+//   zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
 
-  if (globals->haveZconsForcePolicy()){
-    zconsForcePolicy->setData(globals->getZconsForcePolicy());
-  }
-  else{
-    sprintf(painCave.errMsg,
-            "ZConstraint Warning: User does not set force Subtraction policy, "
-            "PolicyByMass is used\n");
-    painCave.isFatal = 0;
-    simError(); 
-    zconsForcePolicy->setData("BYMASS");
-  }
+//   if (globals->haveZconsForcePolicy()){
+//     zconsForcePolicy->setData(globals->getZconsForcePolicy());
+//   }
+//   else{
+//     sprintf(painCave.errMsg,
+//             "ZConstraint Warning: User does not set force Subtraction policy, "
+//             "PolicyByMass is used\n");
+//     painCave.isFatal = 0;
+//     simError(); 
+//     zconsForcePolicy->setData("BYMASS");
+//   }
 
-  theInfo.addProperty(zconsForcePolicy);
+//   theInfo.addProperty(zconsForcePolicy);
 
-  //Determine the name of ouput file and add it into SimInfo's property list 
-  //Be careful, do not use inFileName, since it is a pointer which
-  //point to a string at master node, and slave nodes do not contain that string
+//   //Determine the name of ouput file and add it into SimInfo's property list 
+//   //Be careful, do not use inFileName, since it is a pointer which
+//   //point to a string at master node, and slave nodes do not contain that string
 
-  string zconsOutput(theInfo.finalName);
+//   string zconsOutput(theInfo.finalName);
 
-  zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
+//   zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
 
-  StringData* zconsFilename = new StringData();
-  zconsFilename->setID(ZCONSFILENAME_ID);
-  zconsFilename->setData(zconsOutput);
+//   StringData* zconsFilename = new StringData();
+//   zconsFilename->setID(ZCONSFILENAME_ID);
+//   zconsFilename->setData(zconsOutput);
 
-  theInfo.addProperty(zconsFilename);
+//   theInfo.addProperty(zconsFilename);
 
-  //setup index, pos and other parameters of z-constraint molecules
-  nZConstraints = globals->getNzConstraints();
-  theInfo.nZconstraints = nZConstraints;
+//   //setup index, pos and other parameters of z-constraint molecules
+//   nZConstraints = globals->getNzConstraints();
+//   theInfo.nZconstraints = nZConstraints;
 
-  zconStamp = globals->getZconStamp();
-  ZConsParaItem tempParaItem;
+//   zconStamp = globals->getZconStamp();
+//   ZConsParaItem tempParaItem;
 
-  ZConsParaData* zconsParaData = new ZConsParaData();
-  zconsParaData->setID(ZCONSPARADATA_ID);
+//   ZConsParaData* zconsParaData = new ZConsParaData();
+//   zconsParaData->setID(ZCONSPARADATA_ID);
 
-  for (int i = 0; i < nZConstraints; i++){
-    tempParaItem.havingZPos = zconStamp[i]->haveZpos();
-    tempParaItem.zPos = zconStamp[i]->getZpos();
-    tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
-    tempParaItem.kRatio = zconStamp[i]->getKratio();
+//   for (int i = 0; i < nZConstraints; i++){
+//     tempParaItem.havingZPos = zconStamp[i]->haveZpos();
+//     tempParaItem.zPos = zconStamp[i]->getZpos();
+//     tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
+//     tempParaItem.kRatio = zconStamp[i]->getKratio();
 
-    zconsParaData->addItem(tempParaItem);
-  }
+//     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(); 
-  }
+//   //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();
+//   //sort the parameters by index of molecules
+//   zconsParaData->sortByIndex();
   
-  //push data into siminfo, therefore, we can retrieve later
-  theInfo.addProperty(zconsParaData);
-}
+//   //push data into siminfo, therefore, we can retrieve later
+//   theInfo.addProperty(zconsParaData);
+// }