--- trunk/OOPSE/libmdtools/SimSetup.cpp	2003/09/25 19:27:15	787
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2003/10/30 18:59:20	845
@@ -1,10 +1,9 @@
 #include <algorithm>
-#include <cstdlib>
+#include <stdlib.h>
 #include <iostream>
-#include <cmath>
+#include <math.h>
 #include <string>
 #include <sprng.h> 
-
 #include "SimSetup.hpp"
 #include "ReadWrite.hpp"
 #include "parse_me.h"
@@ -22,7 +21,9 @@
 #define NVT_ENS        1
 #define NPTi_ENS       2
 #define NPTf_ENS       3
+#define NPTxyz_ENS     4
 
+
 #define FF_DUFF 0
 #define FF_LJ   1
 #define FF_EAM  2
@@ -30,6 +31,8 @@ SimSetup::SimSetup(){
 using namespace std;
 
 SimSetup::SimSetup(){
+  
+  initSuspend = false;
   isInfoArray = 0;
   nInfo = 1;
 
@@ -52,6 +55,7 @@ void SimSetup::setSimInfo(SimInfo* the_info, int theNi
   info = the_info;
   nInfo = theNinfo;
   isInfoArray = 1;
+  initSuspend = true;
 }
 
 
@@ -99,16 +103,19 @@ void SimSetup::createSim(void){
 
   sysObjectsCreation();
 
-  // check on the post processing info
-
-  finalInfoCheck();
-
   // initialize the system coordinates
 
-  if (!isInfoArray){
+  if ( !initSuspend ){
     initSystemCoords();
+
+    if( !(globals->getUseInitTime()) )
+      info[0].currentTime = 0.0;
   }  
+
+  // check on the post processing info
 
+  finalInfoCheck();
+
   // make the output filenames
 
   makeOutNames();
@@ -600,6 +607,9 @@ void SimSetup::gatherInfo(void){
   }
   else if (!strcasecmp(ensemble, "NPTf")){
     ensembleCase = NPTf_ENS;
+  }
+  else if (!strcasecmp(ensemble, "NPTxyz")){
+    ensembleCase = NPTxyz_ENS;
   }
   else{
     sprintf(painCave.errMsg,
@@ -686,58 +696,12 @@ void SimSetup::gatherInfo(void){
     }
 
     // check for the temperature set flag
-
+    
     if (globals->haveTempSet())
       info[i].setTemp = globals->getTempSet();
-
-    // get some of the tricky things that may still be in the globals
-
-    double boxVector[3];
-    if (globals->haveBox()){
-      boxVector[0] = globals->getBox();
-      boxVector[1] = globals->getBox();
-      boxVector[2] = globals->getBox();
-
-      info[i].setBox(boxVector);
-    }
-    else if (globals->haveDensity()){
-      double vol;
-      vol = (double) tot_nmol / globals->getDensity();
-      boxVector[0] = pow(vol, (1.0 / 3.0));
-      boxVector[1] = boxVector[0];
-      boxVector[2] = boxVector[0];
-
-      info[i].setBox(boxVector);
-    }
-    else{
-      if (!globals->haveBoxX()){
-        sprintf(painCave.errMsg,
-                "SimSetup error, no periodic BoxX size given.\n");
-        painCave.isFatal = 1;
-        simError();
-      }
-      boxVector[0] = globals->getBoxX();
-
-      if (!globals->haveBoxY()){
-        sprintf(painCave.errMsg,
-                "SimSetup error, no periodic BoxY size given.\n");
-        painCave.isFatal = 1;
-        simError();
-      }
-      boxVector[1] = globals->getBoxY();
-
-      if (!globals->haveBoxZ()){
-        sprintf(painCave.errMsg,
-                "SimSetup error, no periodic BoxZ size given.\n");
-        painCave.isFatal = 1;
-        simError();
-      }
-      boxVector[2] = globals->getBoxZ();
-
-      info[i].setBox(boxVector);
-    }
+    
   }
-
+  
   //setup seed for random number generator
   int seedValue;
 
@@ -841,7 +805,7 @@ void SimSetup::finalInfoCheck(void){
         theEst = globals->getEST();
       }
 
-      info[i].setEcr(theEcr, theEst);
+      info[i].setDefaultEcr(theEcr, theEst);
 
       if (!globals->haveDielectric()){
         sprintf(painCave.errMsg,
@@ -886,9 +850,10 @@ void SimSetup::finalInfoCheck(void){
           theEst = globals->getEST();
         }
 
-        info[i].setEcr(theEcr, theEst);
+        info[i].setDefaultEcr(theEcr, theEst);
       }
     }
+    info[i].checkCutOffs();
   }
 
 #ifdef IS_MPI
@@ -1346,6 +1311,7 @@ void SimSetup::makeIntegrator(void){
   NVT<RealIntegrator>* myNVT = NULL;
   NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
   NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
+  NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
   
   for (k = 0; k < nInfo; k++){
     switch (ensembleCase){
@@ -1449,6 +1415,7 @@ void SimSetup::makeIntegrator(void){
 
         if (globals->haveTauThermostat())
           myNPTf->setTauThermostat(globals->getTauThermostat());
+
         else{
           sprintf(painCave.errMsg,
                   "SimSetup error: If you use an NPT\n"
@@ -1459,6 +1426,7 @@ void SimSetup::makeIntegrator(void){
 
         if (globals->haveTauBarostat())
           myNPTf->setTauBarostat(globals->getTauBarostat());
+
         else{
           sprintf(painCave.errMsg,
                   "SimSetup error: If you use an NPT\n"
@@ -1470,6 +1438,49 @@ void SimSetup::makeIntegrator(void){
 	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;
+
       default:
         sprintf(painCave.errMsg,
                 "SimSetup Error. Unrecognized ensemble in case statement.\n");