--- trunk/OOPSE/libmdtools/SimSetup.cpp	2003/09/23 20:34:31	782
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2003/10/27 22:07:48	823
@@ -4,7 +4,6 @@
 #include <cmath>
 #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;
 }
 
 
@@ -90,7 +94,6 @@ void SimSetup::createSim(void){
 #endif // is_mpi
 
 void SimSetup::createSim(void){
-  int i, j, k, globalAtomIndex;
 
   // gather all of the information from the Bass file
 
@@ -106,8 +109,11 @@ void SimSetup::createSim(void){
 
   // initialize the system coordinates
 
-  if (!isInfoArray){
+  if ( !initSuspend ){
     initSystemCoords();
+
+    if( !(globals->getUseInitTime()) )
+      info[0].currentTime = 0.0;
   }  
 
   // make the output filenames
@@ -129,7 +135,7 @@ void SimSetup::makeMolecules(void){
 
 
 void SimSetup::makeMolecules(void){
-  int k, l;
+  int k;
   int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
   molInit molInfo;
   DirectionalAtom* dAtom;
@@ -551,7 +557,7 @@ void SimSetup::gatherInfo(void){
 
 
 void SimSetup::gatherInfo(void){
-  int i, j, k;
+  int i;
 
   ensembleCase = -1;
   ffCase = -1;
@@ -602,6 +608,9 @@ void SimSetup::gatherInfo(void){
   else if (!strcasecmp(ensemble, "NPTf")){
     ensembleCase = NPTf_ENS;
   }
+  else if (!strcasecmp(ensemble, "NPTxyz")){
+    ensembleCase = NPTxyz_ENS;
+  }
   else{
     sprintf(painCave.errMsg,
             "SimSetup Warning. Unrecognized Ensemble -> %s, "
@@ -914,7 +923,6 @@ void SimSetup::initSystemCoords(void){
     if (worldRank == 0){
 #endif //is_mpi
       inName = globals->getInitialConfig();
-      double* tempDouble = new double[1000000];
       fileInit = new InitializeFromFile(inName);
 #ifdef IS_MPI
     }
@@ -932,7 +940,7 @@ void SimSetup::initSystemCoords(void){
 
     sprintf(painCave.errMsg,
             "Cannot intialize a parallel simulation without an initial configuration file.\n");
-    painCave.isFatal;
+    painCave.isFatal = 1;;
     simError();
 
 #else
@@ -1158,7 +1166,7 @@ void SimSetup::calcSysValues(void){
 }
 
 void SimSetup::calcSysValues(void){
-  int i, j, k;
+  int i;
 
   int* molMembershipArray;
 
@@ -1257,7 +1265,11 @@ void SimSetup::makeSysArrays(void){
 
 
 void SimSetup::makeSysArrays(void){
-  int i, j, k, l;
+ 
+#ifndef IS_MPI
+  int k, j;
+#endif // is_mpi
+  int i, l;
 
   Atom** the_atoms;
   Molecule* the_molecules;
@@ -1344,6 +1356,7 @@ 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){
@@ -1466,6 +1479,49 @@ 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: