--- trunk/OOPSE/libmdtools/SimInfo.cpp	2003/07/31 19:59:34	660
+++ trunk/OOPSE/libmdtools/SimInfo.cpp	2003/09/15 16:52:02	763
@@ -26,16 +26,20 @@ SimInfo::SimInfo(){
 SimInfo::SimInfo(){
   excludes = NULL;
   n_constraints = 0;
+  nZconstraints = 0;
   n_oriented = 0;
   n_dipoles = 0;
   ndf = 0;
   ndfRaw = 0;
+  nZconstraints = 0;
   the_integrator = NULL;
   setTemp = 0;
   thermalTime = 0.0;
   currentTime = 0.0;
   rCut = 0.0;
+  origRcut = -1.0;
   ecr = 0.0;
+  origEcr = -1.0;
   est = 0.0;
   oldEcr = 0.0;
   oldRcut = 0.0;
@@ -54,17 +58,21 @@ SimInfo::SimInfo(){
   useGB = 0;
   useEAM = 0;
 
+  myConfiguration = new SimState();
+
   wrapMeSimInfo( this );
 }
+
 
 SimInfo::~SimInfo(){
 
+  delete myConfiguration;
+
   map<string, GenericData*>::iterator i;
   
   for(i = properties.begin(); i != properties.end(); i++)
     delete (*i).second;
-
-  
+    
 }
 
 void SimInfo::setBox(double newBox[3]) {
@@ -302,6 +310,8 @@ void SimInfo::calcBoxL( void ){
   dsq = dx*dx + dy*dy + dz*dz;
   boxL[2] = sqrt( dsq );
   if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2];
+  
+  checkCutOffs();
 
 }
 
@@ -356,7 +366,7 @@ int SimInfo::getNDF(){
   ndf = ndf_local;
 #endif
 
-  ndf = ndf - 3;
+  ndf = ndf - 3 - nZconstraints;
 
   return ndf;
 }
@@ -468,11 +478,13 @@ void SimInfo::checkCutOffs( void ){
 
   int cutChanged = 0;
 
+
+
   if( boxIsInit ){
     
     //we need to check cutOffs against the box
-    
-    if( maxCutoff > rCut ){
+   
+    if(( maxCutoff > rCut )&&(usePBC)){
       if( rCut < origRcut ){
 	rCut = origRcut;
 	if (rCut > maxCutoff) rCut = maxCutoff;
@@ -501,7 +513,7 @@ void SimInfo::checkCutOffs( void ){
     }
 
 
-    if (rCut > maxCutoff) {
+    if ((rCut > maxCutoff)&&(usePBC)) {
       sprintf( painCave.errMsg,
                "New Box size is setting the long range cutoff radius "
 	       "to %lf\n",
@@ -587,4 +599,9 @@ vector<GenericData*> SimInfo::getProperties(){
   return result;
 }
 
+double SimInfo::matTrace3(double m[3][3]){
+  double trace;
+  trace = m[0][0] + m[1][1] + m[2][2];
 
+  return trace;
+}