--- trunk/OOPSE/libmdtools/SimInfo.cpp	2003/08/07 21:47:18	670
+++ trunk/OOPSE/libmdtools/SimInfo.cpp	2003/09/19 14:55:41	770
@@ -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;
@@ -362,7 +366,7 @@ int SimInfo::getNDF(){
   ndf = ndf_local;
 #endif
 
-  ndf = ndf - 3;
+  ndf = ndf - 3 - nZconstraints;
 
   return ndf;
 }
@@ -381,7 +385,23 @@ int SimInfo::getNDFraw() {
 
   return ndfRaw;
 }
- 
+
+int SimInfo::getNDFtranslational() {
+  int ndfTrans_local, ndfTrans;
+
+  ndfTrans_local = 3 * n_atoms - n_constraints;
+
+#ifdef IS_MPI
+  MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
+#else
+  ndfTrans = ndfTrans_local;
+#endif
+
+  ndfTrans = ndfTrans - 3 - nZconstraints;
+
+  return ndfTrans;
+}
+
 void SimInfo::refreshSim(){
 
   simtype fInfo;
@@ -437,7 +457,7 @@ void SimInfo::refreshSim(){
 
   this->ndf = this->getNDF();
   this->ndfRaw = this->getNDFraw();
-
+  this->ndfTrans = this->getNDFtranslational();
 }
 
 
@@ -473,13 +493,11 @@ void SimInfo::checkCutOffs( void ){
 void SimInfo::checkCutOffs( void ){
 
   int cutChanged = 0;
-
-
-
+  
   if( boxIsInit ){
     
     //we need to check cutOffs against the box
-   
+    
     if(( maxCutoff > rCut )&&(usePBC)){
       if( rCut < origRcut ){
 	rCut = origRcut;
@@ -487,65 +505,70 @@ void SimInfo::checkCutOffs( void ){
 	
 	sprintf( painCave.errMsg,
 		 "New Box size is setting the long range cutoff radius "
-		 "to %lf\n",
-		 rCut );
+		 "to %lf at time %lf\n",
+		 rCut, currentTime );
 	painCave.isFatal = 0;
 	simError();
       }
     }
-
+    
     if( maxCutoff > ecr ){
       if( ecr < origEcr ){
-	rCut = origEcr;
+	ecr = origEcr;
 	if (ecr > maxCutoff) ecr = maxCutoff;
 	
 	sprintf( painCave.errMsg,
 		 "New Box size is setting the electrostaticCutoffRadius "
-		 "to %lf\n",
-		 ecr );
+		 "to %lf at time %lf\n",
+		 ecr, currentTime );
 	painCave.isFatal = 0;
 	simError();
       }
     }
-
-
+    
+    
     if ((rCut > maxCutoff)&&(usePBC)) {
       sprintf( painCave.errMsg,
                "New Box size is setting the long range cutoff radius "
-	       "to %lf\n",
-               maxCutoff );
+	       "to %lf at time %lf\n",
+               maxCutoff, currentTime );
       painCave.isFatal = 0;
       simError();
       rCut = maxCutoff;
     }
-
+    
     if( ecr > maxCutoff){
       sprintf( painCave.errMsg,
                "New Box size is setting the electrostaticCutoffRadius "
-               "to %lf\n",
-               maxCutoff  );
+               "to %lf at time %lf\n",
+               maxCutoff, currentTime  );
       painCave.isFatal = 0;
       simError();      
       ecr = maxCutoff;
     }
 
+    if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
     
-  }
-   
-
-  if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1;
-
-  // rlist is the 1.0 plus max( rcut, ecr )
-  
-  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
-
-  if( cutChanged ){
+    // rlist is the 1.0 plus max( rcut, ecr )
     
-    notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
+    ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
+    
+    if( cutChanged ){
+      
+      notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
+    }
+    
+    oldEcr = ecr;
+    oldRcut = rCut;
+    
+  } else {
+    // initialize this stuff before using it, OK?
+    sprintf( painCave.errMsg,
+             "Trying to check cutoffs without a box. Be smarter.\n" );
+    painCave.isFatal = 1;
+    simError();      
   }
-
-  oldEcr = ecr;
-  oldRcut = rCut;
+  
 }
 
 void SimInfo::addProperty(GenericData* prop){
@@ -595,4 +618,9 @@ 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;
+}