--- trunk/OOPSE/libmdtools/SimInfo.cpp	2003/07/21 16:23:57	642
+++ trunk/OOPSE/libmdtools/SimInfo.cpp	2003/09/16 20:02:11	767
@@ -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;
@@ -54,9 +58,23 @@ 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]) {
   
   int i, j;
@@ -292,6 +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();
 
 }
 
@@ -346,7 +366,7 @@ int SimInfo::getNDF(){
   ndf = ndf_local;
 #endif
 
-  ndf = ndf - 3;
+  ndf = ndf - 3 - nZconstraints;
 
   return ndf;
 }
@@ -365,7 +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;
@@ -421,7 +457,7 @@ void SimInfo::refreshSim(){
 
   this->ndf = this->getNDF();
   this->ndfRaw = this->getNDFraw();
-
+  this->ndfTrans = this->getNDFtranslational();
 }
 
 
@@ -458,11 +494,13 @@ 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;
@@ -478,7 +516,7 @@ void SimInfo::checkCutOffs( void ){
 
     if( maxCutoff > ecr ){
       if( ecr < origEcr ){
-	rCut = origEcr;
+	ecr = origEcr;
 	if (ecr > maxCutoff) ecr = maxCutoff;
 	
 	sprintf( painCave.errMsg,
@@ -491,7 +529,7 @@ 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",
@@ -511,21 +549,81 @@ void SimInfo::checkCutOffs( void ){
       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){
+
+  map<string, GenericData*>::iterator result;
+  result = properties.find(prop->getID());
+  
+  //we can't simply use  properties[prop->getID()] = prop,
+  //it will cause memory leak if we already contain a propery which has the same name of prop
+  
+  if(result != properties.end()){
+    
+    delete (*result).second;
+    (*result).second = prop;
+      
+  }
+  else{
+
+    properties[prop->getID()] = prop;
+
+  }
+    
+}
+
+GenericData* SimInfo::getProperty(const string& propName){
+ 
+  map<string, GenericData*>::iterator result;
+  
+  //string lowerCaseName = ();
+  
+  result = properties.find(propName);
+  
+  if(result != properties.end()) 
+    return (*result).second;  
+  else   
+    return NULL;  
+}
+
+vector<GenericData*> SimInfo::getProperties(){
+
+  vector<GenericData*> result;
+  map<string, GenericData*>::iterator i;
+  
+  for(i = properties.begin(); i != properties.end(); i++)
+    result.push_back((*i).second);
+    
+  return result;
+}
+
+double SimInfo::matTrace3(double m[3][3]){
+  double trace;
+  trace = m[0][0] + m[1][1] + m[2][2];
+
+  return trace;
+}