--- trunk/OOPSE/libmdtools/SimInfo.cpp	2003/04/04 19:16:11	457
+++ trunk/OOPSE/libmdtools/SimInfo.cpp	2003/04/08 22:38:43	482
@@ -16,6 +16,8 @@ SimInfo::SimInfo(){
   n_constraints = 0;
   n_oriented = 0;
   n_dipoles = 0;
+  ndf = 0;
+  ndfRaw = 0;
   the_integrator = NULL;
   setTemp = 0;
   thermalTime = 0.0;
@@ -33,10 +35,56 @@ void SimInfo::setBox(double newBox[3]) {
 }
 
 void SimInfo::setBox(double newBox[3]) {
+  double smallestBox, maxCutoff;
+  int status;
   box_x = newBox[0];
   box_y = newBox[1];
   box_z = newBox[2];
   setFortranBoxSize(newBox);
+
+  smallestBox = box_x;
+  if (box_y < smallestBox) smallestBox = box_y;
+  if (box_z < smallestBox) smallestBox = box_z;
+
+  maxCutoff = smallestBox / 2.0;
+
+  if (rList > maxCutoff) {
+    sprintf( painCave.errMsg,
+             "New Box size is forcing neighborlist radius down to %lf\n",
+             maxCutoff );
+    painCave.isFatal = 0;
+    simError();
+
+    rList = maxCutoff;
+
+    sprintf( painCave.errMsg,
+             "New Box size is forcing cutoff radius down to %lf\n",
+             maxCutoff - 1.0 );
+    painCave.isFatal = 0;
+    simError();
+
+    rCut = rList - 1.0;
+
+    // list radius changed so we have to refresh the simulation structure.
+    refreshSim();
+  }
+
+  if (rCut > maxCutoff) {
+    sprintf( painCave.errMsg,
+             "New Box size is forcing cutoff radius down to %lf\n",
+             maxCutoff );
+    painCave.isFatal = 0;
+    simError();
+
+    status = 0;
+    LJ_new_rcut(&rCut, &status);
+    if (status != 0) {
+      sprintf( painCave.errMsg,
+               "Error in recomputing LJ shifts based on new rcut\n");
+      painCave.isFatal = 1;
+      simError();
+    }
+  }
 }
 
 void SimInfo::getBox(double theBox[3]) {
@@ -44,12 +92,47 @@ void SimInfo::getBox(double theBox[3]) {
   theBox[1] = box_y;
   theBox[2] = box_z;
 }
+ 
+int SimInfo::getNDF(){
+  int ndf_local, ndf;
   
+  ndf_local = 3 * n_atoms + 3 * n_oriented - n_constraints;
+
+#ifdef IS_MPI
+  MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
+#else
+  ndf = ndf_local;
+#endif
+
+  ndf = ndf - 3;
+
+  return ndf;
+}
+
+int SimInfo::getNDFraw() {
+  int ndfRaw_local, ndfRaw;
+
+  // Raw degrees of freedom that we have to set
+  ndfRaw_local = 3 * n_atoms + 3 * n_oriented;
+  
+#ifdef IS_MPI
+  MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
+#else
+  ndfRaw = ndfRaw_local;
+#endif
+
+  return ndfRaw;
+}
+ 
 void SimInfo::refreshSim(){
 
   simtype fInfo;
   int isError;
   int* excl;
+  
+  fInfo.rrf = 0.0;
+  fInfo.rt = 0.0;
+  fInfo.dielect = 0.0;
 
   fInfo.box[0] = box_x;
   fInfo.box[1] = box_y;
@@ -57,10 +140,13 @@ void SimInfo::refreshSim(){
 
   fInfo.rlist = rList;
   fInfo.rcut = rCut;
-  fInfo.rrf = ecr;
-  fInfo.rt = ecr - est;
-  fInfo.dielect = dielectric;
 
+  if( useDipole ){
+    fInfo.rrf = ecr;
+    fInfo.rt = ecr - est;
+    if( useReactionField )fInfo.dielect = dielectric;
+  }
+
   fInfo.SIM_uses_PBC = usePBC;
   //fInfo.SIM_uses_LJ = 0;
   fInfo.SIM_uses_LJ = useLJ;
@@ -102,5 +188,9 @@ void SimInfo::refreshSim(){
 	   "succesfully sent the simulation information to fortran.\n");
   MPIcheckPoint();
 #endif // is_mpi
+
+  this->ndf = this->getNDF();
+  this->ndfRaw = this->getNDFraw();
+
 }