--- trunk/OOPSE/libmdtools/SimInfo.cpp	2003/03/24 18:33:51	393
+++ trunk/OOPSE/libmdtools/SimInfo.cpp	2003/04/04 19:47:19	458
@@ -16,9 +16,12 @@ SimInfo::SimInfo(){
   n_constraints = 0;
   n_oriented = 0;
   n_dipoles = 0;
+  ndf = 0;
+  ndfRaw = 0;
   the_integrator = NULL;
   setTemp = 0;
   thermalTime = 0.0;
+  rCut = 0.0;
 
   usePBC = 0;
   useLJ = 0; 
@@ -28,15 +31,58 @@ SimInfo::SimInfo(){
   useGB = 0;
   useEAM = 0;
 
+  wrapMeSimInfo( this );
+}
 
+void SimInfo::setBox(double newBox[3]) {
+  box_x = newBox[0];
+  box_y = newBox[1];
+  box_z = newBox[2];
+  setFortranBoxSize(newBox);
+}
 
-  wrapMeSimInfo( this );
+void SimInfo::getBox(double theBox[3]) {
+  theBox[0] = box_x;
+  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.box[0] = box_x;
   fInfo.box[1] = box_y;
@@ -44,34 +90,37 @@ void SimInfo::refreshSim(){
 
   fInfo.rlist = rList;
   fInfo.rcut = rCut;
-  fInfo.rrf = rRF;
-  fInfo.rt = 0.95 * rRF;
+  fInfo.rrf = ecr;
+  fInfo.rt = ecr - est;
   fInfo.dielect = dielectric;
- 
 
   fInfo.SIM_uses_PBC = usePBC;
+  //fInfo.SIM_uses_LJ = 0;
   fInfo.SIM_uses_LJ = useLJ;
   fInfo.SIM_uses_sticky = useSticky;
-  fInfo.SIM_uses_dipoles = 0;
-  //  fInfo.SIM_uses_dipoles = useDipole;
+  //fInfo.SIM_uses_sticky = 0;
+  fInfo.SIM_uses_dipoles = useDipole;
+  //fInfo.SIM_uses_dipoles = 0;
+  //fInfo.SIM_uses_RF = useReactionField;
   fInfo.SIM_uses_RF = 0;
-  //  fInfo.SIM_uses_RF = useReactionField;
   fInfo.SIM_uses_GB = useGB;
   fInfo.SIM_uses_EAM = useEAM;
 
+  excl = Exclude::getArray();
 
   isError = 0;
 
-  fInfo;
-  n_atoms; 
-  identArray;
-  n_exclude;
-  excludes;
-  nGlobalExcludes;
-  globalExcludes;
-  isError;
+//   fInfo;
+//   n_atoms; 
+//   identArray;
+//   n_exclude;
+//   excludes;
+//   nGlobalExcludes;
+//   globalExcludes;
+//   isError;
 
-  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excludes, &nGlobalExcludes, globalExcludes, &isError );
+  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excl, 
+		  &nGlobalExcludes, globalExcludes, &isError );
 
   if( isError ){
 
@@ -86,5 +135,9 @@ void SimInfo::refreshSim(){
 	   "succesfully sent the simulation information to fortran.\n");
   MPIcheckPoint();
 #endif // is_mpi
+
+  ndf = this->getNDF();
+  ndfRaw = this->getNDFraw();
+
 }