--- trunk/OOPSE/libmdtools/SimInfo.cpp	2003/03/21 17:42:12	378
+++ trunk/OOPSE/libmdtools/SimInfo.cpp	2003/04/11 15:16:59	490
@@ -9,6 +9,10 @@
 
 #include "fortranWrappers.hpp"
 
+#ifdef IS_MPI
+#include "mpiSimulation.hpp"
+#endif
+
 SimInfo* currentInfo;
 
 SimInfo::SimInfo(){
@@ -16,9 +20,12 @@ 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 +35,109 @@ SimInfo::SimInfo(){
   useGB = 0;
   useEAM = 0;
 
+  wrapMeSimInfo( this );
+}
 
+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);
 
-  wrapMeSimInfo( this );
+  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]) {
+  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 n_global;
+  int* excl;
+  
+  fInfo.rrf = 0.0;
+  fInfo.rt = 0.0;
+  fInfo.dielect = 0.0;
 
   fInfo.box[0] = box_x;
   fInfo.box[1] = box_y;
@@ -44,33 +145,39 @@ void SimInfo::refreshSim(){
 
   fInfo.rlist = rList;
   fInfo.rcut = rCut;
-  fInfo.rrf = rRF;
-  fInfo.rt = 0.95 * rRF;
-  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;
   fInfo.SIM_uses_sticky = useSticky;
+  //fInfo.SIM_uses_sticky = 0;
   fInfo.SIM_uses_dipoles = useDipole;
-  fInfo.SIM_uses_RF = useReactionField;
+  //fInfo.SIM_uses_dipoles = 0;
+  //fInfo.SIM_uses_RF = useReactionField;
+  fInfo.SIM_uses_RF = 0;
   fInfo.SIM_uses_GB = useGB;
   fInfo.SIM_uses_EAM = useEAM;
 
+  excl = Exclude::getArray();
 
+#ifdef IS_MPI
+  n_global = mpiSim->getTotAtoms();
+#else
+  n_global = n_atoms;
+#endif
+
   isError = 0;
 
-  fInfo;
-  n_atoms; 
-  identArray;
-  n_exclude;
-  excludes;
-  nGlobalExcludes;
-  globalExcludes;
-  isError;
+  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, 
+		  &nGlobalExcludes, globalExcludes, molMembershipArray, 
+                  &isError );
 
-  setFsimulation( &fInfo, &n_atoms, identArray, &n_exclude, excludes, &nGlobalExcludes, globalExcludes, &isError );
-
   if( isError ){
 
     sprintf( painCave.errMsg,
@@ -84,5 +191,9 @@ void SimInfo::refreshSim(){
 	   "succesfully sent the simulation information to fortran.\n");
   MPIcheckPoint();
 #endif // is_mpi
+
+  this->ndf = this->getNDF();
+  this->ndfRaw = this->getNDFraw();
+
 }