--- trunk/OOPSE/libmdtools/Thermo.cpp	2003/03/26 15:37:05	403
+++ trunk/OOPSE/libmdtools/Thermo.cpp	2003/04/03 13:43:02	444
@@ -10,6 +10,7 @@ using namespace std;
 #include "Thermo.hpp"
 #include "SRI.hpp"
 #include "Integrator.hpp"
+#include "simError.h"
 
 #ifdef IS_MPI
 #define __C
@@ -86,17 +87,26 @@ double Thermo::getPotential(){
   double potential_local;
   double potential;
   int el, nSRI;
-  SRI** sris;
+  Molecule* molecules;
 
-  sris = entry_plug->sr_interactions;
+  molecules = entry_plug->molecules;
   nSRI = entry_plug->n_SRI;
 
   potential_local = 0.0;
+  potential = 0.0;
   potential_local += entry_plug->lrPot;
 
-  for( el=0; el<nSRI; el++ ){    
-    potential_local += sris[el]->get_potential();
+  for( el=0; el<entry_plug->n_mol; el++ ){    
+    potential_local += molecules[el].getPotential();
   }
+
+#ifdef IS_MPI
+  /*
+  std::cerr << "node " << worldRank << ": before LONG RANGE pot = " << entry_plug->lrPot 
+	    << "; pot_local = " << potential_local 
+	    << "; pot = " << potential << "\n";
+  */
+#endif
 
   // Get total potential for entire system from MPI.
 #ifdef IS_MPI
@@ -105,6 +115,12 @@ double Thermo::getPotential(){
   potential = potential_local; 
 #endif // is_mpi
 
+#ifdef IS_MPI
+  /*
+  std::cerr << "node " << worldRank << ": after pot = " << potential << "\n";
+  */
+#endif
+
   return potential;
 }
 
@@ -196,7 +212,7 @@ void Thermo::velocitize() {
 
     av2 = 2.0 * kebar / atoms[vr]->getMass();
     vbar = sqrt( av2 );
-
+ 
 //     vbar = sqrt( 8.31451e-7 * temperature / atoms[vr]->getMass() );
     
     // picks random velocities from a gaussian distribution