--- trunk/OOPSE/libmdtools/SimSetup.cpp	2004/05/20 20:24:07	1180
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2004/05/27 18:59:17	1203
@@ -950,14 +950,35 @@ void SimSetup::gatherInfo(void){
     info[i].orthoTolerance = globals->getOrthoBoxTolerance();
 
     // check for thermodynamic integration
-    if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
-      info[i].thermIntLambda = globals->getThermIntLambda();
-      info[i].thermIntK = globals->getThermIntK();
-      info[i].useThermInt = 1;
-      
-      Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
-      info[i].restraint = myRestraint;
+    if (globals->getUseThermInt()) {
+      if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
+	info[i].useThermInt = globals->getUseThermInt();
+	info[i].thermIntLambda = globals->getThermIntLambda();
+	info[i].thermIntK = globals->getThermIntK();
+	
+	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
+	info[i].restraint = myRestraint;
+      }
+      else {
+	sprintf(painCave.errMsg,
+		"SimSetup Error:\n"
+		"\tKeyword useThermInt was set to 'true' but\n"
+		"\tthermodynamicIntegrationLambda (and/or\n"
+		"\tthermodynamicIntegrationK) was not specified.\n"
+		"\tPlease provide a lambda value and k value in your .bass file.\n");
+	painCave.isFatal = 1;
+	simError();    
+      }
     }
+    else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
+	sprintf(painCave.errMsg,
+		"SimSetup Warning: If you want to use Thermodynamic\n"
+		"\tIntegration, set useThermInt to 'true' in your .bass file.\n"
+		"\tThe useThermInt keyword is 'false' by default, so your\n"
+		"\tlambda and/or k values are being ignored.\n");
+	painCave.isFatal = 0;
+	simError();   
+    }
   }
   
   //setup seed for random number generator
@@ -1429,21 +1450,33 @@ void SimSetup::calcSysValues(void){
 }
 
 void SimSetup::calcSysValues(void){
-  int i;
+  int i, j;
+  int ncutgroups, atomsingroups, ngroupsinstamp;
 
   int* molMembershipArray;
+  CutoffGroupStamp* cg;
 
   tot_atoms = 0;
   tot_bonds = 0;
   tot_bends = 0;
   tot_torsions = 0;
   tot_rigid = 0;
+  tot_groups = 0;
   for (i = 0; i < n_components; i++){
     tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
     tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
     tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
     tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
     tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
+
+    ncutgroups = comp_stamps[i]->getNCutoffGroups();
+    atomsingroups = 0;
+    for (j=0; j < ncutgroups; j++) {
+      cg = comp_stamps[i]->getCutoffGroup(j);
+      atomsingroups += cg->getNMembers();
+    }
+    ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
+    tot_groups += components_nmol[i] * ngroupsinstamp;    
   }
   
   tot_SRI = tot_bonds + tot_bends + tot_torsions;
@@ -1456,7 +1489,7 @@ void SimSetup::calcSysValues(void){
     info[i].n_torsions = tot_torsions;
     info[i].n_SRI = tot_SRI;
     info[i].n_mol = tot_nmol;
-
+    info[i].ngroup = tot_groups;
     info[i].molMembershipArray = molMembershipArray;
   }
 }
@@ -1510,7 +1543,7 @@ void SimSetup::mpiMolDivide(void){
   }
   local_SRI = local_bonds + local_bends + local_torsions;
 
-  info[0].n_atoms = mpiSim->getMyNlocal();  
+  info[0].n_atoms = mpiSim->getNAtomsLocal();  
   
 
   if (local_atoms != info[0].n_atoms){
@@ -1558,7 +1591,7 @@ void SimSetup::makeSysArrays(void){
 
 
     molIndex = 0;
-    for (i = 0; i < mpiSim->getTotNmol(); i++){
+    for (i = 0; i < mpiSim->getNMolGlobal(); i++){
       if (mol2proc[i] == worldRank){
         the_molecules[molIndex].setStampID(molCompType[i]);
         the_molecules[molIndex].setMyIndex(molIndex);