--- trunk/OOPSE/libmdtools/Thermo.cpp	2003/07/15 17:10:50	611
+++ trunk/OOPSE/libmdtools/Thermo.cpp	2003/07/15 17:57:04	614
@@ -19,8 +19,8 @@ Thermo::Thermo( SimInfo* the_entry_plug ) { 
 
 #define BASE_SEED 123456789
 
-Thermo::Thermo( SimInfo* the_entry_plug ) { 
-  entry_plug = the_entry_plug;
+Thermo::Thermo( SimInfo* the_info ) { 
+  info = the_info;
   int baseSeed = BASE_SEED;
   
   gaussStream = new gaussianSPRNG( baseSeed );
@@ -45,8 +45,8 @@ double Thermo::getKinetic(){
   Atom** atoms;
 
   
-  n_atoms = entry_plug->n_atoms;
-  atoms = entry_plug->atoms;
+  n_atoms = info->n_atoms;
+  atoms = info->atoms;
 
   kinetic = 0.0;
   kinetic_global = 0.0;
@@ -88,14 +88,14 @@ double Thermo::getPotential(){
   int el, nSRI;
   Molecule* molecules;
 
-  molecules = entry_plug->molecules;
-  nSRI = entry_plug->n_SRI;
+  molecules = info->molecules;
+  nSRI = info->n_SRI;
 
   potential_local = 0.0;
   potential = 0.0;
-  potential_local += entry_plug->lrPot;
+  potential_local += info->lrPot;
 
-  for( el=0; el<entry_plug->n_mol; el++ ){    
+  for( el=0; el<info->n_mol; el++ ){    
     potential_local += molecules[el].getPotential();
   }
 
@@ -129,7 +129,7 @@ double Thermo::getTemperature(){
   const double kb = 1.9872179E-3; // boltzman's constant in kcal/(mol K)
   double temperature;
   
-  temperature = ( 2.0 * this->getKinetic() ) / ((double)entry_plug->ndf * kb );
+  temperature = ( 2.0 * this->getKinetic() ) / ((double)info->ndf * kb );
   return temperature;
 }
 
@@ -151,7 +151,7 @@ double Thermo::getVolume() {
 
 double Thermo::getVolume() {
 
-  return entry_plug->boxVol;
+  return info->boxVol;
 }
 
 double Thermo::getPressure() {
@@ -180,12 +180,12 @@ void Thermo::getPressureTensor(double press[3][3]){
   double molmass, volume;
   double vcom[3];
   double p_local[9], p_global[9];
-  int i, j, k, l, nMols;
+  int i, j, k, nMols;
   Molecule* molecules;
 
-  nMols = entry_plug->n_mol;
-  molecules = entry_plug->molecules;
-  //tau = entry_plug->tau;
+  nMols = info->n_mol;
+  molecules = info->molecules;
+  //tau = info->tau;
 
   // use velocities of molecular centers of mass and molecular masses:
   for (i=0; i < 9; i++) {    
@@ -222,7 +222,8 @@ void Thermo::getPressureTensor(double press[3][3]){
   for(i = 0; i < 3; i++) {
     for (j = 0; j < 3; j++) {
       k = 3*i + j;
-      press[i][j] = (p_global[k] + entry_plug->tau[k]*e_convert) / volume;
+      press[i][j] = (p_global[k] + info->tau[k]*e_convert) / volume;
+
     }
   }
 }
@@ -244,14 +245,14 @@ void Thermo::velocitize() {
   int n_oriented;
   int n_constraints;
 
-  atoms         = entry_plug->atoms;
-  n_atoms       = entry_plug->n_atoms;
-  temperature   = entry_plug->target_temp;
-  n_oriented    = entry_plug->n_oriented;
-  n_constraints = entry_plug->n_constraints;
+  atoms         = info->atoms;
+  n_atoms       = info->n_atoms;
+  temperature   = info->target_temp;
+  n_oriented    = info->n_oriented;
+  n_constraints = info->n_constraints;
   
-  kebar = kb * temperature * (double)entry_plug->ndf / 
-    ( 2.0 * (double)entry_plug->ndfRaw );
+  kebar = kb * temperature * (double)info->ndf / 
+    ( 2.0 * (double)info->ndfRaw );
   
   for(vr = 0; vr < n_atoms; vr++){
     
@@ -322,8 +323,8 @@ void Thermo::getCOMVel(double vdrift[3]){
   // We are very careless here with the distinction between n_atoms and n_local
   // We should really fix this before someone pokes an eye out.
 
-  n_atoms = entry_plug->n_atoms;  
-  atoms   = entry_plug->atoms;
+  n_atoms = info->n_atoms;  
+  atoms   = info->atoms;
 
   mtot_local = 0.0;
   vdrift_local[0] = 0.0;