--- trunk/OOPSE/libmdtools/Molecule.cpp	2004/04/14 16:32:15	1109
+++ trunk/OOPSE/libmdtools/Molecule.cpp	2004/04/15 16:18:26	1113
@@ -58,6 +58,9 @@ void Molecule::initialize( molInit &theInit ){
   myRigidBodies = theInit.myRigidBodies;
 
   myIntegrableObjects = theInit.myIntegrableObjects;
+
+  for (int i = 0; i < myRigidBodies.size(); i++) 
+      myRigidBodies[i]->calcRefCoords();
     
 }
 
@@ -132,15 +135,15 @@ void Molecule::moveCOM(double delta[3]){
   double aPos[3];
   int i, j;
 
-  for(i=0; i<nAtoms; i++) {
-    if(myAtoms[i] != NULL ) {
+  for(i=0; i<myIntegrableObjects.size(); i++) {
+    if(myIntegrableObjects[i] != NULL ) {
       
-      myAtoms[i]->getPos( aPos );
+      myIntegrableObjects[i]->getPos( aPos );
       
       for (j=0; j< 3; j++) 
         aPos[j] += delta[j];
 
-      myAtoms[i]->setPos( aPos );
+      myIntegrableObjects[i]->setPos( aPos );
     }
   }
 
@@ -173,13 +176,13 @@ void Molecule::getCOM( double COM[3] ) {
 
   mtot   = 0.0;
 
-  for (i=0; i < nAtoms; i++) {
-    if (myAtoms[i] != NULL) {
+  for (i=0; i < myIntegrableObjects.size(); i++) {
+    if (myIntegrableObjects[i] != NULL) {
 
-      mass = myAtoms[i]->getMass();
+      mass = myIntegrableObjects[i]->getMass();
       mtot   += mass;
       
-      myAtoms[i]->getPos( aPos );
+      myIntegrableObjects[i]->getPos( aPos );
 
       for( j = 0; j < 3; j++) 
         COM[j] += aPos[j] * mass;
@@ -203,13 +206,13 @@ double Molecule::getCOMvel( double COMvel[3] ) {
 
   mtot   = 0.0;
 
-  for (i=0; i < nAtoms; i++) {
-    if (myAtoms[i] != NULL) {
+  for (i=0; i < myIntegrableObjects.size(); i++) {
+    if (myIntegrableObjects[i] != NULL) {
 
-      mass = myAtoms[i]->getMass();
+      mass = myIntegrableObjects[i]->getMass();
       mtot   += mass;
 
-      myAtoms[i]->getVel(aVel);
+      myIntegrableObjects[i]->getVel(aVel);
 
       for (j=0; j<3; j++) 
         COMvel[j] += aVel[j]*mass;
@@ -226,15 +229,12 @@ double Molecule::getTotalMass()
 
 double Molecule::getTotalMass()
 {
-  int natoms;
-  Atom** atoms;
+
   double totalMass;
   
-  natoms = getNAtoms();
-  atoms = getMyAtoms();
   totalMass = 0;
-  for(int i =0; i < natoms; i++){
-    totalMass += atoms[i]->getMass();
+  for(int i =0; i < myIntegrableObjects.size(); i++){
+    totalMass += myIntegrableObjects[i]->getMass();
   }
 
   return totalMass;