--- trunk/OOPSE/libmdtools/Molecule.cpp	2003/07/15 15:50:55	610
+++ trunk/OOPSE/libmdtools/Molecule.cpp	2004/04/14 16:32:15	1109
@@ -1,4 +1,4 @@
-#include <cstdlib>
+#include <stdlib.h>
 
 
 #include "Molecule.hpp"
@@ -15,8 +15,6 @@ Molecule::Molecule( void ){
 
 }
 
-
-
 Molecule::~Molecule( void ){
   int i;
   
@@ -40,10 +38,6 @@ Molecule::~Molecule( void ){
     delete[] myTorsions;
   }
 
-  if( myExcludes != NULL ){
-    for(i=0; i<nExcludes; i++) if(myExcludes[i] != NULL ) delete myExcludes[i];
-    delete[] myExcludes;
-  }
 }
 
 
@@ -54,14 +48,16 @@ void Molecule::initialize( molInit &theInit ){
   nBonds = theInit.nBonds;
   nBends = theInit.nBends;
   nTorsions = theInit.nTorsions;
-  nExcludes = theInit.nExcludes;
+  nRigidBodies = theInit.nRigidBodies;
   nOriented = theInit.nOriented;
 
   myAtoms = theInit.myAtoms;
   myBonds = theInit.myBonds;
   myBends = theInit.myBends;
   myTorsions = theInit.myTorsions;
-  myExcludes = theInit.myExcludes;
+  myRigidBodies = theInit.myRigidBodies;
+
+  myIntegrableObjects = theInit.myIntegrableObjects;
     
 }
 
@@ -69,6 +65,10 @@ void Molecule::calcForces( void ){
   
   int i;
 
+  for(i=0; i<myRigidBodies.size(); i++) {
+    myRigidBodies[i]->updateAtoms();
+  }
+
   for(i=0; i<nBonds; i++){
     myBonds[i]->calc_forces();
   }
@@ -80,6 +80,9 @@ void Molecule::calcForces( void ){
   for(i=0; i<nTorsions; i++){
     myTorsions[i]->calc_forces();
   }
+
+  // Rigid Body forces and torques are done after the fortran force loop
+
 }
 
 
@@ -87,6 +90,10 @@ double Molecule::getPotential( void ){
   
   int i;
   double myPot = 0.0;
+
+  for(i=0; i<myRigidBodies.size(); i++) {
+    myRigidBodies[i]->updateAtoms();
+  }
    
   for(i=0; i<nBonds; i++){
     myPot += myBonds[i]->get_potential();
@@ -118,6 +125,7 @@ void Molecule::printMe( void ){
   for(i=0; i<nTorsions; i++){
     myTorsions[i]->printMe();
   }
+
 }
 
 void Molecule::moveCOM(double delta[3]){
@@ -135,8 +143,25 @@ void Molecule::moveCOM(double delta[3]){
       myAtoms[i]->setPos( aPos );
     }
   }
+
+  for(i=0; i<myRigidBodies.size(); i++) {
+
+      myRigidBodies[i]->getPos( aPos );
+
+      for (j=0; j< 3; j++) 
+        aPos[j] += delta[j];
+      
+      myRigidBodies[i]->setPos( aPos );
+    }
 }
 
+void Molecule::atoms2rigidBodies( void ) {
+  int i;
+  for (i = 0; i < myRigidBodies.size(); i++) {
+    myRigidBodies[i]->calcForcesAndTorques();   
+  }
+}
+
 void Molecule::getCOM( double COM[3] ) {
 
   double mass, mtot;
@@ -198,3 +223,19 @@ double Molecule::getCOMvel( double COMvel[3] ) {
   return mtot;
 
 }
+
+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();
+  }
+
+  return totalMass;
+}