--- trunk/OOPSE/libmdtools/Molecule.cpp	2003/10/28 16:03:37	829
+++ trunk/OOPSE/libmdtools/Molecule.cpp	2004/04/15 16:18:26	1113
@@ -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 +48,19 @@ 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;
+
+  for (int i = 0; i < myRigidBodies.size(); i++) 
+      myRigidBodies[i]->calcRefCoords();
     
 }
 
@@ -69,6 +68,10 @@ 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 +83,9 @@ 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 +93,10 @@ 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();
@@ -118,25 +128,43 @@ void Molecule::printMe( void ){
   for(i=0; i<nTorsions; i++){
     myTorsions[i]->printMe();
   }
+
 }
 
 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 );
     }
   }
+
+  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;
@@ -148,13 +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;
@@ -178,13 +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;
@@ -201,15 +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;