--- trunk/OOPSE/libmdtools/Molecule.cpp	2003/04/03 21:12:51	450
+++ trunk/OOPSE/libmdtools/Molecule.cpp	2004/04/27 16:26:44	1136
@@ -1,4 +1,4 @@
-#include <cstdlib>
+#include <stdlib.h>
 
 
 #include "Molecule.hpp"
@@ -15,8 +15,6 @@ Molecule::Molecule( void ){
 
 }
 
-
-
 Molecule::~Molecule( void ){
   int i;
   
@@ -40,35 +38,54 @@ Molecule::~Molecule( void ){
     delete[] myTorsions;
   }
 
-  if( myExcludes != NULL ){
-    for(i=0; i<nExcludes; i++) if(myExcludes[i] != NULL ) delete myExcludes[i];
-    delete[] myExcludes;
-  }
 }
 
 
 void Molecule::initialize( molInit &theInit ){
-
+  double totMass;
+  
   nAtoms = theInit.nAtoms;
   nMembers = nAtoms;
   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();
+
+
+  //the mass ratio will never change during the simulation. Thus, we could
+  //just calculate it at the begining of the simulation
+  totMass = getTotalMass();
+  for(int i = 0; i < nAtoms; i ++)
+    myAtoms[i]->setMassRatio(myAtoms[i]->getMass()/totMass);  
 }
 
 void Molecule::calcForces( void ){
   
   int i;
+  double com[3];
 
+  for(i=0; i<myRigidBodies.size(); i++) {
+    myRigidBodies[i]->updateAtoms();
+  }
+
+  //calculate the center of mass of the molecule
+  getCOM(com);  
+  for(int i = 0; i < nAtoms; i ++)
+    myAtoms[i]->setRc(com);  
+  
+
   for(i=0; i<nBonds; i++){
     myBonds[i]->calc_forces();
   }
@@ -80,6 +97,9 @@ 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 +107,10 @@ 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();
@@ -118,50 +142,114 @@ void Molecule::printMe( void ){
   for(i=0; i<nTorsions; i++){
     myTorsions[i]->printMe();
   }
+
 }
 
 void Molecule::moveCOM(double delta[3]){
-  double x, y, z;
-  int i;
+  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 ) {
+      
+      myIntegrableObjects[i]->getPos( aPos );
+      
+      for (j=0; j< 3; j++) 
+        aPos[j] += delta[j];
 
-      x = myAtoms[i]->getX() + delta[0];
-      y = myAtoms[i]->getY() + delta[1];
-      z = myAtoms[i]->getZ() + delta[2];
+      myIntegrableObjects[i]->setPos( aPos );
+    }
+  }
 
-      myAtoms[i]->setX(x);
-      myAtoms[i]->setY(y);
-      myAtoms[i]->setZ(z);
+  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;
-  int i;
+  double aPos[3];
+  int i, j;
 
-  COM[0] = 0.0;
-  COM[1] = 0.0;
-  COM[2] = 0.0;
+  for (j=0; j<3; j++) 
+    COM[j] = 0.0;
+
   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;
-      COM[0] += myAtoms[i]->getX() * mass;
-      COM[1] += myAtoms[i]->getY() * mass;
-      COM[2] += myAtoms[i]->getZ() * mass;
+      
+      myIntegrableObjects[i]->getPos( aPos );
 
+      for( j = 0; j < 3; j++) 
+        COM[j] += aPos[j] * mass;
+
     }
   }
 
-  COM[0] /= mtot;
-  COM[1] /= mtot;
-  COM[2] /= mtot;
+  for (j = 0; j < 3; j++) 
+    COM[j] /= mtot; 
+}
+
+double Molecule::getCOMvel( double COMvel[3] ) {
+
+  double mass, mtot;
+  double aVel[3];
+  int i, j;
+
+
+  for (j=0; j<3; j++) 
+    COMvel[j] = 0.0;
+
+  mtot   = 0.0;
+
+  for (i=0; i < myIntegrableObjects.size(); i++) {
+    if (myIntegrableObjects[i] != NULL) {
+
+      mass = myIntegrableObjects[i]->getMass();
+      mtot   += mass;
+
+      myIntegrableObjects[i]->getVel(aVel);
+
+      for (j=0; j<3; j++) 
+        COMvel[j] += aVel[j]*mass;
+
+    }
+  }
+
+  for (j=0; j<3; j++) 
+    COMvel[j] /= mtot;
  
+  return mtot;
+
 }
+
+double Molecule::getTotalMass()
+{
+
+  double totalMass;
+  
+  totalMass = 0;
+  for(int i =0; i < myIntegrableObjects.size(); i++){
+    totalMass += myIntegrableObjects[i]->getMass();
+  }
+
+  return totalMass;
+}