--- trunk/OOPSE/libmdtools/Molecule.cpp	2004/04/12 20:32:20	1097
+++ trunk/OOPSE/libmdtools/Molecule.cpp	2004/05/11 21:14:26	1158
@@ -12,12 +12,8 @@ Molecule::Molecule( void ){
   myBonds = NULL;
   myBends = NULL;
   myTorsions = NULL;
-  myRigidBodies = NULL;
-
 }
 
-
-
 Molecule::~Molecule( void ){
   int i;
   
@@ -41,17 +37,17 @@ Molecule::~Molecule( void ){
     delete[] myTorsions;
   }
 
-  if( myRigidBodies != NULL ){
-    for(i=0; i<nRigidBodies; i++) if(myRigidBodies[i] != NULL ) 
-      delete myRigidBodies[i];
-    delete[] myRigidBodies;
-  }
-  
 }
 
 
 void Molecule::initialize( molInit &theInit ){
 
+  CutoffGroup* curCutoffGroup;
+  vector<CutoffGroup*>::iterator iterCutoff;
+  Atom* cutoffAtom;
+  vector<Atom*>::iterator iterAtom;
+  int atomIndex;
+  
   nAtoms = theInit.nAtoms;
   nMembers = nAtoms;
   nBonds = theInit.nBonds;
@@ -59,23 +55,56 @@ void Molecule::initialize( molInit &theInit ){
   nTorsions = theInit.nTorsions;
   nRigidBodies = theInit.nRigidBodies;
   nOriented = theInit.nOriented;
+  nCutoffGroups = theInit.nCutoffGroups;
 
   myAtoms = theInit.myAtoms;
   myBonds = theInit.myBonds;
   myBends = theInit.myBends;
   myTorsions = theInit.myTorsions;
   myRigidBodies = theInit.myRigidBodies;
-    
+
+  myIntegrableObjects = theInit.myIntegrableObjects;
+
+  for (int i = 0; i < myRigidBodies.size(); i++) 
+      myRigidBodies[i]->calcRefCoords();
+
+  myCutoffGroups = theInit.myCutoffGroups;
+
+  //creat a global index set of atoms which belong to cutoff group. 
+  //it will be use to speed up the query whether an atom belongs to cutoff group or not
+  cutoffAtomSet.clear();
+
+  for(curCutoffGroup = beginCutoffGroup(iterCutoff); curCutoffGroup != NULL;
+                                                  curCutoffGroup = nextCutoffGroup(iterCutoff)){
+
+      for(cutoffAtom = curCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL; 
+                                           cutoffAtom = curCutoffGroup->nextAtom(iterAtom)){
+#ifdef IS_MPI
+        atomIndex = cutoffAtom->getGlobalIndex();
+#else
+        atomIndex = cutoffAtom->getIndex();
+#endif
+        cutoffAtomSet.insert(atomIndex);
+     }// end for(cutoffAtom)    
+  }//end for(curCutoffGroup)
+  
 }
 
 void Molecule::calcForces( void ){
   
   int i;
+  double com[3];
 
-  for(i=0; i<nRigidBodies; i++) {
+  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();
   }
@@ -97,6 +126,10 @@ 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();
@@ -135,22 +168,20 @@ 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<nRigidBodies; i++) {
+  for(i=0; i<myRigidBodies.size(); i++) {
 
-    if (myRigidBodies[i] != NULL) {
-      
       myRigidBodies[i]->getPos( aPos );
 
       for (j=0; j< 3; j++) 
@@ -158,15 +189,12 @@ void Molecule::moveCOM(double delta[3]){
       
       myRigidBodies[i]->setPos( aPos );
     }
-  }  
 }
 
 void Molecule::atoms2rigidBodies( void ) {
   int i;
-  for (i = 0; i < nRigidBodies; i++) {
-    if (myRigidBodies[i] != NULL) {
-      myRigidBodies[i]->calcForcesAndTorques();   
-    }
+  for (i = 0; i < myRigidBodies.size(); i++) {
+    myRigidBodies[i]->calcForcesAndTorques();   
   }
 }
 
@@ -181,13 +209,13 @@ 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;
@@ -211,13 +239,13 @@ 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;
@@ -234,15 +262,12 @@ 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;