--- trunk/OOPSE/libmdtools/Molecule.cpp	2003/03/27 21:07:14	428
+++ trunk/OOPSE/libmdtools/Molecule.cpp	2004/05/11 21:14:26	1158
@@ -1,7 +1,8 @@
-#include <cstdlib>
+#include <stdlib.h>
 
 
 #include "Molecule.hpp"
+#include "simError.h"
 
 
 
@@ -11,11 +12,8 @@ Molecule::Molecule( void ){
   myBonds = NULL;
   myBends = NULL;
   myTorsions = NULL;
-
 }
 
-
-
 Molecule::~Molecule( void ){
   int i;
   
@@ -39,35 +37,74 @@ 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 ){
 
+  CutoffGroup* curCutoffGroup;
+  vector<CutoffGroup*>::iterator iterCutoff;
+  Atom* cutoffAtom;
+  vector<Atom*>::iterator iterAtom;
+  int atomIndex;
+  
   nAtoms = theInit.nAtoms;
   nMembers = nAtoms;
   nBonds = theInit.nBonds;
   nBends = theInit.nBends;
   nTorsions = theInit.nTorsions;
-  nExcludes = theInit.nExcludes;
+  nRigidBodies = theInit.nRigidBodies;
   nOriented = theInit.nOriented;
+  nCutoffGroups = theInit.nCutoffGroups;
 
   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();
+
+  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<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();
   }
@@ -79,6 +116,9 @@ 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
+
 }
 
 
@@ -86,6 +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();
@@ -101,3 +145,130 @@ double Molecule::getPotential( void ){
 
   return myPot;
 }
+
+void Molecule::printMe( void ){
+  
+  int i;
+
+  for(i=0; i<nBonds; i++){
+    myBonds[i]->printMe();
+  }
+
+  for(i=0; i<nBends; i++){
+    myBends[i]->printMe();
+  }
+
+  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<myIntegrableObjects.size(); i++) {
+    if(myIntegrableObjects[i] != NULL ) {
+      
+      myIntegrableObjects[i]->getPos( aPos );
+      
+      for (j=0; j< 3; j++) 
+        aPos[j] += delta[j];
+
+      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;
+  double aPos[3];
+  int i, j;
+
+  for (j=0; j<3; j++) 
+    COM[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]->getPos( aPos );
+
+      for( j = 0; j < 3; j++) 
+        COM[j] += aPos[j] * mass;
+
+    }
+  }
+
+  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;
+}