--- trunk/OOPSE/libmdtools/Molecule.cpp	2003/03/27 20:48:37	427
+++ trunk/OOPSE/libmdtools/Molecule.cpp	2003/04/09 04:06:43	483
@@ -2,6 +2,7 @@
 
 
 #include "Molecule.hpp"
+#include "simError.h"
 
 
 
@@ -60,7 +61,7 @@ void Molecule::initialize( molInit &theInit ){
   myBonds = theInit.myBonds;
   myBends = theInit.myBends;
   myTorsions = theInit.myTorsions;
-  myExcludes = theInit.myExcludses;
+  myExcludes = theInit.myExcludes;
     
 }
 
@@ -82,7 +83,7 @@ void Molecule::getPotential( void ){
 }
 
 
-void Molecule::getPotential( void ){
+double Molecule::getPotential( void ){
   
   int i;
   double myPot = 0.0;
@@ -101,3 +102,107 @@ void 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 x, y, z;
+  int i;
+
+  for(i=0; i<nAtoms; i++) {
+    if(myAtoms[i] != NULL ) {
+
+      x = myAtoms[i]->getX() + delta[0];
+      y = myAtoms[i]->getY() + delta[1];
+      z = myAtoms[i]->getZ() + delta[2];
+
+      myAtoms[i]->setX(x);
+      myAtoms[i]->setY(y);
+      myAtoms[i]->setZ(z);
+    }
+  }
+}
+
+void Molecule::getCOM( double COM[3] ) {
+
+  double mass, mtot;
+  int i;
+
+  COM[0] = 0.0;
+  COM[1] = 0.0;
+  COM[2] = 0.0;
+  mtot   = 0.0;
+
+  for (i=0; i < nAtoms; i++) {
+    if (myAtoms[i] != NULL) {
+
+      mass = myAtoms[i]->getMass();
+      mtot   += mass;
+      COM[0] += myAtoms[i]->getX() * mass;
+      COM[1] += myAtoms[i]->getY() * mass;
+      COM[2] += myAtoms[i]->getZ() * mass;
+
+    }
+  }
+
+  COM[0] /= mtot;
+  COM[1] /= mtot;
+  COM[2] /= mtot;
+ 
+}
+
+double Molecule::getCOMvel( double COMvel[3] ) {
+
+  double mass, mtot;
+  int i;
+
+  COMvel[0] = 0.0;
+  COMvel[1] = 0.0;
+  COMvel[2] = 0.0;
+  mtot   = 0.0;
+
+  for (i=0; i < nAtoms; i++) {
+    if (myAtoms[i] != NULL) {
+      
+      mass = myAtoms[i]->getMass();
+      mtot   += mass;
+      COMvel[0] += myAtoms[i]->get_vx() * mass;
+      COMvel[1] += myAtoms[i]->get_vy() * mass;
+      COMvel[2] += myAtoms[i]->get_vz() * mass;
+
+    }
+  }
+
+  COMvel[0] /= mtot;
+  COMvel[1] /= mtot;
+  COMvel[2] /= mtot;
+ 
+  return mtot;
+
+}
+
+void Molecule::atomicRollCall(int* molMembership) {
+  int i, which;
+
+  for (i=0; i < nAtoms; i++) {
+    if (myAtoms[i] != NULL) {
+      which = myAtoms[i]->getIndex();
+      molMembership[which] = myIndex;
+    }
+  }
+}