--- trunk/OOPSE/libmdtools/Molecule.cpp	2003/03/27 20:48:37	427
+++ trunk/OOPSE/libmdtools/Molecule.cpp	2003/07/15 15:50:55	610
@@ -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::calcForces( void ){
 }
 
 
-void Molecule::getPotential( void ){
+double Molecule::getPotential( void ){
   
   int i;
   double myPot = 0.0;
@@ -101,3 +102,99 @@ 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 aPos[3];
+  int i, j;
+
+  for(i=0; i<nAtoms; i++) {
+    if(myAtoms[i] != NULL ) {
+      
+      myAtoms[i]->getPos( aPos );
+      
+      for (j=0; j< 3; j++) 
+        aPos[j] += delta[j];
+
+      myAtoms[i]->setPos( aPos );
+    }
+  }
+}
+
+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 < nAtoms; i++) {
+    if (myAtoms[i] != NULL) {
+
+      mass = myAtoms[i]->getMass();
+      mtot   += mass;
+      
+      myAtoms[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 < nAtoms; i++) {
+    if (myAtoms[i] != NULL) {
+
+      mass = myAtoms[i]->getMass();
+      mtot   += mass;
+
+      myAtoms[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;
+
+}