--- trunk/OOPSE/libmdtools/Atom.cpp	2003/03/26 21:04:38	409
+++ trunk/OOPSE/libmdtools/Atom.cpp	2003/07/14 21:48:43	599
@@ -1,5 +1,18 @@
+#include <iostream>
+
+using namespace std;
+
 #include "Atom.hpp"
 
+double* Atom::pos; // the position array
+double* Atom::vel; // the velocity array
+double* Atom::frc; // the forc array
+double* Atom::trq; // the torque vector  ( space fixed )
+double* Atom::Amat; // the rotation matrix
+double* Atom::mu;   // the array of dipole moments
+double* Atom::ul;   // the lab frame unit directional vector
+int Atom::nElements;
+
 Atom::Atom(int theIndex) {
   c_n_hyd = 0; 
   has_dipole = 0;
@@ -25,9 +38,11 @@ Atom::Atom(int theIndex) {
   Azz = Axx+8;
 }
 
-void Atom::createArrays (int nElements) {
+void Atom::createArrays (int the_nElements) {
   int i;
   
+  nElements = the_nElements;
+
   pos = new double[nElements*3];
   vel = new double[nElements*3];
   frc = new double[nElements*3];
@@ -117,11 +132,11 @@ void Atom::addAtoms(int nAdded, double* Apos, double* 
 
   for(i = 0; i < 3*nAdded; i++) {
     j = i + 3*nElements;
-    new_pos[j] = pos[i];
-    new_vel[j] = vel[i];
-    new_frc[j] = frc[i];
-    new_trq[j] = trq[i];
-    new_ul[j] = ul[i]; 
+    new_pos[j] = Apos[i];
+    new_vel[j] = Avel[i];
+    new_frc[j] = Afrc[i];
+    new_trq[j] = Atrq[i];
+    new_ul[j] = Aul[i]; 
   }
 
   for (i = 0; i < 9*nElements; i++) {
@@ -130,7 +145,7 @@ void Atom::addAtoms(int nAdded, double* Apos, double* 
 
   for(i = 0; i < 9*nAdded; i++) {
     j = i + 9*nElements;
-    new_Amat[j] = Amat[i];
+    new_Amat[j] = AAmat[i];
   }
 
   for (i = 0; i < nElements; i++) {
@@ -139,7 +154,7 @@ void Atom::addAtoms(int nAdded, double* Apos, double* 
 
   for(i = 0; i < nAdded; i++) {
     j = i + nElements;
-    new_mu[j] = mu[i];
+    new_mu[j] = Amu[i];
   }
 
   delete[] pos;
@@ -228,4 +243,47 @@ void Atom::deleteRange(int startIndex, int stopIndex) 
   mu = new_mu;
 
   nElements = nNew;
+}
+
+
+void Atom::getPos( double theP[3] ){
+  
+  theP[0] = pos[offsetX];
+  theP[1] = pos[offsetY];
+  theP[2] = pos[offsetZ];
 }
+
+void Atom::setPos( double theP[3] ){
+  
+  pos[offsetX] = theP[0];
+  pos[offsetY] = theP[1];
+  pos[offsetZ] = theP[2];
+}
+
+void Atom::getVel( double theV[3] ){
+  
+  theV[0] = vel[offsetX];
+  theV[1] = vel[offsetY];
+  theV[2] = vel[offsetZ];
+}
+
+void Atom::setVel( double theV[3] ){
+  
+  vel[offsetX] = theV[0];
+  vel[offsetY] = theV[1];
+  vel[offsetZ] = theV[2];
+}
+
+void Atom::getFrc( double theF[3] ){
+  
+  theF[0] = frc[offsetX];
+  theF[1] = frc[offsetY];
+  theF[2] = frc[offsetZ];
+}
+
+void Atom::addFrc( double theF[3] ){
+  
+  frc[offsetX] += theF[0];
+  frc[offsetY] += theF[1];
+  frc[offsetZ] += theF[2];
+}