--- trunk/OOPSE/libmdtools/NVT.cpp	2003/06/20 16:49:33	560
+++ trunk/OOPSE/libmdtools/NVT.cpp	2003/06/20 20:29:36	561
@@ -6,11 +6,14 @@
 #include "Thermo.hpp"
 #include "ReadWrite.hpp"
 #include "Integrator.hpp"
-#include "NVT.hpp"
- 
+#include "simError.h" 
+
+
 // Basic thermostating via Hoover, Phys.Rev.A, 1985, Vol. 31 (5) 1695-1697
 
-NVT::NVT() {
+NVT::NVT ( SimInfo *theInfo, ForceFields* the_ff):
+  Integrator( theInfo, the_ff )
+{
   zeta = 0.0;
   have_tau_thermostat = 0;
   have_target_temp = 0;
@@ -24,7 +27,10 @@ void NVT::moveA() {
   DirectionalAtom* dAtom;
   double Tb[3];
   double ji[3];
+  double ke;
+  double angle;
 
+
   ke = tStats->getKinetic() * eConvert;
   zeta += dt2 * ( (2.0 * ke  -  NkBT) / qmass );
 
@@ -68,23 +74,23 @@ void NVT::moveA() {
       
       // rotate about the x-axis      
       angle = dt2 * ji[0] / dAtom->getIxx();
-      this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] ); 
+      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); 
       
       // rotate about the y-axis
       angle = dt2 * ji[1] / dAtom->getIyy();
-      this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] );
+      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
       
       // rotate about the z-axis
       angle = dt * ji[2] / dAtom->getIzz();
-      this->rotate( 0, 1, angle, ji, &aMat[aMatIndex] );
+      this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] );
       
       // rotate about the y-axis
       angle = dt2 * ji[1] / dAtom->getIyy();
-      this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] );
+      this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] );
       
        // rotate about the x-axis
       angle = dt2 * ji[0] / dAtom->getIxx();
-      this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] );
+      this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] );
       
       dAtom->setJx( ji[0] );
       dAtom->setJy( ji[1] );
@@ -94,12 +100,14 @@ void Integrator::moveB( void ){
   }
 }
 
-void Integrator::moveB( void ){
+void NVT::moveB( void ){
   int i,j,k;
   int atomIndex;
   DirectionalAtom* dAtom;
   double Tb[3];
   double ji[3];
+  double ke;
+  
 
   ke = tStats->getKinetic() * eConvert;
   zeta += dt2 * ( (2.0 * ke  -  NkBT) / qmass );
@@ -134,10 +142,6 @@ void Integrator::moveB( void ){
       ji[1] += dt2 * (Tb[1] * eConvert - ji[1]*zeta);
       ji[2] += dt2 * (Tb[2] * eConvert - ji[2]*zeta);
       
-      jx2 = ji[0] * ji[0];
-      jy2 = ji[1] * ji[1];
-      jz2 = ji[2] * ji[2];
-      
       dAtom->setJx( ji[0] );
       dAtom->setJy( ji[1] );
       dAtom->setJz( ji[2] );
@@ -146,8 +150,7 @@ int NVT::readyCheck() {
 }
 
 int NVT::readyCheck() {
-  double NkBT;
-
+ 
   // First check to see if we have a target temperature. 
   // Not having one is fatal. 
   
@@ -164,8 +167,8 @@ int NVT::readyCheck() {
   // and then set NkBT if we do have it.   Unreasonable numbers of DOFs
   // are also fatal.
 
-  if (entry_plug->ndf > 0) {
-    NkBT = (double)entry_plug->ndf * kB * targetTemp;
+  if (info->ndf > 0) {
+    NkBT = (double)info->ndf * kB * targetTemp;
   } else {
     sprintf( painCave.errMsg,
              "NVT error: We got a silly number of degrees of freedom!\n"
@@ -181,7 +184,7 @@ int NVT::readyCheck() {
   if (!have_qmass) {
     if (have_tau_thermostat) {
       sprintf( painCave.errMsg,
-               "NVT info: Setting qMass = %d\n", tauThermostat * NkBT);
+               "NVT info: Setting qMass = %lf\n", tauThermostat * NkBT);
       this->setQmass(tauThermostat * NkBT);      
       painCave.isFatal = 0;
       simError();
@@ -198,4 +201,3 @@ int NVT::readyCheck() {
   return 1;
 }
 
-#endif