--- branches/mmeineke/mdtools/md_code/Symplectic.cpp	2002/07/09 18:40:59	10
+++ trunk/mdtools/md_code/Symplectic.cpp	2003/01/17 21:53:36	238
@@ -4,8 +4,9 @@
 #include "Integrator.hpp"
 #include "Thermo.hpp"
 #include "ReadWrite.hpp"
+#include "ForceField.hpp"
+#include "simError.h"
 
-
 extern "C"{
   
   void v_constrain_a_( double &dt, int &n_atoms, double* mass, 
@@ -34,7 +35,6 @@ Symplectic::Symplectic( SimInfo* the_entry_plug ){
   isFirst = 1;
 
   srInteractions = entry_plug->sr_interactions;
-  longRange      =       entry_plug->longRange;
   nSRI           =           entry_plug->n_SRI;
 
   // give a little love back to the SimInfo object
@@ -120,7 +120,7 @@ void Symplectic::integrate( void ){
   double dt2;                       // half the dt
 
   double vx, vy, vz;    // the velocities
-  double vx2, vy2, vz2; // the square of the velocities
+//  double vx2, vy2, vz2; // the square of the velocities
   double rx, ry, rz;    // the postitions
   
   double ji[3];   // the body frame angular momentum
@@ -129,6 +129,7 @@ void Symplectic::integrate( void ){
   double angle;   // the angle through which to rotate the rotation matrix
   double A[3][3]; // the rotation matrix
 
+  int time;
 
   double dt          = entry_plug->dt;
   double runTime     = entry_plug->run_time;
@@ -141,12 +142,13 @@ void Symplectic::integrate( void ){
   int status_n = (int)( statusTime / dt );
   int vel_n    = (int)( thermalTime / dt );
 
+  ForceFields *ff = entry_plug->
+
   Thermo *tStats = new Thermo( entry_plug );
 
   StatWriter*  e_out    = new StatWriter( entry_plug );
   DumpWriter*  dump_out = new DumpWriter( entry_plug );
 
-
   Atom** atoms = entry_plug->atoms;
   DirectionalAtom* dAtom;
   dt2 = 0.5 * dt;
@@ -154,6 +156,7 @@ void Symplectic::integrate( void ){
   // initialize the forces the before the first step
 
   
+  
   for(i = 0; i < nAtoms; i++){
     atoms[i]->zeroForces();
   }
@@ -170,6 +173,9 @@ void Symplectic::integrate( void ){
     tStats->velocitize();
   }
   
+  dump_out->writeDump( 0.0 );
+  e_out->writeStat( 0.0 );
+
   if( n_constrained ){
 
     double *Rx = new double[nAtoms];
@@ -358,12 +364,14 @@ void Symplectic::integrate( void ){
 	  dAtom->setJz( ji[2] );
 	}
       }
-    
+     
+      time = tl + 1;
+      
       if( entry_plug->setTemp ){
-	if( !(tl % vel_n) ) tStats->velocitize();
+	if( !(time % vel_n) ) tStats->velocitize();
       }
-      if( !(tl % sample_n) ) dump_out->writeDump( tl * dt );
-      if( !(tl % status_n) ) e_out->writeStat( tl * dt );
+      if( !(time % sample_n) ) dump_out->writeDump( time * dt );
+      if( !(time % status_n) ) e_out->writeStat( time * dt );
     }
   }
   else{
@@ -486,9 +494,9 @@ void Symplectic::integrate( void ){
 	atoms[i]->set_vy( vy );
 	atoms[i]->set_vz( vz );
 	
-	vx2 = vx * vx;
-	vy2 = vy * vy;
-	vz2 = vz * vz;
+// 	vx2 = vx * vx;
+// 	vy2 = vy * vy;
+// 	vz2 = vz * vz;
 	
 	if( atoms[i]->isDirectional() ){
 
@@ -521,12 +529,14 @@ void Symplectic::integrate( void ){
 	  dAtom->setJz( ji[2] );
 	}
       }
-    
+      
+      time = tl + 1;
+      
       if( entry_plug->setTemp ){
-	if( !(tl % vel_n) ) tStats->velocitize();
+	if( !(time % vel_n) ) tStats->velocitize();
       }
-      if( !(tl % sample_n) ) dump_out->writeDump( tl * dt );
-      if( !(tl % status_n) ) e_out->writeStat( tl * dt );
+      if( !(time % sample_n) ) dump_out->writeDump( time * dt );
+      if( !(time % status_n) ) e_out->writeStat( time * dt );
     }
   }