--- trunk/mdtools/md_code/Verlet.cpp	2002/07/09 18:40:59	11
+++ trunk/mdtools/md_code/Verlet.cpp	2003/01/27 21:28:19	249
@@ -30,16 +30,17 @@ Verlet::Verlet( SimInfo &info ){
 }
 
   
-Verlet::Verlet( SimInfo &info ){
+Verlet::Verlet( SimInfo &info, ForceFields* the_ff ){
   
   // get what information we need from the SimInfo object
 
   entry_plug = &info;
+  myFF = the_ff;
 
+
   c_natoms = info.n_atoms;
   c_atoms = info.atoms;
   c_sr_interactions = info.sr_interactions;
-  longRange = info.longRange;
   c_n_SRI = info.n_SRI;
   c_is_constrained = 0;
   c_box_x = info.box_x;
@@ -123,89 +124,6 @@ Verlet::~Verlet(){
 }
 
 
-
-void Verlet::integrate_b( double time_length, double dt, 
-			    int n_bond_0, int n_bond_f,
-			    int n_bend_0, int n_bend_f,
-			    int n_torsion_0, int n_torsion_f,
-			    bool do_bonds, bool do_bends, bool do_torsions,
-			    bool do_LRI ){
-  
-//  double percent_tolerance = 0.001;
-//  int max_iterations = 10000;
-
-  int i, j; /* loop counters */
-  double n_loops = time_length / dt;
-  
-  // the first time integrate is called, the forces need to be initialized 
-
-  if(is_first){ 
-    is_first = 0;
-    
-    for(i = 0; i < c_natoms; i++){
-      c_atoms[i]->zeroForces();
-    }
-    
-    if( do_bonds ){
-      for(i = n_bond_0; i <= n_bond_f; i++){
-	c_sr_interactions[i]->calc_forces();
-      }
-    }
-
-    if( do_bends ){
-      for(i = n_bend_0; i <= n_bend_f; i++){
-	c_sr_interactions[i]->calc_forces();
-      }
-    }
-    
-    if( do_torsions ){
-      for(i = n_torsion_0; i <= n_torsion_f; i++){
-	c_sr_interactions[i]->calc_forces();
-      }
-    }
- 
-    if( do_LRI ) longRange->calc_forces();
-  }
-
-  for(i = 0; i < n_loops; i++){
-    
-    move_a( dt );
-    
-    // calculate the forces
-    
-    for(j = 0; j < c_natoms; j++){
-      c_atoms[j]->zeroForces();
-    }
-  
-
-    if( do_bonds ){
-      for(i = n_bond_0; i <= n_bond_f; i++){
-	c_sr_interactions[i]->calc_forces();
-      }
-    }
-
-    if( do_bends ){
-      for(i = n_bend_0; i <= n_bend_f; i++){
-	c_sr_interactions[i]->calc_forces();
-      }
-    }
-    
-    if( do_torsions ){
-      for(i = n_torsion_0; i <= n_torsion_f; i++){
-	c_sr_interactions[i]->calc_forces();
-      }
-    }
-
-    if( do_LRI ) longRange->calc_forces();
-    
-
-    // complete the verlet move
-
-    move_b( dt );
-  }
-}
-
-
 void Verlet::integrate( void ){
   
   int i, j; /* loop counters */
@@ -224,6 +142,8 @@ void Verlet::integrate( void ){
   double *Fy = new double[c_natoms];
   double *Fz = new double[c_natoms];
   
+  int time;
+
   double dt = entry_plug->dt;
   double runTime = entry_plug->run_time;
   double sampleTime = entry_plug->sampleTime;
@@ -243,20 +163,15 @@ void Verlet::integrate( void ){
   // the first time integrate is called, the forces need to be initialized 
 
   
-  for(i = 0; i < c_natoms; i++){
-    c_atoms[i]->zeroForces();
-  }
+  myFF->doForces();
   
-  for(i = 0; i < c_n_SRI; i++){
-    c_sr_interactions[i]->calc_forces();
-  }
-  
-  longRange->calc_forces();
-  
   if( entry_plug->setTemp ){
     tStats->velocitize();
   }
   
+  dump_out->writeDump( 0.0 );
+  e_out->writeStat( 0.0 );
+
   if( c_is_constrained ){
     for(i = 0; i < n_loops; i++){
       
@@ -297,16 +212,8 @@ void Verlet::integrate( void ){
 
       // calculate the forces
       
-      for(j = 0; j < c_natoms; j++){
-	c_atoms[j]->zeroForces();
-      }
+      myFF->doForces();
       
-      for(j = 0; j < c_n_SRI; j++){
-	c_sr_interactions[j]->calc_forces();
-      }
-      
-      longRange->calc_forces();
-      
       // finish the constrain move ( same as above. )
 
       for( j=0; j<c_natoms; j++ ){
@@ -341,12 +248,13 @@ void Verlet::integrate( void ){
 	c_atoms[j]->set_vz(Vz[j]);
       }
       
+      time = i + 1;
+      
       if( entry_plug->setTemp ){
-	if( !(i % vel_n) ) tStats->velocitize();
+	if( !(time % vel_n) ) tStats->velocitize();
       }
-      if( !(i % sample_n) ) dump_out->writeDump( i * dt );
-      if( !(i % status_n) ) e_out->writeStat( i * dt );
-
+      if( !(time % sample_n) ) dump_out->writeDump( time * dt );
+      if( !(time % status_n) ) e_out->writeStat( time * dt );
     }
   }
   else{
@@ -356,25 +264,19 @@ void Verlet::integrate( void ){
       
       // calculate the forces
       
-      for(j = 0; j < c_natoms; j++){
-	c_atoms[j]->zeroForces();
-      }
-      
-      for(j = 0; j < c_n_SRI; j++){
-	c_sr_interactions[j]->calc_forces();
-      }
-      
-      longRange->calc_forces();
+      myFF->doForces();
             
       // complete the verlet move
       
       move_b( dt );
 
+      time = i + 1;
+      
       if( entry_plug->setTemp ){
-	if( !(i % vel_n) ) tStats->velocitize();
+	if( !(time % vel_n) ) tStats->velocitize();
       }
-      if( !(i % sample_n) ) dump_out->writeDump( i * dt );
-      if( !(i % status_n) ) e_out->writeStat( i * dt );
+      if( !(time % sample_n) ) dump_out->writeDump( time * dt );
+      if( !(time % status_n) ) e_out->writeStat( time * dt );
     }
   }
   
@@ -427,7 +329,6 @@ void Verlet::move_b( double dt ){
   const double e_convert = 4.184e-4; // converts kcal/mol -> amu*A^2/fs^2
   
   double vx, vy, vz;
-  double v_sqr;
   int mb;
   double h_dt = 0.5 * dt;