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root/group/trunk/mdtools/md_code/Symplectic.cpp
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Comparing:
branches/mmeineke/mdtools/md_code/Symplectic.cpp (file contents), Revision 10 by mmeineke, Tue Jul 9 18:40:59 2002 UTC vs.
trunk/mdtools/md_code/Symplectic.cpp (file contents), Revision 134 by chuckv, Fri Oct 11 15:09:09 2002 UTC

# Line 120 | Line 120 | void Symplectic::integrate( void ){
120    double dt2;                       // half the dt
121  
122    double vx, vy, vz;    // the velocities
123 <  double vx2, vy2, vz2; // the square of the velocities
123 > //  double vx2, vy2, vz2; // the square of the velocities
124    double rx, ry, rz;    // the postitions
125    
126    double ji[3];   // the body frame angular momentum
# Line 129 | Line 129 | void Symplectic::integrate( void ){
129    double angle;   // the angle through which to rotate the rotation matrix
130    double A[3][3]; // the rotation matrix
131  
132 +  int time;
133  
134    double dt          = entry_plug->dt;
135    double runTime     = entry_plug->run_time;
# Line 170 | Line 171 | void Symplectic::integrate( void ){
171      tStats->velocitize();
172    }
173    
174 +  dump_out->writeDump( 0.0 );
175 +  e_out->writeStat( 0.0 );
176 +
177    if( n_constrained ){
178  
179      double *Rx = new double[nAtoms];
# Line 358 | Line 362 | void Symplectic::integrate( void ){
362            dAtom->setJz( ji[2] );
363          }
364        }
365 <    
366 <      if( entry_plug->setTemp ){
367 <        if( !(tl % vel_n) ) tStats->velocitize();
365 >    
366 >      time = tl + 1;
367 >      
368 >      if( entry_plug->setTemp ){
369 >        if( !(time % vel_n) ) tStats->velocitize();
370        }
371 <      if( !(tl % sample_n) ) dump_out->writeDump( tl * dt );
372 <      if( !(tl % status_n) ) e_out->writeStat( tl * dt );
371 >      if( !(time % sample_n) ) dump_out->writeDump( time * dt );
372 >      if( !(time % status_n) ) e_out->writeStat( time * dt );
373      }
374    }
375    else{
# Line 486 | Line 492 | void Symplectic::integrate( void ){
492          atoms[i]->set_vy( vy );
493          atoms[i]->set_vz( vz );
494          
495 <        vx2 = vx * vx;
496 <        vy2 = vy * vy;
497 <        vz2 = vz * vz;
495 > //      vx2 = vx * vx;
496 > //      vy2 = vy * vy;
497 > //      vz2 = vz * vz;
498          
499          if( atoms[i]->isDirectional() ){
500  
# Line 521 | Line 527 | void Symplectic::integrate( void ){
527            dAtom->setJz( ji[2] );
528          }
529        }
530 <    
530 >      
531 >      time = tl + 1;
532 >      
533        if( entry_plug->setTemp ){
534 <        if( !(tl % vel_n) ) tStats->velocitize();
534 >        if( !(time % vel_n) ) tStats->velocitize();
535        }
536 <      if( !(tl % sample_n) ) dump_out->writeDump( tl * dt );
537 <      if( !(tl % status_n) ) e_out->writeStat( tl * dt );
536 >      if( !(time % sample_n) ) dump_out->writeDump( time * dt );
537 >      if( !(time % status_n) ) e_out->writeStat( time * dt );
538      }
539    }
540  

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