| 10 | 
  | 
#endif // is_mpi | 
| 11 | 
  | 
 | 
| 12 | 
  | 
 | 
| 13 | 
+ | 
#ifdef PROFILE | 
| 14 | 
+ | 
#include "mdProfile.hpp" | 
| 15 | 
+ | 
#endif | 
| 16 | 
+ | 
 | 
| 17 | 
  | 
#include "simError.h" | 
| 18 | 
  | 
#include "ForceFields.hpp" | 
| 19 | 
  | 
#include "Atom.hpp" | 
| 30 | 
  | 
 | 
| 31 | 
  | 
  //calc rCut and rList | 
| 32 | 
  | 
 | 
| 33 | 
< | 
  entry_plug->setRcut( 2.5 * bigSigma );   | 
| 33 | 
> | 
  entry_plug->setDefaultRcut( 2.5 * bigSigma );   | 
| 34 | 
  | 
     | 
| 35 | 
  | 
} | 
| 36 | 
  | 
 | 
| 54 | 
  | 
    entry_plug->atoms[i]->zeroForces();     | 
| 55 | 
  | 
  } | 
| 56 | 
  | 
 | 
| 57 | 
+ | 
#ifdef PROFILE | 
| 58 | 
+ | 
  startProfile(pro7); | 
| 59 | 
+ | 
#endif | 
| 60 | 
+ | 
   | 
| 61 | 
  | 
  for(i=0; i<entry_plug->n_mol; i++ ){ | 
| 62 | 
  | 
    entry_plug->molecules[i].calcForces(); | 
| 63 | 
  | 
  } | 
| 64 | 
  | 
 | 
| 65 | 
+ | 
#ifdef PROFILE | 
| 66 | 
+ | 
  endProfile( pro7 ); | 
| 67 | 
+ | 
#endif | 
| 68 | 
+ | 
 | 
| 69 | 
  | 
  config = entry_plug->getConfiguration(); | 
| 70 | 
  | 
   | 
| 71 | 
  | 
  frc = config->getFrcArray(); | 
| 81 | 
  | 
    entry_plug->tau[i] = 0.0; | 
| 82 | 
  | 
  } | 
| 83 | 
  | 
 | 
| 84 | 
+ | 
 | 
| 85 | 
+ | 
#ifdef PROFILE | 
| 86 | 
+ | 
  startProfile(pro8); | 
| 87 | 
+ | 
#endif | 
| 88 | 
+ | 
 | 
| 89 | 
  | 
  fortranForceLoop( pos, | 
| 90 | 
  | 
                    A, | 
| 91 | 
  | 
                    u_l, | 
| 97 | 
  | 
                    &passedCalcStress, | 
| 98 | 
  | 
                    &isError ); | 
| 99 | 
  | 
 | 
| 100 | 
+ | 
#ifdef PROFILE | 
| 101 | 
+ | 
  endProfile(pro8); | 
| 102 | 
+ | 
#endif | 
| 103 | 
+ | 
 | 
| 104 | 
+ | 
 | 
| 105 | 
  | 
  if( isError ){ | 
| 106 | 
  | 
    sprintf( painCave.errMsg, | 
| 107 | 
  | 
             "Error returned from the fortran force calculation.\n" ); |