| 30 | 
  | 
  n_dipoles = 0; | 
| 31 | 
  | 
  ndf = 0; | 
| 32 | 
  | 
  ndfRaw = 0; | 
| 33 | 
+ | 
  nZconstraints = 0; | 
| 34 | 
  | 
  the_integrator = NULL; | 
| 35 | 
  | 
  setTemp = 0; | 
| 36 | 
  | 
  thermalTime = 0.0; | 
| 55 | 
  | 
  useGB = 0; | 
| 56 | 
  | 
  useEAM = 0; | 
| 57 | 
  | 
 | 
| 58 | 
+ | 
  myConfiguration = new SimState(); | 
| 59 | 
+ | 
 | 
| 60 | 
  | 
  wrapMeSimInfo( this ); | 
| 61 | 
  | 
} | 
| 62 | 
  | 
 | 
| 63 | 
+ | 
 | 
| 64 | 
+ | 
SimInfo::~SimInfo(){ | 
| 65 | 
+ | 
 | 
| 66 | 
+ | 
  delete myConfiguration; | 
| 67 | 
+ | 
 | 
| 68 | 
+ | 
  map<string, GenericData*>::iterator i; | 
| 69 | 
+ | 
   | 
| 70 | 
+ | 
  for(i = properties.begin(); i != properties.end(); i++) | 
| 71 | 
+ | 
    delete (*i).second; | 
| 72 | 
+ | 
     | 
| 73 | 
+ | 
} | 
| 74 | 
+ | 
 | 
| 75 | 
  | 
void SimInfo::setBox(double newBox[3]) { | 
| 76 | 
  | 
   | 
| 77 | 
  | 
  int i, j; | 
| 307 | 
  | 
  dsq = dx*dx + dy*dy + dz*dz; | 
| 308 | 
  | 
  boxL[2] = sqrt( dsq ); | 
| 309 | 
  | 
  if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; | 
| 310 | 
+ | 
   | 
| 311 | 
+ | 
  checkCutOffs(); | 
| 312 | 
  | 
 | 
| 313 | 
  | 
} | 
| 314 | 
  | 
 | 
| 363 | 
  | 
  ndf = ndf_local; | 
| 364 | 
  | 
#endif | 
| 365 | 
  | 
 | 
| 366 | 
< | 
  ndf = ndf - 3; | 
| 366 | 
> | 
  ndf = ndf - 3 - nZconstraints; | 
| 367 | 
  | 
 | 
| 368 | 
  | 
  return ndf; | 
| 369 | 
  | 
} | 
| 475 | 
  | 
 | 
| 476 | 
  | 
  int cutChanged = 0; | 
| 477 | 
  | 
 | 
| 478 | 
+ | 
 | 
| 479 | 
+ | 
 | 
| 480 | 
  | 
  if( boxIsInit ){ | 
| 481 | 
  | 
     | 
| 482 | 
  | 
    //we need to check cutOffs against the box | 
| 483 | 
< | 
     | 
| 484 | 
< | 
    if( maxCutoff > rCut ){ | 
| 483 | 
> | 
    | 
| 484 | 
> | 
    if(( maxCutoff > rCut )&&(usePBC)){ | 
| 485 | 
  | 
      if( rCut < origRcut ){ | 
| 486 | 
  | 
        rCut = origRcut; | 
| 487 | 
  | 
        if (rCut > maxCutoff) rCut = maxCutoff; | 
| 510 | 
  | 
    } | 
| 511 | 
  | 
 | 
| 512 | 
  | 
 | 
| 513 | 
< | 
    if (rCut > maxCutoff) { | 
| 513 | 
> | 
    if ((rCut > maxCutoff)&&(usePBC)) { | 
| 514 | 
  | 
      sprintf( painCave.errMsg, | 
| 515 | 
  | 
               "New Box size is setting the long range cutoff radius " | 
| 516 | 
  | 
               "to %lf\n", |