| 63 | 
  | 
  useReactionField = 0; | 
| 64 | 
  | 
  useGB = 0; | 
| 65 | 
  | 
  useEAM = 0; | 
| 66 | 
+ | 
  useMolecularCutoffs = 0; | 
| 67 | 
  | 
 | 
| 68 | 
  | 
  excludes = Exclude::Instance(); | 
| 69 | 
  | 
 | 
| 349 | 
  | 
  // entire system: | 
| 350 | 
  | 
 | 
| 351 | 
  | 
  ndf = ndf - 3 - nZconstraints; | 
| 351 | 
– | 
 | 
| 352 | 
– | 
  std::cerr << "ndf = " << ndf; | 
| 352 | 
  | 
 | 
| 353 | 
  | 
  return ndf; | 
| 354 | 
  | 
} | 
| 437 | 
  | 
  //fInfo.SIM_uses_RF = 0; | 
| 438 | 
  | 
  fInfo.SIM_uses_GB = useGB; | 
| 439 | 
  | 
  fInfo.SIM_uses_EAM = useEAM; | 
| 440 | 
+ | 
  fInfo.SIM_uses_molecular_cutoffs = useMolecularCutoffs; | 
| 441 | 
  | 
 | 
| 442 | 
  | 
  n_exclude = excludes->getSize(); | 
| 443 | 
  | 
  excl = excludes->getFortranArray(); | 
| 512 | 
  | 
               "\tCurrent Value of LJrcut = %G at time %G\n " | 
| 513 | 
  | 
               "\tThis is larger than half of at least one of the\n" | 
| 514 | 
  | 
               "\tperiodic box vectors.  Right now, the Box matrix is:\n" | 
| 515 | 
< | 
               "\n, %G" | 
| 515 | 
> | 
               "\n" | 
| 516 | 
  | 
               "\t[ %G %G %G ]\n" | 
| 517 | 
  | 
               "\t[ %G %G %G ]\n" | 
| 518 | 
  | 
               "\t[ %G %G %G ]\n", | 
| 519 | 
< | 
               rCut, currentTime, maxCutoff, | 
| 519 | 
> | 
               rCut, currentTime, | 
| 520 | 
  | 
               Hmat[0][0], Hmat[0][1], Hmat[0][2], | 
| 521 | 
  | 
               Hmat[1][0], Hmat[1][1], Hmat[1][2], | 
| 522 | 
  | 
               Hmat[2][0], Hmat[2][1], Hmat[2][2]); |