| 39 | 
  | 
  bool haveMaxLength; | 
| 40 | 
  | 
  double maxLength; | 
| 41 | 
  | 
   | 
| 42 | 
+ | 
  bool separateOut; | 
| 43 | 
+ | 
  bool havePairCorrs; | 
| 44 | 
+ | 
  bool haveStaticCorrs; | 
| 45 | 
+ | 
 | 
| 46 | 
  | 
  int nBins; | 
| 47 | 
  | 
 | 
| 48 | 
  | 
  vector<PairCorrList> theList; | 
| 63 | 
  | 
   | 
| 64 | 
  | 
  // first things first, all of the initializations | 
| 65 | 
  | 
 | 
| 66 | 
< | 
  printf("Initializing stuff ....\n"); | 
| 63 | 
< | 
  fflush(sdtout); | 
| 66 | 
> | 
  fflush(stdout); | 
| 67 | 
  | 
  srand48( 1337 );          // the random number generator. | 
| 68 | 
  | 
  initSimError();           // the error handler | 
| 69 | 
  | 
 | 
| 75 | 
  | 
  | 
| 76 | 
  | 
  havePrefix = false; | 
| 77 | 
  | 
  haveMaxLength = false; | 
| 78 | 
+ | 
 | 
| 79 | 
+ | 
  haveStaticCorrs = false; | 
| 80 | 
+ | 
  havePairCorrs = false; | 
| 81 | 
+ | 
  separateOut = false; | 
| 82 | 
  | 
   | 
| 83 | 
  | 
  maxLength = 1.0; | 
| 84 | 
  | 
  nBins = 100; | 
| 85 | 
  | 
 | 
| 86 | 
< | 
  programName = argv[0]; /*save the program name in case we need it*/ | 
| 86 | 
> | 
  programName = argV[0]; /*save the program name in case we need it*/ | 
| 87 | 
  | 
 | 
| 88 | 
  | 
  for( i = 1; i < argC; i++){ | 
| 89 | 
  | 
     | 
| 121 | 
  | 
 | 
| 122 | 
  | 
          pairType = gofr; | 
| 123 | 
  | 
          theList.push_back(PairCorrList( pairType, pair1, pair2 )); | 
| 124 | 
+ | 
          havePairCorrs = true; | 
| 125 | 
  | 
        } | 
| 126 | 
  | 
 | 
| 127 | 
  | 
        else if( !strcmp( argV[i], "--version") ){ | 
| 250 | 
  | 
            } | 
| 251 | 
  | 
             | 
| 252 | 
  | 
            done = true; | 
| 253 | 
+ | 
 | 
| 254 | 
+ | 
            break; | 
| 255 | 
+ | 
 | 
| 256 | 
+ | 
          case 's': | 
| 257 | 
+ | 
            // -s turn on separate output files | 
| 258 | 
  | 
 | 
| 259 | 
+ | 
            separateOut = true; | 
| 260 | 
  | 
            break; | 
| 261 | 
  | 
 | 
| 262 | 
  | 
          case 'n': | 
| 408 | 
  | 
  theCorrs.setNbins( nBins ); | 
| 409 | 
  | 
  theCorrs.setFrames( infoArray, nFrames, reader ); | 
| 410 | 
  | 
  theCorrs.setPairCorrList( theList ); | 
| 411 | 
< | 
  theCorrs.initCorrelations( outPrefix ); | 
| 411 | 
> | 
  theCorrs.initCorrelations( outPrefix, separateOut, havePairCorrs, | 
| 412 | 
> | 
                             haveStaticCorrs ); | 
| 413 | 
  | 
 | 
| 414 | 
  | 
  printf("done\n"); | 
| 415 | 
  | 
  fflush(stdout); | 
| 444 | 
  | 
                "   long:\n" | 
| 445 | 
  | 
                "   -----\n" | 
| 446 | 
  | 
                "   --gofr <atom1> <atom2>    g(r) for atom1 and atom2\n" | 
| 447 | 
< | 
                "                                *note: \"_ALL_\" matches all atoms/n" | 
| 447 | 
> | 
                "                                *note: \"_ALL_\" matches all atoms\n" | 
| 448 | 
  | 
                "   --version                 displays the version number\n" | 
| 449 | 
  | 
                "   --help                    displays this help message.\n" | 
| 450 | 
  | 
                 |