| 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 |  |  |