| 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 |
|
|