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 |
|
|