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 |
+ |
if( !strcmp( argV[i], "--gofrTheta" ) ){ |
128 |
+ |
|
129 |
+ |
i++; |
130 |
+ |
if( i>=argC ){ |
131 |
+ |
sprintf( painCave.errMsg, |
132 |
+ |
"\n" |
133 |
+ |
"not enough arguments for --gofrTheta\n"); |
134 |
+ |
usage(); |
135 |
+ |
painCave.isFatal = 1; |
136 |
+ |
simError(); |
137 |
+ |
} |
138 |
+ |
pair1 = argV[i]; |
139 |
+ |
|
140 |
+ |
i++; |
141 |
+ |
if( i>=argC ){ |
142 |
+ |
sprintf( painCave.errMsg, |
143 |
+ |
"\n" |
144 |
+ |
"not enough arguments for --gofrTheta\n"); |
145 |
+ |
usage(); |
146 |
+ |
painCave.isFatal = 1; |
147 |
+ |
simError(); |
148 |
+ |
} |
149 |
+ |
pair2 = argV[i]; |
150 |
+ |
|
151 |
+ |
pairType = gofrTheta; |
152 |
+ |
theList.push_back(PairCorrList( pairType, pair1, pair2 )); |
153 |
+ |
havePairCorrs = true; |
154 |
+ |
} |
155 |
+ |
|
156 |
+ |
if( !strcmp( argV[i], "--gofrOmega" ) ){ |
157 |
+ |
|
158 |
+ |
i++; |
159 |
+ |
if( i>=argC ){ |
160 |
+ |
sprintf( painCave.errMsg, |
161 |
+ |
"\n" |
162 |
+ |
"not enough arguments for --gofrOmega\n"); |
163 |
+ |
usage(); |
164 |
+ |
painCave.isFatal = 1; |
165 |
+ |
simError(); |
166 |
+ |
} |
167 |
+ |
pair1 = argV[i]; |
168 |
+ |
|
169 |
+ |
i++; |
170 |
+ |
if( i>=argC ){ |
171 |
+ |
sprintf( painCave.errMsg, |
172 |
+ |
"\n" |
173 |
+ |
"not enough arguments for --gofrOmega\n"); |
174 |
+ |
usage(); |
175 |
+ |
painCave.isFatal = 1; |
176 |
+ |
simError(); |
177 |
+ |
} |
178 |
+ |
pair2 = argV[i]; |
179 |
+ |
|
180 |
+ |
pairType = gofrOmega; |
181 |
+ |
theList.push_back(PairCorrList( pairType, pair1, pair2 )); |
182 |
+ |
havePairCorrs = true; |
183 |
+ |
} |
184 |
+ |
|
185 |
|
else if( !strcmp( argV[i], "--version") ){ |
186 |
|
|
187 |
|
printf("\n" |
311 |
|
|
312 |
|
break; |
313 |
|
|
314 |
+ |
case 's': |
315 |
+ |
// -s turn on separate output files |
316 |
+ |
|
317 |
+ |
separateOut = true; |
318 |
+ |
break; |
319 |
+ |
|
320 |
|
case 'n': |
321 |
|
// -n <int> set <int> to the nBins |
322 |
|
|
466 |
|
theCorrs.setNbins( nBins ); |
467 |
|
theCorrs.setFrames( infoArray, nFrames, reader ); |
468 |
|
theCorrs.setPairCorrList( theList ); |
469 |
< |
theCorrs.initCorrelations( outPrefix ); |
469 |
> |
theCorrs.initCorrelations( outPrefix, separateOut, havePairCorrs, |
470 |
> |
haveStaticCorrs ); |
471 |
|
|
472 |
|
printf("done\n"); |
473 |
|
fflush(stdout); |
501 |
|
"\n" |
502 |
|
" long:\n" |
503 |
|
" -----\n" |
504 |
< |
" --gofr <atom1> <atom2> g(r) for atom1 and atom2\n" |
505 |
< |
" *note: \"_ALL_\" matches all atoms/n" |
506 |
< |
" --version displays the version number\n" |
507 |
< |
" --help displays this help message.\n" |
504 |
> |
" --gofr <atom1> <atom2> g(r) for atom1 and atom2\n" |
505 |
> |
" *note: \"_ALL_\" matches all atoms\n" |
506 |
> |
" --gofrTheta <atom1> <atom2> g(r, theta) for atom1 and atom2\n" |
507 |
> |
" *note: \"_ALL_\" matches all atoms\n" |
508 |
> |
" --gofrOmega <atom1> <atom2> g(r, omega) for atom1 and atom2\n" |
509 |
> |
" *note: \"_ALL_\" matches all atoms\n" |
510 |
> |
" --version displays the version number\n" |
511 |
> |
" --help displays this help message.\n" |
512 |
|
|
513 |
|
"\n" |
514 |
|
"\n", |