| 1 |
#define _FILE_OFFSET_BITS 64 |
| 2 |
|
| 3 |
#include <stdio.h> |
| 4 |
#include <stdlib.h> |
| 5 |
#include <string.h> |
| 6 |
|
| 7 |
|
| 8 |
#include "params.h" |
| 9 |
#include "tcProps.h" |
| 10 |
#include "readWrite.h" |
| 11 |
#include "scdCorr.h" |
| 12 |
#include "directorHead.h" |
| 13 |
#include "directorWhole.h" |
| 14 |
|
| 15 |
|
| 16 |
#define VERSION_MAJOR 0 |
| 17 |
#define VERSION_MINOR 1 |
| 18 |
|
| 19 |
char *programName; /*the name of the program */ |
| 20 |
void usage(void); |
| 21 |
|
| 22 |
int main( int argC, char *argV[] ){ |
| 23 |
|
| 24 |
// list of 'a priori' constants |
| 25 |
|
| 26 |
const int nLipAtoms = NL_ATOMS; |
| 27 |
const int nBonds = NBONDS; |
| 28 |
const int nLipids = NLIPIDS; |
| 29 |
const int nSSD = NSSD; |
| 30 |
const int nAtoms = nLipAtoms * nLipids + nSSD; |
| 31 |
|
| 32 |
// different needed variables |
| 33 |
|
| 34 |
struct atomCoord atoms[nAtoms]; |
| 35 |
int i,j,k; |
| 36 |
|
| 37 |
char* outPrefix; // the output prefix |
| 38 |
char currentFlag; // used in parsing the flags |
| 39 |
int done = 0; // multipurpose boolean |
| 40 |
int havePrefix; // boolean for the output prefix |
| 41 |
int haveMaxLength; |
| 42 |
char* conversionCheck; |
| 43 |
int conversionError; |
| 44 |
int optionError; |
| 45 |
char* pair1; |
| 46 |
char* pair2; |
| 47 |
int scdCorr; |
| 48 |
double startTime; |
| 49 |
double maxLength; |
| 50 |
int directorHead, directorWhole; |
| 51 |
|
| 52 |
// system initialization |
| 53 |
|
| 54 |
isScanned = 0; |
| 55 |
fileOpen = 0; |
| 56 |
nFrames = 0; |
| 57 |
frameTimes = NULL; |
| 58 |
|
| 59 |
outPrefix = NULL; |
| 60 |
inName = NULL; |
| 61 |
|
| 62 |
haveMaxLength = 0; |
| 63 |
conversionError = 0; |
| 64 |
optionError = 0; |
| 65 |
havePrefix = 0; |
| 66 |
scdCorr = 0; |
| 67 |
startTime = 0.0; |
| 68 |
directorHead = 0; |
| 69 |
directorWhole = 0; |
| 70 |
|
| 71 |
|
| 72 |
// parse the command line |
| 73 |
|
| 74 |
programName = argV[0]; /*save the program name in case we need it*/ |
| 75 |
|
| 76 |
for( i = 1; i < argC; i++){ |
| 77 |
|
| 78 |
if(argV[i][0] =='-'){ |
| 79 |
|
| 80 |
// parse the option |
| 81 |
|
| 82 |
if(argV[i][1] == '-' ){ |
| 83 |
|
| 84 |
// parse long word options |
| 85 |
|
| 86 |
if( !strcmp( argV[i], "--gofr" ) ){ |
| 87 |
|
| 88 |
i++; |
| 89 |
if( i>=argC ){ |
| 90 |
fprintf( stderr, |
| 91 |
"\n" |
| 92 |
"not enough arguments for --gofr\n"); |
| 93 |
usage(); |
| 94 |
exit(0); |
| 95 |
} |
| 96 |
pair1 = argV[i]; |
| 97 |
|
| 98 |
i++; |
| 99 |
if( i>=argC ){ |
| 100 |
fprintf( stderr, |
| 101 |
"\n" |
| 102 |
"not enough arguments for --gofr\n"); |
| 103 |
usage(); |
| 104 |
exit(0); |
| 105 |
} |
| 106 |
pair2 = argV[i]; |
| 107 |
|
| 108 |
} |
| 109 |
|
| 110 |
else if( !strcmp( argV[i], "--gofrTheta" ) ){ |
| 111 |
|
| 112 |
i++; |
| 113 |
if( i>=argC ){ |
| 114 |
fprintf( stderr, |
| 115 |
"\n" |
| 116 |
"not enough arguments for --gofrTheta\n"); |
| 117 |
usage(); |
| 118 |
exit(0); |
| 119 |
} |
| 120 |
pair1 = argV[i]; |
| 121 |
|
| 122 |
i++; |
| 123 |
if( i>=argC ){ |
| 124 |
fprintf( stderr, |
| 125 |
"\n" |
| 126 |
"not enough arguments for --gofrTheta\n"); |
| 127 |
usage(); |
| 128 |
exit(0); |
| 129 |
} |
| 130 |
pair2 = argV[i]; |
| 131 |
|
| 132 |
} |
| 133 |
|
| 134 |
else if( !strcmp( argV[i], "--gofrOmega" ) ){ |
| 135 |
|
| 136 |
i++; |
| 137 |
if( i>=argC ){ |
| 138 |
fprintf( stderr, |
| 139 |
"\n" |
| 140 |
"not enough arguments for --gofrOmega\n"); |
| 141 |
usage(); |
| 142 |
exit(0); |
| 143 |
} |
| 144 |
pair1 = argV[i]; |
| 145 |
|
| 146 |
i++; |
| 147 |
if( i>=argC ){ |
| 148 |
fprintf( stderr, |
| 149 |
"\n" |
| 150 |
"not enough arguments for --gofrOmega\n"); |
| 151 |
usage(); |
| 152 |
exit(0); |
| 153 |
} |
| 154 |
pair2 = argV[i]; |
| 155 |
|
| 156 |
} |
| 157 |
|
| 158 |
else if( !strcmp( argV[i], "--version") ){ |
| 159 |
|
| 160 |
printf("\n" |
| 161 |
"tcProps version %d.%d\n" |
| 162 |
"\n", |
| 163 |
VERSION_MAJOR, VERSION_MINOR ); |
| 164 |
exit(0); |
| 165 |
|
| 166 |
} |
| 167 |
|
| 168 |
else if( !strcmp( argV[i], "--help") ){ |
| 169 |
|
| 170 |
usage(); |
| 171 |
exit(0); |
| 172 |
} |
| 173 |
|
| 174 |
// anything else is an error |
| 175 |
|
| 176 |
else{ |
| 177 |
fprintf( stderr, |
| 178 |
"Invalid option \"%s\"\n", argV[i] ); |
| 179 |
usage(); |
| 180 |
exit(0); |
| 181 |
} |
| 182 |
} |
| 183 |
|
| 184 |
else{ |
| 185 |
|
| 186 |
// parse single character options |
| 187 |
|
| 188 |
done =0; |
| 189 |
j = 1; |
| 190 |
currentFlag = argV[i][j]; |
| 191 |
while( (currentFlag != '\0') && (!done) ){ |
| 192 |
|
| 193 |
switch(currentFlag){ |
| 194 |
|
| 195 |
case 'o': |
| 196 |
// -o <prefix> => the output prefix. |
| 197 |
|
| 198 |
j++; |
| 199 |
currentFlag = argV[i][j]; |
| 200 |
|
| 201 |
if( currentFlag != '\0' ) optionError = 1; |
| 202 |
|
| 203 |
if( optionError ){ |
| 204 |
fprintf( stderr, |
| 205 |
"\n" |
| 206 |
"The -o flag should end an option sequence.\n" |
| 207 |
" example: -r <outname> *NOT* -or <outname>\n" ); |
| 208 |
usage(); |
| 209 |
exit(0); |
| 210 |
} |
| 211 |
|
| 212 |
i++; |
| 213 |
if( i>=argC ){ |
| 214 |
fprintf( stderr, |
| 215 |
"\n" |
| 216 |
"not enough arguments for -o\n"); |
| 217 |
usage(); |
| 218 |
exit(0); |
| 219 |
} |
| 220 |
|
| 221 |
outPrefix = argV[i]; |
| 222 |
if( outPrefix[0] == '-' ) optionError = 1; |
| 223 |
|
| 224 |
if( optionError ){ |
| 225 |
fprintf( stderr, |
| 226 |
"\n" |
| 227 |
"\"%s\" is not a valid out prefix/name.\n" |
| 228 |
"Out prefix/name should not begin with a dash.\n", |
| 229 |
outPrefix ); |
| 230 |
usage(); |
| 231 |
exit(0); |
| 232 |
} |
| 233 |
|
| 234 |
havePrefix = 1; |
| 235 |
done = 1; |
| 236 |
break; |
| 237 |
|
| 238 |
case 'l': |
| 239 |
// -l <double> set <double> to the maxLength |
| 240 |
|
| 241 |
haveMaxLength = 1; |
| 242 |
j++; |
| 243 |
currentFlag = argV[i][j]; |
| 244 |
|
| 245 |
if( currentFlag != '\0' ) optionError = 1; |
| 246 |
|
| 247 |
if( optionError ){ |
| 248 |
fprintf( stderr, |
| 249 |
"\n" |
| 250 |
"The -l flag should end an option sequence.\n" |
| 251 |
" example: -sl <double> *NOT* -ls <double>\n" ); |
| 252 |
usage(); |
| 253 |
exit(0); |
| 254 |
} |
| 255 |
|
| 256 |
i++; |
| 257 |
if( i>=argC ){ |
| 258 |
fprintf( stderr, |
| 259 |
"\n" |
| 260 |
"not enough arguments for -l\n"); |
| 261 |
usage(); |
| 262 |
exit(0); |
| 263 |
} |
| 264 |
|
| 265 |
maxLength = atof( argV[i] ); |
| 266 |
|
| 267 |
done = 1; |
| 268 |
|
| 269 |
break; |
| 270 |
|
| 271 |
case 't': |
| 272 |
// -t <double> set <double> to the startTime |
| 273 |
|
| 274 |
j++; |
| 275 |
currentFlag = argV[i][j]; |
| 276 |
|
| 277 |
if( currentFlag != '\0' ) optionError = 1; |
| 278 |
|
| 279 |
if( optionError ){ |
| 280 |
fprintf( stderr, |
| 281 |
"\n" |
| 282 |
"The -t flag should end an option sequence.\n" |
| 283 |
" example: -st <double> *NOT* -ts <double>\n" ); |
| 284 |
usage(); |
| 285 |
exit(0); |
| 286 |
} |
| 287 |
|
| 288 |
i++; |
| 289 |
if( i>=argC ){ |
| 290 |
fprintf( stderr, |
| 291 |
"\n" |
| 292 |
"not enough arguments for -t\n"); |
| 293 |
usage(); |
| 294 |
exit(0); |
| 295 |
} |
| 296 |
|
| 297 |
startTime = atof( argV[i] ); |
| 298 |
done = 1; |
| 299 |
break; |
| 300 |
|
| 301 |
case 's': |
| 302 |
// -s turn on Scd corr |
| 303 |
|
| 304 |
scdCorr = 1; |
| 305 |
break; |
| 306 |
|
| 307 |
case 'h': |
| 308 |
// -h turn on director head |
| 309 |
|
| 310 |
directorHead = 1; |
| 311 |
break; |
| 312 |
|
| 313 |
case 'w': |
| 314 |
// -h turn on director head |
| 315 |
|
| 316 |
directorWhole = 1; |
| 317 |
break; |
| 318 |
|
| 319 |
|
| 320 |
default: |
| 321 |
|
| 322 |
fprintf( stderr, |
| 323 |
"\n" |
| 324 |
"Bad option \"-%c\"\n", currentFlag); |
| 325 |
usage(); |
| 326 |
exit(0); |
| 327 |
} |
| 328 |
j++; |
| 329 |
currentFlag = argV[i][j]; |
| 330 |
} |
| 331 |
} |
| 332 |
} |
| 333 |
|
| 334 |
else{ |
| 335 |
|
| 336 |
if( inName != NULL ){ |
| 337 |
fprintf( stderr, |
| 338 |
"Error at \"%s\", program does not currently support\n" |
| 339 |
"more than one input dump file.\n" |
| 340 |
"\n", |
| 341 |
argV[i]); |
| 342 |
usage(); |
| 343 |
exit(0); |
| 344 |
} |
| 345 |
|
| 346 |
inName = argV[i]; |
| 347 |
|
| 348 |
} |
| 349 |
} |
| 350 |
|
| 351 |
if( inName == NULL ){ |
| 352 |
fprintf( stderr, |
| 353 |
"Error, dump file is needed to run.\n" ); |
| 354 |
usage(); |
| 355 |
exit(0); |
| 356 |
} |
| 357 |
|
| 358 |
if( outPrefix == NULL ) |
| 359 |
outPrefix = inName; |
| 360 |
|
| 361 |
|
| 362 |
// initialize the arrays |
| 363 |
|
| 364 |
for(i=0;i<nLipids;i++){ |
| 365 |
|
| 366 |
atoms[nLipAtoms*i+0].type = HEAD; |
| 367 |
atoms[nLipAtoms*i+0].mass = 72; |
| 368 |
atoms[nLipAtoms*i+0].u[0] = 0.0; |
| 369 |
atoms[nLipAtoms*i+0].u[1] = 0.0; |
| 370 |
atoms[nLipAtoms*i+0].u[2] = 1.0; |
| 371 |
|
| 372 |
|
| 373 |
|
| 374 |
atoms[nLipAtoms*i+1].type = CH2; |
| 375 |
atoms[nLipAtoms*i+1].mass = 14.03; |
| 376 |
|
| 377 |
atoms[nLipAtoms*i+2].type = CH; |
| 378 |
atoms[nLipAtoms*i+2].mass = 13.02; |
| 379 |
|
| 380 |
atoms[nLipAtoms*i+3].type = CH2; |
| 381 |
atoms[nLipAtoms*i+3].mass = 14.03; |
| 382 |
|
| 383 |
atoms[nLipAtoms*i+4].type = CH2; |
| 384 |
atoms[nLipAtoms*i+4].mass = 14.03; |
| 385 |
|
| 386 |
atoms[nLipAtoms*i+5].type = CH2; |
| 387 |
atoms[nLipAtoms*i+5].mass = 14.03; |
| 388 |
|
| 389 |
atoms[nLipAtoms*i+6].type = CH2; |
| 390 |
atoms[nLipAtoms*i+6].mass = 14.03; |
| 391 |
|
| 392 |
atoms[nLipAtoms*i+7].type = CH2; |
| 393 |
atoms[nLipAtoms*i+7].mass = 14.03; |
| 394 |
|
| 395 |
atoms[nLipAtoms*i+8].type = CH2; |
| 396 |
atoms[nLipAtoms*i+8].mass = 14.03; |
| 397 |
|
| 398 |
atoms[nLipAtoms*i+9].type = CH2; |
| 399 |
atoms[nLipAtoms*i+9].mass = 14.03; |
| 400 |
|
| 401 |
atoms[nLipAtoms*i+10].type = CH3; |
| 402 |
atoms[nLipAtoms*i+10].mass = 15.04; |
| 403 |
|
| 404 |
atoms[nLipAtoms*i+11].type = CH2; |
| 405 |
atoms[nLipAtoms*i+11].mass = 14.03; |
| 406 |
|
| 407 |
atoms[nLipAtoms*i+12].type = CH2; |
| 408 |
atoms[nLipAtoms*i+12].mass = 14.03; |
| 409 |
|
| 410 |
atoms[nLipAtoms*i+13].type = CH2; |
| 411 |
atoms[nLipAtoms*i+13].mass = 14.03; |
| 412 |
|
| 413 |
atoms[nLipAtoms*i+14].type = CH2; |
| 414 |
atoms[nLipAtoms*i+14].mass = 14.03; |
| 415 |
|
| 416 |
atoms[nLipAtoms*i+15].type = CH2; |
| 417 |
atoms[nLipAtoms*i+15].mass = 14.03; |
| 418 |
|
| 419 |
atoms[nLipAtoms*i+16].type = CH2; |
| 420 |
atoms[nLipAtoms*i+16].mass = 14.03; |
| 421 |
|
| 422 |
atoms[nLipAtoms*i+17].type = CH2; |
| 423 |
atoms[nLipAtoms*i+17].mass = 14.03; |
| 424 |
|
| 425 |
atoms[nLipAtoms*i+18].type = CH3; |
| 426 |
atoms[nLipAtoms*i+18].mass = 15.04; |
| 427 |
} |
| 428 |
|
| 429 |
for(i=(nLipAtoms*nLipids);i<nAtoms;i++){ |
| 430 |
atoms[i].type = SSD; |
| 431 |
atoms[i].mass = 18.03; |
| 432 |
atoms[i].u[0] = 0.0; |
| 433 |
atoms[i].u[1] = 0.0; |
| 434 |
atoms[i].u[2] = 1.0; |
| 435 |
} |
| 436 |
|
| 437 |
// read and set the frames |
| 438 |
|
| 439 |
openFile(); |
| 440 |
|
| 441 |
fprintf( stdout, |
| 442 |
"\n" |
| 443 |
"Counting the number of frames in \"%s\"...", |
| 444 |
inName ); |
| 445 |
fflush(stdout); |
| 446 |
|
| 447 |
setFrames(); |
| 448 |
|
| 449 |
fprintf( stdout, |
| 450 |
"done.\n" |
| 451 |
"nFrames = %d.\n", |
| 452 |
nFrames ); |
| 453 |
fflush(stdout); |
| 454 |
|
| 455 |
if(scdCorr){ |
| 456 |
|
| 457 |
fprintf ( stdout, |
| 458 |
"Calculating the Scd correlation\n" ); |
| 459 |
fflush( stdout ); |
| 460 |
|
| 461 |
calcScdCorr( startTime, atoms, outPrefix ); |
| 462 |
} |
| 463 |
|
| 464 |
if(directorHead){ |
| 465 |
|
| 466 |
fprintf ( stdout, |
| 467 |
"Calculating the Head director\n" ); |
| 468 |
fflush( stdout ); |
| 469 |
|
| 470 |
calcDirHeadCorr( startTime, atoms, outPrefix ); |
| 471 |
} |
| 472 |
|
| 473 |
if(directorWhole){ |
| 474 |
|
| 475 |
fprintf ( stdout, |
| 476 |
"Calculating the bilayer director\n" ); |
| 477 |
fflush( stdout ); |
| 478 |
|
| 479 |
calcDirWholeCorr( startTime, atoms, outPrefix ); |
| 480 |
} |
| 481 |
|
| 482 |
|
| 483 |
closeFile(); |
| 484 |
|
| 485 |
} |
| 486 |
|
| 487 |
|
| 488 |
/*************************************************************************** |
| 489 |
* prints out the usage for the command line arguments, then exits. |
| 490 |
***************************************************************************/ |
| 491 |
|
| 492 |
void usage(){ |
| 493 |
(void)fprintf(stdout, |
| 494 |
"\n" |
| 495 |
"The proper usage is: %s [options] <input_file>\n" |
| 496 |
"\n" |
| 497 |
"Options:\n" |
| 498 |
"\n" |
| 499 |
" short:\n" |
| 500 |
" ------\n" |
| 501 |
" -o <name> The output prefix\n" |
| 502 |
" -t <time> Set the start time for correlations\n" |
| 503 |
" -l <maxLength> set the maximum value of r\n" |
| 504 |
" *Defaults to 1/2 smallest length of first frame.\n" |
| 505 |
" -s Calculate the Scd chain correlation.\n" |
| 506 |
" -h Calculate the directors for the head groups\n" |
| 507 |
" -w Calculate the director fro the bilayers\n" |
| 508 |
"\n" |
| 509 |
" long:\n" |
| 510 |
" -----\n" |
| 511 |
" --gofr <atom1> <atom2> g(r) for atom1 and atom2\n" |
| 512 |
" --gofrTheta <atom1> <atom2> g(r, theta) for atom1 and atom2\n" |
| 513 |
" --gofrOmega <atom1> <atom2> g(r, omega) for atom1 and atom2\n" |
| 514 |
" --version displays the version number\n" |
| 515 |
" --help displays this help message.\n" |
| 516 |
|
| 517 |
"\n" |
| 518 |
"\n", |
| 519 |
programName); |
| 520 |
} |
