| 1 |
#include <iostream> |
| 2 |
#include <stdio.h> |
| 3 |
#include <stdlib.h> |
| 4 |
#include <string.h> |
| 5 |
#include <math.h> |
| 6 |
|
| 7 |
#include "simError.h" |
| 8 |
#include "SimInfo.hpp" |
| 9 |
#include "ReadWrite.hpp" |
| 10 |
|
| 11 |
#include "MoLocator.hpp" |
| 12 |
#include "latticeBuilder.hpp" |
| 13 |
#include "QuickBass.hpp" |
| 14 |
|
| 15 |
#define VERSION_MAJOR 0 |
| 16 |
#define VERSION_MINOR 1 |
| 17 |
|
| 18 |
char *programName; /*the name of the program */ |
| 19 |
void usage(void); |
| 20 |
int buildLatticeBilayer( double aLat, |
| 21 |
double bLat, |
| 22 |
double leafSpacing); |
| 23 |
using namespace std; |
| 24 |
|
| 25 |
int main(int argC,char* argV[]){ |
| 26 |
|
| 27 |
int i,j; // loop counters |
| 28 |
|
| 29 |
char* outPrefix; // the output prefix |
| 30 |
|
| 31 |
char* conversionCheck; |
| 32 |
bool conversionError; |
| 33 |
bool optionError; |
| 34 |
|
| 35 |
char currentFlag; // used in parsing the flags |
| 36 |
bool done = false; // multipurpose boolean |
| 37 |
bool havePrefix; // boolean for the output prefix |
| 38 |
|
| 39 |
char* lipidName; |
| 40 |
char* waterName; |
| 41 |
bool haveWaterName, haveLipidName; |
| 42 |
|
| 43 |
bool haveSpacing, haveAlat, haveBlat; |
| 44 |
double aLat, bLat, leafSpacing; |
| 45 |
|
| 46 |
char* inName; |
| 47 |
|
| 48 |
// first things first, all of the initializations |
| 49 |
|
| 50 |
fflush(stdout); |
| 51 |
srand48( 1337 ); // the random number generator. |
| 52 |
initSimError(); // the error handler |
| 53 |
|
| 54 |
outPrefix = NULL; |
| 55 |
inName = NULL; |
| 56 |
|
| 57 |
conversionError = false; |
| 58 |
optionError = false; |
| 59 |
|
| 60 |
havePrefix = false; |
| 61 |
haveAlat = false; |
| 62 |
haveBlat = false; |
| 63 |
haveSpacing = false; |
| 64 |
|
| 65 |
programName = argV[0]; /*save the program name in case we need it*/ |
| 66 |
|
| 67 |
for( i = 1; i < argC; i++){ |
| 68 |
|
| 69 |
if(argV[i][0] =='-'){ |
| 70 |
|
| 71 |
// parse the option |
| 72 |
|
| 73 |
if(argV[i][1] == '-' ){ |
| 74 |
|
| 75 |
// parse long word options |
| 76 |
|
| 77 |
if( !strcmp( argV[i], "--version") ){ |
| 78 |
|
| 79 |
printf("\n" |
| 80 |
"staticProps version %d.%d\n" |
| 81 |
"\n", |
| 82 |
VERSION_MAJOR, VERSION_MINOR ); |
| 83 |
exit(0); |
| 84 |
|
| 85 |
} |
| 86 |
|
| 87 |
else if( !strcmp( argV[i], "--help") ){ |
| 88 |
|
| 89 |
usage(); |
| 90 |
exit(0); |
| 91 |
} |
| 92 |
|
| 93 |
// anything else is an error |
| 94 |
|
| 95 |
else{ |
| 96 |
fprintf( stderr, |
| 97 |
"Invalid option \"%s\"\n", argV[i] ); |
| 98 |
usage(); |
| 99 |
exit(0); |
| 100 |
} |
| 101 |
} |
| 102 |
|
| 103 |
else{ |
| 104 |
|
| 105 |
// parse single character options |
| 106 |
|
| 107 |
done =0; |
| 108 |
j = 1; |
| 109 |
currentFlag = argV[i][j]; |
| 110 |
while( (currentFlag != '\0') && (!done) ){ |
| 111 |
|
| 112 |
switch(currentFlag){ |
| 113 |
|
| 114 |
case 'o': |
| 115 |
// -o <prefix> => the output prefix. |
| 116 |
|
| 117 |
j++; |
| 118 |
currentFlag = argV[i][j]; |
| 119 |
|
| 120 |
if( currentFlag != '\0' ) optionError = true; |
| 121 |
|
| 122 |
if( optionError ){ |
| 123 |
sprintf( painCave.errMsg, |
| 124 |
"\n" |
| 125 |
"The -o flag should end an option sequence.\n" |
| 126 |
" example: -r <outname> *NOT* -or <outname>\n" ); |
| 127 |
usage(); |
| 128 |
painCave.isFatal = 1; |
| 129 |
simError(); |
| 130 |
} |
| 131 |
|
| 132 |
i++; |
| 133 |
if( i>=argC ){ |
| 134 |
sprintf( painCave.errMsg, |
| 135 |
"\n" |
| 136 |
"not enough arguments for -o\n"); |
| 137 |
usage(); |
| 138 |
painCave.isFatal = 1; |
| 139 |
simError(); |
| 140 |
} |
| 141 |
|
| 142 |
outPrefix = argV[i]; |
| 143 |
if( outPrefix[0] == '-' ) optionError = true; |
| 144 |
|
| 145 |
if( optionError ){ |
| 146 |
sprintf( painCave.errMsg, |
| 147 |
"\n" |
| 148 |
"\"%s\" is not a valid out prefix/name.\n" |
| 149 |
"Out prefix/name should not begin with a dash.\n", |
| 150 |
outPrefix ); |
| 151 |
usage(); |
| 152 |
painCave.isFatal = 1; |
| 153 |
simError(); |
| 154 |
} |
| 155 |
|
| 156 |
havePrefix = true; |
| 157 |
done = true; |
| 158 |
break; |
| 159 |
|
| 160 |
case 'l': |
| 161 |
// -l <lipidName> => the lipid name. |
| 162 |
|
| 163 |
j++; |
| 164 |
currentFlag = argV[i][j]; |
| 165 |
|
| 166 |
if( currentFlag != '\0' ) optionError = true; |
| 167 |
|
| 168 |
if( optionError ){ |
| 169 |
sprintf( painCave.errMsg, |
| 170 |
"\n" |
| 171 |
"The -l flag should end an option sequence.\n" |
| 172 |
" example: -rl <lipidName> *NOT* -lr <lipidName>\n" ); |
| 173 |
usage(); |
| 174 |
painCave.isFatal = 1; |
| 175 |
simError(); |
| 176 |
} |
| 177 |
|
| 178 |
i++; |
| 179 |
if( i>=argC ){ |
| 180 |
sprintf( painCave.errMsg, |
| 181 |
"\n" |
| 182 |
"not enough arguments for -l\n"); |
| 183 |
usage(); |
| 184 |
painCave.isFatal = 1; |
| 185 |
simError(); |
| 186 |
} |
| 187 |
|
| 188 |
lipidName = argV[i]; |
| 189 |
if( lipidName[0] == '-' ) optionError = true; |
| 190 |
|
| 191 |
if( optionError ){ |
| 192 |
sprintf( painCave.errMsg, |
| 193 |
"\n" |
| 194 |
"\"%s\" is not a valid lipidName.\n" |
| 195 |
"lipidName should not begin with a dash.\n", |
| 196 |
lipidName ); |
| 197 |
usage(); |
| 198 |
painCave.isFatal = 1; |
| 199 |
simError(); |
| 200 |
} |
| 201 |
|
| 202 |
haveLipidName = true; |
| 203 |
done = true; |
| 204 |
break; |
| 205 |
|
| 206 |
case 'w': |
| 207 |
// -w <waterName> => the water name. |
| 208 |
|
| 209 |
j++; |
| 210 |
currentFlag = argV[i][j]; |
| 211 |
|
| 212 |
if( currentFlag != '\0' ) optionError = true; |
| 213 |
|
| 214 |
if( optionError ){ |
| 215 |
sprintf( painCave.errMsg, |
| 216 |
"\n" |
| 217 |
"The -w flag should end an option sequence.\n" |
| 218 |
" example: -rw <waterName> *NOT* -lw <waterName>\n" ); |
| 219 |
usage(); |
| 220 |
painCave.isFatal = 1; |
| 221 |
simError(); |
| 222 |
} |
| 223 |
|
| 224 |
i++; |
| 225 |
if( i>=argC ){ |
| 226 |
sprintf( painCave.errMsg, |
| 227 |
"\n" |
| 228 |
"not enough arguments for -w\n"); |
| 229 |
usage(); |
| 230 |
painCave.isFatal = 1; |
| 231 |
simError(); |
| 232 |
} |
| 233 |
|
| 234 |
waterName = argV[i]; |
| 235 |
if( waterName[0] == '-' ) optionError = true; |
| 236 |
|
| 237 |
if( optionError ){ |
| 238 |
sprintf( painCave.errMsg, |
| 239 |
"\n" |
| 240 |
"\"%s\" is not a valid waterName.\n" |
| 241 |
"waterName should not begin with a dash.\n", |
| 242 |
waterName ); |
| 243 |
usage(); |
| 244 |
painCave.isFatal = 1; |
| 245 |
simError(); |
| 246 |
} |
| 247 |
|
| 248 |
haveWaterName = true; |
| 249 |
done = true; |
| 250 |
break; |
| 251 |
|
| 252 |
|
| 253 |
case 'h': |
| 254 |
// -h <double> set <double> to the hex lattice spacing |
| 255 |
|
| 256 |
haveAlat = true; |
| 257 |
haveBlat = true; |
| 258 |
j++; |
| 259 |
currentFlag = argV[i][j]; |
| 260 |
|
| 261 |
if( currentFlag != '\0' ) optionError = true; |
| 262 |
|
| 263 |
if( optionError ){ |
| 264 |
sprintf( painCave.errMsg, |
| 265 |
"\n" |
| 266 |
"The -h flag should end an option sequence.\n" |
| 267 |
" example: -sh <double> *NOT* -hs <double>\n" ); |
| 268 |
usage(); |
| 269 |
painCave.isFatal = 1; |
| 270 |
simError(); |
| 271 |
} |
| 272 |
|
| 273 |
i++; |
| 274 |
if( i>=argC ){ |
| 275 |
sprintf( painCave.errMsg, |
| 276 |
"\n" |
| 277 |
"not enough arguments for -h\n"); |
| 278 |
usage(); |
| 279 |
painCave.isFatal = 1; |
| 280 |
simError(); |
| 281 |
} |
| 282 |
|
| 283 |
bLat = strtod( argV[i], &conversionCheck); |
| 284 |
if( conversionCheck == argV[i] ) conversionError = true; |
| 285 |
if( *conversionCheck != '\0' ) conversionError = true; |
| 286 |
|
| 287 |
if( conversionError ){ |
| 288 |
sprintf( painCave.errMsg, |
| 289 |
"Error converting \"%s\" to a double for \"h\".\n", |
| 290 |
argV[i] ); |
| 291 |
usage(); |
| 292 |
painCave.isFatal = 1; |
| 293 |
simError(); |
| 294 |
} |
| 295 |
|
| 296 |
aLat = sqrt( 3.0 ) * bLat; |
| 297 |
|
| 298 |
done = true; |
| 299 |
|
| 300 |
break; |
| 301 |
|
| 302 |
case 'a': |
| 303 |
// -a <double> set <double> to the aLat |
| 304 |
|
| 305 |
haveAlat = true; |
| 306 |
j++; |
| 307 |
currentFlag = argV[i][j]; |
| 308 |
|
| 309 |
if( currentFlag != '\0' ) optionError = true; |
| 310 |
|
| 311 |
if( optionError ){ |
| 312 |
sprintf( painCave.errMsg, |
| 313 |
"\n" |
| 314 |
"The -a flag should end an option sequence.\n" |
| 315 |
" example: -sa <double> *NOT* -as <double>\n" ); |
| 316 |
usage(); |
| 317 |
painCave.isFatal = 1; |
| 318 |
simError(); |
| 319 |
} |
| 320 |
|
| 321 |
i++; |
| 322 |
if( i>=argC ){ |
| 323 |
sprintf( painCave.errMsg, |
| 324 |
"\n" |
| 325 |
"not enough arguments for -a\n"); |
| 326 |
usage(); |
| 327 |
painCave.isFatal = 1; |
| 328 |
simError(); |
| 329 |
} |
| 330 |
|
| 331 |
aLat = strtod( argV[i], &conversionCheck); |
| 332 |
if( conversionCheck == argV[i] ) conversionError = true; |
| 333 |
if( *conversionCheck != '\0' ) conversionError = true; |
| 334 |
|
| 335 |
if( conversionError ){ |
| 336 |
sprintf( painCave.errMsg, |
| 337 |
"Error converting \"%s\" to a double for \"a\".\n", |
| 338 |
argV[i] ); |
| 339 |
usage(); |
| 340 |
painCave.isFatal = 1; |
| 341 |
simError(); |
| 342 |
} |
| 343 |
|
| 344 |
done = true; |
| 345 |
|
| 346 |
break; |
| 347 |
|
| 348 |
case 'b': |
| 349 |
// -b <double> set <double> to the bLat |
| 350 |
|
| 351 |
haveBlat = true; |
| 352 |
j++; |
| 353 |
currentFlag = argV[i][j]; |
| 354 |
|
| 355 |
if( currentFlag != '\0' ) optionError = true; |
| 356 |
|
| 357 |
if( optionError ){ |
| 358 |
sprintf( painCave.errMsg, |
| 359 |
"\n" |
| 360 |
"The -b flag should end an option sequence.\n" |
| 361 |
" example: -sb <double> *NOT* -bs <double>\n" ); |
| 362 |
usage(); |
| 363 |
painCave.isFatal = 1; |
| 364 |
simError(); |
| 365 |
} |
| 366 |
|
| 367 |
i++; |
| 368 |
if( i>=argC ){ |
| 369 |
sprintf( painCave.errMsg, |
| 370 |
"\n" |
| 371 |
"not enough arguments for -b\n"); |
| 372 |
usage(); |
| 373 |
painCave.isFatal = 1; |
| 374 |
simError(); |
| 375 |
} |
| 376 |
|
| 377 |
bLat = strtod( argV[i], &conversionCheck); |
| 378 |
if( conversionCheck == argV[i] ) conversionError = true; |
| 379 |
if( *conversionCheck != '\0' ) conversionError = true; |
| 380 |
|
| 381 |
if( conversionError ){ |
| 382 |
sprintf( painCave.errMsg, |
| 383 |
"Error converting \"%s\" to a double for \"a\".\n", |
| 384 |
argV[i] ); |
| 385 |
usage(); |
| 386 |
painCave.isFatal = 1; |
| 387 |
simError(); |
| 388 |
} |
| 389 |
|
| 390 |
done = true; |
| 391 |
|
| 392 |
break; |
| 393 |
|
| 394 |
case 's': |
| 395 |
// -s <double> set <double> to the leafSpacing |
| 396 |
|
| 397 |
haveSpacing = true; |
| 398 |
j++; |
| 399 |
currentFlag = argV[i][j]; |
| 400 |
|
| 401 |
if( currentFlag != '\0' ) optionError = true; |
| 402 |
|
| 403 |
if( optionError ){ |
| 404 |
sprintf( painCave.errMsg, |
| 405 |
"\n" |
| 406 |
"The -s flag should end an option sequence.\n" |
| 407 |
" example: -rs <double> *NOT* -sr <double>\n" ); |
| 408 |
usage(); |
| 409 |
painCave.isFatal = 1; |
| 410 |
simError(); |
| 411 |
} |
| 412 |
|
| 413 |
i++; |
| 414 |
if( i>=argC ){ |
| 415 |
sprintf( painCave.errMsg, |
| 416 |
"\n" |
| 417 |
"not enough arguments for -s\n"); |
| 418 |
usage(); |
| 419 |
painCave.isFatal = 1; |
| 420 |
simError(); |
| 421 |
} |
| 422 |
|
| 423 |
leafSpacing = strtod( argV[i], &conversionCheck); |
| 424 |
if( conversionCheck == argV[i] ) conversionError = true; |
| 425 |
if( *conversionCheck != '\0' ) conversionError = true; |
| 426 |
|
| 427 |
if( conversionError ){ |
| 428 |
sprintf( painCave.errMsg, |
| 429 |
"Error converting \"%s\" to a double for \"s\".\n", |
| 430 |
argV[i] ); |
| 431 |
usage(); |
| 432 |
painCave.isFatal = 1; |
| 433 |
simError(); |
| 434 |
} |
| 435 |
|
| 436 |
done = true; |
| 437 |
|
| 438 |
break; |
| 439 |
|
| 440 |
default: |
| 441 |
|
| 442 |
sprintf(painCave.errMsg, |
| 443 |
"\n" |
| 444 |
"Bad option \"-%c\"\n", currentFlag); |
| 445 |
usage(); |
| 446 |
painCave.isFatal = 1; |
| 447 |
simError(); |
| 448 |
} |
| 449 |
j++; |
| 450 |
currentFlag = argV[i][j]; |
| 451 |
} |
| 452 |
} |
| 453 |
} |
| 454 |
|
| 455 |
else{ |
| 456 |
|
| 457 |
if( inName != NULL ){ |
| 458 |
sprintf( painCave.errMsg, |
| 459 |
"Error at \"%s\", program does not currently support\n" |
| 460 |
"more than one input bass file.\n" |
| 461 |
"\n", |
| 462 |
argV[i]); |
| 463 |
usage(); |
| 464 |
painCave.isFatal = 1; |
| 465 |
simError(); |
| 466 |
} |
| 467 |
|
| 468 |
inName = argV[i]; |
| 469 |
|
| 470 |
} |
| 471 |
} |
| 472 |
|
| 473 |
if( inName == NULL ){ |
| 474 |
sprintf( painCave.errMsg, |
| 475 |
"Error, bass file is needed to run.\n" ); |
| 476 |
usage(); |
| 477 |
painCave.isFatal = 1; |
| 478 |
simError(); |
| 479 |
} |
| 480 |
|
| 481 |
// if no output prefix is given default to "donkey". |
| 482 |
|
| 483 |
if( !havePrefix ){ |
| 484 |
outPrefix = strdup( "donkey" ); |
| 485 |
} |
| 486 |
|
| 487 |
|
| 488 |
if( !haveWaterName ){ |
| 489 |
sprintf( painCave.errMsg, |
| 490 |
"Error, the water name is needed to run.\n" |
| 491 |
); |
| 492 |
usage(); |
| 493 |
painCave.isFatal = 1; |
| 494 |
simError(); |
| 495 |
} |
| 496 |
|
| 497 |
if( !haveLipidName ){ |
| 498 |
sprintf( painCave.errMsg, |
| 499 |
"Error, the lipid name is needed to run.\n" |
| 500 |
); |
| 501 |
usage(); |
| 502 |
painCave.isFatal = 1; |
| 503 |
simError(); |
| 504 |
} |
| 505 |
|
| 506 |
if( !haveAlat ){ |
| 507 |
sprintf( painCave.errMsg, |
| 508 |
"Error, the hexagonal lattice parameter, a, is needed to run.\n" |
| 509 |
); |
| 510 |
usage(); |
| 511 |
painCave.isFatal = 1; |
| 512 |
simError(); |
| 513 |
} |
| 514 |
|
| 515 |
if( !haveBlat ){ |
| 516 |
sprintf( painCave.errMsg, |
| 517 |
"Error, the hexagonal lattice parameter, b, is needed to run.\n" |
| 518 |
); |
| 519 |
usage(); |
| 520 |
painCave.isFatal = 1; |
| 521 |
simError(); |
| 522 |
} |
| 523 |
|
| 524 |
|
| 525 |
if( !haveSpacing ){ |
| 526 |
sprintf( painCave.errMsg, |
| 527 |
"Error, the leaf spaceing is needed to run.\n" |
| 528 |
); |
| 529 |
usage(); |
| 530 |
painCave.isFatal = 1; |
| 531 |
simError(); |
| 532 |
} |
| 533 |
|
| 534 |
bsInfo.outPrefix = outPrefix; |
| 535 |
strcpy(bsInfo.waterName, waterName); |
| 536 |
strcpy(bsInfo.lipidName, lipidName); |
| 537 |
|
| 538 |
parseBuildBass( inName ); |
| 539 |
|
| 540 |
buildLatticeBilayer( aLat, bLat, leafSpacing ); |
| 541 |
|
| 542 |
return 0; |
| 543 |
} |
| 544 |
|
| 545 |
int buildLatticeBilayer(double aLat, |
| 546 |
double bLat, |
| 547 |
double leafSpacing){ |
| 548 |
|
| 549 |
typedef struct{ |
| 550 |
double rot[3][3]; |
| 551 |
double pos[3]; |
| 552 |
} coord; |
| 553 |
|
| 554 |
const double waterRho = 0.0334; // number density per cubic angstrom |
| 555 |
const double waterVol = 4.0 / waterRho; // volume occupied by 4 waters |
| 556 |
|
| 557 |
double waterCell[3]; |
| 558 |
|
| 559 |
double *posX, *posY, *posZ; |
| 560 |
double pos[3], posA[3], posB[3]; |
| 561 |
|
| 562 |
const double waterFudge = 5.0; |
| 563 |
|
| 564 |
int i,j,k,l; |
| 565 |
int nAtoms, atomIndex, molIndex, molID; |
| 566 |
int* molSeq; |
| 567 |
int* molMap; |
| 568 |
int* molStart; |
| 569 |
int testTot, done; |
| 570 |
int nCells, nCellsX, nCellsY, nCellsZ; |
| 571 |
int nx, ny; |
| 572 |
double boxX, boxY, boxZ; |
| 573 |
double unitVector[3]; |
| 574 |
int which; |
| 575 |
int targetWaters; |
| 576 |
|
| 577 |
Atom** atoms; |
| 578 |
SimInfo* simnfo; |
| 579 |
SimInfo* testInfo; |
| 580 |
coord testSite; |
| 581 |
SimState* theConfig; |
| 582 |
DumpWriter* writer; |
| 583 |
|
| 584 |
MoleculeStamp* lipidStamp; |
| 585 |
MoleculeStamp* waterStamp; |
| 586 |
MoLocator *lipidLocate; |
| 587 |
MoLocator *waterLocate; |
| 588 |
int foundLipid, foundWater; |
| 589 |
int nLipids, lipidNatoms, nWaters, waterNatoms; |
| 590 |
int targetNlipids, targetNwaters; |
| 591 |
double targetWaterLipidRatio; |
| 592 |
double maxZ, minZ, zHeight; |
| 593 |
|
| 594 |
// create the simInfo objects |
| 595 |
|
| 596 |
simnfo = new SimInfo; |
| 597 |
|
| 598 |
// set the the lipidStamp |
| 599 |
|
| 600 |
foundLipid = 0; |
| 601 |
foundWater = 0; |
| 602 |
for(i=0; i<bsInfo.nComponents; i++){ |
| 603 |
if( !strcmp( bsInfo.compStamps[i]->getID(), bsInfo.lipidName ) ){ |
| 604 |
|
| 605 |
foundLipid = 1; |
| 606 |
lipidStamp = bsInfo.compStamps[i]; |
| 607 |
targetNlipids = bsInfo.componentsNmol[i]; |
| 608 |
lipidNatoms = lipidStamp->getNAtoms(); |
| 609 |
} |
| 610 |
if( !strcmp( bsInfo.compStamps[i]->getID(), bsInfo.waterName ) ){ |
| 611 |
|
| 612 |
foundWater = 1; |
| 613 |
|
| 614 |
waterStamp = bsInfo.compStamps[i]; |
| 615 |
targetNwaters = bsInfo.componentsNmol[i]; |
| 616 |
waterNatoms = waterStamp->getNAtoms(); |
| 617 |
} |
| 618 |
} |
| 619 |
if( !foundLipid ){ |
| 620 |
sprintf(painCave.errMsg, |
| 621 |
"Could not find lipid \"%s\" in the bass file.\n", |
| 622 |
bsInfo.lipidName ); |
| 623 |
painCave.isFatal = 1; |
| 624 |
simError(); |
| 625 |
} |
| 626 |
if( !foundWater ){ |
| 627 |
sprintf(painCave.errMsg, |
| 628 |
"Could not find solvent \"%s\" in the bass file.\n", |
| 629 |
bsInfo.waterName ); |
| 630 |
painCave.isFatal = 1; |
| 631 |
simError(); |
| 632 |
} |
| 633 |
|
| 634 |
//create the Molocator arrays |
| 635 |
|
| 636 |
lipidLocate = new MoLocator( lipidStamp ); |
| 637 |
waterLocate = new MoLocator( waterStamp ); |
| 638 |
|
| 639 |
// gather info about the lipid |
| 640 |
|
| 641 |
testInfo = new SimInfo(); |
| 642 |
testInfo->n_atoms = lipidNatoms; |
| 643 |
theConfig = testInfo->getConfiguration(); |
| 644 |
theConfig->createArrays( lipidNatoms ); |
| 645 |
testInfo->atoms = new Atom*[lipidNatoms]; |
| 646 |
atoms = testInfo->atoms; |
| 647 |
|
| 648 |
testSite.pos[0] = 0.0; |
| 649 |
testSite.pos[1] = 0.0; |
| 650 |
testSite.pos[2] = 0.0; |
| 651 |
|
| 652 |
unitVector[0] = 0.0; |
| 653 |
unitVector[1] = 0.0; |
| 654 |
unitVector[2] = 1.0; |
| 655 |
|
| 656 |
getUnitRot(unitVector, testSite.rot ); |
| 657 |
lipidLocate->placeMol( testSite.pos, testSite.rot, atoms, 0, theConfig ); |
| 658 |
|
| 659 |
minZ = 0.0; |
| 660 |
maxZ = 0.0; |
| 661 |
double myPos[3]; |
| 662 |
for(i=0;i<lipidNatoms;i++){ |
| 663 |
atoms[i]->getPos( myPos ); |
| 664 |
minZ = (minZ > myPos[2]) ? myPos[2] : minZ; |
| 665 |
maxZ = (maxZ < myPos[2]) ? myPos[2] : maxZ; |
| 666 |
} |
| 667 |
zHeight = maxZ - minZ; |
| 668 |
|
| 669 |
nCells = (int) sqrt( (double)targetNlipids * bLat / (4.0 * aLat) ); |
| 670 |
|
| 671 |
nx = nCells; |
| 672 |
ny = (int) ((double)nCells * aLat / bLat); |
| 673 |
|
| 674 |
boxX = nx * aLat; |
| 675 |
boxY = ny * bLat; |
| 676 |
|
| 677 |
nLipids = 4 * nx * ny; |
| 678 |
coord* lipidSites = new coord[nLipids]; |
| 679 |
|
| 680 |
unitVector[0] = 0.0; |
| 681 |
unitVector[1] = 0.0; |
| 682 |
|
| 683 |
which = 0; |
| 684 |
|
| 685 |
for (i = 0; i < nx; i++) { |
| 686 |
for (j = 0; j < ny; j++ ) { |
| 687 |
for (k = 0; k < 2; k++) { |
| 688 |
|
| 689 |
lipidSites[which].pos[0] = (double)i * aLat; |
| 690 |
lipidSites[which].pos[1] = (double)j * bLat; |
| 691 |
lipidSites[which].pos[2] = ((double)k - 0.5) * (leafSpacing - maxZ); |
| 692 |
|
| 693 |
unitVector[2] = 2.0 * (double)k - 1.0; |
| 694 |
|
| 695 |
getUnitRot( unitVector, lipidSites[which].rot ); |
| 696 |
|
| 697 |
which++; |
| 698 |
|
| 699 |
lipidSites[which].pos[0] = aLat * ((double)i + 0.5); |
| 700 |
lipidSites[which].pos[1] = bLat * ((double)j + 0.5); |
| 701 |
lipidSites[which].pos[2] = ((double)k - 0.5) * (leafSpacing - maxZ); |
| 702 |
|
| 703 |
unitVector[2] = 2.0 * (double)k - 1.0; |
| 704 |
|
| 705 |
getUnitRot( unitVector, lipidSites[which].rot ); |
| 706 |
|
| 707 |
which++; |
| 708 |
} |
| 709 |
} |
| 710 |
} |
| 711 |
|
| 712 |
targetWaterLipidRatio = (double)targetNwaters / (double)targetNlipids; |
| 713 |
|
| 714 |
targetWaters = targetWaterLipidRatio * nLipids; |
| 715 |
|
| 716 |
// guess the size of the water box |
| 717 |
|
| 718 |
nCellsX = (int)ceil(boxX / pow(waterVol, ( 1.0 / 3.0 )) ); |
| 719 |
nCellsY = (int)ceil(boxY / pow(waterVol, ( 1.0 / 3.0 )) ); |
| 720 |
|
| 721 |
done = 0; |
| 722 |
nCellsZ = 0; |
| 723 |
while( !done ){ |
| 724 |
|
| 725 |
nCellsZ++; |
| 726 |
testTot = 4 * nCellsX * nCellsY * nCellsZ; |
| 727 |
|
| 728 |
if( testTot >= targetWaters ) done = 1; |
| 729 |
} |
| 730 |
|
| 731 |
nWaters = nCellsX * nCellsY * nCellsZ * 4; |
| 732 |
|
| 733 |
coord* waterSites = new coord[nWaters]; |
| 734 |
|
| 735 |
waterCell[0] = boxX / nCellsX; |
| 736 |
waterCell[1] = boxY / nCellsY; |
| 737 |
waterCell[2] = 4.0 / (waterRho * waterCell[0] * waterCell[1]); |
| 738 |
|
| 739 |
Lattice *myORTHO; |
| 740 |
myORTHO = new Lattice( ORTHORHOMBIC_LATTICE_TYPE, waterCell); |
| 741 |
myORTHO->setStartZ( leafSpacing / 2.0 + waterFudge); |
| 742 |
|
| 743 |
boxZ = waterCell[2] * nCellsZ + leafSpacing; |
| 744 |
|
| 745 |
// create an fcc lattice in the water box. |
| 746 |
|
| 747 |
which = 0; |
| 748 |
for( i=0; i < nCellsX; i++ ){ |
| 749 |
for( j=0; j < nCellsY; j++ ){ |
| 750 |
for( k=0; k < nCellsZ; k++ ){ |
| 751 |
|
| 752 |
myORTHO->getLatticePoints(&posX, &posY, &posZ, i, j, k); |
| 753 |
for(l=0; l<4; l++){ |
| 754 |
waterSites[which].pos[0] = posX[l]; |
| 755 |
waterSites[which].pos[1] = posY[l]; |
| 756 |
waterSites[which].pos[2] = posZ[l]; |
| 757 |
which++; |
| 758 |
} |
| 759 |
} |
| 760 |
} |
| 761 |
} |
| 762 |
|
| 763 |
// create the real Atom arrays |
| 764 |
|
| 765 |
nAtoms = 0; |
| 766 |
molIndex = 0; |
| 767 |
molStart = new int[nLipids + nWaters]; |
| 768 |
|
| 769 |
for(j=0; j<nLipids; j++){ |
| 770 |
molStart[molIndex] = nAtoms; |
| 771 |
molIndex++; |
| 772 |
nAtoms += lipidNatoms; |
| 773 |
} |
| 774 |
|
| 775 |
for(j=0; j<nWaters; j++){ |
| 776 |
molStart[molIndex] = nAtoms; |
| 777 |
molIndex++; |
| 778 |
nAtoms += waterNatoms; |
| 779 |
} |
| 780 |
|
| 781 |
theConfig = simnfo->getConfiguration(); |
| 782 |
theConfig->createArrays( nAtoms ); |
| 783 |
simnfo->atoms = new Atom*[nAtoms]; |
| 784 |
atoms = simnfo->atoms; |
| 785 |
|
| 786 |
|
| 787 |
// wrap back to <0,0,0> as center |
| 788 |
|
| 789 |
double Hmat[3][3]; |
| 790 |
|
| 791 |
Hmat[0][0] = boxX; |
| 792 |
Hmat[0][1] = 0.0; |
| 793 |
Hmat[0][2] = 0.0; |
| 794 |
|
| 795 |
Hmat[1][0] = 0.0; |
| 796 |
Hmat[1][1] = boxY; |
| 797 |
Hmat[1][2] = 0.0; |
| 798 |
|
| 799 |
Hmat[2][0] = 0.0; |
| 800 |
Hmat[2][1] = 0.0; |
| 801 |
Hmat[2][2] = boxZ; |
| 802 |
|
| 803 |
bsInfo.boxX = boxX; |
| 804 |
bsInfo.boxY = boxY; |
| 805 |
bsInfo.boxZ = boxZ; |
| 806 |
|
| 807 |
simnfo->setBoxM( Hmat ); |
| 808 |
|
| 809 |
for(j=0;j<nLipids;j++) |
| 810 |
simnfo->wrapVector( lipidSites[j].pos ); |
| 811 |
|
| 812 |
for(j=0;j<nWaters;j++) |
| 813 |
simnfo->wrapVector( waterSites[j].pos ); |
| 814 |
|
| 815 |
// initialize lipid positions |
| 816 |
|
| 817 |
molIndex = 0; |
| 818 |
for(i=0; i<nLipids; i++ ){ |
| 819 |
lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms, |
| 820 |
molStart[molIndex], theConfig ); |
| 821 |
molIndex++; |
| 822 |
} |
| 823 |
|
| 824 |
// initialize the water positions |
| 825 |
|
| 826 |
for(i=0; i<nWaters; i++){ |
| 827 |
|
| 828 |
getRandomRot( waterSites[i].rot ); |
| 829 |
waterLocate->placeMol( waterSites[i].pos, waterSites[i].rot, atoms, |
| 830 |
molStart[molIndex], theConfig ); |
| 831 |
molIndex++; |
| 832 |
} |
| 833 |
|
| 834 |
// set up the SimInfo object |
| 835 |
|
| 836 |
Hmat[0][0] = boxX; |
| 837 |
Hmat[0][1] = 0.0; |
| 838 |
Hmat[0][2] = 0.0; |
| 839 |
|
| 840 |
Hmat[1][0] = 0.0; |
| 841 |
Hmat[1][1] = boxY; |
| 842 |
Hmat[1][2] = 0.0; |
| 843 |
|
| 844 |
Hmat[2][0] = 0.0; |
| 845 |
Hmat[2][1] = 0.0; |
| 846 |
Hmat[2][2] = boxZ; |
| 847 |
|
| 848 |
|
| 849 |
bsInfo.boxX = boxX; |
| 850 |
bsInfo.boxY = boxY; |
| 851 |
bsInfo.boxZ = boxZ; |
| 852 |
|
| 853 |
simnfo->setBoxM( Hmat ); |
| 854 |
|
| 855 |
sprintf( simnfo->sampleName, "%s.dump", bsInfo.outPrefix ); |
| 856 |
sprintf( simnfo->finalName, "%s.init", bsInfo.outPrefix ); |
| 857 |
|
| 858 |
// set up the writer and write out |
| 859 |
|
| 860 |
writer = new DumpWriter( simnfo ); |
| 861 |
writer->writeFinal( 0.0 ); |
| 862 |
|
| 863 |
return 1; |
| 864 |
} |
| 865 |
|
| 866 |
|
| 867 |
/*************************************************************************** |
| 868 |
* prints out the usage for the command line arguments, then exits. |
| 869 |
***************************************************************************/ |
| 870 |
|
| 871 |
void usage(){ |
| 872 |
(void)fprintf(stdout, |
| 873 |
"\n" |
| 874 |
"The proper usage is: %s [options] <input_file>\n" |
| 875 |
"\n" |
| 876 |
"Options:\n" |
| 877 |
"\n" |
| 878 |
" short:\n" |
| 879 |
" ------\n" |
| 880 |
" -o <name> The output prefix\n" |
| 881 |
" -l <lipidName> The name of the lipid molecule specified in the BASS file.\n" |
| 882 |
" -w <waterName> The name of the water molecule specified in the BASS file.\n" |
| 883 |
" -s <double> The leaf spaceing of the bilayer.\n" |
| 884 |
" -a <double> The hexagonal lattice constant, a, for the bilayer leaf.\n" |
| 885 |
" -b <double> The hexagonal lattice constant, b, for the bilayer leaf.\n" |
| 886 |
" -h <double> Use to set a and b for a normal hex lattice with spacing <double>\n" |
| 887 |
|
| 888 |
"\n" |
| 889 |
" long:\n" |
| 890 |
" -----\n" |
| 891 |
|
| 892 |
" --version displays the version number\n" |
| 893 |
" --help displays this help message.\n" |
| 894 |
"\n" |
| 895 |
"\n", |
| 896 |
programName); |
| 897 |
} |
