| 1 |
#include <iostream> |
| 2 |
#include <vector> |
| 3 |
#include <algorithm> |
| 4 |
|
| 5 |
#include <stdio.h> |
| 6 |
#include <stdlib.h> |
| 7 |
#include <string.h> |
| 8 |
#include <math.h> |
| 9 |
|
| 10 |
#include "simError.h" |
| 11 |
#include "SimInfo.hpp" |
| 12 |
#include "ReadWrite.hpp" |
| 13 |
#include "SimSetup.hpp" |
| 14 |
|
| 15 |
#include "MoLocator.hpp" |
| 16 |
#include "latticeBuilder.hpp" |
| 17 |
|
| 18 |
#define RAND_SEED 31337 // \/\/007! |
| 19 |
|
| 20 |
#define VERSION_MAJOR 0 |
| 21 |
#define VERSION_MINOR 1 |
| 22 |
|
| 23 |
class SortCond{ |
| 24 |
|
| 25 |
public: |
| 26 |
bool operator()(const pair<int, double>& p1, const pair<int, double>& p2){ |
| 27 |
return p1.second < p2.second; |
| 28 |
} |
| 29 |
|
| 30 |
|
| 31 |
}; |
| 32 |
|
| 33 |
|
| 34 |
void buildMap( double &x, double &y, double &z, |
| 35 |
double boxX, double boxY, double boxZ ); |
| 36 |
|
| 37 |
int buildRandomBilayer( double waterCell, |
| 38 |
double waterBuffer, |
| 39 |
double lipidBuffer, |
| 40 |
char* waterName, |
| 41 |
char* lipidName ); |
| 42 |
|
| 43 |
|
| 44 |
char *programName; /*the name of the program */ |
| 45 |
void usage(void); |
| 46 |
using namespace std; |
| 47 |
SimInfo* mainInfo; |
| 48 |
|
| 49 |
int main(int argC,char* argV[]){ |
| 50 |
|
| 51 |
int i,j; // loop counters |
| 52 |
|
| 53 |
char* outPrefix; // the output prefix |
| 54 |
|
| 55 |
char* conversionCheck; |
| 56 |
bool conversionError; |
| 57 |
bool optionError; |
| 58 |
|
| 59 |
char currentFlag; // used in parsing the flags |
| 60 |
bool done = false; // multipurpose boolean |
| 61 |
bool havePrefix; // boolean for the output prefix |
| 62 |
|
| 63 |
char* lipidName; |
| 64 |
char* waterName; |
| 65 |
bool haveWaterName, haveLipidName; |
| 66 |
|
| 67 |
double waterLattice, waterBuffer, lipidBuffer; |
| 68 |
|
| 69 |
char* inName; |
| 70 |
|
| 71 |
SimSetup* simInit; |
| 72 |
|
| 73 |
// first things first, all of the initializations |
| 74 |
|
| 75 |
fflush(stdout); |
| 76 |
srand48( 1337 ); // the random number generator. |
| 77 |
initSimError(); // the error handler |
| 78 |
|
| 79 |
outPrefix = NULL; |
| 80 |
inName = NULL; |
| 81 |
|
| 82 |
conversionError = false; |
| 83 |
optionError = false; |
| 84 |
|
| 85 |
havePrefix = false; |
| 86 |
|
| 87 |
waterBuffer = 5.0; |
| 88 |
lipidBuffer = 6.0; |
| 89 |
waterLattice = 4.929; |
| 90 |
|
| 91 |
programName = argV[0]; /*save the program name in case we need it*/ |
| 92 |
|
| 93 |
for( i = 1; i < argC; i++){ |
| 94 |
|
| 95 |
if(argV[i][0] =='-'){ |
| 96 |
|
| 97 |
// parse the option |
| 98 |
|
| 99 |
if(argV[i][1] == '-' ){ |
| 100 |
|
| 101 |
// parse long word options |
| 102 |
|
| 103 |
if( !strcmp( argV[i], "--version") ){ |
| 104 |
|
| 105 |
printf("\n" |
| 106 |
"randomBilayer version %d.%d\n" |
| 107 |
"\n", |
| 108 |
VERSION_MAJOR, VERSION_MINOR ); |
| 109 |
exit(0); |
| 110 |
|
| 111 |
} |
| 112 |
|
| 113 |
else if( !strcmp( argV[i], "--help") ){ |
| 114 |
|
| 115 |
usage(); |
| 116 |
exit(0); |
| 117 |
} |
| 118 |
|
| 119 |
else if (!strcmp( argV[i], "--lipidBuffer" )){ |
| 120 |
|
| 121 |
i++; |
| 122 |
if( i>=argC ){ |
| 123 |
sprintf( painCave.errMsg, |
| 124 |
"\n" |
| 125 |
"not enough arguments for -lipidBuffer\n"); |
| 126 |
usage(); |
| 127 |
painCave.isFatal = 1; |
| 128 |
simError(); |
| 129 |
} |
| 130 |
|
| 131 |
lipidBuffer = atof( argV[i] ); |
| 132 |
} |
| 133 |
|
| 134 |
else if (!strcmp( argV[i], "--waterBuffer" )){ |
| 135 |
|
| 136 |
i++; |
| 137 |
if( i>=argC ){ |
| 138 |
sprintf( painCave.errMsg, |
| 139 |
"\n" |
| 140 |
"not enough arguments for --waterBuffer\n"); |
| 141 |
usage(); |
| 142 |
painCave.isFatal = 1; |
| 143 |
simError(); |
| 144 |
} |
| 145 |
|
| 146 |
waterBuffer = atof( argV[i] ); |
| 147 |
} |
| 148 |
|
| 149 |
else if (!strcmp( argV[i], "--waterLattice" )){ |
| 150 |
|
| 151 |
i++; |
| 152 |
if( i>=argC ){ |
| 153 |
sprintf( painCave.errMsg, |
| 154 |
"\n" |
| 155 |
"not enough arguments for -waterLattice\n"); |
| 156 |
usage(); |
| 157 |
painCave.isFatal = 1; |
| 158 |
simError(); |
| 159 |
} |
| 160 |
|
| 161 |
waterLattice = atof( argV[i] ); |
| 162 |
} |
| 163 |
|
| 164 |
|
| 165 |
|
| 166 |
// anything else is an error |
| 167 |
|
| 168 |
else{ |
| 169 |
fprintf( stderr, |
| 170 |
"Invalid option \"%s\"\n", argV[i] ); |
| 171 |
usage(); |
| 172 |
exit(0); |
| 173 |
} |
| 174 |
} |
| 175 |
|
| 176 |
else{ |
| 177 |
|
| 178 |
// parse single character options |
| 179 |
|
| 180 |
done =0; |
| 181 |
j = 1; |
| 182 |
currentFlag = argV[i][j]; |
| 183 |
while( (currentFlag != '\0') && (!done) ){ |
| 184 |
|
| 185 |
switch(currentFlag){ |
| 186 |
|
| 187 |
case 'o': |
| 188 |
// -o <prefix> => the output prefix. |
| 189 |
|
| 190 |
j++; |
| 191 |
currentFlag = argV[i][j]; |
| 192 |
|
| 193 |
if( currentFlag != '\0' ) optionError = true; |
| 194 |
|
| 195 |
if( optionError ){ |
| 196 |
sprintf( painCave.errMsg, |
| 197 |
"\n" |
| 198 |
"The -o flag should end an option sequence.\n" |
| 199 |
" example: -r <outname> *NOT* -or <outname>\n" ); |
| 200 |
usage(); |
| 201 |
painCave.isFatal = 1; |
| 202 |
simError(); |
| 203 |
} |
| 204 |
|
| 205 |
i++; |
| 206 |
if( i>=argC ){ |
| 207 |
sprintf( painCave.errMsg, |
| 208 |
"\n" |
| 209 |
"not enough arguments for -o\n"); |
| 210 |
usage(); |
| 211 |
painCave.isFatal = 1; |
| 212 |
simError(); |
| 213 |
} |
| 214 |
|
| 215 |
outPrefix = argV[i]; |
| 216 |
if( outPrefix[0] == '-' ) optionError = true; |
| 217 |
|
| 218 |
if( optionError ){ |
| 219 |
sprintf( painCave.errMsg, |
| 220 |
"\n" |
| 221 |
"\"%s\" is not a valid out prefix/name.\n" |
| 222 |
"Out prefix/name should not begin with a dash.\n", |
| 223 |
outPrefix ); |
| 224 |
usage(); |
| 225 |
painCave.isFatal = 1; |
| 226 |
simError(); |
| 227 |
} |
| 228 |
|
| 229 |
havePrefix = true; |
| 230 |
done = true; |
| 231 |
break; |
| 232 |
|
| 233 |
case 'l': |
| 234 |
// -l <lipidName> => the lipid name. |
| 235 |
|
| 236 |
j++; |
| 237 |
currentFlag = argV[i][j]; |
| 238 |
|
| 239 |
if( currentFlag != '\0' ) optionError = true; |
| 240 |
|
| 241 |
if( optionError ){ |
| 242 |
sprintf( painCave.errMsg, |
| 243 |
"\n" |
| 244 |
"The -l flag should end an option sequence.\n" |
| 245 |
" example: -rl <lipidName> *NOT* -lr <lipidName>\n" ); |
| 246 |
usage(); |
| 247 |
painCave.isFatal = 1; |
| 248 |
simError(); |
| 249 |
} |
| 250 |
|
| 251 |
i++; |
| 252 |
if( i>=argC ){ |
| 253 |
sprintf( painCave.errMsg, |
| 254 |
"\n" |
| 255 |
"not enough arguments for -l\n"); |
| 256 |
usage(); |
| 257 |
painCave.isFatal = 1; |
| 258 |
simError(); |
| 259 |
} |
| 260 |
|
| 261 |
lipidName = argV[i]; |
| 262 |
if( lipidName[0] == '-' ) optionError = true; |
| 263 |
|
| 264 |
if( optionError ){ |
| 265 |
sprintf( painCave.errMsg, |
| 266 |
"\n" |
| 267 |
"\"%s\" is not a valid lipidName.\n" |
| 268 |
"lipidName should not begin with a dash.\n", |
| 269 |
lipidName ); |
| 270 |
usage(); |
| 271 |
painCave.isFatal = 1; |
| 272 |
simError(); |
| 273 |
} |
| 274 |
|
| 275 |
haveLipidName = true; |
| 276 |
done = true; |
| 277 |
break; |
| 278 |
|
| 279 |
case 'w': |
| 280 |
// -w <waterName> => the water name. |
| 281 |
|
| 282 |
j++; |
| 283 |
currentFlag = argV[i][j]; |
| 284 |
|
| 285 |
if( currentFlag != '\0' ) optionError = true; |
| 286 |
|
| 287 |
if( optionError ){ |
| 288 |
sprintf( painCave.errMsg, |
| 289 |
"\n" |
| 290 |
"The -w flag should end an option sequence.\n" |
| 291 |
" example: -rw <waterName> *NOT* -lw <waterName>\n" ); |
| 292 |
usage(); |
| 293 |
painCave.isFatal = 1; |
| 294 |
simError(); |
| 295 |
} |
| 296 |
|
| 297 |
i++; |
| 298 |
if( i>=argC ){ |
| 299 |
sprintf( painCave.errMsg, |
| 300 |
"\n" |
| 301 |
"not enough arguments for -w\n"); |
| 302 |
usage(); |
| 303 |
painCave.isFatal = 1; |
| 304 |
simError(); |
| 305 |
} |
| 306 |
|
| 307 |
waterName = argV[i]; |
| 308 |
if( waterName[0] == '-' ) optionError = true; |
| 309 |
|
| 310 |
if( optionError ){ |
| 311 |
sprintf( painCave.errMsg, |
| 312 |
"\n" |
| 313 |
"\"%s\" is not a valid waterName.\n" |
| 314 |
"waterName should not begin with a dash.\n", |
| 315 |
waterName ); |
| 316 |
usage(); |
| 317 |
painCave.isFatal = 1; |
| 318 |
simError(); |
| 319 |
} |
| 320 |
|
| 321 |
haveWaterName = true; |
| 322 |
done = true; |
| 323 |
break; |
| 324 |
|
| 325 |
default: |
| 326 |
|
| 327 |
sprintf(painCave.errMsg, |
| 328 |
"\n" |
| 329 |
"Bad option \"-%c\"\n", currentFlag); |
| 330 |
usage(); |
| 331 |
painCave.isFatal = 1; |
| 332 |
simError(); |
| 333 |
} |
| 334 |
j++; |
| 335 |
currentFlag = argV[i][j]; |
| 336 |
} |
| 337 |
} |
| 338 |
} |
| 339 |
|
| 340 |
else{ |
| 341 |
|
| 342 |
if( inName != NULL ){ |
| 343 |
sprintf( painCave.errMsg, |
| 344 |
"Error at \"%s\", program does not currently support\n" |
| 345 |
"more than one input bass file.\n" |
| 346 |
"\n", |
| 347 |
argV[i]); |
| 348 |
usage(); |
| 349 |
painCave.isFatal = 1; |
| 350 |
simError(); |
| 351 |
} |
| 352 |
|
| 353 |
inName = argV[i]; |
| 354 |
|
| 355 |
} |
| 356 |
} |
| 357 |
|
| 358 |
if( inName == NULL ){ |
| 359 |
sprintf( painCave.errMsg, |
| 360 |
"Error, bass file is needed to run.\n" ); |
| 361 |
usage(); |
| 362 |
painCave.isFatal = 1; |
| 363 |
simError(); |
| 364 |
} |
| 365 |
|
| 366 |
// if no output prefix is given default to "donkey". |
| 367 |
|
| 368 |
if( !havePrefix ){ |
| 369 |
outPrefix = strdup( "donkey" ); |
| 370 |
} |
| 371 |
|
| 372 |
if( !haveWaterName ){ |
| 373 |
sprintf( painCave.errMsg, |
| 374 |
"Error, the water name is needed to run.\n" |
| 375 |
); |
| 376 |
usage(); |
| 377 |
painCave.isFatal = 1; |
| 378 |
simError(); |
| 379 |
} |
| 380 |
|
| 381 |
if( !haveLipidName ){ |
| 382 |
sprintf( painCave.errMsg, |
| 383 |
"Error, the lipid name is needed to run.\n" |
| 384 |
); |
| 385 |
usage(); |
| 386 |
painCave.isFatal = 1; |
| 387 |
simError(); |
| 388 |
} |
| 389 |
|
| 390 |
|
| 391 |
// create and initialize the info object |
| 392 |
|
| 393 |
mainInfo = new SimInfo(); |
| 394 |
simInit = new SimSetup(); |
| 395 |
simInit->setSimInfo( mainInfo ); |
| 396 |
simInit->suspendInit(); |
| 397 |
simInit->parseFile( inName ); |
| 398 |
simInit->createSim(); |
| 399 |
|
| 400 |
delete simInit; |
| 401 |
|
| 402 |
sprintf( mainInfo->statusName, "%s.stat", outPrefix ); |
| 403 |
sprintf( mainInfo->sampleName, "%s.dump", outPrefix ); |
| 404 |
sprintf( mainInfo->finalName, "%s.init", outPrefix ); |
| 405 |
|
| 406 |
buildRandomBilayer( waterLattice, waterBuffer, lipidBuffer, |
| 407 |
waterName, lipidName ); |
| 408 |
|
| 409 |
return 0; |
| 410 |
} |
| 411 |
|
| 412 |
int buildRandomBilayer( double waterCell, |
| 413 |
double water_padding, |
| 414 |
double lipid_spaceing, |
| 415 |
char* waterName, |
| 416 |
char* lipidName ){ |
| 417 |
|
| 418 |
typedef struct{ |
| 419 |
double rot[3][3]; |
| 420 |
double pos[3]; |
| 421 |
} coord; |
| 422 |
|
| 423 |
Lattice myFCC( FCC_LATTICE_TYPE, waterCell ); |
| 424 |
double *posX, *posY, *posZ; |
| 425 |
double pos[3], posA[3], posB[3]; |
| 426 |
|
| 427 |
int i,j,k, l, m; |
| 428 |
int nAtoms, atomIndex, molIndex, molID; |
| 429 |
int* molSeq; |
| 430 |
int* molMap; |
| 431 |
int* molStart; |
| 432 |
int* cardDeck; |
| 433 |
int deckSize; |
| 434 |
int rSite, rCard; |
| 435 |
double cell; |
| 436 |
int nCells, nSites, siteIndex; |
| 437 |
|
| 438 |
coord testSite; |
| 439 |
|
| 440 |
Atom** atoms; |
| 441 |
SimInfo* simnfo; |
| 442 |
SimState* theConfig; |
| 443 |
DumpWriter* writer; |
| 444 |
|
| 445 |
MoleculeStamp* lipidStamp; |
| 446 |
MoleculeStamp* waterStamp; |
| 447 |
MoLocator *lipidLocate; |
| 448 |
MoLocator *waterLocate; |
| 449 |
int foundLipid, foundWater; |
| 450 |
int nLipids, lipidNatoms, nWaters, waterNatoms; |
| 451 |
double testBox, maxLength; |
| 452 |
|
| 453 |
double waterRho, waterVol; |
| 454 |
|
| 455 |
|
| 456 |
srand48( RAND_SEED ); |
| 457 |
|
| 458 |
// calculate the water parameters |
| 459 |
|
| 460 |
waterVol = waterCell * waterCell * waterCell; |
| 461 |
waterRho = 4.0 / waterVol; |
| 462 |
|
| 463 |
// set the the lipidStamp |
| 464 |
|
| 465 |
foundLipid = 0; |
| 466 |
foundWater = 0; |
| 467 |
for(i=0; i<mainInfo->nComponents; i++){ |
| 468 |
|
| 469 |
if( !strcmp( mainInfo->compStamps[i]->getID(), lipidName ) ){ |
| 470 |
|
| 471 |
foundLipid = 1; |
| 472 |
lipidStamp = mainInfo->compStamps[i]; |
| 473 |
nLipids = mainInfo->componentsNmol[i]; |
| 474 |
} |
| 475 |
if( !strcmp( mainInfo->compStamps[i]->getID(), waterName ) ){ |
| 476 |
|
| 477 |
foundWater = 1; |
| 478 |
|
| 479 |
waterStamp = mainInfo->compStamps[i]; |
| 480 |
nWaters = mainInfo->componentsNmol[i]; |
| 481 |
} |
| 482 |
} |
| 483 |
if( !foundLipid ){ |
| 484 |
sprintf(painCave.errMsg, |
| 485 |
"randomBilayer error: Could not find lipid \"%s\" in the bass file.\n", |
| 486 |
lipidName ); |
| 487 |
painCave.isFatal = 1; |
| 488 |
simError(); |
| 489 |
} |
| 490 |
if( !foundWater ){ |
| 491 |
sprintf(painCave.errMsg, |
| 492 |
"randomBilayer error: Could not find solvent \"%s\" in the bass file.\n", |
| 493 |
waterName ); |
| 494 |
painCave.isFatal = 1; |
| 495 |
simError(); |
| 496 |
} |
| 497 |
|
| 498 |
//create the temp Molocator and atom Arrays |
| 499 |
|
| 500 |
lipidLocate = new MoLocator( lipidStamp ); |
| 501 |
lipidNatoms = lipidStamp->getNAtoms(); |
| 502 |
maxLength = lipidLocate->getMaxLength(); |
| 503 |
|
| 504 |
waterLocate = new MoLocator( waterStamp ); |
| 505 |
waterNatoms = waterStamp->getNAtoms(); |
| 506 |
|
| 507 |
// create a test box |
| 508 |
|
| 509 |
SimInfo* testInfo; |
| 510 |
|
| 511 |
testInfo = new SimInfo(); |
| 512 |
testInfo->n_atoms = lipidNatoms; |
| 513 |
theConfig = testInfo->getConfiguration(); |
| 514 |
theConfig->createArrays( lipidNatoms ); |
| 515 |
testInfo->atoms = new Atom*[lipidNatoms]; |
| 516 |
atoms = testInfo->atoms; |
| 517 |
|
| 518 |
// create the test box for initial water displacement |
| 519 |
|
| 520 |
testBox = maxLength + waterCell * 10.0; // pad with 4 cells |
| 521 |
nCells = (int)( testBox / waterCell + 1.0 ); |
| 522 |
int testWaters = 4 * nCells * nCells * nCells; |
| 523 |
|
| 524 |
double* waterX = new double[testWaters]; |
| 525 |
double* waterY = new double[testWaters]; |
| 526 |
double* waterZ = new double[testWaters]; |
| 527 |
|
| 528 |
double x0 = 0.0 - ( testBox * 0.5 ); |
| 529 |
double y0 = 0.0 - ( testBox * 0.5 ); |
| 530 |
double z0 = 0.0 - ( testBox * 0.5 ); |
| 531 |
|
| 532 |
|
| 533 |
// create an fcc lattice in the water box. |
| 534 |
|
| 535 |
int ndx = 0; |
| 536 |
for( i=0; i < nCells; i++ ){ |
| 537 |
for( j=0; j < nCells; j++ ){ |
| 538 |
for( k=0; k < nCells; k++ ){ |
| 539 |
|
| 540 |
myFCC.getLatticePoints(&posX, &posY, &posZ, i, j, k); |
| 541 |
for(l=0; l<4; l++){ |
| 542 |
waterX[ndx]=posX[l]; |
| 543 |
waterY[ndx]=posY[l]; |
| 544 |
waterZ[ndx]=posZ[l]; |
| 545 |
ndx++; |
| 546 |
} |
| 547 |
} |
| 548 |
} |
| 549 |
} |
| 550 |
|
| 551 |
// calculate the number of water's displaced by our lipid. |
| 552 |
|
| 553 |
testSite.rot[0][0] = 1.0; |
| 554 |
testSite.rot[0][1] = 0.0; |
| 555 |
testSite.rot[0][2] = 0.0; |
| 556 |
|
| 557 |
testSite.rot[1][0] = 0.0; |
| 558 |
testSite.rot[1][1] = 1.0; |
| 559 |
testSite.rot[1][2] = 0.0; |
| 560 |
|
| 561 |
testSite.rot[2][0] = 0.0; |
| 562 |
testSite.rot[2][1] = 0.0; |
| 563 |
testSite.rot[2][2] = 1.0; |
| 564 |
|
| 565 |
testSite.pos[0] = 0.0; |
| 566 |
testSite.pos[1] = 0.0; |
| 567 |
testSite.pos[2] = 0.0; |
| 568 |
|
| 569 |
lipidLocate->placeMol( testSite.pos, testSite.rot, atoms, 0, theConfig ); |
| 570 |
|
| 571 |
int *isActive = new int[testWaters]; |
| 572 |
for(i=0; i<testWaters; i++) isActive[i] = 1; |
| 573 |
|
| 574 |
int n_deleted = 0; |
| 575 |
double dx, dy, dz; |
| 576 |
double dx2, dy2, dz2, dSqr; |
| 577 |
double rCutSqr = water_padding * water_padding; |
| 578 |
|
| 579 |
for(i=0; ( (i<testWaters) && isActive[i] ); i++){ |
| 580 |
for(j=0; ( (j<lipidNatoms) && isActive[i] ); j++){ |
| 581 |
|
| 582 |
atoms[j]->getPos( pos ); |
| 583 |
|
| 584 |
dx = waterX[i] - pos[0]; |
| 585 |
dy = waterY[i] - pos[1]; |
| 586 |
dz = waterZ[i] - pos[2]; |
| 587 |
|
| 588 |
buildMap( dx, dy, dz, testBox, testBox, testBox ); |
| 589 |
|
| 590 |
dx2 = dx * dx; |
| 591 |
dy2 = dy * dy; |
| 592 |
dz2 = dz * dz; |
| 593 |
|
| 594 |
dSqr = dx2 + dy2 + dz2; |
| 595 |
if( dSqr < rCutSqr ){ |
| 596 |
isActive[i] = 0; |
| 597 |
n_deleted++; |
| 598 |
} |
| 599 |
} |
| 600 |
} |
| 601 |
|
| 602 |
int targetWaters = nWaters + n_deleted * nLipids; |
| 603 |
|
| 604 |
targetWaters = (int) ( targetWaters * 1.2 ); |
| 605 |
|
| 606 |
// find the best box size for the sim |
| 607 |
|
| 608 |
int nCellsX, nCellsY, nCellsZ; |
| 609 |
|
| 610 |
const double boxTargetX = 66.22752; |
| 611 |
const double boxTargetY = 60.53088; |
| 612 |
|
| 613 |
// nCellsX = (int)ceil(boxTargetX / waterCell); |
| 614 |
// nCellsY = (int)ceil(boxTargetY / waterCell); |
| 615 |
|
| 616 |
int testTot; |
| 617 |
int done = 0; |
| 618 |
nCellsX = 0; |
| 619 |
nCellsY = 0; |
| 620 |
nCellsZ = 0; |
| 621 |
while( !done ){ |
| 622 |
|
| 623 |
nCellsX++; |
| 624 |
nCellsY++; |
| 625 |
nCellsZ++; |
| 626 |
testTot = 4 * nCellsX * nCellsY * nCellsZ; |
| 627 |
|
| 628 |
if( testTot >= targetWaters ) done = 1; |
| 629 |
} |
| 630 |
|
| 631 |
// create the new water box to the new specifications |
| 632 |
|
| 633 |
int newWaters = nCellsX * nCellsY * nCellsZ * 4; |
| 634 |
|
| 635 |
delete[] waterX; |
| 636 |
delete[] waterY; |
| 637 |
delete[] waterZ; |
| 638 |
|
| 639 |
coord* waterSites = new coord[newWaters]; |
| 640 |
|
| 641 |
double box_x = waterCell * nCellsX; |
| 642 |
double box_y = waterCell * nCellsY; |
| 643 |
double box_z = waterCell * nCellsZ; |
| 644 |
|
| 645 |
// create an fcc lattice in the water box. |
| 646 |
|
| 647 |
ndx = 0; |
| 648 |
for( i=0; i < nCellsX; i++ ){ |
| 649 |
for( j=0; j < nCellsY; j++ ){ |
| 650 |
for( k=0; k < nCellsZ; k++ ){ |
| 651 |
|
| 652 |
myFCC.getLatticePoints(&posX, &posY, &posZ, i, j, k); |
| 653 |
for(l=0; l<4; l++){ |
| 654 |
waterSites[ndx].pos[0] = posX[l]; |
| 655 |
waterSites[ndx].pos[1] = posY[l]; |
| 656 |
waterSites[ndx].pos[2] = posZ[l]; |
| 657 |
ndx++; |
| 658 |
} |
| 659 |
} |
| 660 |
} |
| 661 |
} |
| 662 |
|
| 663 |
coord* lipidSites = new coord[nLipids]; |
| 664 |
|
| 665 |
// start a 3D RSA for the for the lipid placements |
| 666 |
|
| 667 |
|
| 668 |
int reject; |
| 669 |
int testDX, acceptedDX; |
| 670 |
SimInfo* testInfo2; |
| 671 |
|
| 672 |
nAtoms = nLipids * lipidNatoms; |
| 673 |
testInfo2 = new SimInfo(); |
| 674 |
testInfo2->n_atoms = nAtoms; |
| 675 |
theConfig = testInfo2->getConfiguration(); |
| 676 |
theConfig->createArrays( nAtoms ); |
| 677 |
testInfo2->atoms = new Atom*[nAtoms]; |
| 678 |
atoms = testInfo2->atoms; |
| 679 |
|
| 680 |
rCutSqr = lipid_spaceing * lipid_spaceing; |
| 681 |
|
| 682 |
for(i=0; i<nLipids; i++ ){ |
| 683 |
done = 0; |
| 684 |
while( !done ){ |
| 685 |
|
| 686 |
lipidSites[i].pos[0] = drand48() * box_x; |
| 687 |
lipidSites[i].pos[1] = drand48() * box_y; |
| 688 |
lipidSites[i].pos[2] = drand48() * box_z; |
| 689 |
|
| 690 |
getRandomRot( lipidSites[i].rot ); |
| 691 |
|
| 692 |
ndx = i * lipidNatoms; |
| 693 |
|
| 694 |
lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms, |
| 695 |
ndx, theConfig ); |
| 696 |
|
| 697 |
reject = 0; |
| 698 |
for( j=0; !reject && j<i; j++){ |
| 699 |
for(k=0; !reject && k<lipidNatoms; k++){ |
| 700 |
|
| 701 |
acceptedDX = j*lipidNatoms + k; |
| 702 |
for(l=0; !reject && l<lipidNatoms; l++){ |
| 703 |
|
| 704 |
testDX = ndx + l; |
| 705 |
|
| 706 |
atoms[testDX]->getPos( posA ); |
| 707 |
atoms[acceptedDX]->getPos( posB ); |
| 708 |
|
| 709 |
dx = posA[0] - posB[0]; |
| 710 |
dy = posA[1] - posB[1]; |
| 711 |
dz = posA[2] - posB[2]; |
| 712 |
|
| 713 |
buildMap( dx, dy, dz, box_x, box_y, box_z ); |
| 714 |
|
| 715 |
dx2 = dx * dx; |
| 716 |
dy2 = dy * dy; |
| 717 |
dz2 = dz * dz; |
| 718 |
|
| 719 |
dSqr = dx2 + dy2 + dz2; |
| 720 |
if( dSqr < rCutSqr ) reject = 1; |
| 721 |
} |
| 722 |
} |
| 723 |
} |
| 724 |
|
| 725 |
if( reject ){ |
| 726 |
|
| 727 |
for(j=0; j< lipidNatoms; j++) delete atoms[ndx+j]; |
| 728 |
} |
| 729 |
else{ |
| 730 |
done = 1; |
| 731 |
std::cout << (i+1) << " has been accepted\n"; |
| 732 |
std::cout.flush(); |
| 733 |
} |
| 734 |
} |
| 735 |
} |
| 736 |
|
| 737 |
|
| 738 |
// // zSort of the lipid positions |
| 739 |
|
| 740 |
|
| 741 |
// vector< pair<int,double> >zSortArray; |
| 742 |
// for(i=0;i<nLipids;i++) |
| 743 |
// zSortArray.push_back( make_pair(i, lipidSites[i].pos[2]) ); |
| 744 |
|
| 745 |
// sort(zSortArray.begin(),zSortArray.end(),SortCond()); |
| 746 |
|
| 747 |
// ofstream outFile( "./zipper.bass", ios::app); |
| 748 |
|
| 749 |
// for(i=0; i<nLipids; i++){ |
| 750 |
// outFile << "zConstraint[" << i << "]{\n" |
| 751 |
// << " molIndex = " << zSortArray[i].first << ";\n" |
| 752 |
// << " zPos = "; |
| 753 |
|
| 754 |
// if(i<32) outFile << "60.0;\n"; |
| 755 |
// else outFile << "100.0;\n"; |
| 756 |
|
| 757 |
// outFile << " kRatio = 0.5;\n" |
| 758 |
// << "}\n"; |
| 759 |
// } |
| 760 |
|
| 761 |
// outFile.close(); |
| 762 |
|
| 763 |
|
| 764 |
// cut out the waters that overlap with the lipids. |
| 765 |
|
| 766 |
|
| 767 |
delete[] isActive; |
| 768 |
isActive = new int[newWaters]; |
| 769 |
for(i=0; i<newWaters; i++) isActive[i] = 1; |
| 770 |
int n_active = newWaters; |
| 771 |
rCutSqr = water_padding * water_padding; |
| 772 |
|
| 773 |
for(i=0; ( (i<newWaters) && isActive[i] ); i++){ |
| 774 |
for(j=0; ( (j<nAtoms) && isActive[i] ); j++){ |
| 775 |
|
| 776 |
atoms[j]->getPos( pos ); |
| 777 |
|
| 778 |
dx = waterSites[i].pos[0] - pos[0]; |
| 779 |
dy = waterSites[i].pos[1] - pos[1]; |
| 780 |
dz = waterSites[i].pos[2] - pos[2]; |
| 781 |
|
| 782 |
buildMap( dx, dy, dz, box_x, box_y, box_z ); |
| 783 |
|
| 784 |
dx2 = dx * dx; |
| 785 |
dy2 = dy * dy; |
| 786 |
dz2 = dz * dz; |
| 787 |
|
| 788 |
dSqr = dx2 + dy2 + dz2; |
| 789 |
if( dSqr < rCutSqr ){ |
| 790 |
isActive[i] = 0; |
| 791 |
n_active--; |
| 792 |
|
| 793 |
|
| 794 |
} |
| 795 |
} |
| 796 |
} |
| 797 |
|
| 798 |
|
| 799 |
|
| 800 |
|
| 801 |
if( n_active < nWaters ){ |
| 802 |
|
| 803 |
sprintf( painCave.errMsg, |
| 804 |
"Too many waters were removed, edit code and try again.\n" ); |
| 805 |
|
| 806 |
painCave.isFatal = 1; |
| 807 |
simError(); |
| 808 |
} |
| 809 |
|
| 810 |
int quickKill; |
| 811 |
while( n_active > nWaters ){ |
| 812 |
|
| 813 |
quickKill = (int)(drand48()*newWaters); |
| 814 |
|
| 815 |
if( isActive[quickKill] ){ |
| 816 |
isActive[quickKill] = 0; |
| 817 |
n_active--; |
| 818 |
|
| 819 |
} |
| 820 |
} |
| 821 |
|
| 822 |
if( n_active != nWaters ){ |
| 823 |
|
| 824 |
sprintf( painCave.errMsg, |
| 825 |
"QuickKill didn't work right. n_active = %d, and nWaters = %d\n", |
| 826 |
n_active, nWaters ); |
| 827 |
painCave.isFatal = 1; |
| 828 |
simError(); |
| 829 |
} |
| 830 |
|
| 831 |
// clean up our messes before building the final system. |
| 832 |
|
| 833 |
testInfo->getConfiguration()->destroyArrays(); |
| 834 |
testInfo2->getConfiguration()->destroyArrays(); |
| 835 |
|
| 836 |
// create the real Atom arrays |
| 837 |
|
| 838 |
nAtoms = 0; |
| 839 |
molIndex = 0; |
| 840 |
molStart = new int[nLipids + nWaters]; |
| 841 |
|
| 842 |
for(j=0; j<nLipids; j++){ |
| 843 |
molStart[molIndex] = nAtoms; |
| 844 |
molIndex++; |
| 845 |
nAtoms += lipidNatoms; |
| 846 |
} |
| 847 |
|
| 848 |
for(j=0; j<nWaters; j++){ |
| 849 |
molStart[molIndex] = nAtoms; |
| 850 |
molIndex++; |
| 851 |
nAtoms += waterNatoms; |
| 852 |
} |
| 853 |
|
| 854 |
theConfig = mainInfo->getConfiguration(); |
| 855 |
theConfig->createArrays( nAtoms ); |
| 856 |
mainInfo->atoms = new Atom*[nAtoms]; |
| 857 |
atoms = mainInfo->atoms; |
| 858 |
mainInfo->n_atoms = nAtoms; |
| 859 |
|
| 860 |
// set up the SimInfo object |
| 861 |
|
| 862 |
double Hmat[3][3]; |
| 863 |
|
| 864 |
Hmat[0][0] = box_x; |
| 865 |
Hmat[0][1] = 0.0; |
| 866 |
Hmat[0][2] = 0.0; |
| 867 |
|
| 868 |
Hmat[1][0] = 0.0; |
| 869 |
Hmat[1][1] = box_y; |
| 870 |
Hmat[1][2] = 0.0; |
| 871 |
|
| 872 |
Hmat[2][0] = 0.0; |
| 873 |
Hmat[2][1] = 0.0; |
| 874 |
Hmat[2][2] = box_z; |
| 875 |
|
| 876 |
mainInfo->setBoxM( Hmat ); |
| 877 |
|
| 878 |
// center the system on (0,0,0) |
| 879 |
|
| 880 |
for(j=0;j<nLipids;j++){ |
| 881 |
|
| 882 |
mainInfo->wrapVector( lipidSites[j].pos ); |
| 883 |
} |
| 884 |
|
| 885 |
for(j=0;j<newWaters;j++){ |
| 886 |
|
| 887 |
mainInfo->wrapVector( waterSites[j].pos ); |
| 888 |
} |
| 889 |
|
| 890 |
// initialize lipid positions |
| 891 |
|
| 892 |
molIndex = 0; |
| 893 |
for(i=0; i<nLipids; i++ ){ |
| 894 |
lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms, |
| 895 |
molStart[molIndex], theConfig ); |
| 896 |
molIndex++; |
| 897 |
} |
| 898 |
|
| 899 |
// initialize the water positions |
| 900 |
|
| 901 |
for(i=0; i<newWaters; i++){ |
| 902 |
|
| 903 |
if( isActive[i] ){ |
| 904 |
|
| 905 |
getRandomRot( waterSites[i].rot ); |
| 906 |
waterLocate->placeMol( waterSites[i].pos, waterSites[i].rot, atoms, |
| 907 |
molStart[molIndex], theConfig ); |
| 908 |
molIndex++; |
| 909 |
} |
| 910 |
} |
| 911 |
|
| 912 |
|
| 913 |
|
| 914 |
// set up the writer and write out |
| 915 |
|
| 916 |
writer = new DumpWriter( mainInfo ); |
| 917 |
writer->writeFinal( 0.0 ); |
| 918 |
|
| 919 |
return 1; |
| 920 |
} |
| 921 |
|
| 922 |
void buildMap( double &x, double &y, double &z, |
| 923 |
double boxX, double boxY, double boxZ ){ |
| 924 |
|
| 925 |
if(x < 0) x -= boxX * (double)( (int)( (x / boxX) - 0.5 ) ); |
| 926 |
else x -= boxX * (double)( (int)( (x / boxX ) + 0.5)); |
| 927 |
|
| 928 |
if(y < 0) y -= boxY * (double)( (int)( (y / boxY) - 0.5 ) ); |
| 929 |
else y -= boxY * (double)( (int)( (y / boxY ) + 0.5)); |
| 930 |
|
| 931 |
if(z < 0) z -= boxZ * (double)( (int)( (z / boxZ) - 0.5 ) ); |
| 932 |
else z -= boxZ * (double)( (int)( (z / boxZ ) + 0.5)); |
| 933 |
} |
| 934 |
|
| 935 |
/*************************************************************************** |
| 936 |
* prints out the usage for the command line arguments, then exits. |
| 937 |
***************************************************************************/ |
| 938 |
|
| 939 |
void usage(){ |
| 940 |
(void)fprintf(stdout, |
| 941 |
"\n" |
| 942 |
"The proper usage is: %s [options] <input_file>\n" |
| 943 |
"\n" |
| 944 |
"Options:\n" |
| 945 |
"\n" |
| 946 |
" short:\n" |
| 947 |
" ------\n" |
| 948 |
" -o <name> The output prefix\n" |
| 949 |
" -l <lipidName> The name of the lipid molecule specified in the BASS file.\n" |
| 950 |
" -w <waterName> The name of the water molecule specified in the BASS file.\n" |
| 951 |
|
| 952 |
"\n" |
| 953 |
" long:\n" |
| 954 |
" -----\n" |
| 955 |
|
| 956 |
" --version displays the version number\n" |
| 957 |
" --help displays this help message.\n" |
| 958 |
" --waterBuffer <#> sets the distance of closest approach of the water around the lipid\n" |
| 959 |
" defaults to 5.0\n" |
| 960 |
" --lipidBuffer <#> sets the distance of closest approach between two lipids\n" |
| 961 |
" defaults to 6.0\n" |
| 962 |
" --waterLattice <#> sets the water lattice spacing\n" |
| 963 |
" defaults to 4.929 ( 1 g/cm^3 )\n" |
| 964 |
"\n" |
| 965 |
"\n", |
| 966 |
programName); |
| 967 |
} |
