| 1 |
#include <iostream> |
| 2 |
|
| 3 |
#include <cstdlib> |
| 4 |
#include <cstring> |
| 5 |
#include <cmath> |
| 6 |
|
| 7 |
#include "simError.h" |
| 8 |
#include "SimInfo.hpp" |
| 9 |
#include "ReadWrite.hpp" |
| 10 |
|
| 11 |
#include "MoLocator.hpp" |
| 12 |
#include "sysBuild.hpp" |
| 13 |
#include "bilayerSys.hpp" |
| 14 |
|
| 15 |
|
| 16 |
|
| 17 |
void map( double &x, double &y, double &z, |
| 18 |
double boxX, double boxY, double boxZ ); |
| 19 |
|
| 20 |
int buildRandomBilayer( void ); |
| 21 |
|
| 22 |
void getRandomRot( double rot[3][3] ); |
| 23 |
|
| 24 |
int buildBilayer( int isRandom ){ |
| 25 |
|
| 26 |
if( isRandom ){ |
| 27 |
return buildRandomBilayer(); |
| 28 |
} |
| 29 |
else{ |
| 30 |
sprintf( painCave.errMsg, |
| 31 |
"Cannot currently create a non-random bilayer.\n" ); |
| 32 |
painCave.isFatal = 1; |
| 33 |
simError(); |
| 34 |
return 0; |
| 35 |
} |
| 36 |
} |
| 37 |
|
| 38 |
|
| 39 |
int buildRandomBilayer( void ){ |
| 40 |
|
| 41 |
typedef struct{ |
| 42 |
double rot[3][3]; |
| 43 |
double pos[3]; |
| 44 |
} coord; |
| 45 |
|
| 46 |
|
| 47 |
const double waterRho = 0.0334; // number density per cubic angstrom |
| 48 |
const double waterVol = 4.0 / waterRho; // volume occupied by 4 waters |
| 49 |
const double waterCell = 4.929; // fcc unit cell length |
| 50 |
|
| 51 |
const double water_padding = 2.5; |
| 52 |
const double lipid_spaceing = 5.0; |
| 53 |
|
| 54 |
|
| 55 |
int i,j,k, l; |
| 56 |
int nAtoms, atomIndex, molIndex, molID; |
| 57 |
int* molSeq; |
| 58 |
int* molMap; |
| 59 |
int* molStart; |
| 60 |
int* cardDeck; |
| 61 |
int deckSize; |
| 62 |
int rSite, rCard; |
| 63 |
double cell; |
| 64 |
int nCells, nSites, siteIndex; |
| 65 |
|
| 66 |
coord testSite; |
| 67 |
|
| 68 |
Atom** atoms; |
| 69 |
SimInfo* simnfo; |
| 70 |
DumpWriter* writer; |
| 71 |
|
| 72 |
MoleculeStamp* lipidStamp; |
| 73 |
MoleculeStamp* waterStamp; |
| 74 |
MoLocator *lipidLocate; |
| 75 |
MoLocator *waterLocate; |
| 76 |
int foundLipid, foundWater; |
| 77 |
int nLipids, lipidNatoms, nWaters, waterNatoms; |
| 78 |
double testBox, maxLength; |
| 79 |
|
| 80 |
srand48( RAND_SEED ); |
| 81 |
|
| 82 |
|
| 83 |
// set the the lipidStamp |
| 84 |
|
| 85 |
foundLipid = 0; |
| 86 |
foundWater = 0; |
| 87 |
for(i=0; i<bsInfo.nComponents; i++){ |
| 88 |
if( !strcmp( bsInfo.compStamps[i]->getID(), bsInfo.lipidName ) ){ |
| 89 |
|
| 90 |
foundLipid = 1; |
| 91 |
lipidStamp = bsInfo.compStamps[i]; |
| 92 |
nLipids = bsInfo.componentsNmol[i]; |
| 93 |
} |
| 94 |
if( !strcmp( bsInfo.compStamps[i]->getID(), bsInfo.waterName ) ){ |
| 95 |
|
| 96 |
foundWater = 1; |
| 97 |
|
| 98 |
waterStamp = bsInfo.compStamps[i]; |
| 99 |
nWaters = bsInfo.componentsNmol[i]; |
| 100 |
} |
| 101 |
} |
| 102 |
if( !foundLipid ){ |
| 103 |
sprintf(painCave.errMsg, |
| 104 |
"Could not find lipid \"%s\" in the bass file.\n", |
| 105 |
bsInfo.lipidName ); |
| 106 |
painCave.isFatal = 1; |
| 107 |
simError(); |
| 108 |
} |
| 109 |
if( !foundWater ){ |
| 110 |
sprintf(painCave.errMsg, |
| 111 |
"Could not find solvent \"%s\" in the bass file.\n", |
| 112 |
bsInfo.waterName ); |
| 113 |
painCave.isFatal = 1; |
| 114 |
simError(); |
| 115 |
} |
| 116 |
|
| 117 |
//create the temp Molocator and atom Arrays |
| 118 |
|
| 119 |
lipidLocate = new MoLocator( lipidStamp ); |
| 120 |
lipidNatoms = lipidStamp->getNAtoms(); |
| 121 |
maxLength = lipidLocate->getMaxLength(); |
| 122 |
|
| 123 |
waterLocate = new MoLocator( waterStamp ); |
| 124 |
waterNatoms = waterStamp->getNAtoms(); |
| 125 |
|
| 126 |
nAtoms = nLipids * lipidNatoms; |
| 127 |
|
| 128 |
Atom::createArrays( nAtoms ); |
| 129 |
atoms = new Atom*[nAtoms]; |
| 130 |
|
| 131 |
// create the test box for initial water displacement |
| 132 |
|
| 133 |
testBox = maxLength + waterCell * 4.0; // pad with 4 cells |
| 134 |
nCells = (int)( testBox / waterCell + 1.0 ); |
| 135 |
int testWaters = 4 * nCells * nCells * nCells; |
| 136 |
|
| 137 |
double* waterX = new double[testWaters]; |
| 138 |
double* waterY = new double[testWaters]; |
| 139 |
double* waterZ = new double[testWaters]; |
| 140 |
|
| 141 |
double x0 = 0.0 - ( testBox * 0.5 ); |
| 142 |
double y0 = 0.0 - ( testBox * 0.5 ); |
| 143 |
double z0 = 0.0 - ( testBox * 0.5 ); |
| 144 |
|
| 145 |
|
| 146 |
// create an fcc lattice in the water box. |
| 147 |
|
| 148 |
int ndx = 0; |
| 149 |
for( i=0; i < nCells; i++ ){ |
| 150 |
for( j=0; j < nCells; j++ ){ |
| 151 |
for( k=0; k < nCells; k++ ){ |
| 152 |
|
| 153 |
waterX[ndx] = i * waterCell + x0; |
| 154 |
waterY[ndx] = j * waterCell + y0; |
| 155 |
waterZ[ndx] = k * waterCell + z0; |
| 156 |
ndx++; |
| 157 |
|
| 158 |
waterX[ndx] = i * waterCell + 0.5 * waterCell + x0; |
| 159 |
waterY[ndx] = j * waterCell + 0.5 * waterCell + y0; |
| 160 |
waterZ[ndx] = k * waterCell + z0; |
| 161 |
ndx++; |
| 162 |
|
| 163 |
waterX[ndx] = i * waterCell + x0; |
| 164 |
waterY[ndx] = j * waterCell + 0.5 * waterCell + y0; |
| 165 |
waterZ[ndx] = k * waterCell + 0.5 * waterCell + z0; |
| 166 |
ndx++; |
| 167 |
|
| 168 |
waterX[ndx] = i * waterCell + 0.5 * waterCell + x0; |
| 169 |
waterY[ndx] = j * waterCell + y0; |
| 170 |
waterZ[ndx] = k * waterCell + 0.5 * waterCell + z0; |
| 171 |
ndx++; |
| 172 |
} |
| 173 |
} |
| 174 |
} |
| 175 |
|
| 176 |
// calculate the number of water's displaced by our lipid. |
| 177 |
|
| 178 |
testSite.rot[0][0] = 1.0; |
| 179 |
testSite.rot[0][1] = 0.0; |
| 180 |
testSite.rot[0][2] = 0.0; |
| 181 |
|
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testSite.rot[1][0] = 0.0; |
| 183 |
testSite.rot[1][1] = 1.0; |
| 184 |
testSite.rot[1][2] = 0.0; |
| 185 |
|
| 186 |
testSite.rot[2][0] = 0.0; |
| 187 |
testSite.rot[2][1] = 0.0; |
| 188 |
testSite.rot[2][2] = 1.0; |
| 189 |
|
| 190 |
testSite.pos[0] = 0.0; |
| 191 |
testSite.pos[1] = 0.0; |
| 192 |
testSite.pos[2] = 0.0; |
| 193 |
|
| 194 |
lipidLocate->placeMol( testSite.pos, testSite.rot, atoms, 0 ); |
| 195 |
|
| 196 |
int *isActive = new int[testWaters]; |
| 197 |
for(i=0; i<testWaters; i++) isActive[i] = 1; |
| 198 |
|
| 199 |
int n_deleted = 0; |
| 200 |
double dx, dy, dz; |
| 201 |
double dx2, dy2, dz2, dSqr; |
| 202 |
double rCutSqr = water_padding * water_padding; |
| 203 |
|
| 204 |
for(i=0; ( (i<testWaters) && isActive[i] ); i++){ |
| 205 |
for(j=0; ( (j<lipidNatoms) && isActive[i] ); j++){ |
| 206 |
|
| 207 |
dx = waterX[i] - atoms[j]->getX(); |
| 208 |
dy = waterY[i] - atoms[j]->getY(); |
| 209 |
dz = waterZ[i] - atoms[j]->getZ(); |
| 210 |
|
| 211 |
map( dx, dy, dz, testBox, testBox, testBox ); |
| 212 |
|
| 213 |
dx2 = dx * dx; |
| 214 |
dy2 = dy * dy; |
| 215 |
dz2 = dz * dz; |
| 216 |
|
| 217 |
dSqr = dx2 + dy2 + dz2; |
| 218 |
if( dSqr < rCutSqr ){ |
| 219 |
isActive[i] = 0; |
| 220 |
n_deleted++; |
| 221 |
} |
| 222 |
} |
| 223 |
} |
| 224 |
|
| 225 |
int targetWaters = nWaters + n_deleted * nLipids; |
| 226 |
|
| 227 |
// find the best box size for the sim |
| 228 |
|
| 229 |
int testTot; |
| 230 |
int done = 0; |
| 231 |
ndx = 0; |
| 232 |
while( !done ){ |
| 233 |
|
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ndx++; |
| 235 |
testTot = 4 * ndx * ndx * ndx; |
| 236 |
|
| 237 |
if( testTot >= targetWaters ) done = 1; |
| 238 |
} |
| 239 |
|
| 240 |
nCells = ndx; |
| 241 |
|
| 242 |
|
| 243 |
// create the new water box to the new specifications |
| 244 |
|
| 245 |
int newWaters = nCells * nCells * nCells * 4; |
| 246 |
|
| 247 |
delete[] waterX; |
| 248 |
delete[] waterY; |
| 249 |
delete[] waterZ; |
| 250 |
|
| 251 |
coord* waterSites = new coord[newWaters]; |
| 252 |
|
| 253 |
double box_x = waterCell * nCells; |
| 254 |
double box_y = waterCell * nCells; |
| 255 |
double box_z = waterCell * nCells; |
| 256 |
|
| 257 |
// create an fcc lattice in the water box. |
| 258 |
|
| 259 |
ndx = 0; |
| 260 |
for( i=0; i < nCells; i++ ){ |
| 261 |
for( j=0; j < nCells; j++ ){ |
| 262 |
for( k=0; k < nCells; k++ ){ |
| 263 |
|
| 264 |
waterSites[ndx].pos[0] = i * waterCell; |
| 265 |
waterSites[ndx].pos[1] = j * waterCell; |
| 266 |
waterSites[ndx].pos[2] = k * waterCell; |
| 267 |
ndx++; |
| 268 |
|
| 269 |
waterSites[ndx].pos[0] = i * waterCell + 0.5 * waterCell; |
| 270 |
waterSites[ndx].pos[1] = j * waterCell + 0.5 * waterCell; |
| 271 |
waterSites[ndx].pos[2] = k * waterCell; |
| 272 |
ndx++; |
| 273 |
|
| 274 |
waterSites[ndx].pos[0] = i * waterCell; |
| 275 |
waterSites[ndx].pos[1] = j * waterCell + 0.5 * waterCell; |
| 276 |
waterSites[ndx].pos[2] = k * waterCell + 0.5 * waterCell; |
| 277 |
ndx++; |
| 278 |
|
| 279 |
waterSites[ndx].pos[0] = i * waterCell + 0.5 * waterCell; |
| 280 |
waterSites[ndx].pos[1] = j * waterCell; |
| 281 |
waterSites[ndx].pos[2] = k * waterCell + 0.5 * waterCell; |
| 282 |
ndx++; |
| 283 |
} |
| 284 |
} |
| 285 |
} |
| 286 |
|
| 287 |
|
| 288 |
// clear up memory from the test box |
| 289 |
|
| 290 |
for(i=0; i<lipidNatoms; i++ ) delete atoms[i]; |
| 291 |
|
| 292 |
coord* lipidSites = new coord[nLipids]; |
| 293 |
|
| 294 |
// start a 3D RSA for the for the lipid placements |
| 295 |
|
| 296 |
|
| 297 |
int reject; |
| 298 |
int testDX, acceptedDX; |
| 299 |
|
| 300 |
rCutSqr = lipid_spaceing * lipid_spaceing; |
| 301 |
|
| 302 |
for(i=0; i<nLipids; i++ ){ |
| 303 |
done = 0; |
| 304 |
while( !done ){ |
| 305 |
|
| 306 |
lipidSites[i].pos[0] = drand48() * box_x; |
| 307 |
lipidSites[i].pos[1] = drand48() * box_y; |
| 308 |
lipidSites[i].pos[2] = drand48() * box_z; |
| 309 |
|
| 310 |
getRandomRot( lipidSites[i].rot ); |
| 311 |
|
| 312 |
ndx = i * lipidNatoms; |
| 313 |
|
| 314 |
lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms, |
| 315 |
ndx ); |
| 316 |
|
| 317 |
reject = 0; |
| 318 |
for( j=0; !reject && j<i; j++){ |
| 319 |
for(k=0; !reject && k<lipidNatoms; k++){ |
| 320 |
|
| 321 |
acceptedDX = j*lipidNatoms + k; |
| 322 |
for(l=0; !reject && l<lipidNatoms; l++){ |
| 323 |
|
| 324 |
testDX = ndx + l; |
| 325 |
|
| 326 |
dx = atoms[testDX]->getX() - atoms[acceptedDX]->getX(); |
| 327 |
dy = atoms[testDX]->getY() - atoms[acceptedDX]->getY(); |
| 328 |
dz = atoms[testDX]->getZ() - atoms[acceptedDX]->getZ(); |
| 329 |
|
| 330 |
map( dx, dy, dz, box_x, box_y, box_z ); |
| 331 |
|
| 332 |
dx2 = dx * dx; |
| 333 |
dy2 = dy * dy; |
| 334 |
dz2 = dz * dz; |
| 335 |
|
| 336 |
dSqr = dx2 + dy2 + dz2; |
| 337 |
if( dSqr < rCutSqr ) reject = 1; |
| 338 |
} |
| 339 |
} |
| 340 |
} |
| 341 |
|
| 342 |
if( reject ){ |
| 343 |
|
| 344 |
for(j=0; j< lipidNatoms; j++) delete atoms[ndx+j]; |
| 345 |
} |
| 346 |
else{ |
| 347 |
done = 1; |
| 348 |
std::cout << i << " has been accepted\n"; |
| 349 |
} |
| 350 |
} |
| 351 |
} |
| 352 |
|
| 353 |
// cut out the waters that overlap with the lipids. |
| 354 |
|
| 355 |
delete[] isActive; |
| 356 |
isActive = new int[newWaters]; |
| 357 |
for(i=0; i<newWaters; i++) isActive[i] = 1; |
| 358 |
int n_active = newWaters; |
| 359 |
rCutSqr = water_padding * water_padding; |
| 360 |
|
| 361 |
for(i=0; ( (i<newWaters) && isActive[i] ); i++){ |
| 362 |
for(j=0; ( (j<nAtoms) && isActive[i] ); j++){ |
| 363 |
|
| 364 |
dx = waterSites[i].pos[0] - atoms[j]->getX(); |
| 365 |
dy = waterSites[i].pos[1] - atoms[j]->getY(); |
| 366 |
dz = waterSites[i].pos[2] - atoms[j]->getZ(); |
| 367 |
|
| 368 |
map( dx, dy, dz, box_x, box_y, box_z ); |
| 369 |
|
| 370 |
dx2 = dx * dx; |
| 371 |
dy2 = dy * dy; |
| 372 |
dz2 = dz * dz; |
| 373 |
|
| 374 |
dSqr = dx2 + dy2 + dz2; |
| 375 |
if( dSqr < rCutSqr ){ |
| 376 |
isActive[i] = 0; |
| 377 |
n_active--; |
| 378 |
} |
| 379 |
} |
| 380 |
} |
| 381 |
|
| 382 |
if( n_active < nWaters ){ |
| 383 |
|
| 384 |
sprintf( painCave.errMsg, |
| 385 |
"Too many waters were removed, edit code and try again.\n" ); |
| 386 |
|
| 387 |
painCave.isFatal = 1; |
| 388 |
simError(); |
| 389 |
} |
| 390 |
|
| 391 |
int quickKill; |
| 392 |
while( n_active > nWaters ){ |
| 393 |
|
| 394 |
quickKill = (int)(drand48()*newWaters); |
| 395 |
|
| 396 |
if( isActive[quickKill] ){ |
| 397 |
isActive[quickKill] = 0; |
| 398 |
n_active--; |
| 399 |
} |
| 400 |
} |
| 401 |
|
| 402 |
if( n_active != nWaters ){ |
| 403 |
|
| 404 |
sprintf( painCave.errMsg, |
| 405 |
"QuickKill didn't work right. n_active = %d, and nWaters = %d\n", |
| 406 |
n_active, nWaters ); |
| 407 |
painCave.isFatal = 1; |
| 408 |
simError(); |
| 409 |
} |
| 410 |
|
| 411 |
// clean up our messes before building the final system. |
| 412 |
|
| 413 |
for(i=0; i<nAtoms; i++){ |
| 414 |
|
| 415 |
delete atoms[i]; |
| 416 |
} |
| 417 |
Atom::destroyArrays(); |
| 418 |
|
| 419 |
|
| 420 |
// create the real Atom arrays |
| 421 |
|
| 422 |
nAtoms = 0; |
| 423 |
molIndex = 0; |
| 424 |
molStart = new int[nLipids + nWaters]; |
| 425 |
|
| 426 |
for(j=0; j<nLipids; j++){ |
| 427 |
molStart[molIndex] = nAtoms; |
| 428 |
molIndex++; |
| 429 |
nAtoms += lipidNatoms; |
| 430 |
} |
| 431 |
|
| 432 |
for(j=0; j<nWaters; j++){ |
| 433 |
molStart[molIndex] = nAtoms; |
| 434 |
molIndex++; |
| 435 |
nAtoms += waterNatoms; |
| 436 |
} |
| 437 |
|
| 438 |
|
| 439 |
Atom::createArrays( nAtoms ); |
| 440 |
atoms = new Atom*[nAtoms]; |
| 441 |
|
| 442 |
|
| 443 |
// initialize lipid positions |
| 444 |
|
| 445 |
molIndex = 0; |
| 446 |
for(i=0; i<nLipids; i++ ){ |
| 447 |
lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms, |
| 448 |
molStart[molIndex] ); |
| 449 |
molIndex++; |
| 450 |
} |
| 451 |
|
| 452 |
// initialize the water positions |
| 453 |
|
| 454 |
for(i=0; i<newWaters; i++){ |
| 455 |
|
| 456 |
if( isActive[i] ){ |
| 457 |
|
| 458 |
getRandomRot( waterSites[i].rot ); |
| 459 |
waterLocate->placeMol( waterSites[i].pos, waterSites[i].rot, atoms, |
| 460 |
molStart[molIndex] ); |
| 461 |
molIndex++; |
| 462 |
} |
| 463 |
} |
| 464 |
|
| 465 |
// set up the SimInfo object |
| 466 |
|
| 467 |
bsInfo.boxX = box_x; |
| 468 |
bsInfo.boxY = box_y; |
| 469 |
bsInfo.boxZ = box_z; |
| 470 |
|
| 471 |
simnfo = new SimInfo(); |
| 472 |
simnfo->n_atoms = nAtoms; |
| 473 |
simnfo->box_x = bsInfo.boxX; |
| 474 |
simnfo->box_y = bsInfo.boxY; |
| 475 |
simnfo->box_z = bsInfo.boxZ; |
| 476 |
|
| 477 |
sprintf( simnfo->sampleName, "%s.dump", bsInfo.outPrefix ); |
| 478 |
sprintf( simnfo->finalName, "%s.init", bsInfo.outPrefix ); |
| 479 |
|
| 480 |
simnfo->atoms = atoms; |
| 481 |
|
| 482 |
// set up the writer and write out |
| 483 |
|
| 484 |
writer = new DumpWriter( simnfo ); |
| 485 |
writer->writeFinal(); |
| 486 |
|
| 487 |
// clean up the memory |
| 488 |
|
| 489 |
// if( molMap != NULL ) delete[] molMap; |
| 490 |
// if( cardDeck != NULL ) delete[] cardDeck; |
| 491 |
// if( locate != NULL ){ |
| 492 |
// for(i=0; i<bsInfo.nComponents; i++){ |
| 493 |
// delete locate[i]; |
| 494 |
// } |
| 495 |
// delete[] locate; |
| 496 |
// } |
| 497 |
// if( atoms != NULL ){ |
| 498 |
// for(i=0; i<nAtoms; i++){ |
| 499 |
// delete atoms[i]; |
| 500 |
// } |
| 501 |
// Atom::destroyArrays(); |
| 502 |
// delete[] atoms; |
| 503 |
// } |
| 504 |
// if( molSeq != NULL ) delete[] molSeq; |
| 505 |
// if( simnfo != NULL ) delete simnfo; |
| 506 |
// if( writer != NULL ) delete writer; |
| 507 |
|
| 508 |
return 1; |
| 509 |
} |
| 510 |
|
| 511 |
|
| 512 |
|
| 513 |
int Old_buildRandomBilayer( void ){ |
| 514 |
|
| 515 |
int i,j,k; |
| 516 |
int nAtoms, atomIndex, molIndex, molID; |
| 517 |
int* molSeq; |
| 518 |
int* molMap; |
| 519 |
int* molStart; |
| 520 |
int* cardDeck; |
| 521 |
int deckSize; |
| 522 |
int rSite, rCard; |
| 523 |
double cell; |
| 524 |
int nCells, nSites, siteIndex; |
| 525 |
double rot[3][3]; |
| 526 |
double pos[3]; |
| 527 |
|
| 528 |
Atom** atoms; |
| 529 |
SimInfo* simnfo; |
| 530 |
DumpWriter* writer; |
| 531 |
MoLocator** locate; |
| 532 |
|
| 533 |
// initialize functions and variables |
| 534 |
|
| 535 |
srand48( RAND_SEED ); |
| 536 |
molSeq = NULL; |
| 537 |
molStart = NULL; |
| 538 |
molMap = NULL; |
| 539 |
cardDeck = NULL; |
| 540 |
atoms = NULL; |
| 541 |
locate = NULL; |
| 542 |
simnfo = NULL; |
| 543 |
writer = NULL; |
| 544 |
|
| 545 |
// calculate the number of cells in the fcc box |
| 546 |
|
| 547 |
nCells = 0; |
| 548 |
nSites = 0; |
| 549 |
while( nSites < bsInfo.totNmol ){ |
| 550 |
nCells++; |
| 551 |
nSites = 4.0 * pow( (double)nCells, 3.0 ); |
| 552 |
} |
| 553 |
|
| 554 |
|
| 555 |
// create the molMap and cardDeck arrays |
| 556 |
|
| 557 |
molMap = new int[nSites]; |
| 558 |
cardDeck = new int[nSites]; |
| 559 |
|
| 560 |
for(i=0; i<nSites; i++){ |
| 561 |
molMap[i] = -1; |
| 562 |
cardDeck[i] = i; |
| 563 |
} |
| 564 |
|
| 565 |
// randomly place the molecules on the sites |
| 566 |
|
| 567 |
deckSize = nSites; |
| 568 |
for(i=0; i<bsInfo.totNmol; i++){ |
| 569 |
rCard = (int)( deckSize * drand48() ); |
| 570 |
rSite = cardDeck[rCard]; |
| 571 |
molMap[rSite] = i; |
| 572 |
|
| 573 |
// book keep the card deck; |
| 574 |
|
| 575 |
deckSize--; |
| 576 |
cardDeck[rCard] = cardDeck[deckSize]; |
| 577 |
} |
| 578 |
|
| 579 |
|
| 580 |
// create the MoLocator and Atom arrays |
| 581 |
|
| 582 |
nAtoms = 0; |
| 583 |
molIndex = 0; |
| 584 |
locate = new MoLocator*[bsInfo.nComponents]; |
| 585 |
molSeq = new int[bsInfo.totNmol]; |
| 586 |
molStart = new int[bsInfo.totNmol]; |
| 587 |
for(i=0; i<bsInfo.nComponents; i++){ |
| 588 |
locate[i] = new MoLocator( bsInfo.compStamps[i] ); |
| 589 |
for(j=0; j<bsInfo.componentsNmol[i]; j++){ |
| 590 |
molSeq[molIndex] = i; |
| 591 |
molStart[molIndex] = nAtoms; |
| 592 |
molIndex++; |
| 593 |
nAtoms += bsInfo.compStamps[i]->getNAtoms(); |
| 594 |
} |
| 595 |
} |
| 596 |
|
| 597 |
Atom::createArrays( nAtoms ); |
| 598 |
atoms = new Atom*[nAtoms]; |
| 599 |
|
| 600 |
|
| 601 |
// place the molecules at each FCC site |
| 602 |
|
| 603 |
cell = 5.0; |
| 604 |
for(i=0; i<bsInfo.nComponents; i++){ |
| 605 |
if(cell < locate[i]->getMaxLength() ) cell = locate[i]->getMaxLength(); |
| 606 |
} |
| 607 |
cell *= 1.2; // add a little buffer |
| 608 |
|
| 609 |
cell *= M_SQRT2; |
| 610 |
|
| 611 |
siteIndex = 0; |
| 612 |
for(i=0; i<nCells; i++){ |
| 613 |
for(j=0; j<nCells; j++){ |
| 614 |
for(k=0; k<nCells; k++){ |
| 615 |
|
| 616 |
if( molMap[siteIndex] >= 0 ){ |
| 617 |
pos[0] = i * cell; |
| 618 |
pos[1] = j * cell; |
| 619 |
pos[2] = k * cell; |
| 620 |
|
| 621 |
getRandomRot( rot ); |
| 622 |
molID = molSeq[molMap[siteIndex]]; |
| 623 |
atomIndex = molStart[ molMap[siteIndex] ]; |
| 624 |
locate[molID]->placeMol( pos, rot, atoms, atomIndex ); |
| 625 |
} |
| 626 |
siteIndex++; |
| 627 |
|
| 628 |
if( molMap[siteIndex] >= 0 ){ |
| 629 |
pos[0] = i * cell + (0.5 * cell); |
| 630 |
pos[1] = j * cell; |
| 631 |
pos[2] = k * cell + (0.5 * cell); |
| 632 |
|
| 633 |
getRandomRot( rot ); |
| 634 |
molID = molSeq[molMap[siteIndex]]; |
| 635 |
atomIndex = molStart[ molMap[siteIndex] ]; |
| 636 |
locate[molID]->placeMol( pos, rot, atoms, atomIndex ); |
| 637 |
} |
| 638 |
siteIndex++; |
| 639 |
|
| 640 |
if( molMap[siteIndex] >= 0 ){ |
| 641 |
pos[0] = i * cell + (0.5 * cell); |
| 642 |
pos[1] = j * cell + (0.5 * cell); |
| 643 |
pos[2] = k * cell; |
| 644 |
|
| 645 |
getRandomRot( rot ); |
| 646 |
molID = molSeq[molMap[siteIndex]]; |
| 647 |
atomIndex = molStart[ molMap[siteIndex] ]; |
| 648 |
locate[molID]->placeMol( pos, rot, atoms, atomIndex ); |
| 649 |
} |
| 650 |
siteIndex++; |
| 651 |
|
| 652 |
if( molMap[siteIndex] >= 0 ){ |
| 653 |
pos[0] = i * cell; |
| 654 |
pos[1] = j * cell + (0.5 * cell); |
| 655 |
pos[2] = k * cell + (0.5 * cell); |
| 656 |
|
| 657 |
getRandomRot( rot ); |
| 658 |
molID = molSeq[molMap[siteIndex]]; |
| 659 |
atomIndex = molStart[ molMap[siteIndex] ]; |
| 660 |
locate[molID]->placeMol( pos, rot, atoms, atomIndex ); |
| 661 |
} |
| 662 |
siteIndex++; |
| 663 |
} |
| 664 |
} |
| 665 |
} |
| 666 |
|
| 667 |
// set up the SimInfo object |
| 668 |
|
| 669 |
bsInfo.boxX = nCells * cell; |
| 670 |
bsInfo.boxY = nCells * cell; |
| 671 |
bsInfo.boxZ = nCells * cell; |
| 672 |
|
| 673 |
simnfo = new SimInfo(); |
| 674 |
simnfo->n_atoms = nAtoms; |
| 675 |
simnfo->box_x = bsInfo.boxX; |
| 676 |
simnfo->box_y = bsInfo.boxY; |
| 677 |
simnfo->box_z = bsInfo.boxZ; |
| 678 |
|
| 679 |
sprintf( simnfo->sampleName, "%s.dump", bsInfo.outPrefix ); |
| 680 |
sprintf( simnfo->finalName, "%s.init", bsInfo.outPrefix ); |
| 681 |
|
| 682 |
simnfo->atoms = atoms; |
| 683 |
|
| 684 |
// set up the writer and write out |
| 685 |
|
| 686 |
writer = new DumpWriter( simnfo ); |
| 687 |
writer->writeFinal(); |
| 688 |
|
| 689 |
// clean up the memory |
| 690 |
|
| 691 |
if( molMap != NULL ) delete[] molMap; |
| 692 |
if( cardDeck != NULL ) delete[] cardDeck; |
| 693 |
if( locate != NULL ){ |
| 694 |
for(i=0; i<bsInfo.nComponents; i++){ |
| 695 |
delete locate[i]; |
| 696 |
} |
| 697 |
delete[] locate; |
| 698 |
} |
| 699 |
if( atoms != NULL ){ |
| 700 |
for(i=0; i<nAtoms; i++){ |
| 701 |
delete atoms[i]; |
| 702 |
} |
| 703 |
Atom::destroyArrays(); |
| 704 |
delete[] atoms; |
| 705 |
} |
| 706 |
if( molSeq != NULL ) delete[] molSeq; |
| 707 |
if( simnfo != NULL ) delete simnfo; |
| 708 |
if( writer != NULL ) delete writer; |
| 709 |
|
| 710 |
return 1; |
| 711 |
} |
| 712 |
|
| 713 |
|
| 714 |
void getRandomRot( double rot[3][3] ){ |
| 715 |
|
| 716 |
double theta, phi, psi; |
| 717 |
double cosTheta; |
| 718 |
|
| 719 |
// select random phi, psi, and cosTheta |
| 720 |
|
| 721 |
phi = 2.0 * M_PI * drand48(); |
| 722 |
psi = 2.0 * M_PI * drand48(); |
| 723 |
cosTheta = (2.0 * drand48()) - 1.0; // sample cos -1 to 1 |
| 724 |
|
| 725 |
theta = acos( cosTheta ); |
| 726 |
|
| 727 |
rot[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
| 728 |
rot[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
| 729 |
rot[0][2] = sin(theta) * sin(psi); |
| 730 |
|
| 731 |
rot[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
| 732 |
rot[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
| 733 |
rot[1][2] = sin(theta) * cos(psi); |
| 734 |
|
| 735 |
rot[2][0] = sin(phi) * sin(theta); |
| 736 |
rot[2][1] = -cos(phi) * sin(theta); |
| 737 |
rot[2][2] = cos(theta); |
| 738 |
} |
| 739 |
|
| 740 |
|
| 741 |
|
| 742 |
void map( double &x, double &y, double &z, |
| 743 |
double boxX, double boxY, double boxZ ){ |
| 744 |
|
| 745 |
if(x < 0) x -= boxX * (double)( (int)( (x / boxX) - 0.5 ) ); |
| 746 |
else x -= boxX * (double)( (int)( (x / boxX ) + 0.5)); |
| 747 |
|
| 748 |
if(y < 0) y -= boxY * (double)( (int)( (y / boxY) - 0.5 ) ); |
| 749 |
else y -= boxY * (double)( (int)( (y / boxY ) + 0.5)); |
| 750 |
|
| 751 |
if(z < 0) z -= boxZ * (double)( (int)( (z / boxZ) - 0.5 ) ); |
| 752 |
else z -= boxZ * (double)( (int)( (z / boxZ ) + 0.5)); |
| 753 |
} |
