| 1 |
|
| 2 |
#include <iostream> |
| 3 |
#include <vector> |
| 4 |
#include <algorithm> |
| 5 |
|
| 6 |
#include <cstdlib> |
| 7 |
#include <cstring> |
| 8 |
#include <cmath> |
| 9 |
|
| 10 |
|
| 11 |
#include "simError.h" |
| 12 |
#include "SimInfo.hpp" |
| 13 |
#include "ReadWrite.hpp" |
| 14 |
|
| 15 |
#include "MoLocator.hpp" |
| 16 |
#include "sysBuild.hpp" |
| 17 |
#include "bilayerSys.hpp" |
| 18 |
|
| 19 |
#include "latticeBuilder.hpp" |
| 20 |
|
| 21 |
class SortCond{ |
| 22 |
|
| 23 |
public: |
| 24 |
bool operator()(const pair<int, double>& p1, const pair<int, double>& p2){ |
| 25 |
return p1.second < p2.second; |
| 26 |
} |
| 27 |
|
| 28 |
|
| 29 |
}; |
| 30 |
|
| 31 |
|
| 32 |
void buildMap( double &x, double &y, double &z, |
| 33 |
double boxX, double boxY, double boxZ ); |
| 34 |
|
| 35 |
int buildRandomBilayer( void ); |
| 36 |
int buildLatticeBilayer( int isHexLattice, |
| 37 |
double hexSpacing, |
| 38 |
double aLat, |
| 39 |
double bLat, |
| 40 |
int targetNlipid, |
| 41 |
double targetWaterLipidRatio, |
| 42 |
double leafSpacing); |
| 43 |
|
| 44 |
void getRandomRot( double rot[3][3] ); |
| 45 |
void getEulerRot( double theta, double phi, double psi, double rot[3][3] ); |
| 46 |
void getUnitRot( double unit[3], double rot[3][3] ); |
| 47 |
|
| 48 |
int buildBilayer( int isRandom ){ |
| 49 |
|
| 50 |
if( isRandom ){ |
| 51 |
return buildRandomBilayer(); |
| 52 |
} |
| 53 |
else{ |
| 54 |
|
| 55 |
|
| 56 |
|
| 57 |
return buildLatticeBilayer(); |
| 58 |
} |
| 59 |
} |
| 60 |
|
| 61 |
|
| 62 |
int buildRandomBilayer( void ){ |
| 63 |
|
| 64 |
typedef struct{ |
| 65 |
double rot[3][3]; |
| 66 |
double pos[3]; |
| 67 |
} coord; |
| 68 |
|
| 69 |
|
| 70 |
|
| 71 |
const double waterRho = 0.0334; // number density per cubic angstrom |
| 72 |
const double waterVol = 4.0 / waterRho; // volume occupied by 4 waters |
| 73 |
const double waterCell = 4.929; // fcc unit cell length |
| 74 |
|
| 75 |
Lattice myFCC( FCC_LATTICE_TYPE, waterCell ); |
| 76 |
double *posX, *posY, *posZ; |
| 77 |
double pos[3], posA[3], posB[3]; |
| 78 |
|
| 79 |
const double water_padding = 6.0; |
| 80 |
const double lipid_spaceing = 8.0; |
| 81 |
|
| 82 |
|
| 83 |
int i,j,k, l, m; |
| 84 |
int nAtoms, atomIndex, molIndex, molID; |
| 85 |
int* molSeq; |
| 86 |
int* molMap; |
| 87 |
int* molStart; |
| 88 |
int* cardDeck; |
| 89 |
int deckSize; |
| 90 |
int rSite, rCard; |
| 91 |
double cell; |
| 92 |
int nCells, nSites, siteIndex; |
| 93 |
|
| 94 |
coord testSite; |
| 95 |
|
| 96 |
Atom** atoms; |
| 97 |
SimInfo* simnfo; |
| 98 |
SimState* theConfig; |
| 99 |
DumpWriter* writer; |
| 100 |
|
| 101 |
MoleculeStamp* lipidStamp; |
| 102 |
MoleculeStamp* waterStamp; |
| 103 |
MoLocator *lipidLocate; |
| 104 |
MoLocator *waterLocate; |
| 105 |
int foundLipid, foundWater; |
| 106 |
int nLipids, lipidNatoms, nWaters, waterNatoms; |
| 107 |
double testBox, maxLength; |
| 108 |
|
| 109 |
srand48( RAND_SEED ); |
| 110 |
|
| 111 |
|
| 112 |
// create the simInfo objects |
| 113 |
|
| 114 |
simnfo = new SimInfo[3]; |
| 115 |
|
| 116 |
|
| 117 |
// set the the lipidStamp |
| 118 |
|
| 119 |
foundLipid = 0; |
| 120 |
foundWater = 0; |
| 121 |
for(i=0; i<bsInfo.nComponents; i++){ |
| 122 |
if( !strcmp( bsInfo.compStamps[i]->getID(), bsInfo.lipidName ) ){ |
| 123 |
|
| 124 |
foundLipid = 1; |
| 125 |
lipidStamp = bsInfo.compStamps[i]; |
| 126 |
nLipids = bsInfo.componentsNmol[i]; |
| 127 |
} |
| 128 |
if( !strcmp( bsInfo.compStamps[i]->getID(), bsInfo.waterName ) ){ |
| 129 |
|
| 130 |
foundWater = 1; |
| 131 |
|
| 132 |
waterStamp = bsInfo.compStamps[i]; |
| 133 |
nWaters = bsInfo.componentsNmol[i]; |
| 134 |
} |
| 135 |
} |
| 136 |
if( !foundLipid ){ |
| 137 |
sprintf(painCave.errMsg, |
| 138 |
"Could not find lipid \"%s\" in the bass file.\n", |
| 139 |
bsInfo.lipidName ); |
| 140 |
painCave.isFatal = 1; |
| 141 |
simError(); |
| 142 |
} |
| 143 |
if( !foundWater ){ |
| 144 |
sprintf(painCave.errMsg, |
| 145 |
"Could not find solvent \"%s\" in the bass file.\n", |
| 146 |
bsInfo.waterName ); |
| 147 |
painCave.isFatal = 1; |
| 148 |
simError(); |
| 149 |
} |
| 150 |
|
| 151 |
//create the temp Molocator and atom Arrays |
| 152 |
|
| 153 |
lipidLocate = new MoLocator( lipidStamp ); |
| 154 |
lipidNatoms = lipidStamp->getNAtoms(); |
| 155 |
maxLength = lipidLocate->getMaxLength(); |
| 156 |
|
| 157 |
waterLocate = new MoLocator( waterStamp ); |
| 158 |
waterNatoms = waterStamp->getNAtoms(); |
| 159 |
|
| 160 |
nAtoms = lipidNatoms; |
| 161 |
|
| 162 |
simnfo[0].n_atoms = nAtoms; |
| 163 |
simnfo[0].atoms=new Atom*[nAtoms]; |
| 164 |
|
| 165 |
theConfig = simnfo[0].getConfiguration(); |
| 166 |
theConfig->createArrays( simnfo[0].n_atoms ); |
| 167 |
|
| 168 |
atoms=simnfo[0].atoms; |
| 169 |
|
| 170 |
|
| 171 |
// create the test box for initial water displacement |
| 172 |
|
| 173 |
testBox = maxLength + waterCell * 4.0; // pad with 4 cells |
| 174 |
nCells = (int)( testBox / waterCell + 1.0 ); |
| 175 |
int testWaters = 4 * nCells * nCells * nCells; |
| 176 |
|
| 177 |
double* waterX = new double[testWaters]; |
| 178 |
double* waterY = new double[testWaters]; |
| 179 |
double* waterZ = new double[testWaters]; |
| 180 |
|
| 181 |
double x0 = 0.0 - ( testBox * 0.5 ); |
| 182 |
double y0 = 0.0 - ( testBox * 0.5 ); |
| 183 |
double z0 = 0.0 - ( testBox * 0.5 ); |
| 184 |
|
| 185 |
|
| 186 |
// create an fcc lattice in the water box. |
| 187 |
|
| 188 |
int ndx = 0; |
| 189 |
for( i=0; i < nCells; i++ ){ |
| 190 |
for( j=0; j < nCells; j++ ){ |
| 191 |
for( k=0; k < nCells; k++ ){ |
| 192 |
|
| 193 |
myFCC.getLatticePoints(&posX, &posY, &posZ, i, j, k); |
| 194 |
for(l=0; l<4; l++){ |
| 195 |
waterX[ndx]=posX[l]; |
| 196 |
waterY[ndx]=posY[l]; |
| 197 |
waterZ[ndx]=posZ[l]; |
| 198 |
ndx++; |
| 199 |
} |
| 200 |
} |
| 201 |
} |
| 202 |
} |
| 203 |
|
| 204 |
// calculate the number of water's displaced by our lipid. |
| 205 |
|
| 206 |
testSite.rot[0][0] = 1.0; |
| 207 |
testSite.rot[0][1] = 0.0; |
| 208 |
testSite.rot[0][2] = 0.0; |
| 209 |
|
| 210 |
testSite.rot[1][0] = 0.0; |
| 211 |
testSite.rot[1][1] = 1.0; |
| 212 |
testSite.rot[1][2] = 0.0; |
| 213 |
|
| 214 |
testSite.rot[2][0] = 0.0; |
| 215 |
testSite.rot[2][1] = 0.0; |
| 216 |
testSite.rot[2][2] = 1.0; |
| 217 |
|
| 218 |
testSite.pos[0] = 0.0; |
| 219 |
testSite.pos[1] = 0.0; |
| 220 |
testSite.pos[2] = 0.0; |
| 221 |
|
| 222 |
lipidLocate->placeMol( testSite.pos, testSite.rot, atoms, 0, theConfig ); |
| 223 |
|
| 224 |
int *isActive = new int[testWaters]; |
| 225 |
for(i=0; i<testWaters; i++) isActive[i] = 1; |
| 226 |
|
| 227 |
int n_deleted = 0; |
| 228 |
double dx, dy, dz; |
| 229 |
double dx2, dy2, dz2, dSqr; |
| 230 |
double rCutSqr = water_padding * water_padding; |
| 231 |
|
| 232 |
for(i=0; ( (i<testWaters) && isActive[i] ); i++){ |
| 233 |
for(j=0; ( (j<lipidNatoms) && isActive[i] ); j++){ |
| 234 |
|
| 235 |
atoms[j]->getPos( pos ); |
| 236 |
|
| 237 |
dx = waterX[i] - pos[0]; |
| 238 |
dy = waterY[i] - pos[1]; |
| 239 |
dz = waterZ[i] - pos[2]; |
| 240 |
|
| 241 |
buildMap( dx, dy, dz, testBox, testBox, testBox ); |
| 242 |
|
| 243 |
dx2 = dx * dx; |
| 244 |
dy2 = dy * dy; |
| 245 |
dz2 = dz * dz; |
| 246 |
|
| 247 |
dSqr = dx2 + dy2 + dz2; |
| 248 |
if( dSqr < rCutSqr ){ |
| 249 |
isActive[i] = 0; |
| 250 |
n_deleted++; |
| 251 |
} |
| 252 |
} |
| 253 |
} |
| 254 |
|
| 255 |
int targetWaters = nWaters + n_deleted * nLipids; |
| 256 |
|
| 257 |
targetWaters = (int) ( targetWaters * 1.2 ); |
| 258 |
|
| 259 |
// find the best box size for the sim |
| 260 |
|
| 261 |
int nCellsX, nCellsY, nCellsZ; |
| 262 |
|
| 263 |
const double boxTargetX = 66.22752; |
| 264 |
const double boxTargetY = 60.53088; |
| 265 |
|
| 266 |
nCellsX = (int)ceil(boxTargetX / waterCell); |
| 267 |
nCellsY = (int)ceil(boxTargetY / waterCell); |
| 268 |
|
| 269 |
int testTot; |
| 270 |
int done = 0; |
| 271 |
nCellsZ = 0; |
| 272 |
while( !done ){ |
| 273 |
|
| 274 |
nCellsZ++; |
| 275 |
testTot = 4 * nCellsX * nCellsY * nCellsZ; |
| 276 |
|
| 277 |
if( testTot >= targetWaters ) done = 1; |
| 278 |
} |
| 279 |
|
| 280 |
// create the new water box to the new specifications |
| 281 |
|
| 282 |
int newWaters = nCellsX * nCellsY * nCellsZ * 4; |
| 283 |
|
| 284 |
delete[] waterX; |
| 285 |
delete[] waterY; |
| 286 |
delete[] waterZ; |
| 287 |
|
| 288 |
coord* waterSites = new coord[newWaters]; |
| 289 |
|
| 290 |
double box_x = waterCell * nCellsX; |
| 291 |
double box_y = waterCell * nCellsY; |
| 292 |
double box_z = waterCell * nCellsZ; |
| 293 |
|
| 294 |
// create an fcc lattice in the water box. |
| 295 |
|
| 296 |
ndx = 0; |
| 297 |
for( i=0; i < nCellsX; i++ ){ |
| 298 |
for( j=0; j < nCellsY; j++ ){ |
| 299 |
for( k=0; k < nCellsZ; k++ ){ |
| 300 |
|
| 301 |
myFCC.getLatticePoints(&posX, &posY, &posZ, i, j, k); |
| 302 |
for(l=0; l<4; l++){ |
| 303 |
waterSites[ndx].pos[0] = posX[l]; |
| 304 |
waterSites[ndx].pos[1] = posY[l]; |
| 305 |
waterSites[ndx].pos[2] = posZ[l]; |
| 306 |
ndx++; |
| 307 |
} |
| 308 |
} |
| 309 |
} |
| 310 |
} |
| 311 |
|
| 312 |
coord* lipidSites = new coord[nLipids]; |
| 313 |
|
| 314 |
// start a 3D RSA for the for the lipid placements |
| 315 |
|
| 316 |
|
| 317 |
int reject; |
| 318 |
int testDX, acceptedDX; |
| 319 |
|
| 320 |
nAtoms = nLipids * lipidNatoms; |
| 321 |
|
| 322 |
simnfo[1].n_atoms = nAtoms; |
| 323 |
simnfo[1].atoms=new Atom*[nAtoms]; |
| 324 |
|
| 325 |
theConfig = simnfo[1].getConfiguration(); |
| 326 |
theConfig->createArrays( simnfo[1].n_atoms ); |
| 327 |
|
| 328 |
atoms=simnfo[1].atoms; |
| 329 |
|
| 330 |
rCutSqr = lipid_spaceing * lipid_spaceing; |
| 331 |
|
| 332 |
for(i=0; i<nLipids; i++ ){ |
| 333 |
done = 0; |
| 334 |
while( !done ){ |
| 335 |
|
| 336 |
lipidSites[i].pos[0] = drand48() * box_x; |
| 337 |
lipidSites[i].pos[1] = drand48() * box_y; |
| 338 |
lipidSites[i].pos[2] = drand48() * box_z; |
| 339 |
|
| 340 |
getRandomRot( lipidSites[i].rot ); |
| 341 |
|
| 342 |
ndx = i * lipidNatoms; |
| 343 |
|
| 344 |
lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms, |
| 345 |
ndx, theConfig ); |
| 346 |
|
| 347 |
reject = 0; |
| 348 |
for( j=0; !reject && j<i; j++){ |
| 349 |
for(k=0; !reject && k<lipidNatoms; k++){ |
| 350 |
|
| 351 |
acceptedDX = j*lipidNatoms + k; |
| 352 |
for(l=0; !reject && l<lipidNatoms; l++){ |
| 353 |
|
| 354 |
testDX = ndx + l; |
| 355 |
|
| 356 |
atoms[testDX]->getPos( posA ); |
| 357 |
atoms[acceptedDX]->getPos( posB ); |
| 358 |
|
| 359 |
dx = posA[0] - posB[0]; |
| 360 |
dy = posA[1] - posB[1]; |
| 361 |
dz = posA[2] - posB[2]; |
| 362 |
|
| 363 |
buildMap( dx, dy, dz, box_x, box_y, box_z ); |
| 364 |
|
| 365 |
dx2 = dx * dx; |
| 366 |
dy2 = dy * dy; |
| 367 |
dz2 = dz * dz; |
| 368 |
|
| 369 |
dSqr = dx2 + dy2 + dz2; |
| 370 |
if( dSqr < rCutSqr ) reject = 1; |
| 371 |
} |
| 372 |
} |
| 373 |
} |
| 374 |
|
| 375 |
if( reject ){ |
| 376 |
|
| 377 |
for(j=0; j< lipidNatoms; j++) delete atoms[ndx+j]; |
| 378 |
} |
| 379 |
else{ |
| 380 |
done = 1; |
| 381 |
std::cout << (i+1) << " has been accepted\n"; |
| 382 |
} |
| 383 |
} |
| 384 |
} |
| 385 |
|
| 386 |
|
| 387 |
// zSort of the lipid positions |
| 388 |
|
| 389 |
|
| 390 |
vector< pair<int,double> >zSortArray; |
| 391 |
for(i=0;i<nLipids;i++) |
| 392 |
zSortArray.push_back( make_pair(i, lipidSites[i].pos[2]) ); |
| 393 |
|
| 394 |
sort(zSortArray.begin(),zSortArray.end(),SortCond()); |
| 395 |
|
| 396 |
ofstream outFile( "./zipper.bass", ios::app); |
| 397 |
|
| 398 |
for(i=0; i<nLipids; i++){ |
| 399 |
outFile << "zConstraint[" << i << "]{\n" |
| 400 |
<< " molIndex = " << zSortArray[i].first << ";\n" |
| 401 |
<< " zPos = "; |
| 402 |
|
| 403 |
if(i<32) outFile << "60.0;\n"; |
| 404 |
else outFile << "100.0;\n"; |
| 405 |
|
| 406 |
outFile << " kRatio = 0.5;\n" |
| 407 |
<< "}\n"; |
| 408 |
} |
| 409 |
|
| 410 |
outFile.close(); |
| 411 |
|
| 412 |
|
| 413 |
// cut out the waters that overlap with the lipids. |
| 414 |
|
| 415 |
|
| 416 |
delete[] isActive; |
| 417 |
isActive = new int[newWaters]; |
| 418 |
for(i=0; i<newWaters; i++) isActive[i] = 1; |
| 419 |
int n_active = newWaters; |
| 420 |
rCutSqr = water_padding * water_padding; |
| 421 |
|
| 422 |
for(i=0; ( (i<newWaters) && isActive[i] ); i++){ |
| 423 |
for(j=0; ( (j<nAtoms) && isActive[i] ); j++){ |
| 424 |
|
| 425 |
atoms[j]->getPos( pos ); |
| 426 |
|
| 427 |
dx = waterSites[i].pos[0] - pos[0]; |
| 428 |
dy = waterSites[i].pos[1] - pos[1]; |
| 429 |
dz = waterSites[i].pos[2] - pos[2]; |
| 430 |
|
| 431 |
buildMap( dx, dy, dz, box_x, box_y, box_z ); |
| 432 |
|
| 433 |
dx2 = dx * dx; |
| 434 |
dy2 = dy * dy; |
| 435 |
dz2 = dz * dz; |
| 436 |
|
| 437 |
dSqr = dx2 + dy2 + dz2; |
| 438 |
if( dSqr < rCutSqr ){ |
| 439 |
isActive[i] = 0; |
| 440 |
n_active--; |
| 441 |
|
| 442 |
|
| 443 |
} |
| 444 |
} |
| 445 |
} |
| 446 |
|
| 447 |
|
| 448 |
|
| 449 |
|
| 450 |
if( n_active < nWaters ){ |
| 451 |
|
| 452 |
sprintf( painCave.errMsg, |
| 453 |
"Too many waters were removed, edit code and try again.\n" ); |
| 454 |
|
| 455 |
painCave.isFatal = 1; |
| 456 |
simError(); |
| 457 |
} |
| 458 |
|
| 459 |
int quickKill; |
| 460 |
while( n_active > nWaters ){ |
| 461 |
|
| 462 |
quickKill = (int)(drand48()*newWaters); |
| 463 |
|
| 464 |
if( isActive[quickKill] ){ |
| 465 |
isActive[quickKill] = 0; |
| 466 |
n_active--; |
| 467 |
|
| 468 |
} |
| 469 |
} |
| 470 |
|
| 471 |
if( n_active != nWaters ){ |
| 472 |
|
| 473 |
sprintf( painCave.errMsg, |
| 474 |
"QuickKill didn't work right. n_active = %d, and nWaters = %d\n", |
| 475 |
n_active, nWaters ); |
| 476 |
painCave.isFatal = 1; |
| 477 |
simError(); |
| 478 |
} |
| 479 |
|
| 480 |
// clean up our messes before building the final system. |
| 481 |
|
| 482 |
simnfo[0].getConfiguration()->destroyArrays(); |
| 483 |
simnfo[1].getConfiguration()->destroyArrays(); |
| 484 |
|
| 485 |
// create the real Atom arrays |
| 486 |
|
| 487 |
nAtoms = 0; |
| 488 |
molIndex = 0; |
| 489 |
molStart = new int[nLipids + nWaters]; |
| 490 |
|
| 491 |
for(j=0; j<nLipids; j++){ |
| 492 |
molStart[molIndex] = nAtoms; |
| 493 |
molIndex++; |
| 494 |
nAtoms += lipidNatoms; |
| 495 |
} |
| 496 |
|
| 497 |
for(j=0; j<nWaters; j++){ |
| 498 |
molStart[molIndex] = nAtoms; |
| 499 |
molIndex++; |
| 500 |
nAtoms += waterNatoms; |
| 501 |
} |
| 502 |
|
| 503 |
theConfig = simnfo[2].getConfiguration(); |
| 504 |
theConfig->createArrays( nAtoms ); |
| 505 |
simnfo[2].atoms = new Atom*[nAtoms]; |
| 506 |
atoms = simnfo[2].atoms; |
| 507 |
simnfo[2].n_atoms = nAtoms; |
| 508 |
|
| 509 |
// initialize lipid positions |
| 510 |
|
| 511 |
molIndex = 0; |
| 512 |
for(i=0; i<nLipids; i++ ){ |
| 513 |
lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms, |
| 514 |
molStart[molIndex], theConfig ); |
| 515 |
molIndex++; |
| 516 |
} |
| 517 |
|
| 518 |
// initialize the water positions |
| 519 |
|
| 520 |
for(i=0; i<newWaters; i++){ |
| 521 |
|
| 522 |
if( isActive[i] ){ |
| 523 |
|
| 524 |
getRandomRot( waterSites[i].rot ); |
| 525 |
waterLocate->placeMol( waterSites[i].pos, waterSites[i].rot, atoms, |
| 526 |
molStart[molIndex], theConfig ); |
| 527 |
molIndex++; |
| 528 |
} |
| 529 |
} |
| 530 |
|
| 531 |
// set up the SimInfo object |
| 532 |
|
| 533 |
double Hmat[3][3]; |
| 534 |
|
| 535 |
Hmat[0][0] = box_x; |
| 536 |
Hmat[0][1] = 0.0; |
| 537 |
Hmat[0][2] = 0.0; |
| 538 |
|
| 539 |
Hmat[1][0] = 0.0; |
| 540 |
Hmat[1][1] = box_y; |
| 541 |
Hmat[1][2] = 0.0; |
| 542 |
|
| 543 |
Hmat[2][0] = 0.0; |
| 544 |
Hmat[2][1] = 0.0; |
| 545 |
Hmat[2][2] = box_z; |
| 546 |
|
| 547 |
|
| 548 |
bsInfo.boxX = box_x; |
| 549 |
bsInfo.boxY = box_y; |
| 550 |
bsInfo.boxZ = box_z; |
| 551 |
|
| 552 |
simnfo[2].setBoxM( Hmat ); |
| 553 |
|
| 554 |
sprintf( simnfo[2].sampleName, "%s.dump", bsInfo.outPrefix ); |
| 555 |
sprintf( simnfo[2].finalName, "%s.init", bsInfo.outPrefix ); |
| 556 |
|
| 557 |
// set up the writer and write out |
| 558 |
|
| 559 |
writer = new DumpWriter( &simnfo[2] ); |
| 560 |
writer->writeFinal( 0.0 ); |
| 561 |
|
| 562 |
// clean up the memory |
| 563 |
|
| 564 |
// if( molMap != NULL ) delete[] molMap; |
| 565 |
// if( cardDeck != NULL ) delete[] cardDeck; |
| 566 |
// if( locate != NULL ){ |
| 567 |
// for(i=0; i<bsInfo.nComponents; i++){ |
| 568 |
// delete locate[i]; |
| 569 |
// } |
| 570 |
// delete[] locate; |
| 571 |
// } |
| 572 |
// if( atoms != NULL ){ |
| 573 |
// for(i=0; i<nAtoms; i++){ |
| 574 |
// delete atoms[i]; |
| 575 |
// } |
| 576 |
// Atom::destroyArrays(); |
| 577 |
// delete[] atoms; |
| 578 |
// } |
| 579 |
// if( molSeq != NULL ) delete[] molSeq; |
| 580 |
// if( simnfo != NULL ) delete simnfo; |
| 581 |
// if( writer != NULL ) delete writer; |
| 582 |
|
| 583 |
return 1; |
| 584 |
} |
| 585 |
|
| 586 |
int buildLatticeBilayer(int isHexLattice, |
| 587 |
double hexSpacing, |
| 588 |
double aLat, |
| 589 |
double bLat, |
| 590 |
int targetNlipid, |
| 591 |
double targetWaterLipidRatio, |
| 592 |
double leafSpacing){ |
| 593 |
|
| 594 |
typedef struct{ |
| 595 |
double rot[3][3]; |
| 596 |
double pos[3]; |
| 597 |
} coord; |
| 598 |
|
| 599 |
const double waterRho = 0.0334; // number density per cubic angstrom |
| 600 |
const double waterVol = 4.0 / waterRho; // volume occupied by 4 waters |
| 601 |
|
| 602 |
double waterCell[3]; |
| 603 |
|
| 604 |
double *posX, *posY, *posZ; |
| 605 |
double pos[3], posA[3], posB[3]; |
| 606 |
|
| 607 |
const double waterFudge = 5.0; |
| 608 |
|
| 609 |
int i,j,k,l; |
| 610 |
int nAtoms, atomIndex, molIndex, molID; |
| 611 |
int* molSeq; |
| 612 |
int* molMap; |
| 613 |
int* molStart; |
| 614 |
int testTot, done; |
| 615 |
int nCells, nCellsX, nCellsY, nCellsZ; |
| 616 |
int nx, ny; |
| 617 |
double boxX, boxY, boxZ; |
| 618 |
double unitVector[3]; |
| 619 |
int which; |
| 620 |
int targetWaters; |
| 621 |
|
| 622 |
|
| 623 |
|
| 624 |
coord testSite; |
| 625 |
|
| 626 |
Atom** atoms; |
| 627 |
SimInfo* simnfo; |
| 628 |
SimState* theConfig; |
| 629 |
DumpWriter* writer; |
| 630 |
|
| 631 |
MoleculeStamp* lipidStamp; |
| 632 |
MoleculeStamp* waterStamp; |
| 633 |
MoLocator *lipidLocate; |
| 634 |
MoLocator *waterLocate; |
| 635 |
int foundLipid, foundWater; |
| 636 |
int nLipids, lipidNatoms, nWaters, waterNatoms; |
| 637 |
|
| 638 |
srand48( RAND_SEED ); |
| 639 |
|
| 640 |
// create the simInfo objects |
| 641 |
|
| 642 |
simnfo = new SimInfo; |
| 643 |
|
| 644 |
// set the the lipidStamp |
| 645 |
|
| 646 |
foundLipid = 0; |
| 647 |
foundWater = 0; |
| 648 |
for(i=0; i<bsInfo.nComponents; i++){ |
| 649 |
if( !strcmp( bsInfo.compStamps[i]->getID(), bsInfo.lipidName ) ){ |
| 650 |
|
| 651 |
foundLipid = 1; |
| 652 |
lipidStamp = bsInfo.compStamps[i]; |
| 653 |
nLipids = bsInfo.componentsNmol[i]; |
| 654 |
lipidNatoms = lipidStamp->getNAtoms(); |
| 655 |
} |
| 656 |
if( !strcmp( bsInfo.compStamps[i]->getID(), bsInfo.waterName ) ){ |
| 657 |
|
| 658 |
foundWater = 1; |
| 659 |
|
| 660 |
waterStamp = bsInfo.compStamps[i]; |
| 661 |
nWaters = bsInfo.componentsNmol[i]; |
| 662 |
waterNatoms = waterStamp->getNAtoms(); |
| 663 |
} |
| 664 |
} |
| 665 |
if( !foundLipid ){ |
| 666 |
sprintf(painCave.errMsg, |
| 667 |
"Could not find lipid \"%s\" in the bass file.\n", |
| 668 |
bsInfo.lipidName ); |
| 669 |
painCave.isFatal = 1; |
| 670 |
simError(); |
| 671 |
} |
| 672 |
if( !foundWater ){ |
| 673 |
sprintf(painCave.errMsg, |
| 674 |
"Could not find solvent \"%s\" in the bass file.\n", |
| 675 |
bsInfo.waterName ); |
| 676 |
painCave.isFatal = 1; |
| 677 |
simError(); |
| 678 |
} |
| 679 |
|
| 680 |
//create the Molocator arrays |
| 681 |
|
| 682 |
lipidLocate = new MoLocator( lipidStamp ); |
| 683 |
waterLocate = new MoLocator( waterStamp ); |
| 684 |
|
| 685 |
|
| 686 |
// set up the bilayer leaves |
| 687 |
|
| 688 |
if (isHexLattice) { |
| 689 |
aLat = sqrt(3.0)*hexSpacing; |
| 690 |
bLat = hexSpacing; |
| 691 |
} |
| 692 |
|
| 693 |
nCells = (int) sqrt( (double)targetNlipid * bLat / (4.0 * aLat) ); |
| 694 |
|
| 695 |
nx = nCells; |
| 696 |
ny = (int) ((double)nCells * aLat / bLat); |
| 697 |
|
| 698 |
boxX = nx * aLat; |
| 699 |
boxY = ny * bLat; |
| 700 |
|
| 701 |
nLipids = 4 * nx * ny; |
| 702 |
coord* lipidSites = new coord[nLipids]; |
| 703 |
|
| 704 |
unitVector[0] = 0.0; |
| 705 |
unitVector[1] = 0.0; |
| 706 |
|
| 707 |
which = 0; |
| 708 |
|
| 709 |
for (i = 0; i < nx; i++) { |
| 710 |
for (j = 0; j < ny; j++ ) { |
| 711 |
for (k = 0; k < 2; k++) { |
| 712 |
|
| 713 |
lipidSites[which].pos[0] = (double)i * aLat; |
| 714 |
lipidSites[which].pos[1] = (double)j * bLat; |
| 715 |
lipidSites[which].pos[2] = ((double)k - 0.5) * (leafSpacing / 2.0); |
| 716 |
|
| 717 |
unitVector[2] = 2.0 * (double)k - 1.0; |
| 718 |
|
| 719 |
getUnitRot( unitVector, lipidSites[which].rot ); |
| 720 |
|
| 721 |
which++; |
| 722 |
|
| 723 |
lipidSites[which].pos[0] = aLat * ((double)i + 0.5); |
| 724 |
lipidSites[which].pos[1] = bLat * ((double)j + 0.5); |
| 725 |
lipidSites[which].pos[2] = ((double)k - 0.5) * (leafSpacing / 2.0); |
| 726 |
|
| 727 |
unitVector[2] = 2.0 * (double)k - 1.0; |
| 728 |
|
| 729 |
getUnitRot( unitVector, lipidSites[which].rot ); |
| 730 |
|
| 731 |
which++; |
| 732 |
} |
| 733 |
} |
| 734 |
} |
| 735 |
|
| 736 |
targetWaters = targetWaterLipidRatio * nLipids; |
| 737 |
|
| 738 |
// guess the size of the water box |
| 739 |
|
| 740 |
|
| 741 |
|
| 742 |
nCellsX = (int)ceil(boxX / pow(waterVol, ( 1.0 / 3.0 )) ); |
| 743 |
nCellsY = (int)ceil(boxY / pow(waterVol, ( 1.0 / 3.0 )) ); |
| 744 |
|
| 745 |
done = 0; |
| 746 |
nCellsZ = 0; |
| 747 |
while( !done ){ |
| 748 |
|
| 749 |
nCellsZ++; |
| 750 |
testTot = 4 * nCellsX * nCellsY * nCellsZ; |
| 751 |
|
| 752 |
if( testTot >= targetWaters ) done = 1; |
| 753 |
} |
| 754 |
|
| 755 |
nWaters = nCellsX * nCellsY * nCellsZ * 4; |
| 756 |
|
| 757 |
coord* waterSites = new coord[nWaters]; |
| 758 |
|
| 759 |
waterCell[0] = boxX / nCellsX; |
| 760 |
waterCell[1] = boxY / nCellsY; |
| 761 |
waterCell[2] = 4.0 / (waterRho * waterCell[0] * waterCell[1]); |
| 762 |
|
| 763 |
Lattice *myORTHO; |
| 764 |
myORTHO = new Lattice( ORTHORHOMBIC_LATTICE_TYPE, waterCell); |
| 765 |
myORTHO->setStartZ( leafSpacing / 2.0 + waterFudge); |
| 766 |
|
| 767 |
boxZ = waterCell[2] * nCellsZ; |
| 768 |
|
| 769 |
// create an fcc lattice in the water box. |
| 770 |
|
| 771 |
which = 0; |
| 772 |
for( i=0; i < nCellsX; i++ ){ |
| 773 |
for( j=0; j < nCellsY; j++ ){ |
| 774 |
for( k=0; k < nCellsZ; k++ ){ |
| 775 |
|
| 776 |
myORTHO->getLatticePoints(&posX, &posY, &posZ, i, j, k); |
| 777 |
for(l=0; l<4; l++){ |
| 778 |
waterSites[which].pos[0] = posX[l]; |
| 779 |
waterSites[which].pos[1] = posY[l]; |
| 780 |
waterSites[which].pos[2] = posZ[l]; |
| 781 |
which++; |
| 782 |
} |
| 783 |
} |
| 784 |
} |
| 785 |
} |
| 786 |
|
| 787 |
// create the real Atom arrays |
| 788 |
|
| 789 |
nAtoms = 0; |
| 790 |
molIndex = 0; |
| 791 |
molStart = new int[nLipids + nWaters]; |
| 792 |
|
| 793 |
for(j=0; j<nLipids; j++){ |
| 794 |
molStart[molIndex] = nAtoms; |
| 795 |
molIndex++; |
| 796 |
nAtoms += lipidNatoms; |
| 797 |
} |
| 798 |
|
| 799 |
for(j=0; j<nWaters; j++){ |
| 800 |
molStart[molIndex] = nAtoms; |
| 801 |
molIndex++; |
| 802 |
nAtoms += waterNatoms; |
| 803 |
} |
| 804 |
|
| 805 |
theConfig = simnfo->getConfiguration(); |
| 806 |
theConfig->createArrays( nAtoms ); |
| 807 |
simnfo->atoms = new Atom*[nAtoms]; |
| 808 |
atoms = simnfo->atoms; |
| 809 |
|
| 810 |
// initialize lipid positions |
| 811 |
|
| 812 |
molIndex = 0; |
| 813 |
for(i=0; i<nLipids; i++ ){ |
| 814 |
lipidLocate->placeMol( lipidSites[i].pos, lipidSites[i].rot, atoms, |
| 815 |
molStart[molIndex], theConfig ); |
| 816 |
molIndex++; |
| 817 |
} |
| 818 |
|
| 819 |
// initialize the water positions |
| 820 |
|
| 821 |
for(i=0; i<nWaters; i++){ |
| 822 |
|
| 823 |
getRandomRot( waterSites[i].rot ); |
| 824 |
waterLocate->placeMol( waterSites[i].pos, waterSites[i].rot, atoms, |
| 825 |
molStart[molIndex], theConfig ); |
| 826 |
molIndex++; |
| 827 |
} |
| 828 |
|
| 829 |
// set up the SimInfo object |
| 830 |
|
| 831 |
double Hmat[3][3]; |
| 832 |
|
| 833 |
Hmat[0][0] = boxX; |
| 834 |
Hmat[0][1] = 0.0; |
| 835 |
Hmat[0][2] = 0.0; |
| 836 |
|
| 837 |
Hmat[1][0] = 0.0; |
| 838 |
Hmat[1][1] = boxY; |
| 839 |
Hmat[1][2] = 0.0; |
| 840 |
|
| 841 |
Hmat[2][0] = 0.0; |
| 842 |
Hmat[2][1] = 0.0; |
| 843 |
Hmat[2][2] = boxZ; |
| 844 |
|
| 845 |
|
| 846 |
bsInfo.boxX = boxX; |
| 847 |
bsInfo.boxY = boxY; |
| 848 |
bsInfo.boxZ = boxZ; |
| 849 |
|
| 850 |
simnfo->setBoxM( Hmat ); |
| 851 |
|
| 852 |
sprintf( simnfo->sampleName, "%s.dump", bsInfo.outPrefix ); |
| 853 |
sprintf( simnfo->finalName, "%s.init", bsInfo.outPrefix ); |
| 854 |
|
| 855 |
// set up the writer and write out |
| 856 |
|
| 857 |
writer = new DumpWriter( simnfo ); |
| 858 |
writer->writeFinal( 0.0 ); |
| 859 |
|
| 860 |
return 1; |
| 861 |
} |
| 862 |
|
| 863 |
|
| 864 |
void getRandomRot( double rot[3][3] ){ |
| 865 |
|
| 866 |
double theta, phi, psi; |
| 867 |
double cosTheta; |
| 868 |
|
| 869 |
// select random phi, psi, and cosTheta |
| 870 |
|
| 871 |
phi = 2.0 * M_PI * drand48(); |
| 872 |
psi = 2.0 * M_PI * drand48(); |
| 873 |
cosTheta = (2.0 * drand48()) - 1.0; // sample cos -1 to 1 |
| 874 |
|
| 875 |
theta = acos( cosTheta ); |
| 876 |
|
| 877 |
getEulerRot( theta, phi, psi, rot ); |
| 878 |
} |
| 879 |
|
| 880 |
|
| 881 |
void getEulerRot( double theta, double phi, double psi, double rot[3][3] ){ |
| 882 |
|
| 883 |
rot[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
| 884 |
rot[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
| 885 |
rot[0][2] = sin(theta) * sin(psi); |
| 886 |
|
| 887 |
rot[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
| 888 |
rot[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
| 889 |
rot[1][2] = sin(theta) * cos(psi); |
| 890 |
|
| 891 |
rot[2][0] = sin(phi) * sin(theta); |
| 892 |
rot[2][1] = -cos(phi) * sin(theta); |
| 893 |
rot[2][2] = cos(theta); |
| 894 |
} |
| 895 |
|
| 896 |
|
| 897 |
void getUnitRot( double u[3], double rot[3][3] ){ |
| 898 |
|
| 899 |
double theta, phi, psi; |
| 900 |
|
| 901 |
theta = acos(u[2]); |
| 902 |
phi = atan(u[1] / u[0]); |
| 903 |
psi = 0.0; |
| 904 |
|
| 905 |
getEulerRot( theta, phi, psi, rot ); |
| 906 |
} |
| 907 |
|
| 908 |
|
| 909 |
|
| 910 |
void buildMap( double &x, double &y, double &z, |
| 911 |
double boxX, double boxY, double boxZ ){ |
| 912 |
|
| 913 |
if(x < 0) x -= boxX * (double)( (int)( (x / boxX) - 0.5 ) ); |
| 914 |
else x -= boxX * (double)( (int)( (x / boxX ) + 0.5)); |
| 915 |
|
| 916 |
if(y < 0) y -= boxY * (double)( (int)( (y / boxY) - 0.5 ) ); |
| 917 |
else y -= boxY * (double)( (int)( (y / boxY ) + 0.5)); |
| 918 |
|
| 919 |
if(z < 0) z -= boxZ * (double)( (int)( (z / boxZ) - 0.5 ) ); |
| 920 |
else z -= boxZ * (double)( (int)( (z / boxZ ) + 0.5)); |
| 921 |
} |
