| 1 |
#include <iostream> |
| 2 |
#include <cstdlib> |
| 3 |
#include <cstring> |
| 4 |
#include <cstdio> |
| 5 |
#include <cmath> |
| 6 |
|
| 7 |
#include "SimSetup.hpp" |
| 8 |
#include "SimInfo.hpp" |
| 9 |
#include "Atom.hpp" |
| 10 |
#include "Integrator.hpp" |
| 11 |
#include "Thermo.hpp" |
| 12 |
#include "ReadWrite.hpp" |
| 13 |
|
| 14 |
|
| 15 |
void map( double &x, double &y, double &z, |
| 16 |
double boxX, double boxY, double boxZ ); |
| 17 |
|
| 18 |
void rotate( double &x, double &y, double &z, |
| 19 |
double theta, double phi, double psi ); |
| 20 |
|
| 21 |
char* program_name; |
| 22 |
using namespace std; |
| 23 |
|
| 24 |
int main(int argc,char* argv[]){ |
| 25 |
|
| 26 |
int i, j, k, l; |
| 27 |
unsigned int n_atoms, eo, xo; |
| 28 |
char* in_name; |
| 29 |
SimSetup* startMe; |
| 30 |
SimInfo* entry_plug; |
| 31 |
Thermo* tStats; |
| 32 |
|
| 33 |
int lipidNAtoms; |
| 34 |
Atom** lipidAtoms; |
| 35 |
|
| 36 |
int tot_Natoms; |
| 37 |
Atom** totAtoms; |
| 38 |
|
| 39 |
const double water_rho = 0.0334; // number density per cubic angstrom |
| 40 |
const double water_vol = 4.0 / water_rho; // volume occupied by 4 waters |
| 41 |
const double water_cell = 4.929; // fcc unit cell length |
| 42 |
|
| 43 |
int n_lipids = 50; |
| 44 |
double water_ratio = 25.0; // water to lipid ratio |
| 45 |
int n_h2o_target = (int)( n_lipids * water_ratio + 0.5 ); |
| 46 |
|
| 47 |
std::cerr << "n_lipids = " << n_lipids << "\n"; |
| 48 |
|
| 49 |
double water_shell = 10.0; |
| 50 |
double water_padding = 2.5; |
| 51 |
double lipid_spaceing = 2.5; |
| 52 |
|
| 53 |
srand48( 1337 ); // initialize the random number generator. |
| 54 |
|
| 55 |
program_name = argv[0]; /*save the program name in case we need it*/ |
| 56 |
if( argc < 3 ){ |
| 57 |
cerr<< "Error, input and output bass files are needed to run.\n" |
| 58 |
<< program_name << " <input.bass> <output.bass>\n"; |
| 59 |
|
| 60 |
exit(8); |
| 61 |
} |
| 62 |
|
| 63 |
in_name = argv[1]; |
| 64 |
char* out_name = argv[2]; |
| 65 |
entry_plug = new SimInfo; |
| 66 |
|
| 67 |
startMe = new SimSetup; |
| 68 |
startMe->setSimInfo( entry_plug ); |
| 69 |
startMe->parseFile( in_name ); |
| 70 |
startMe->createSim(); |
| 71 |
|
| 72 |
delete startMe; |
| 73 |
|
| 74 |
lipidAtoms = entry_plug->atoms; |
| 75 |
lipidNAtoms = entry_plug->n_atoms; |
| 76 |
|
| 77 |
|
| 78 |
// find the width, height, and length of the molecule |
| 79 |
|
| 80 |
double min_x, min_y, min_z; |
| 81 |
double max_x, max_y, max_z; |
| 82 |
double test_x, test_y, test_z; |
| 83 |
|
| 84 |
max_x = min_x = lipidAtoms[0]->getX(); |
| 85 |
max_y = min_y = lipidAtoms[0]->getY(); |
| 86 |
max_z = min_z = lipidAtoms[0]->getZ(); |
| 87 |
|
| 88 |
for(i=0; i<lipidNAtoms; i++){ |
| 89 |
|
| 90 |
test_x = lipidAtoms[i]->getX(); |
| 91 |
test_y = lipidAtoms[i]->getY(); |
| 92 |
test_z = lipidAtoms[i]->getZ(); |
| 93 |
|
| 94 |
if( test_x < min_x ) min_x = test_x; |
| 95 |
if( test_y < min_y ) min_y = test_y; |
| 96 |
if( test_z < min_z ) min_z = test_z; |
| 97 |
|
| 98 |
if( test_x > max_x ) max_x = test_x; |
| 99 |
if( test_y > max_y ) max_y = test_y; |
| 100 |
if( test_z > max_z ) max_z = test_z; |
| 101 |
} |
| 102 |
|
| 103 |
double ml2 = pow((max_x - min_x), 2 ) + pow((max_y - min_y), 2 ) |
| 104 |
+ pow((max_x - min_x), 2 ); |
| 105 |
double max_length = sqrt( ml2 ); |
| 106 |
|
| 107 |
|
| 108 |
// from this information, create the test box |
| 109 |
|
| 110 |
|
| 111 |
double box_x; |
| 112 |
double box_y; |
| 113 |
double box_z; |
| 114 |
|
| 115 |
box_x = box_y = box_z = max_length + water_cell * 4.0; // pad with 4 cells |
| 116 |
|
| 117 |
int n_cellX = (int)(box_x / water_cell + 1.0 ); |
| 118 |
int n_cellY = (int)(box_y / water_cell + 1.0 ); |
| 119 |
int n_cellZ = (int)(box_z / water_cell + 1.0 ); |
| 120 |
|
| 121 |
box_x = water_cell * n_cellX; |
| 122 |
box_y = water_cell * n_cellY; |
| 123 |
box_z = water_cell * n_cellZ; |
| 124 |
|
| 125 |
int n_water = n_cellX * n_cellY * n_cellZ * 4; |
| 126 |
|
| 127 |
double *waterX = new double[n_water]; |
| 128 |
double *waterY = new double[n_water]; |
| 129 |
double *waterZ = new double[n_water]; |
| 130 |
|
| 131 |
|
| 132 |
// find the center of the test lipid, and make it the center of our |
| 133 |
// soon to be created water box. |
| 134 |
|
| 135 |
|
| 136 |
double cx, cy, cz; |
| 137 |
|
| 138 |
cx = 0.0; |
| 139 |
cy = 0.0; |
| 140 |
cz = 0.0; |
| 141 |
for(i=0; i<lipidNAtoms; i++){ |
| 142 |
cx += lipidAtoms[i]->getX(); |
| 143 |
cy += lipidAtoms[i]->getY(); |
| 144 |
cz += lipidAtoms[i]->getZ(); |
| 145 |
} |
| 146 |
cx /= lipidNAtoms; |
| 147 |
cy /= lipidNAtoms; |
| 148 |
cz /= lipidNAtoms; |
| 149 |
|
| 150 |
double x0 = cx - ( box_x * 0.5 ); |
| 151 |
double y0 = cy - ( box_y * 0.5 ); |
| 152 |
double z0 = cz - ( box_z * 0.5 ); |
| 153 |
|
| 154 |
|
| 155 |
// create an fcc lattice in the water box. |
| 156 |
|
| 157 |
|
| 158 |
int ndx = 0; |
| 159 |
for( i=0; i < n_cellX; i++ ){ |
| 160 |
for( j=0; j < n_cellY; j++ ){ |
| 161 |
for( k=0; k < n_cellZ; k++ ){ |
| 162 |
|
| 163 |
waterX[ndx] = i * water_cell + x0; |
| 164 |
waterY[ndx] = j * water_cell + y0; |
| 165 |
waterZ[ndx] = k * water_cell + z0; |
| 166 |
ndx++; |
| 167 |
|
| 168 |
waterX[ndx] = i * water_cell + 0.5 * water_cell + x0; |
| 169 |
waterY[ndx] = j * water_cell + 0.5 * water_cell + y0; |
| 170 |
waterZ[ndx] = k * water_cell + z0; |
| 171 |
ndx++; |
| 172 |
|
| 173 |
waterX[ndx] = i * water_cell + x0; |
| 174 |
waterY[ndx] = j * water_cell + 0.5 * water_cell + y0; |
| 175 |
waterZ[ndx] = k * water_cell + 0.5 * water_cell + z0; |
| 176 |
ndx++; |
| 177 |
|
| 178 |
waterX[ndx] = i * water_cell + 0.5 * water_cell + x0; |
| 179 |
waterY[ndx] = j * water_cell + y0; |
| 180 |
waterZ[ndx] = k * water_cell + 0.5 * water_cell + z0; |
| 181 |
ndx++; |
| 182 |
} |
| 183 |
} |
| 184 |
} |
| 185 |
|
| 186 |
|
| 187 |
// calculate the number of water's displaced by our molecule. |
| 188 |
|
| 189 |
int *isActive = new int[n_water]; |
| 190 |
for(i=0; i<n_water; i++) isActive[i] = 1; |
| 191 |
|
| 192 |
int n_deleted = 0; |
| 193 |
double dx, dy, dz; |
| 194 |
double dx2, dy2, dz2, dSqr; |
| 195 |
double rCutSqr = water_padding * water_padding; |
| 196 |
|
| 197 |
for(i=0; ( (i<n_water) && isActive[i] ); i++){ |
| 198 |
for(j=0; ( (j<lipidNAtoms) && isActive[i] ); j++){ |
| 199 |
|
| 200 |
dx = waterX[i] - lipidAtoms[j]->getX(); |
| 201 |
dy = waterY[i] - lipidAtoms[j]->getY(); |
| 202 |
dz = waterZ[i] - lipidAtoms[j]->getZ(); |
| 203 |
|
| 204 |
map( dx, dy, dz, box_x, box_y, box_z ); |
| 205 |
|
| 206 |
dx2 = dx * dx; |
| 207 |
dy2 = dy * dy; |
| 208 |
dz2 = dz * dz; |
| 209 |
|
| 210 |
dSqr = dx2 + dy2 + dz2; |
| 211 |
if( dSqr < rCutSqr ){ |
| 212 |
isActive[i] = 0; |
| 213 |
n_deleted++; |
| 214 |
} |
| 215 |
} |
| 216 |
} |
| 217 |
|
| 218 |
std::cerr << "nTarget before: " << n_h2o_target; |
| 219 |
|
| 220 |
n_h2o_target += n_deleted * n_lipids; |
| 221 |
|
| 222 |
std::cerr << ", after: " << n_h2o_target << ", n_deleted: " << n_deleted |
| 223 |
<< "\n"; |
| 224 |
|
| 225 |
// find a box size that best suits the number of waters we need. |
| 226 |
|
| 227 |
int done = 0; |
| 228 |
|
| 229 |
if( n_water < n_h2o_target ){ |
| 230 |
|
| 231 |
int n_generated = n_cellX; |
| 232 |
int n_test, nx, ny, nz; |
| 233 |
nx = n_cellX; |
| 234 |
ny = n_cellY; |
| 235 |
nz = n_cellZ; |
| 236 |
|
| 237 |
n_test = 4 * nx * ny * nz; |
| 238 |
|
| 239 |
while( n_test < n_h2o_target ){ |
| 240 |
|
| 241 |
nz++; |
| 242 |
n_test = 4 * nx * ny * nz; |
| 243 |
} |
| 244 |
|
| 245 |
int n_diff, goodX, goodY, goodZ; |
| 246 |
|
| 247 |
n_diff = n_test - n_h2o_target; |
| 248 |
goodX = nx; |
| 249 |
goodY = ny; |
| 250 |
goodZ = nz; |
| 251 |
|
| 252 |
int test_diff; |
| 253 |
int n_limit = nz; |
| 254 |
nz = n_cellZ; |
| 255 |
|
| 256 |
for( i=n_generated; i<=n_limit; i++ ){ |
| 257 |
for( j=i; j<=n_limit; j++ ){ |
| 258 |
for( k=j; k<=n_limit; k++ ){ |
| 259 |
|
| 260 |
n_test = 4 * i * j * k; |
| 261 |
|
| 262 |
if( n_test > n_h2o_target ){ |
| 263 |
|
| 264 |
test_diff = n_test - n_h2o_target; |
| 265 |
|
| 266 |
if( test_diff < n_diff ){ |
| 267 |
|
| 268 |
n_diff = test_diff; |
| 269 |
goodX = nx; |
| 270 |
goodY = ny; |
| 271 |
goodZ = nz; |
| 272 |
} |
| 273 |
} |
| 274 |
} |
| 275 |
} |
| 276 |
} |
| 277 |
|
| 278 |
n_cellX = goodX; |
| 279 |
n_cellY = goodY; |
| 280 |
n_cellZ = goodZ; |
| 281 |
} |
| 282 |
|
| 283 |
// we now have the best box size for the simulation. Next we |
| 284 |
// recreate the water box to the new specifications. |
| 285 |
|
| 286 |
n_water = n_cellX * n_cellY * n_cellZ * 4; |
| 287 |
|
| 288 |
std::cerr << "new waters = " << n_water << "\n"; |
| 289 |
|
| 290 |
delete[] waterX; |
| 291 |
delete[] waterY; |
| 292 |
delete[] waterZ; |
| 293 |
|
| 294 |
waterX = new double[n_water]; |
| 295 |
waterY = new double[n_water]; |
| 296 |
waterZ = new double[n_water]; |
| 297 |
|
| 298 |
box_x = water_cell * n_cellX; |
| 299 |
box_y = water_cell * n_cellY; |
| 300 |
box_z = water_cell * n_cellZ; |
| 301 |
|
| 302 |
x0 = 0.0; |
| 303 |
y0 = 0.0; |
| 304 |
z0 = 0.0; |
| 305 |
|
| 306 |
cx = ( box_x * 0.5 ); |
| 307 |
cy = ( box_y * 0.5 ); |
| 308 |
cz = ( box_z * 0.5 ); |
| 309 |
|
| 310 |
// create an fcc lattice in the water box. |
| 311 |
|
| 312 |
ndx = 0; |
| 313 |
for( i=0; i < n_cellX; i++ ){ |
| 314 |
for( j=0; j < n_cellY; j++ ){ |
| 315 |
for( k=0; k < n_cellZ; k++ ){ |
| 316 |
|
| 317 |
waterX[ndx] = i * water_cell + x0; |
| 318 |
waterY[ndx] = j * water_cell + y0; |
| 319 |
waterZ[ndx] = k * water_cell + z0; |
| 320 |
ndx++; |
| 321 |
|
| 322 |
waterX[ndx] = i * water_cell + 0.5 * water_cell + x0; |
| 323 |
waterY[ndx] = j * water_cell + 0.5 * water_cell + y0; |
| 324 |
waterZ[ndx] = k * water_cell + z0; |
| 325 |
ndx++; |
| 326 |
|
| 327 |
waterX[ndx] = i * water_cell + x0; |
| 328 |
waterY[ndx] = j * water_cell + 0.5 * water_cell + y0; |
| 329 |
waterZ[ndx] = k * water_cell + 0.5 * water_cell + z0; |
| 330 |
ndx++; |
| 331 |
|
| 332 |
waterX[ndx] = i * water_cell + 0.5 * water_cell + x0; |
| 333 |
waterY[ndx] = j * water_cell + y0; |
| 334 |
waterZ[ndx] = k * water_cell + 0.5 * water_cell + z0; |
| 335 |
ndx++; |
| 336 |
} |
| 337 |
} |
| 338 |
} |
| 339 |
|
| 340 |
// ************************************************************** |
| 341 |
|
| 342 |
|
| 343 |
|
| 344 |
// start a 3D RSA for the for the lipid placements |
| 345 |
|
| 346 |
srand48( 1337 ); |
| 347 |
|
| 348 |
int rsaNAtoms = n_lipids * lipidNAtoms; |
| 349 |
Atom** rsaAtoms = new Atom*[rsaNAtoms]; |
| 350 |
|
| 351 |
DirectionalAtom* dAtom; |
| 352 |
DirectionalAtom* dAtomNew; |
| 353 |
|
| 354 |
double rotMat[3][3]; |
| 355 |
double unitRotMat[3][3]; |
| 356 |
|
| 357 |
unitRotMat[0][0] = 1.0; |
| 358 |
unitRotMat[0][1] = 0.0; |
| 359 |
unitRotMat[0][2] = 0.0; |
| 360 |
|
| 361 |
unitRotMat[1][0] = 0.0; |
| 362 |
unitRotMat[1][1] = 1.0; |
| 363 |
unitRotMat[1][2] = 0.0; |
| 364 |
|
| 365 |
unitRotMat[2][0] = 0.0; |
| 366 |
unitRotMat[2][1] = 0.0; |
| 367 |
unitRotMat[2][2] = 1.0; |
| 368 |
|
| 369 |
ndx = 0; |
| 370 |
for(i=0; i<n_lipids; i++ ){ |
| 371 |
for(j=0; j<lipidNAtoms; j++){ |
| 372 |
|
| 373 |
if( lipidAtoms[j]->isDirectional() ){ |
| 374 |
dAtom = (DirectionalAtom *)lipidAtoms[j]; |
| 375 |
|
| 376 |
dAtomNew = new DirectionalAtom(); |
| 377 |
dAtomNew->setSUx( dAtom->getSUx() ); |
| 378 |
dAtomNew->setSUx( dAtom->getSUx() ); |
| 379 |
dAtomNew->setSUx( dAtom->getSUx() ); |
| 380 |
|
| 381 |
dAtom->getA( rotMat ); |
| 382 |
dAtomNew->setA( rotMat ); |
| 383 |
|
| 384 |
rsaAtoms[ndx] = dAtomNew; |
| 385 |
} |
| 386 |
else{ |
| 387 |
|
| 388 |
rsaAtoms[ndx] = new GeneralAtom(); |
| 389 |
} |
| 390 |
|
| 391 |
rsaAtoms[ndx]->setType( lipidAtoms[j]->getType() ); |
| 392 |
|
| 393 |
ndx++; |
| 394 |
} |
| 395 |
} |
| 396 |
|
| 397 |
double testX, testY, testZ; |
| 398 |
double theta, phi, psi; |
| 399 |
double tempX, tempY, tempZ; |
| 400 |
int reject; |
| 401 |
int testDX, acceptedDX; |
| 402 |
|
| 403 |
rCutSqr = lipid_spaceing * lipid_spaceing; |
| 404 |
|
| 405 |
for(i=0; i<n_lipids; i++ ){ |
| 406 |
done = 0; |
| 407 |
while( !done ){ |
| 408 |
|
| 409 |
testX = drand48() * box_x; |
| 410 |
testY = drand48() * box_y; |
| 411 |
testZ = drand48() * box_z; |
| 412 |
|
| 413 |
theta = drand48() * 2.0 * M_PI; |
| 414 |
phi = drand48() * 2.0 * M_PI; |
| 415 |
psi = drand48() * 2.0 * M_PI; |
| 416 |
|
| 417 |
ndx = i * lipidNAtoms; |
| 418 |
for(j=0; j<lipidNAtoms; j++){ |
| 419 |
|
| 420 |
tempX = lipidAtoms[j]->getX(); |
| 421 |
tempY = lipidAtoms[j]->getY(); |
| 422 |
tempZ = lipidAtoms[j]->getZ(); |
| 423 |
|
| 424 |
rotate( tempX, tempY, tempZ, theta, phi, psi ); |
| 425 |
|
| 426 |
rsaAtoms[ndx + j]->setX( tempX + testX ); |
| 427 |
rsaAtoms[ndx + j]->setY( tempY + testY ); |
| 428 |
rsaAtoms[ndx + j]->setZ( tempZ + testZ ); |
| 429 |
} |
| 430 |
|
| 431 |
reject = 0; |
| 432 |
for( j=0; !reject && j<i; j++){ |
| 433 |
for(k=0; !reject && k<lipidNAtoms; k++){ |
| 434 |
|
| 435 |
acceptedDX = j*lipidNAtoms + k; |
| 436 |
for(l=0; !reject && l<lipidNAtoms; l++){ |
| 437 |
|
| 438 |
testDX = ndx + l; |
| 439 |
|
| 440 |
dx = rsaAtoms[testDX]->getX() - rsaAtoms[acceptedDX]->getX(); |
| 441 |
dy = rsaAtoms[testDX]->getY() - rsaAtoms[acceptedDX]->getY(); |
| 442 |
dz = rsaAtoms[testDX]->getZ() - rsaAtoms[acceptedDX]->getZ(); |
| 443 |
|
| 444 |
map( dx, dy, dz, box_x, box_y, box_z ); |
| 445 |
|
| 446 |
dx2 = dx * dx; |
| 447 |
dy2 = dy * dy; |
| 448 |
dz2 = dz * dz; |
| 449 |
|
| 450 |
dSqr = dx2 + dy2 + dz2; |
| 451 |
if( dSqr < rCutSqr ) reject = 1; |
| 452 |
} |
| 453 |
} |
| 454 |
} |
| 455 |
|
| 456 |
if( !reject ){ |
| 457 |
done = 1; |
| 458 |
std::cerr << i << " has been accepted\n"; |
| 459 |
} |
| 460 |
} |
| 461 |
} |
| 462 |
|
| 463 |
// cut out the waters that overlap with the lipids. |
| 464 |
|
| 465 |
delete[] isActive; |
| 466 |
isActive = new int[n_water]; |
| 467 |
for(i=0; i<n_water; i++) isActive[i] = 1; |
| 468 |
int n_active = n_water; |
| 469 |
rCutSqr = water_padding * water_padding; |
| 470 |
|
| 471 |
for(i=0; ( (i<n_water) && isActive[i] ); i++){ |
| 472 |
for(j=0; ( (j<rsaNAtoms) && isActive[i] ); j++){ |
| 473 |
|
| 474 |
dx = waterX[i] - rsaAtoms[j]->getX(); |
| 475 |
dy = waterY[i] - rsaAtoms[j]->getY(); |
| 476 |
dz = waterZ[i] - rsaAtoms[j]->getZ(); |
| 477 |
|
| 478 |
map( dx, dy, dz, box_x, box_y, box_z ); |
| 479 |
|
| 480 |
dx2 = dx * dx; |
| 481 |
dy2 = dy * dy; |
| 482 |
dz2 = dz * dz; |
| 483 |
|
| 484 |
dSqr = dx2 + dy2 + dz2; |
| 485 |
if( dSqr < rCutSqr ){ |
| 486 |
isActive[i] = 0; |
| 487 |
n_active--; |
| 488 |
} |
| 489 |
} |
| 490 |
} |
| 491 |
|
| 492 |
std::cerr << "final n_waters = " << n_active << "\n"; |
| 493 |
|
| 494 |
// place all of the waters and lipids into one new array |
| 495 |
|
| 496 |
int new_nAtoms = rsaNAtoms + n_active; |
| 497 |
Atom** new_atoms = new Atom*[new_nAtoms]; |
| 498 |
|
| 499 |
ndx = 0; |
| 500 |
for(i=0; i<rsaNAtoms; i++ ){ |
| 501 |
|
| 502 |
if( rsaAtoms[i]->isDirectional() ){ |
| 503 |
dAtom = (DirectionalAtom *)rsaAtoms[i]; |
| 504 |
|
| 505 |
dAtomNew = new DirectionalAtom(); |
| 506 |
dAtomNew->setSUx( dAtom->getSUx() ); |
| 507 |
dAtomNew->setSUx( dAtom->getSUx() ); |
| 508 |
dAtomNew->setSUx( dAtom->getSUx() ); |
| 509 |
|
| 510 |
dAtom->getA( rotMat ); |
| 511 |
dAtomNew->setA( rotMat ); |
| 512 |
|
| 513 |
new_atoms[ndx] = dAtomNew; |
| 514 |
} |
| 515 |
else{ |
| 516 |
|
| 517 |
new_atoms[ndx] = new GeneralAtom(); |
| 518 |
} |
| 519 |
|
| 520 |
new_atoms[ndx]->setType( rsaAtoms[i]->getType() ); |
| 521 |
|
| 522 |
new_atoms[ndx]->setX( rsaAtoms[i]->getX() ); |
| 523 |
new_atoms[ndx]->setY( rsaAtoms[i]->getY() ); |
| 524 |
new_atoms[ndx]->setZ( rsaAtoms[i]->getZ() ); |
| 525 |
|
| 526 |
new_atoms[ndx]->set_vx( 0.0 ); |
| 527 |
new_atoms[ndx]->set_vy( 0.0 ); |
| 528 |
new_atoms[ndx]->set_vz( 0.0 ); |
| 529 |
|
| 530 |
ndx++; |
| 531 |
} |
| 532 |
|
| 533 |
for(i=0; i<n_water; i++){ |
| 534 |
if(isActive[i]){ |
| 535 |
|
| 536 |
new_atoms[ndx] = new DirectionalAtom(); |
| 537 |
new_atoms[ndx]->setType( "SSD" ); |
| 538 |
|
| 539 |
new_atoms[ndx]->setX( waterX[i] ); |
| 540 |
new_atoms[ndx]->setY( waterY[i] ); |
| 541 |
new_atoms[ndx]->setZ( waterZ[i] ); |
| 542 |
|
| 543 |
new_atoms[ndx]->set_vx( 0.0 ); |
| 544 |
new_atoms[ndx]->set_vy( 0.0 ); |
| 545 |
new_atoms[ndx]->set_vz( 0.0 ); |
| 546 |
|
| 547 |
dAtom = (DirectionalAtom *) new_atoms[ndx]; |
| 548 |
|
| 549 |
dAtom->setSUx( 0.0 ); |
| 550 |
dAtom->setSUy( 0.0 ); |
| 551 |
dAtom->setSUz( 1.0 ); |
| 552 |
|
| 553 |
dAtom->setA( unitRotMat ); |
| 554 |
|
| 555 |
ndx++; |
| 556 |
} |
| 557 |
} |
| 558 |
|
| 559 |
entry_plug->n_atoms = new_nAtoms; |
| 560 |
entry_plug->atoms = new_atoms; |
| 561 |
|
| 562 |
entry_plug->box_x = box_x; |
| 563 |
entry_plug->box_y = box_y; |
| 564 |
entry_plug->box_z = box_z; |
| 565 |
|
| 566 |
DumpWriter* xyz_out = new DumpWriter( entry_plug ); |
| 567 |
xyz_out->writeFinal(); |
| 568 |
delete xyz_out; |
| 569 |
|
| 570 |
FILE* out_file; |
| 571 |
|
| 572 |
out_file = fopen( out_name, "w" ); |
| 573 |
|
| 574 |
fprintf(out_file, |
| 575 |
"#include \"water.mdl\"\n" |
| 576 |
"#include \"lipid.mdl\"\n" |
| 577 |
"\n" |
| 578 |
"nComponents = 2;\n" |
| 579 |
"component{\n" |
| 580 |
" type = \"theLipid\";\n" |
| 581 |
" nMol = %d;\n" |
| 582 |
"}\n" |
| 583 |
"\n" |
| 584 |
"component{\n" |
| 585 |
" type = \"SSD_water\";\n" |
| 586 |
" nMol = %d;\n" |
| 587 |
"}\n" |
| 588 |
"\n" |
| 589 |
"initialConfig = \"%s\";\n" |
| 590 |
"\n" |
| 591 |
"boxX = %lf;\n" |
| 592 |
"boxY = %lf;\n" |
| 593 |
"boxZ = %lf;\n", |
| 594 |
n_lipids, n_active, entry_plug->finalName, |
| 595 |
box_x, box_y, box_z ); |
| 596 |
|
| 597 |
fclose( out_file ); |
| 598 |
|
| 599 |
return 0; |
| 600 |
} |
| 601 |
|
| 602 |
|
| 603 |
void map( double &x, double &y, double &z, |
| 604 |
double boxX, double boxY, double boxZ ){ |
| 605 |
|
| 606 |
if(x < 0) x -= boxX * (double)( (int)( (x / boxX) - 0.5 ) ); |
| 607 |
else x -= boxX * (double)( (int)( (x / boxX ) + 0.5)); |
| 608 |
|
| 609 |
if(y < 0) y -= boxY * (double)( (int)( (y / boxY) - 0.5 ) ); |
| 610 |
else y -= boxY * (double)( (int)( (y / boxY ) + 0.5)); |
| 611 |
|
| 612 |
if(z < 0) z -= boxZ * (double)( (int)( (z / boxZ) - 0.5 ) ); |
| 613 |
else z -= boxZ * (double)( (int)( (z / boxZ ) + 0.5)); |
| 614 |
} |
| 615 |
|
| 616 |
|
| 617 |
void rotate( double &x, double &y, double &z, |
| 618 |
double theta, double phi, double psi ){ |
| 619 |
|
| 620 |
double newX, newY, newZ; |
| 621 |
|
| 622 |
double A[3][3]; |
| 623 |
|
| 624 |
A[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
| 625 |
A[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
| 626 |
A[0][2] = sin(theta) * sin(psi); |
| 627 |
|
| 628 |
A[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
| 629 |
A[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
| 630 |
A[1][2] = sin(theta) * cos(psi); |
| 631 |
|
| 632 |
A[2][0] = sin(phi) * sin(theta); |
| 633 |
A[2][1] = -cos(phi) * sin(theta); |
| 634 |
A[2][2] = cos(theta); |
| 635 |
|
| 636 |
newX = (x * A[0][0]) + (y * A[0][1]) + (z * A[0][2]); |
| 637 |
newY = (x * A[1][0]) + (y * A[1][1]) + (z * A[1][2]); |
| 638 |
newZ = (x * A[2][0]) + (y * A[2][1]) + (z * A[2][2]); |
| 639 |
|
| 640 |
x = newX; |
| 641 |
y = newY; |
| 642 |
z = newZ; |
| 643 |
} |
