| 1 |
#include <iostream> |
| 2 |
|
| 3 |
#include <cstdlib> |
| 4 |
#include <cstring> |
| 5 |
#include <cmath> |
| 6 |
|
| 7 |
|
| 8 |
#include "simError.h" |
| 9 |
#include "SimInfo.hpp" |
| 10 |
#include "ReadWrite.hpp" |
| 11 |
|
| 12 |
#include "latticeBuilder.hpp" |
| 13 |
#include "MoLocator.hpp" |
| 14 |
#include "sysBuild.hpp" |
| 15 |
#include "nanoBuilder.hpp" |
| 16 |
|
| 17 |
nanoBuilder::nanoBuilder(int &hasError){ |
| 18 |
int Errors; |
| 19 |
int foundCore,foundShell; |
| 20 |
int i; |
| 21 |
|
| 22 |
|
| 23 |
|
| 24 |
//Zero variables |
| 25 |
particleRadius = 0.0; |
| 26 |
coreRadius = 0.0; |
| 27 |
vacancyFraction = 0.0; |
| 28 |
vacancyRadius = 0.0; |
| 29 |
shellRadius = 0.0; |
| 30 |
latticeSpacing = 0.0; |
| 31 |
|
| 32 |
buildNmol = 0; |
| 33 |
|
| 34 |
nCoreMolecules = 0; |
| 35 |
nShellMolecules = 0; |
| 36 |
|
| 37 |
atomCount = 0; |
| 38 |
coreAtomCount = 0; |
| 39 |
shellAtomCount = 0; |
| 40 |
|
| 41 |
|
| 42 |
|
| 43 |
moleculeCount = 0; |
| 44 |
foundCore = 0; |
| 45 |
foundShell = 0; |
| 46 |
totalMolecules = 0; |
| 47 |
coreHasOrientation = 0; |
| 48 |
shellHasOrientation = 0; |
| 49 |
nInterface = 0; |
| 50 |
nMol = 0; |
| 51 |
|
| 52 |
hasError = 0; |
| 53 |
Errors = 0; |
| 54 |
|
| 55 |
//Initialize class members from bsInfo struct that sysbuilder provides. |
| 56 |
isRandom = bsInfo.isRandomParticle; |
| 57 |
hasVacancies = bsInfo.hasVacancies; |
| 58 |
latticeType = bsInfo.latticeType; |
| 59 |
particleRadius = bsInfo.particleRadius; |
| 60 |
coreRadius = bsInfo.coreRadius; |
| 61 |
vacancyFraction = bsInfo.vacancyFraction; |
| 62 |
latticeSpacing = bsInfo.latticeSpacing; |
| 63 |
soluteX = bsInfo.soluteX; //Mole fraction for random particle. |
| 64 |
|
| 65 |
|
| 66 |
|
| 67 |
|
| 68 |
|
| 69 |
for (i=0;bsInfo.nComponents;i++){ |
| 70 |
if( !strcmp( bsInfo.compStamps[i]->getID(),bsInfo.coreName )){ |
| 71 |
foundCore = 1; |
| 72 |
coreStamp = bsInfo.compStamps[i]; |
| 73 |
nCoreMolecules = bsInfo.componentsNmol[i]; |
| 74 |
} |
| 75 |
if( !strcmp( bsInfo.compStamps[i]->getID(),bsInfo.shellName)){ |
| 76 |
foundShell = 1; |
| 77 |
shellStamp = bsInfo.compStamps[i]; |
| 78 |
nShellMolecules = bsInfo.componentsNmol[i]; |
| 79 |
|
| 80 |
} |
| 81 |
|
| 82 |
} |
| 83 |
|
| 84 |
|
| 85 |
|
| 86 |
if( !foundCore ){ |
| 87 |
hasError = 1; |
| 88 |
return; |
| 89 |
} |
| 90 |
if( !foundShell ){ |
| 91 |
hasError = 1; |
| 92 |
return; |
| 93 |
} |
| 94 |
|
| 95 |
|
| 96 |
|
| 97 |
Errors = sanityCheck(); |
| 98 |
|
| 99 |
if (Errors){ |
| 100 |
hasError = 1; |
| 101 |
return; |
| 102 |
} |
| 103 |
|
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|
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|
| 106 |
|
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|
| 108 |
|
| 109 |
|
| 110 |
nCoreModelAtoms = coreStamp->getNAtoms(); |
| 111 |
nShellModelAtoms = shellStamp->getNAtoms(); |
| 112 |
|
| 113 |
|
| 114 |
// We assume that if the core or shell model has more then one atom |
| 115 |
// the model has an orientational component... |
| 116 |
if (nCoreModelAtoms > 1) coreHasOrientation = 1; |
| 117 |
if (nShellModelAtoms > 1) shellHasOrientation = 1; |
| 118 |
|
| 119 |
maxModelNatoms = std::max(nCoreModelAtoms,nShellModelAtoms); |
| 120 |
|
| 121 |
/* If we specify a number of atoms in bass, we will try to build a nanopartice |
| 122 |
with that number. |
| 123 |
*/ |
| 124 |
|
| 125 |
|
| 126 |
if ((nShellMolecules != 0) && (nCoreMolecules != 0)){ |
| 127 |
totalMolecules = nShellMolecules + nCoreMolecules; |
| 128 |
nCells = ceil(pow((double)totalMolecules/4.0, 1/3)); |
| 129 |
buildNmol = 1; |
| 130 |
} |
| 131 |
else { |
| 132 |
nCells = 2.0 * particleRadius/latticeSpacing; |
| 133 |
shellRadius = particleRadius - coreRadius; |
| 134 |
} |
| 135 |
|
| 136 |
|
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|
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|
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// Initialize random seed |
| 140 |
srand48( RAND_SEED ); |
| 141 |
|
| 142 |
|
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} |
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|
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|
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nanoBuilder::~nanoBuilder(){ |
| 147 |
} |
| 148 |
|
| 149 |
|
| 150 |
// Checks to make sure we aren't doing something the builder can't do. |
| 151 |
int nanoBuilder::sanityCheck(void){ |
| 152 |
|
| 153 |
// Right now we only do bimetallic nanoparticles |
| 154 |
if (bsInfo.nComponents > 2) return 1; |
| 155 |
|
| 156 |
//Check for vacancies and random |
| 157 |
if (hasVacancies && isRandom) return 1; |
| 158 |
|
| 159 |
// make sure we aren't trying to build a core larger then the total particle size |
| 160 |
if ((coreRadius >= particleRadius) && (particleRadius != 0)) return 1; |
| 161 |
|
| 162 |
// we initialize the lattice spacing to be 0.0, if the lattice spacing is still 0.0 |
| 163 |
// we have a problem |
| 164 |
if (latticeSpacing == 0.0) return 1; |
| 165 |
|
| 166 |
// Check to see if we are specifing the number of atoms in the particle correctly. |
| 167 |
if ((nShellMolecules == 0) && (nCoreMolecules != 0)){ |
| 168 |
cerr << "nShellParticles is zero and nCoreParticles != 0" << "\n"; |
| 169 |
return 1; |
| 170 |
} |
| 171 |
// Make sure there are more then two components if we are building a randomly mixed particle. |
| 172 |
if ((bsInfo.nComponents < 2) && (isRandom)){ |
| 173 |
cerr << "Two Components are needed to build a random particle." << "\n"; |
| 174 |
} |
| 175 |
// Make sure both the core and shell models specify a target nmol. |
| 176 |
if ((nShellMolecules != 0) && (nCoreMolecules == 0)){ |
| 177 |
cerr << "nCoreParticles is zero and nShellParticles != 0" << "\n"; |
| 178 |
return 1; |
| 179 |
} |
| 180 |
|
| 181 |
return 0; |
| 182 |
|
| 183 |
} |
| 184 |
|
| 185 |
|
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|
| 187 |
int nanoBuilder::buildNanoParticle( void ){ |
| 188 |
|
| 189 |
int ix; |
| 190 |
int iy; |
| 191 |
int iz; |
| 192 |
double *rx; |
| 193 |
double *ry; |
| 194 |
double *rz; |
| 195 |
double pos[3]; |
| 196 |
double A[3][3]; |
| 197 |
double HmatI[3][3]; |
| 198 |
|
| 199 |
int nCellSites; |
| 200 |
int iref; |
| 201 |
int appNMols; |
| 202 |
int latticeCount = 0; |
| 203 |
|
| 204 |
int nAtoms; |
| 205 |
int nCoreAtomCounter = 0; |
| 206 |
int nShellAtomCounter = 0; |
| 207 |
int hasError; |
| 208 |
|
| 209 |
int i, j; |
| 210 |
|
| 211 |
int interfaceIndex = 0; |
| 212 |
double dist; |
| 213 |
double distsq; |
| 214 |
int latticeNpoints; |
| 215 |
int shesActualSizetoMe = 0; |
| 216 |
|
| 217 |
DumpWriter* writer; |
| 218 |
SimInfo* simnfo; |
| 219 |
SimState* theConfig; |
| 220 |
|
| 221 |
Lattice *myLattice; |
| 222 |
MoLocator *coreLocate; |
| 223 |
MoLocator *shellLocate; |
| 224 |
|
| 225 |
|
| 226 |
Atom** atoms; |
| 227 |
|
| 228 |
hasError = 0; |
| 229 |
|
| 230 |
myLattice = new Lattice(FCC_LATTICE_TYPE,latticeSpacing); |
| 231 |
/* |
| 232 |
latticeNpoints = myLattice.getNpoints(); |
| 233 |
|
| 234 |
// Initializd atom vector to approximate size. |
| 235 |
switch (buildType){ |
| 236 |
|
| 237 |
case BUILD_NMOL_PARTICLE: |
| 238 |
|
| 239 |
break; |
| 240 |
case BUILD_CORE_SHELL_VACANCY: |
| 241 |
// Make space in the vector for all atoms except the last full cells |
| 242 |
// We will have to add at most (latticeNpoints-1)^3 to vector |
| 243 |
appNMols = latticeNPoints * pow((double)(nCells - 1),3); |
| 244 |
moleculeVector.pushBack(); |
| 245 |
|
| 246 |
default: |
| 247 |
// Make space in the vector for all atoms except the last full cells |
| 248 |
// We will have to add at most (latticeNpoints-1)^3 to vector |
| 249 |
appNMols = latticeNPoints * pow((double)(nCells - 1),3); |
| 250 |
|
| 251 |
} |
| 252 |
*/ |
| 253 |
|
| 254 |
|
| 255 |
|
| 256 |
|
| 257 |
// Create molocator and atom arrays. |
| 258 |
coreLocate = new MoLocator(coreStamp); |
| 259 |
shellLocate = new MoLocator(shellStamp); |
| 260 |
|
| 261 |
|
| 262 |
|
| 263 |
|
| 264 |
|
| 265 |
|
| 266 |
for(iz=-nCells;iz < nCells;iz++){ |
| 267 |
for(iy=-nCells;iy<nCells;iy++){ |
| 268 |
for(ix=-nCells;ix<nCells;ix++){ |
| 269 |
nCellSites = myLattice->getLatticePoints(&rx,&ry,&rz, |
| 270 |
ix,iy,iz); |
| 271 |
for (iref=1;iref<nCellSites;iref++){ |
| 272 |
latticeCount++; |
| 273 |
|
| 274 |
pos[0] = rx[iref]; |
| 275 |
pos[1] = ry[iref]; |
| 276 |
pos[2] = rz[iref]; |
| 277 |
|
| 278 |
distsq = rx[iref]*rx[iref] + ry[iref]*ry[iref] +rz[iref]*rz[iref]; |
| 279 |
dist = sqrt(distsq); |
| 280 |
|
| 281 |
switch(buildType){ |
| 282 |
|
| 283 |
case BUILD_CORE_SHELL: |
| 284 |
nanoBuilder::buildWithCoreShell(dist,pos); |
| 285 |
break; |
| 286 |
case BUILD_CORE_SHELL_VACANCY: |
| 287 |
nanoBuilder::buildWithVacancies(dist,pos); |
| 288 |
break; |
| 289 |
|
| 290 |
case BUILD_RANDOM_PARTICLE: |
| 291 |
nanoBuilder::buildRandomlyMixed(dist,pos); |
| 292 |
break; |
| 293 |
case BUILD_NMOL_PARTICLE: |
| 294 |
nanoBuilder::buildNmolParticle(dist,pos); |
| 295 |
} |
| 296 |
} |
| 297 |
} |
| 298 |
} |
| 299 |
} |
| 300 |
|
| 301 |
|
| 302 |
|
| 303 |
// Create vacancies |
| 304 |
if (hasVacancies) buildVacancies(); |
| 305 |
|
| 306 |
// Find the size of the atom vector not including Null atoms |
| 307 |
for (i=0;i<moleculeVector.size();i++){ |
| 308 |
if (! moleculeVector[i].isVacancy){ |
| 309 |
shesActualSizetoMe++; |
| 310 |
nAtoms = moleculeVector[i].myStamp->getNAtoms(); |
| 311 |
} |
| 312 |
} |
| 313 |
|
| 314 |
// Make a random particle. |
| 315 |
if (isRandom){ |
| 316 |
placeRandom(shesActualSizetoMe); |
| 317 |
|
| 318 |
// Loop back thru and count natoms since they may have changed |
| 319 |
for (i=0;i<moleculeVector.size();i++){ |
| 320 |
if (! moleculeVector[i].isVacancy){ |
| 321 |
shesActualSizetoMe++; |
| 322 |
nAtoms = moleculeVector[i].myStamp->getNAtoms(); |
| 323 |
} |
| 324 |
} |
| 325 |
} |
| 326 |
|
| 327 |
|
| 328 |
// set up the SimInfo object |
| 329 |
|
| 330 |
simnfo = new SimInfo(); |
| 331 |
simnfo->n_atoms = nAtoms; |
| 332 |
|
| 333 |
theConfig = simnfo->getConfiguration(); |
| 334 |
theConfig->createArrays( nAtoms ); |
| 335 |
simnfo->atoms = new Atom*[nAtoms]; |
| 336 |
atoms = simnfo->atoms; |
| 337 |
|
| 338 |
|
| 339 |
shesActualSizetoMe = 0; |
| 340 |
/* Use the information from the molecule vector to place the atoms. |
| 341 |
*/ |
| 342 |
for (i= 0;i<moleculeVector.size();i++){ |
| 343 |
if (! moleculeVector[i].isVacancy) { |
| 344 |
orientationMunger( A ); |
| 345 |
if( moleculeVector[i].isCore){ |
| 346 |
nCoreAtomCounter += nCoreModelAtoms; |
| 347 |
coreLocate->placeMol(moleculeVector[i].pos,A,atoms,nShellAtomCounter, theConfig); |
| 348 |
} |
| 349 |
else { |
| 350 |
nShellAtomCounter += nShellModelAtoms; |
| 351 |
shellLocate->placeMol(moleculeVector[i].pos,A,atoms,nCoreAtomCounter, theConfig); |
| 352 |
} |
| 353 |
shesActualSizetoMe++; |
| 354 |
} |
| 355 |
} |
| 356 |
|
| 357 |
|
| 358 |
// shellLocate.placeMol(pos, A, moleculeVector,shellAtomCount); |
| 359 |
|
| 360 |
for (i=0;i<3;i++) |
| 361 |
for (j=0; j<3; j++) |
| 362 |
simnfo->Hmat[i][j] = 0.0; |
| 363 |
|
| 364 |
simnfo->Hmat[0][0] = 1.0; |
| 365 |
simnfo->Hmat[1][1] = 1.0; |
| 366 |
simnfo->Hmat[2][2] = 1.0; |
| 367 |
|
| 368 |
|
| 369 |
|
| 370 |
sprintf( simnfo->sampleName, "%s.dump", bsInfo.outPrefix ); |
| 371 |
sprintf( simnfo->finalName, "%s.init", bsInfo.outPrefix ); |
| 372 |
|
| 373 |
// set up the writer and write out |
| 374 |
|
| 375 |
writer = new DumpWriter( simnfo ); |
| 376 |
writer->writeFinal(0.0); |
| 377 |
|
| 378 |
// clean up |
| 379 |
|
| 380 |
delete[] myLattice; |
| 381 |
|
| 382 |
return hasError; |
| 383 |
} |
| 384 |
|
| 385 |
// Begin Builder routines-------------------------------> |
| 386 |
|
| 387 |
/* Builds a standard core-shell nanoparticle. |
| 388 |
*/ |
| 389 |
void nanoBuilder::buildWithCoreShell(double dist, double pos[3]){ |
| 390 |
|
| 391 |
|
| 392 |
if ( dist <= particleRadius ){ |
| 393 |
moleculeVector.push_back(myMol); |
| 394 |
|
| 395 |
if (dist <= coreRadius){ |
| 396 |
coreAtomCount += nCoreModelAtoms; |
| 397 |
moleculeVector[moleculeCount].pos[0] = pos[0]; |
| 398 |
moleculeVector[moleculeCount].pos[1] = pos[1]; |
| 399 |
moleculeVector[moleculeCount].pos[2] = pos[2]; |
| 400 |
moleculeVector[moleculeCount].myStamp = coreStamp; |
| 401 |
moleculeVector[moleculeCount].isCore = 1; |
| 402 |
moleculeVector[moleculeCount].isShell = 0; |
| 403 |
|
| 404 |
} |
| 405 |
// Place shell |
| 406 |
else{ |
| 407 |
shellAtomCount += nShellModelAtoms; |
| 408 |
moleculeVector[moleculeCount].pos[0] = pos[0]; |
| 409 |
moleculeVector[moleculeCount].pos[1] = pos[1]; |
| 410 |
moleculeVector[moleculeCount].pos[2] = pos[2]; |
| 411 |
moleculeVector[moleculeCount].myStamp = shellStamp; |
| 412 |
moleculeVector[moleculeCount].isCore = 0; |
| 413 |
moleculeVector[moleculeCount].isShell = 1; |
| 414 |
|
| 415 |
} |
| 416 |
moleculeCount++; |
| 417 |
} |
| 418 |
|
| 419 |
} |
| 420 |
/* |
| 421 |
Builds a core-shell nanoparticle and tracks the number of molecules at the |
| 422 |
interface between the core-shell. These are recorded in vacancyInterface which is just |
| 423 |
an integer vector. |
| 424 |
*/ |
| 425 |
void nanoBuilder::buildWithVacancies(double dist, double pos[3]){ |
| 426 |
if ( dist <= particleRadius ){ |
| 427 |
|
| 428 |
moleculeVector.push_back(myMol); |
| 429 |
if (dist <= coreRadius){ |
| 430 |
|
| 431 |
coreAtomCount += nCoreModelAtoms; |
| 432 |
moleculeVector[moleculeCount].pos[0] = pos[0]; |
| 433 |
moleculeVector[moleculeCount].pos[1] = pos[1]; |
| 434 |
moleculeVector[moleculeCount].pos[2] = pos[2]; |
| 435 |
moleculeVector[moleculeCount].myStamp = coreStamp; |
| 436 |
moleculeVector[moleculeCount].isCore = 1; |
| 437 |
moleculeVector[moleculeCount].isShell = 0; |
| 438 |
|
| 439 |
if ((dist >= coreRadius - vacancyRadius/2.0) && |
| 440 |
(dist <= coreRadius + vacancyRadius/2.0)){ |
| 441 |
|
| 442 |
vacancyInterface.push_back(moleculeCount); |
| 443 |
nInterface++; |
| 444 |
} |
| 445 |
} else { |
| 446 |
// Place shell |
| 447 |
shellAtomCount += nShellModelAtoms; |
| 448 |
moleculeVector[moleculeCount].pos[0] = pos[0]; |
| 449 |
moleculeVector[moleculeCount].pos[1] = pos[1]; |
| 450 |
moleculeVector[moleculeCount].pos[2] = pos[2]; |
| 451 |
moleculeVector[moleculeCount].myStamp = shellStamp; |
| 452 |
moleculeVector[moleculeCount].isCore = 0; |
| 453 |
moleculeVector[moleculeCount].isShell = 1; |
| 454 |
|
| 455 |
} |
| 456 |
moleculeCount++; |
| 457 |
} |
| 458 |
|
| 459 |
|
| 460 |
|
| 461 |
} |
| 462 |
|
| 463 |
/* Builds a core-shell nanoparticle where the number of core and shell |
| 464 |
molecules is known. |
| 465 |
*/ |
| 466 |
void nanoBuilder::buildNmolParticle(double dist, double pos[3]){ |
| 467 |
static int nMolCounter = 0; |
| 468 |
static int nCoreMolCounter = 0; |
| 469 |
|
| 470 |
|
| 471 |
if (nMolCounter < totalMolecules){ |
| 472 |
moleculeVector.push_back(myMol); |
| 473 |
if (nCoreMolCounter < nCoreMolecules){ |
| 474 |
|
| 475 |
coreAtomCount += nCoreModelAtoms; |
| 476 |
moleculeVector[moleculeCount].pos[0] = pos[0]; |
| 477 |
moleculeVector[moleculeCount].pos[1] = pos[1]; |
| 478 |
moleculeVector[moleculeCount].pos[2] = pos[2]; |
| 479 |
moleculeVector[moleculeCount].myStamp = coreStamp; |
| 480 |
moleculeVector[moleculeCount].isCore = 1; |
| 481 |
moleculeVector[moleculeCount].isShell = 0; |
| 482 |
|
| 483 |
|
| 484 |
} else { |
| 485 |
shellAtomCount += nShellModelAtoms; |
| 486 |
moleculeVector[moleculeCount].pos[0] = pos[0]; |
| 487 |
moleculeVector[moleculeCount].pos[1] = pos[1]; |
| 488 |
moleculeVector[moleculeCount].pos[2] = pos[2]; |
| 489 |
moleculeVector[moleculeCount].myStamp = shellStamp; |
| 490 |
moleculeVector[moleculeCount].isCore = 0; |
| 491 |
moleculeVector[moleculeCount].isShell = 1; |
| 492 |
|
| 493 |
|
| 494 |
} |
| 495 |
|
| 496 |
} |
| 497 |
} |
| 498 |
|
| 499 |
|
| 500 |
/* Builds a randomly mixed nanoparticle. We build the particle to be |
| 501 |
entirely the core model, then randomly switch identities after the particle is built. |
| 502 |
*/ |
| 503 |
void nanoBuilder::buildRandomlyMixed(double dist, double pos[3]){ |
| 504 |
|
| 505 |
|
| 506 |
if ( dist <= particleRadius ){ |
| 507 |
moleculeCount++; |
| 508 |
|
| 509 |
|
| 510 |
moleculeVector[moleculeCount].pos[0] = pos[0]; |
| 511 |
moleculeVector[moleculeCount].pos[1] = pos[1]; |
| 512 |
moleculeVector[moleculeCount].pos[2] = pos[2]; |
| 513 |
moleculeVector[moleculeCount].myStamp = coreStamp; |
| 514 |
moleculeVector[moleculeCount].isCore = 1; |
| 515 |
moleculeVector[moleculeCount].isShell = 0; |
| 516 |
|
| 517 |
} |
| 518 |
|
| 519 |
|
| 520 |
|
| 521 |
} |
| 522 |
|
| 523 |
|
| 524 |
// -----------------------END Builder routines. |
| 525 |
|
| 526 |
|
| 527 |
|
| 528 |
//------------------------Begin Helper routines. |
| 529 |
void nanoBuilder::placeRandom(int totalMol){ |
| 530 |
int nSolute; |
| 531 |
int nSolvent; |
| 532 |
int i; |
| 533 |
int notfound; |
| 534 |
double solute_x; |
| 535 |
double solvent_x; |
| 536 |
|
| 537 |
int tester; |
| 538 |
|
| 539 |
nSolute = floor(soluteX * (double)totalMolecules); //CHECK ME |
| 540 |
nSolvent = totalMolecules - nSolute; |
| 541 |
|
| 542 |
solute_x = (double)nSolute/(double)totalMolecules; |
| 543 |
solvent_x = 1.0 - solute_x; |
| 544 |
|
| 545 |
|
| 546 |
|
| 547 |
|
| 548 |
for(i=0;nSolute-1;i++){ |
| 549 |
notfound = 1; |
| 550 |
|
| 551 |
while(notfound){ |
| 552 |
|
| 553 |
tester = floor((double)totalMolecules * drand48()); //Pick a molecule |
| 554 |
|
| 555 |
if (moleculeVector[tester].isCore){ // Make sure we select a core atom to change |
| 556 |
|
| 557 |
moleculeVector[tester].isCore = 0; |
| 558 |
moleculeVector[tester].isShell = 1; |
| 559 |
moleculeVector[tester].myStamp = shellStamp; |
| 560 |
notfound = 0; //set notfound = false. |
| 561 |
} |
| 562 |
|
| 563 |
} |
| 564 |
|
| 565 |
} |
| 566 |
} |
| 567 |
|
| 568 |
|
| 569 |
void nanoBuilder::buildVacancies(void){ |
| 570 |
int i; |
| 571 |
int* VacancyList; //logical nInterface long. |
| 572 |
int notfound; |
| 573 |
int index = 0; |
| 574 |
int nVacancies; |
| 575 |
int tester; |
| 576 |
|
| 577 |
if (nInterface != 0){ |
| 578 |
nVacancies = floor((double)nInterface * vacancyFraction); |
| 579 |
|
| 580 |
VacancyList = new int[nInterface]; |
| 581 |
|
| 582 |
// make vacancy list all false |
| 583 |
for(i=0;i<nInterface-1;i++){ |
| 584 |
VacancyList[i] = 0; |
| 585 |
} |
| 586 |
|
| 587 |
// Build a vacancy list.... |
| 588 |
for(i=0;nVacancies-1;i++){ |
| 589 |
notfound = 1; |
| 590 |
while(notfound){ |
| 591 |
|
| 592 |
tester = floor((double)nInterface * drand48()); |
| 593 |
|
| 594 |
if(! VacancyList[tester]){ |
| 595 |
VacancyList[tester] = 1; |
| 596 |
notfound = 0; |
| 597 |
} |
| 598 |
|
| 599 |
} |
| 600 |
} |
| 601 |
} |
| 602 |
// Loop through and kill the vacancies from atom vector. |
| 603 |
|
| 604 |
for (i=0;i<nInterface;i++){ |
| 605 |
if (VacancyList[i]){ |
| 606 |
moleculeVector[vacancyInterface[i]].isVacancy = 1; |
| 607 |
} // End Vacancy List |
| 608 |
} // for nInterface |
| 609 |
|
| 610 |
|
| 611 |
delete[] VacancyList; |
| 612 |
} |
| 613 |
|
| 614 |
|
| 615 |
|
| 616 |
|
| 617 |
void nanoBuilder::orientationMunger(double rot[3][3]){ |
| 618 |
|
| 619 |
double theta, phi, psi; |
| 620 |
double cosTheta; |
| 621 |
|
| 622 |
// select random phi, psi, and cosTheta |
| 623 |
|
| 624 |
phi = 2.0 * M_PI * drand48(); |
| 625 |
psi = 2.0 * M_PI * drand48(); |
| 626 |
cosTheta = (2.0 * drand48()) - 1.0; // sample cos -1 to 1 |
| 627 |
|
| 628 |
theta = acos( cosTheta ); |
| 629 |
|
| 630 |
rot[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
| 631 |
rot[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
| 632 |
rot[0][2] = sin(theta) * sin(psi); |
| 633 |
|
| 634 |
rot[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
| 635 |
rot[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
| 636 |
rot[1][2] = sin(theta) * cos(psi); |
| 637 |
|
| 638 |
rot[2][0] = sin(phi) * sin(theta); |
| 639 |
rot[2][1] = -cos(phi) * sin(theta); |
| 640 |
rot[2][2] = cos(theta); |
| 641 |
|
| 642 |
} |
| 643 |
|
| 644 |
|
| 645 |
|
| 646 |
|
| 647 |
|
| 648 |
|
| 649 |
|
