| 1 |
#include "latticeBuilder.hpp" |
| 2 |
#include <cmath> |
| 3 |
#include <cstdlib> |
| 4 |
#include "simError.h" |
| 5 |
|
| 6 |
|
| 7 |
Lattice::Lattice(int latticeType, double latticeParameter){ |
| 8 |
int hasError; |
| 9 |
|
| 10 |
latticePosX = NULL; |
| 11 |
latticePosY = NULL; |
| 12 |
latticePosZ = NULL; |
| 13 |
|
| 14 |
startX = 0.0; |
| 15 |
startY = 0.0; |
| 16 |
startZ = 0.0; |
| 17 |
|
| 18 |
switch(latticeType){ |
| 19 |
|
| 20 |
case FCC_LATTICE_TYPE: |
| 21 |
hasError = createFccLattice(latticeParameter); |
| 22 |
break; |
| 23 |
|
| 24 |
case BCC_LATTICE_TYPE: |
| 25 |
hasError = createBccLattice(latticeParameter); |
| 26 |
break; |
| 27 |
|
| 28 |
case HCP_LATTICE_TYPE: |
| 29 |
hasError = createHcpLattice(latticeParameter); |
| 30 |
break; |
| 31 |
|
| 32 |
case HCPWATER_LATTICE_TYPE: |
| 33 |
hasError = createHcpWaterLattice(latticeParameter); |
| 34 |
break; |
| 35 |
|
| 36 |
case ORTHORHOMBIC_LATTICE_TYPE: |
| 37 |
hasError = createFccLattice(latticeParameter); |
| 38 |
break; |
| 39 |
|
| 40 |
|
| 41 |
default: |
| 42 |
//simerror here..... |
| 43 |
; |
| 44 |
} |
| 45 |
|
| 46 |
latticePosX = new double[nCellSites]; |
| 47 |
latticePosY = new double[nCellSites]; |
| 48 |
latticePosZ = new double[nCellSites]; |
| 49 |
|
| 50 |
return; |
| 51 |
} |
| 52 |
|
| 53 |
Lattice::Lattice(int latticeType, double latticeParameters[3]){ |
| 54 |
int hasError; |
| 55 |
|
| 56 |
latticePosX = NULL; |
| 57 |
latticePosY = NULL; |
| 58 |
latticePosZ = NULL; |
| 59 |
|
| 60 |
startX = 0.0; |
| 61 |
startY = 0.0; |
| 62 |
startZ = 0.0; |
| 63 |
|
| 64 |
switch(latticeType){ |
| 65 |
|
| 66 |
case ORTHORHOMBIC_LATTICE_TYPE: |
| 67 |
hasError = createOrthorhombicLattice(latticeParameters); |
| 68 |
break; |
| 69 |
|
| 70 |
|
| 71 |
default: |
| 72 |
//simerror here..... |
| 73 |
; |
| 74 |
} |
| 75 |
|
| 76 |
latticePosX = new double[nCellSites]; |
| 77 |
latticePosY = new double[nCellSites]; |
| 78 |
latticePosZ = new double[nCellSites]; |
| 79 |
|
| 80 |
return; |
| 81 |
} |
| 82 |
|
| 83 |
|
| 84 |
Lattice::~Lattice(void){ |
| 85 |
if (latticePosX != NULL) delete[] latticePosX; |
| 86 |
if (latticePosY != NULL) delete[] latticePosY; |
| 87 |
if (latticePosZ != NULL) delete[] latticePosZ; |
| 88 |
} |
| 89 |
|
| 90 |
|
| 91 |
int Lattice::createFccLattice(double latticeParameter){ |
| 92 |
double cell2; |
| 93 |
double rroot3; |
| 94 |
|
| 95 |
cellLengthX = latticeParameter; |
| 96 |
cellLengthY = latticeParameter; |
| 97 |
cellLengthZ = latticeParameter; |
| 98 |
|
| 99 |
cell2 = 0.5 * latticeParameter; |
| 100 |
rroot3 = 1.0 / sqrt(3.0); |
| 101 |
|
| 102 |
nCellSites = 4; |
| 103 |
// create new unit cells |
| 104 |
thisUnitCell.sx = new double[nCellSites]; |
| 105 |
thisUnitCell.sy = new double[nCellSites]; |
| 106 |
thisUnitCell.sz = new double[nCellSites]; |
| 107 |
thisUnitCell.s_ex = new double[nCellSites]; |
| 108 |
thisUnitCell.s_ey = new double[nCellSites]; |
| 109 |
thisUnitCell.s_ez = new double[nCellSites]; |
| 110 |
|
| 111 |
// add members to each unit cell |
| 112 |
// Molecule 1 |
| 113 |
thisUnitCell.sx[0] = 0.0; |
| 114 |
thisUnitCell.sy[0] = 0.0; |
| 115 |
thisUnitCell.sz[0] = 0.0; |
| 116 |
thisUnitCell.s_ex[0] = rroot3; |
| 117 |
thisUnitCell.s_ey[0] = rroot3; |
| 118 |
thisUnitCell.s_ez[0] = rroot3; |
| 119 |
|
| 120 |
// Molecule 2 |
| 121 |
thisUnitCell.sx[1] = 0.0; |
| 122 |
thisUnitCell.sy[1] = cell2; |
| 123 |
thisUnitCell.sz[1] = cell2; |
| 124 |
thisUnitCell.s_ex[1] = -rroot3; |
| 125 |
thisUnitCell.s_ey[1] = rroot3; |
| 126 |
thisUnitCell.s_ez[1] = -rroot3; |
| 127 |
|
| 128 |
// Molecule 3 |
| 129 |
thisUnitCell.sx[2] = cell2; |
| 130 |
thisUnitCell.sy[2] = cell2; |
| 131 |
thisUnitCell.sz[2] = 0.0; |
| 132 |
thisUnitCell.s_ex[2] = rroot3; |
| 133 |
thisUnitCell.s_ey[2] = -rroot3; |
| 134 |
thisUnitCell.s_ez[2] = -rroot3; |
| 135 |
|
| 136 |
// Molecule 4 |
| 137 |
thisUnitCell.sx[3] = cell2; |
| 138 |
thisUnitCell.sy[3] = 0.0; |
| 139 |
thisUnitCell.sz[3] = cell2; |
| 140 |
thisUnitCell.s_ex[3] = -rroot3; |
| 141 |
thisUnitCell.s_ey[3] = -rroot3; |
| 142 |
thisUnitCell.s_ez[3] = rroot3; |
| 143 |
|
| 144 |
return 0; |
| 145 |
} |
| 146 |
|
| 147 |
|
| 148 |
int Lattice::createOrthorhombicLattice(double latticeParameters[3]){ |
| 149 |
double cellx2, celly2, cellz2; |
| 150 |
double rroot3; |
| 151 |
|
| 152 |
cellLengthX = latticeParameters[0]; |
| 153 |
cellLengthY = latticeParameters[1]; |
| 154 |
cellLengthZ = latticeParameters[2]; |
| 155 |
|
| 156 |
cellx2 = 0.5 * latticeParameters[0]; |
| 157 |
celly2 = 0.5 * latticeParameters[1]; |
| 158 |
cellz2 = 0.5 * latticeParameters[2]; |
| 159 |
rroot3 = 1.0 / sqrt(3.0); |
| 160 |
|
| 161 |
nCellSites = 4; |
| 162 |
// create new unit cells |
| 163 |
thisUnitCell.sx = new double[nCellSites]; |
| 164 |
thisUnitCell.sy = new double[nCellSites]; |
| 165 |
thisUnitCell.sz = new double[nCellSites]; |
| 166 |
thisUnitCell.s_ex = new double[nCellSites]; |
| 167 |
thisUnitCell.s_ey = new double[nCellSites]; |
| 168 |
thisUnitCell.s_ez = new double[nCellSites]; |
| 169 |
|
| 170 |
// add members to each unit cell |
| 171 |
// Molecule 1 |
| 172 |
thisUnitCell.sx[0] = 0.0; |
| 173 |
thisUnitCell.sy[0] = 0.0; |
| 174 |
thisUnitCell.sz[0] = 0.0; |
| 175 |
thisUnitCell.s_ex[0] = rroot3; |
| 176 |
thisUnitCell.s_ey[0] = rroot3; |
| 177 |
thisUnitCell.s_ez[0] = rroot3; |
| 178 |
|
| 179 |
// Molecule 2 |
| 180 |
thisUnitCell.sx[1] = 0.0; |
| 181 |
thisUnitCell.sy[1] = celly2; |
| 182 |
thisUnitCell.sz[1] = cellz2; |
| 183 |
thisUnitCell.s_ex[1] = -rroot3; |
| 184 |
thisUnitCell.s_ey[1] = rroot3; |
| 185 |
thisUnitCell.s_ez[1] = -rroot3; |
| 186 |
|
| 187 |
// Molecule 3 |
| 188 |
thisUnitCell.sx[2] = cellx2; |
| 189 |
thisUnitCell.sy[2] = celly2; |
| 190 |
thisUnitCell.sz[2] = 0.0; |
| 191 |
thisUnitCell.s_ex[2] = rroot3; |
| 192 |
thisUnitCell.s_ey[2] = -rroot3; |
| 193 |
thisUnitCell.s_ez[2] = -rroot3; |
| 194 |
|
| 195 |
// Molecule 4 |
| 196 |
thisUnitCell.sx[3] = cellx2; |
| 197 |
thisUnitCell.sy[3] = 0.0; |
| 198 |
thisUnitCell.sz[3] = cellz2; |
| 199 |
thisUnitCell.s_ex[3] = -rroot3; |
| 200 |
thisUnitCell.s_ey[3] = -rroot3; |
| 201 |
thisUnitCell.s_ez[3] = rroot3; |
| 202 |
|
| 203 |
return 0; |
| 204 |
} |
| 205 |
|
| 206 |
|
| 207 |
// Body centered cubic lattice |
| 208 |
int Lattice::createBccLattice(double latticeParameter){ |
| 209 |
return 0; |
| 210 |
} |
| 211 |
|
| 212 |
|
| 213 |
// Standard HCP lattice |
| 214 |
int Lattice::createHcpLattice(double latticeParameter){ |
| 215 |
return 0; |
| 216 |
} |
| 217 |
|
| 218 |
// HCP contains tetrahedral sites for waters |
| 219 |
int Lattice::createHcpWaterLattice(double latticeParameter){ |
| 220 |
|
| 221 |
return 0; |
| 222 |
|
| 223 |
double rroot3; |
| 224 |
double cell; |
| 225 |
double cell2; |
| 226 |
double cell4; |
| 227 |
double cell16; |
| 228 |
double cell23; |
| 229 |
double cell34; |
| 230 |
double cell09; |
| 231 |
double cell59; |
| 232 |
|
| 233 |
nCellSites = 16; |
| 234 |
|
| 235 |
// create new unit cells |
| 236 |
thisUnitCell.sx = new double[nCellSites]; |
| 237 |
thisUnitCell.sy = new double[nCellSites]; |
| 238 |
thisUnitCell.sz = new double[nCellSites]; |
| 239 |
thisUnitCell.s_ex = new double[nCellSites]; |
| 240 |
thisUnitCell.s_ey = new double[nCellSites]; |
| 241 |
thisUnitCell.s_ez = new double[nCellSites]; |
| 242 |
|
| 243 |
rroot3 = 1.0 / sqrt(3.0); |
| 244 |
cell = latticeParameter; |
| 245 |
cell2 = 0.5 * cell; |
| 246 |
cell4 = 0.25 * cell; |
| 247 |
cell16 = cell / 6.0; |
| 248 |
cell23 = (2.0 * cell) / 3.0; |
| 249 |
cell34 = 0.75 * cell; |
| 250 |
cell09 = 0.11238 * cell; |
| 251 |
cell59 = 0.61238 * cell; |
| 252 |
|
| 253 |
// ** build the unit cell ** |
| 254 |
|
| 255 |
// molecule 1 |
| 256 |
|
| 257 |
thisUnitCell.sx[0] = 0.0; |
| 258 |
thisUnitCell.sy[0] = 0.0; |
| 259 |
thisUnitCell.sz[0] = 0.0; |
| 260 |
|
| 261 |
// molecule 2 |
| 262 |
|
| 263 |
thisUnitCell.sx[1] = cell4; |
| 264 |
thisUnitCell.sy[1] = cell2; |
| 265 |
thisUnitCell.sz[1] = 0.0; |
| 266 |
|
| 267 |
// molecule 3 |
| 268 |
|
| 269 |
thisUnitCell.sx[2] = cell4; |
| 270 |
thisUnitCell.sy[2] = cell16; |
| 271 |
thisUnitCell.sz[2] = cell09; |
| 272 |
|
| 273 |
// molecule 4 |
| 274 |
|
| 275 |
thisUnitCell.sx[3] = 0.0; |
| 276 |
thisUnitCell.sy[3] = cell23; |
| 277 |
thisUnitCell.sz[3] = cell09; |
| 278 |
|
| 279 |
// molecule 5 |
| 280 |
|
| 281 |
thisUnitCell.sx[4] = cell4; |
| 282 |
thisUnitCell.sy[4] = cell16; |
| 283 |
thisUnitCell.sz[4] = cell2; |
| 284 |
|
| 285 |
// molecule 6 |
| 286 |
|
| 287 |
thisUnitCell.sx[5] = 0.0; |
| 288 |
thisUnitCell.sy[5] = cell23; |
| 289 |
thisUnitCell.sz[5] = cell2; |
| 290 |
|
| 291 |
// molecule 7 |
| 292 |
|
| 293 |
thisUnitCell.sx[6] = 0.0; |
| 294 |
thisUnitCell.sy[6] = 0.0; |
| 295 |
thisUnitCell.sz[6] = cell59; |
| 296 |
|
| 297 |
|
| 298 |
// molecule 8 |
| 299 |
|
| 300 |
thisUnitCell.sx[7] = cell4; |
| 301 |
thisUnitCell.sy[7] = cell2; |
| 302 |
thisUnitCell.sz[7] = cell59; |
| 303 |
|
| 304 |
// molecule 9 |
| 305 |
|
| 306 |
thisUnitCell.sz[8] = cell2; |
| 307 |
thisUnitCell.sy[8] = 0.0; |
| 308 |
thisUnitCell.sz[8] = 0.0; |
| 309 |
|
| 310 |
// molecule 10 |
| 311 |
|
| 312 |
thisUnitCell.sz[9] = cell34; |
| 313 |
thisUnitCell.sy[9] = cell2; |
| 314 |
thisUnitCell.sz[9] = 0.0; |
| 315 |
|
| 316 |
// molecule 11 |
| 317 |
|
| 318 |
thisUnitCell.sz[10] = cell34; |
| 319 |
thisUnitCell.sy[10] = cell16; |
| 320 |
thisUnitCell.sz[10] = cell09; |
| 321 |
|
| 322 |
// molecule 12 |
| 323 |
|
| 324 |
thisUnitCell.sz[11] = cell2; |
| 325 |
thisUnitCell.sy[11] = cell23; |
| 326 |
thisUnitCell.sz[11] = cell09; |
| 327 |
|
| 328 |
// molecule 13 |
| 329 |
|
| 330 |
thisUnitCell.sz[12] = cell34; |
| 331 |
thisUnitCell.sy[12] = cell16; |
| 332 |
thisUnitCell.sz[12] = cell2; |
| 333 |
|
| 334 |
// molecule 14 |
| 335 |
|
| 336 |
thisUnitCell.sz[13]= cell2; |
| 337 |
thisUnitCell.sy[13]= cell23; |
| 338 |
thisUnitCell.sz[13]= cell2; |
| 339 |
|
| 340 |
// molecule 15 |
| 341 |
|
| 342 |
thisUnitCell.sz[14] = cell2; |
| 343 |
thisUnitCell.sy[14] = 0.0; |
| 344 |
thisUnitCell.sz[14] = cell59; |
| 345 |
|
| 346 |
// molecule 16 |
| 347 |
|
| 348 |
thisUnitCell.sz[15] = cell34; |
| 349 |
thisUnitCell.sy[15] = cell2; |
| 350 |
thisUnitCell.sz[15] = cell59; |
| 351 |
|
| 352 |
return 0; |
| 353 |
} |
| 354 |
|
| 355 |
|
| 356 |
//Returns lattice points when called repeatedly |
| 357 |
int Lattice::getLatticePoints(double** thePosX, double** thePosY, |
| 358 |
double** thePosZ, |
| 359 |
int ix, int iy, int iz){ |
| 360 |
|
| 361 |
int iref; |
| 362 |
|
| 363 |
for( iref=0;iref < nCellSites;iref++){ |
| 364 |
|
| 365 |
latticePosX[iref] = startX + thisUnitCell.sx[iref] + |
| 366 |
cellLengthX * (double( ix ) - 0.5); |
| 367 |
latticePosY[iref] = startY + thisUnitCell.sy[iref] + |
| 368 |
cellLengthY * (double( iy ) - 0.5); |
| 369 |
latticePosZ[iref] = startZ + thisUnitCell.sz[iref] + |
| 370 |
cellLengthZ * (double( iz ) - 0.5); |
| 371 |
|
| 372 |
} |
| 373 |
|
| 374 |
*thePosX = latticePosX; |
| 375 |
*thePosY = latticePosY; |
| 376 |
*thePosZ = latticePosZ; |
| 377 |
|
| 378 |
return nCellSites; |
| 379 |
} |
| 380 |
|
