| 185 |
|
else |
| 186 |
|
outInitFileName = getPrefix(inputFileName.c_str()) + ".in"; |
| 187 |
|
|
| 188 |
+ |
|
| 189 |
+ |
|
| 190 |
+ |
|
| 191 |
+ |
|
| 192 |
+ |
|
| 193 |
|
//creat Molocator |
| 194 |
|
locator = new MoLocator(oldInfo->getMoleculeStamp(0), oldInfo->getForceField()); |
| 195 |
|
|
| 210 |
|
// Create geometry for nanocrystal |
| 211 |
|
#ifdef HAVE_CGAL |
| 212 |
|
GeometryBuilder myGeometry(rodLength,rodDiameter); |
| 213 |
+ |
if (args_info.genGeomview_given){ |
| 214 |
+ |
if (args_info.genGeomview_flag){ |
| 215 |
+ |
outGeomFileName = getPrefix(inputFileName.c_str()) + ".off"; |
| 216 |
+ |
myGeometry.dumpGeometry(outGeomFileName); |
| 217 |
+ |
} |
| 218 |
+ |
} |
| 219 |
+ |
|
| 220 |
|
#endif |
| 221 |
|
|
| 222 |
|
/* |
| 253 |
|
|
| 254 |
|
|
| 255 |
|
numMol = 0; |
| 256 |
< |
for(int i = 0; i < nx; i++) { |
| 257 |
< |
for(int j = 0; j < ny; j++) { |
| 258 |
< |
for(int k = 0; k < nz; k++) { |
| 256 |
> |
for(int i = -nx; i < nx; i++) { |
| 257 |
> |
for(int j = -ny; j < ny; j++) { |
| 258 |
> |
for(int k = -nz; k < nz; k++) { |
| 259 |
|
//if (oldInfo->getNGlobalMolecules() != numMol) { |
| 260 |
|
|
| 261 |
|
|
| 274 |
|
} |
| 275 |
|
} |
| 276 |
|
} |
| 277 |
+ |
std::cerr << "numMol before is " << numMol << std::endl; |
| 278 |
|
|
| 266 |
– |
|
| 279 |
|
// needed for writing out new md file. |
| 280 |
|
|
| 281 |
|
outPrefix = getPrefix(inputFileName.c_str()) + "_" + latticeType; |
| 299 |
|
Molecule* mol; |
| 300 |
|
SimInfo::MoleculeIterator mi; |
| 301 |
|
mol = NewInfo->beginMolecule(mi); |
| 302 |
< |
|
| 303 |
< |
for(int i = 0; i < nx; i++) { |
| 304 |
< |
for(int j = 0; j < ny; j++) { |
| 305 |
< |
for(int k = 0; k < nz; k++) { |
| 306 |
< |
|
| 307 |
< |
//get the position of the cell sites |
| 308 |
< |
simpleLat->getLatticePointsPos(latticePos, i, j, k); |
| 309 |
< |
|
| 310 |
< |
for(int l = 0; l < numMolPerCell; l++) { |
| 311 |
< |
if (mol != NULL) { |
| 312 |
< |
|
| 313 |
< |
#ifdef HAVE_GCAL |
| 314 |
< |
if (myGeometry.isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){ |
| 315 |
< |
locator->placeMol(latticePos[l], latticeOrt[l], mol); |
| 316 |
< |
} |
| 317 |
< |
#else |
| 318 |
< |
|
| 319 |
< |
locator->placeMol(latticePos[l], latticeOrt[l], mol); |
| 320 |
< |
#endif |
| 321 |
< |
} else { |
| 322 |
< |
std::cerr << std::endl; |
| 323 |
< |
} |
| 312 |
< |
mol = NewInfo->nextMolecule(mi); |
| 302 |
> |
numMol = 0; |
| 303 |
> |
int countMol = 0; |
| 304 |
> |
for(int i = -nx; i < nx; i++) { |
| 305 |
> |
for(int j = -ny; j < ny; j++) { |
| 306 |
> |
for(int k = -nz; k < nz; k++) { |
| 307 |
> |
|
| 308 |
> |
//get the position of the cell sites |
| 309 |
> |
simpleLat->getLatticePointsPos(latticePos, i, j, k); |
| 310 |
> |
|
| 311 |
> |
for(int l = 0; l < numMolPerCell; l++) { |
| 312 |
> |
if (myGeometry.isInsidePolyhedron(latticePos[l][0],latticePos[l][1],latticePos[l][2])){ |
| 313 |
> |
countMol++; |
| 314 |
> |
if (mol != NULL) { |
| 315 |
> |
locator->placeMol(latticePos[l], latticeOrt[l], mol); |
| 316 |
> |
numMol++; |
| 317 |
> |
} else { |
| 318 |
> |
std::cerr<<"Error in placing molecule " << countMol << std::endl; |
| 319 |
> |
} |
| 320 |
> |
mol = NewInfo->nextMolecule(mi); |
| 321 |
> |
} |
| 322 |
> |
|
| 323 |
> |
} |
| 324 |
|
} |
| 325 |
< |
} |
| 315 |
< |
} |
| 325 |
> |
} |
| 326 |
|
} |
| 327 |
|
|
| 328 |
+ |
std::cerr << "numMol after is " << numMol << std::endl; |
| 329 |
|
|
| 319 |
– |
|
| 330 |
|
//fill Hmat |
| 331 |
|
hmat(0, 0)= nx * latticeConstant; |
| 332 |
|
hmat(0, 1) = 0.0; |
