| 190 |
|
int newN; |
| 191 |
|
Atom** atoms; |
| 192 |
|
double pos[3]; |
| 193 |
< |
char atomType[100]; |
| 193 |
> |
char* atomType; |
| 194 |
|
double HMat[3][3]; |
| 195 |
|
int numNonSSD; |
| 196 |
|
int numSSD; |
| 202 |
|
|
| 203 |
|
//Determine the number of SSD molecules and Non-SSD molecules |
| 204 |
|
for (int i = 0; i < info->n_atoms; i++){ |
| 205 |
< |
atoms[i]->getType(); |
| 206 |
< |
if (strcmp(atomType, "SSD") || strcmp(atomType+2, "SSD")) |
| 205 |
> |
atomType = atoms[i]->getType(); |
| 206 |
> |
if (!strcmp(atomType, "SSD") || !strcmp(atomType+2, "SSD")) |
| 207 |
|
numSSD++; |
| 208 |
|
else |
| 209 |
|
numNonSSD++; |
| 231 |
|
|
| 232 |
|
for (int l = 0; l < info->n_atoms; l++){ |
| 233 |
|
atoms[l]->getPos(pos); |
| 234 |
< |
strcpy(atomType, atoms[l]->getType()); |
| 234 |
> |
atomType = atoms[l]->getType(); |
| 235 |
|
|
| 236 |
|
if (periodicBox_given) |
| 237 |
|
info->wrapVector(pos); |
| 276 |
|
atomType, pos[0], pos [1], pos[2], u[0], u[1], u[2] ); |
| 277 |
|
} |
| 278 |
|
else |
| 279 |
< |
sprintf(buffer,"%s\t%lf\t%lf\t%lf\t0.0\t0.0\t0.0\n", |
| 279 |
> |
sprintf(buffer,"%s\t%lf\t%lf\t%lf\n", |
| 280 |
|
atomType,pos[0], pos [1], pos[2]); |
| 281 |
|
} |
| 282 |
|
} |
| 283 |
|
else{ |
| 284 |
< |
sprintf(buffer,"%s\t%lf\t%lf\t%lf\n", |
| 284 |
> |
if (dipole_given) |
| 285 |
> |
sprintf(buffer,"%s\t%lf\t%lf\t%lf\t0.0\t0.0\t0.0\n", |
| 286 |
|
atomType,pos[0], pos [1], pos[2]); |
| 287 |
+ |
|
| 288 |
+ |
else |
| 289 |
+ |
sprintf(buffer,"%s\t%lf\t%lf\t%lf\n", |
| 290 |
+ |
atomType,pos[0], pos [1], pos[2]); |
| 291 |
|
}//end if atoms[i]->isDirectional() |
| 292 |
|
|
| 293 |
|
(*xyzStream) << buffer; |
| 381 |
|
} |
| 382 |
|
else{ |
| 383 |
|
if(mols[i].getGlobalIndex() == zmolIndex[curIndex]){ |
| 384 |
< |
isZmol = zmolIndex[curIndex]; |
| 384 |
> |
isZmol = curIndex; |
| 385 |
|
curIndex ++; |
| 386 |
|
} |
| 387 |
|
else |
