| 279 |
|
//create SimInfo |
| 280 |
|
SimInfo * info = new SimInfo(ff, simParams); |
| 281 |
|
|
| 282 |
< |
//gather parameters (SimCreator only retrieves part of the parameters) |
| 282 |
> |
//gather parameters (SimCreator only retrieves part of the |
| 283 |
> |
//parameters) |
| 284 |
|
gatherParameters(info, mdFileName); |
| 285 |
|
|
| 286 |
|
//divide the molecules and determine the global index of molecules |
| 292 |
|
createMolecules(info); |
| 293 |
|
|
| 294 |
|
|
| 295 |
< |
//allocate memory for DataStorage(circular reference, need to break it) |
| 295 |
> |
//allocate memory for DataStorage(circular reference, need to |
| 296 |
> |
//break it) |
| 297 |
|
info->setSnapshotManager(new SimSnapshotManager(info)); |
| 298 |
|
|
| 299 |
< |
//set the global index of atoms, rigidbodies and cutoffgroups (only need to be set once, the |
| 300 |
< |
//global index will never change again). Local indices of atoms and rigidbodies are already set by |
| 301 |
< |
//MoleculeCreator class which actually delegates the responsibility to LocalIndexManager. |
| 299 |
> |
//set the global index of atoms, rigidbodies and cutoffgroups |
| 300 |
> |
//(only need to be set once, the global index will never change |
| 301 |
> |
//again). Local indices of atoms and rigidbodies are already set |
| 302 |
> |
//by MoleculeCreator class which actually delegates the |
| 303 |
> |
//responsibility to LocalIndexManager. |
| 304 |
|
setGlobalIndex(info); |
| 305 |
|
|
| 306 |
< |
//Alought addExculdePairs is called inside SimInfo's addMolecule method, at that point |
| 307 |
< |
//atoms don't have the global index yet (their global index are all initialized to -1). |
| 308 |
< |
//Therefore we have to call addExcludePairs explicitly here. A way to work around is that |
| 309 |
< |
//we can determine the beginning global indices of atoms before they get created. |
| 306 |
> |
//Although addExcludePairs is called inside SimInfo's addMolecule |
| 307 |
> |
//method, at that point atoms don't have the global index yet |
| 308 |
> |
//(their global index are all initialized to -1). Therefore we |
| 309 |
> |
//have to call addExcludePairs explicitly here. A way to work |
| 310 |
> |
//around is that we can determine the beginning global indices of |
| 311 |
> |
//atoms before they get created. |
| 312 |
|
SimInfo::MoleculeIterator mi; |
| 313 |
|
Molecule* mol; |
| 314 |
|
for (mol= info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) { |
