Révision 5 ase/embed.py
| embed.py (revision 5) | ||
|---|---|---|
| 225 | 225 |
# go over all pairs of atoms |
| 226 | 226 |
for iat_sys in xrange(nat_sys): |
| 227 | 227 |
xyz = positions_new[iat_sys] |
| 228 |
self.atoms_system[iat_sys].set_position(xyz) |
|
| 228 | 229 |
iat_cl = self.atom_map_sys_cl[iat_sys] |
| 229 |
self.atoms_system[iat_sys].set_position(xyz) |
|
| 230 | 230 |
if iat_cl > -1: |
| 231 | 231 |
self.atoms_cluster[iat_cl].set_position(xyz) |
| 232 | 232 |
|
| 233 | 233 |
for cell_L, iat_cl_sys, iat_sys, r, iat in self.linkatoms: |
| 234 | 234 |
# determine position of the link atom |
| 235 |
xyz_cl = self.atoms_system[iat_cl_sys].get_position()
|
|
| 236 |
xyz = self.atoms_system[iat_sys].get_position() - xyz_cl + cell_L
|
|
| 235 |
xyz_cl = positions_new[iat_cl_sys]
|
|
| 236 |
xyz = positions_new[iat_sys] - xyz_cl + cell_L
|
|
| 237 | 237 |
xyz *= r / np.sqrt(np.dot(xyz, xyz)) |
| 238 | 238 |
xyz += xyz_cl |
| 239 | 239 |
# update xyz coordinates of the cluster |
Formats disponibles : Unified diff