Révision d8d92cfb
| b/modules/screening.py | ||
|---|---|---|
| 176 | 176 |
return norm_vec |
| 177 | 177 |
|
| 178 | 178 |
|
| 179 |
def align_molec(molec, ctr_coord, ref_vect): |
|
| 179 |
def align_molec(orig_molec, ctr_coord, ref_vect):
|
|
| 180 | 180 |
"""Align a molecule to a vector by a center. |
| 181 | 181 |
|
| 182 | 182 |
Given a reference vector to be aligned to and some coordinates acting as |
| ... | ... | |
| 188 | 188 |
@param ref_vect: The vector to be aligned with. |
| 189 | 189 |
@return: ase.Atoms of the aligned molecule |
| 190 | 190 |
""" |
| 191 |
from copy import deepcopy |
|
| 191 | 192 |
from ase import Atom |
| 192 | 193 |
from ase.neighborlist import natural_cutoffs, neighbor_list |
| 193 | 194 |
|
| 195 |
molec = deepcopy(orig_molec) |
|
| 194 | 196 |
if len(molec) == 1: |
| 195 | 197 |
err_msg = "Cannot align a single atom" |
| 196 | 198 |
logger.error(err_msg) |
| ... | ... | |
| 532 | 534 |
""" |
| 533 | 535 |
from copy import deepcopy |
| 534 | 536 |
slab_ads_list = [] |
| 535 |
orig_molec = align_molec(orig_molec, ctr_coord, norm_vect)
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|
| 537 |
prealigned_molec = align_molec(orig_molec, ctr_coord, norm_vect)
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|
| 536 | 538 |
# rotation around z |
| 537 | 539 |
for alpha in np.arange(0, 360, 360 / num_pts): |
| 538 | 540 |
# rotation around x' |
| 539 | 541 |
for beta in np.arange(0, 180, 180 / num_pts): |
| 540 | 542 |
# rotation around z' |
| 541 | 543 |
for gamma in np.arange(0, 360, 360 / num_pts): |
| 542 |
molec = deepcopy(orig_molec)
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|
| 544 |
molec = deepcopy(prealigned_molec)
|
|
| 543 | 545 |
molec.euler_rotate(alpha, beta, gamma, center=ctr_coord) |
| 544 | 546 |
slab_molec, collision = correct_coll(molec, slab, |
| 545 | 547 |
ctr_coord, site_coord, |
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