Révision cf980c86
| b/docs/source/inp_ref_manual.rst | ||
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| 174 | 174 |
and negative). |
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When set to False the detection of atomic clashes with the minimum height |
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method is not carried out. |
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| Accepted values: Positive decimal number or "False". Default Value: False
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| Accepted values: Positive decimal number or "False". Default Value: 1.5
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|
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.. warning:: If both the *collision_threshold* and *min_coll_height* are set to |
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"False", atomic clashes will NOT be checked. |
| ... | ... | |
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using the ASANN method. This is specially useful for stepped/kinked surfaces |
| 283 | 283 |
or nanoparticles, where the surface normal has to be defined locally. |
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| Accepted values: a three-dimensional vector (eg. "(1, -2, 4)"), "x", "y", "z", |
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"-x", "-y", "-z" or "ASANN". Default value: z.
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"-x", "-y", "-z" or "auto". Default value: auto.
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|
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| **use_molec_file** (*optional*): Instead of carrying out the ``Screening`` |
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stage using the molecules obtained in ``Isolated``. It uses a single conformer |
| b/modules/dos_input.py | ||
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| 760 | 760 |
def get_min_coll_height(norm_vect): |
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err_msg = num_error % ('min_coll_height', 'decimal number')
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min_coll_height = dos_inp.get('Screening', 'min_coll_height',
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fallback="False")
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fallback="1.5")
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if min_coll_height.lower() in turn_false_answers: |
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return False |
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min_coll_height = try_command(float, [(ValueError, err_msg)], |
| b/modules/screening.py | ||
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| 311 | 311 |
from copy import deepcopy |
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from ase.neighborlist import natural_cutoffs, neighbor_list |
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|
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normal = 0 |
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for i, coord in enumerate(vect): |
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if coord == 0: |
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continue |
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normal = i |
|
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if vect[normal] > 0: |
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surf_height = max(slab_molec[:slab_num_atoms].positions[:, normal]) |
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else: |
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surf_height = min(slab_molec[:slab_num_atoms].positions[:, normal]) |
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|
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# Check structure overlap by height |
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if min_height is not False: |
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cart_axes = [[1.0, 0.0, 0.0], [0.0, 1.0, 0.0], [0.0, 0.0, 1.0], |
| ... | ... | |
| 327 | 337 |
for i, coord in enumerate(vect): |
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if coord == 0: |
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continue |
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if atom.position[i] * coord < min_height * coord:
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|
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if (atom.position[i] - surf_height) * coord < min_height:
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return True |
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|
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# Check structure overlap by sphere collision |
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