Révision b25f77a4
| b/modules/screening.py | ||
|---|---|---|
| 533 | 533 |
conformer. |
| 534 | 534 |
""" |
| 535 | 535 |
from copy import deepcopy |
| 536 |
slab_ads_list = []
|
|
| 536 |
slab_ads_list, coll_confs, dup_confs = [], [], []
|
|
| 537 | 537 |
prealigned_molec = align_molec(orig_molec, ctr_coord, norm_vect) |
| 538 | 538 |
# rotation around z |
| 539 | 539 |
for alpha in np.arange(0, 360, 360 / num_pts): |
| ... | ... | |
| 549 | 549 |
norm_vect, |
| 550 | 550 |
slab_nghbs, molec_nghbs, |
| 551 | 551 |
coll_coeff) |
| 552 |
if not collision and not any([np.allclose(slab_molec.positions, |
|
| 553 |
conf.positions) |
|
| 554 |
for conf in slab_ads_list]): |
|
| 555 |
slab_ads_list.append(slab_molec) |
|
| 556 |
if h_donor is not False: |
|
| 557 |
slab_ads_list.extend(dissociation(slab_molec, h_donor, |
|
| 558 |
h_acceptor, |
|
| 559 |
len(slab))) |
|
| 552 |
if not collision: |
|
| 553 |
if not any([np.allclose(slab_molec.positions, conf.positions) |
|
| 554 |
for conf in slab_ads_list]): |
|
| 555 |
slab_ads_list.append(slab_molec) |
|
| 556 |
else: |
|
| 557 |
dup_confs.append(slab_molec) |
|
| 558 |
# if h_donor is not False: |
|
| 559 |
# slab_ads_list.extend(dissociation(slab_molec, h_donor, |
|
| 560 |
# h_acceptor, |
|
| 561 |
# len(slab))) |
|
| 562 |
else: |
|
| 563 |
coll_confs.append(slab_molec) |
|
| 564 |
return slab_ads_list, coll_confs, dup_confs |
|
| 560 | 565 |
|
| 561 |
return slab_ads_list |
|
| 562 | 566 |
|
| 563 | 567 |
def internal_rotate(molecule, surf, ctr1_mol, ctr2_mol, ctr3_mol, ctr1_surf, |
| 564 | 568 |
ctr2_surf, bond_vector, bond_angle_target, |
| ... | ... | |
| 860 | 864 |
conformer. |
| 861 | 865 |
""" |
| 862 | 866 |
from copy import deepcopy |
| 863 |
slab_ads_list = []
|
|
| 867 |
slab_ads_list, coll_confs, dup_confs = [], [], []
|
|
| 864 | 868 |
# Rotation over bond angle |
| 865 | 869 |
for alpha in np.arange(90, 180+1, 90 / max(1, num_pts-1))[:num_pts]: |
| 866 | 870 |
# Rotation over surf-adsorbate dihedral angle |
| ... | ... | |
| 882 | 886 |
num_pts, min_coll_height, |
| 883 | 887 |
norm_vect, slab_nghbs, |
| 884 | 888 |
molec_nghbs, coll_coeff) |
| 885 |
if not collision and \ |
|
| 886 |
not any([np.allclose(slab_molec.positions, |
|
| 887 |
conf.positions) |
|
| 888 |
for conf in slab_ads_list]): |
|
| 889 |
slab_ads_list.append(slab_molec) |
|
| 890 |
if h_donor is not False: |
|
| 891 |
slab_ads_list.extend(dissociation(slab_molec, h_donor, |
|
| 892 |
h_acceptor, |
|
| 893 |
len(slab))) |
|
| 894 |
|
|
| 895 |
return slab_ads_list |
|
| 889 |
if not collision: |
|
| 890 |
if not any([np.allclose(slab_molec.positions, conf.positions) |
|
| 891 |
for conf in slab_ads_list]): |
|
| 892 |
slab_ads_list.append(slab_molec) |
|
| 893 |
else: |
|
| 894 |
dup_confs.append(slab_molec) |
|
| 895 |
# if h_donor is not False: |
|
| 896 |
# slab_ads_list.extend(dissociation(slab_molec, h_donor, |
|
| 897 |
# h_acceptor, |
|
| 898 |
# len(slab))) |
|
| 899 |
else: |
|
| 900 |
coll_confs.append(slab_molec) |
|
| 901 |
|
|
| 902 |
return slab_ads_list, coll_confs, dup_confs |
|
| 896 | 903 |
|
| 897 | 904 |
|
| 898 | 905 |
def adsorb_confs(conf_list, surf, inp_vars): |
| ... | ... | |
| 922 | 929 |
surf.set_pbc(True) |
| 923 | 930 |
surf.set_cell(inp_vars['pbc_cell']) |
| 924 | 931 |
|
| 925 |
surf_ads_list = []
|
|
| 932 |
surf_ads_list, colli_confs, dupl_confs = [], [], []
|
|
| 926 | 933 |
sites_coords = get_atom_coords(surf, sites) |
| 927 | 934 |
if coll_coeff is not False: |
| 928 | 935 |
surf_cutoffs = natural_cutoffs(surf, mult=coll_coeff) |
| ... | ... | |
| 947 | 954 |
norm_vect = inp_norm_vect |
| 948 | 955 |
for c, ctr in enumerate(molec_ctr_coords): |
| 949 | 956 |
if angles == 'euler': |
| 950 |
surf_ads_list.extend(ads_euler(conf, surf, ctr, site, |
|
| 951 |
num_pts, min_coll_height, |
|
| 952 |
coll_coeff, norm_vect, |
|
| 953 |
surf_nghbs, molec_nghbs, |
|
| 954 |
h_donor, h_acceptor)) |
|
| 957 |
good_confs, coll_confs, dup_confs = ads_euler(conf, surf, |
|
| 958 |
ctr, site, num_pts, min_coll_height, coll_coeff, |
|
| 959 |
norm_vect, surf_nghbs, molec_nghbs, h_donor, h_acceptor) |
|
| 960 |
surf_ads_list.extend(good_confs) |
|
| 961 |
colli_confs.extend(coll_confs) |
|
| 962 |
dupl_confs.extend(dup_confs) |
|
| 963 |
|
|
| 955 | 964 |
elif angles == 'chemcat': |
| 956 | 965 |
mol_ctr1 = molec_ctrs[c] |
| 957 | 966 |
mol_ctr2 = inp_vars["molec_ctrs2"][c] |
| ... | ... | |
| 959 | 968 |
surf_ctr1 = sites[s] |
| 960 | 969 |
surf_ctr2 = inp_vars["surf_ctrs2"][s] |
| 961 | 970 |
max_h = inp_vars["max_helic_angle"] |
| 962 |
surf_ads_list.extend(ads_chemcat(conf, surf, mol_ctr1, |
|
| 963 |
mol_ctr2, mol_ctr3, |
|
| 964 |
surf_ctr1, surf_ctr2, |
|
| 965 |
num_pts, min_coll_height, |
|
| 966 |
coll_coeff, norm_vect, |
|
| 967 |
surf_nghbs, molec_nghbs, |
|
| 968 |
h_donor, h_acceptor, |
|
| 969 |
max_h)) |
|
| 970 |
return surf_ads_list |
|
| 971 |
good_confs, coll_confs, dup_confs = ads_internal(conf, surf, |
|
| 972 |
mol_ctr1, mol_ctr2, mol_ctr3, surf_ctr1, surf_ctr2, |
|
| 973 |
num_pts, min_coll_height, coll_coeff, norm_vect, |
|
| 974 |
surf_nghbs, molec_nghbs, h_donor, h_acceptor, max_h) |
|
| 975 |
surf_ads_list.extend(good_confs) |
|
| 976 |
colli_confs.extend(coll_confs) |
|
| 977 |
dupl_confs.extend(dup_confs) |
|
| 978 |
return surf_ads_list, colli_confs, dupl_confs |
|
| 971 | 979 |
|
| 972 | 980 |
|
| 973 | 981 |
def run_screening(inp_vars): |
| ... | ... | |
| 1016 | 1024 |
inp_vars['confs_per_magn'], |
| 1017 | 1025 |
inp_vars['code']) |
| 1018 | 1026 |
surf = adapt_format('ase', inp_vars['surf_file'], inp_vars['special_atoms'])
|
| 1019 |
surf_ads_list = adsorb_confs(selected_confs, surf, inp_vars) |
|
| 1027 |
surf_ads_list, colli_confs, dupl_confs = adsorb_confs(selected_confs, surf, |
|
| 1028 |
inp_vars) |
|
| 1020 | 1029 |
if len(surf_ads_list) > inp_vars['max_structures']: |
| 1021 | 1030 |
surf_ads_list = random.sample(surf_ads_list, inp_vars['max_structures']) |
| 1022 |
logger.info(f'Generated {len(surf_ads_list)} adsorbate-surface atomic '
|
|
| 1023 |
f'configurations to carry out a calculation of.') |
|
| 1031 |
logger.info(f"Good: {len(surf_ads_list)}, Collision: {len(colli_confs)},"
|
|
| 1032 |
f" Duplicate: {len(dupl_confs)}")
|
|
| 1033 |
# logger.info(f'Generated {len(surf_ads_list)} adsorbate-surface atomic '
|
|
| 1034 |
# f'configurations to carry out a calculation of.') |
|
| 1024 | 1035 |
|
| 1025 | 1036 |
run_calc('screening', inp_vars, surf_ads_list)
|
| 1026 | 1037 |
logger.info('Finished the procedures for the screening of adsorbate-surface'
|
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