Révision a44ad3c2
| b/modules/dos_input.py | ||
|---|---|---|
| 670 | 670 |
def get_coll_thrsld(): |
| 671 | 671 |
err_msg = num_error % ('collision_threshold', 'positive number')
|
| 672 | 672 |
coll_thrsld_str = dos_inp.get('Screening', 'collision_threshold',
|
| 673 |
fallback="1.3")
|
|
| 673 |
fallback="False")
|
|
| 674 | 674 |
if coll_thrsld_str.lower() in turn_false_answers: |
| 675 | 675 |
return False |
| 676 | 676 |
coll_thrsld = try_command(float, [(ValueError, err_msg)], coll_thrsld_str) |
| b/modules/isolated.py | ||
|---|---|---|
| 156 | 156 |
exemplars = clustering(rmsd_mtx) |
| 157 | 157 |
mol_list = confs_to_mol_list(confs, exemplars) |
| 158 | 158 |
ase_atms_list = [rdkit_mol_to_ase_atoms(mol) for mol in mol_list] |
| 159 |
if len(ase_atms_list) == 0: |
|
| 160 |
err_msg = "No configurations were generated: Check the parameters in" \ |
|
| 161 |
"dockonsurf.inp" |
|
| 162 |
logger.error(err_msg) |
|
| 163 |
raise ValueError(err_msg) |
|
| 159 | 164 |
run_calc('isolated', inp_vars, ase_atms_list)
|
| 160 | 165 |
logger.info('Finished the procedures for the isolated molecule section.')
|
| b/modules/screening.py | ||
|---|---|---|
| 1073 | 1073 |
surf_ads_list = adsorb_confs(selected_confs, surf, inp_vars) |
| 1074 | 1074 |
if len(surf_ads_list) > inp_vars['max_structures']: |
| 1075 | 1075 |
surf_ads_list = random.sample(surf_ads_list, inp_vars['max_structures']) |
| 1076 |
elif len(surf_ads_list) == 0: |
|
| 1077 |
err_msg = "No configurations were generated: Check the parameters in" \ |
|
| 1078 |
"dockonsurf.inp" |
|
| 1079 |
logger.error(err_msg) |
|
| 1080 |
raise ValueError(err_msg) |
|
| 1076 | 1081 |
logger.info(f'Generated {len(surf_ads_list)} adsorbate-surface atomic '
|
| 1077 | 1082 |
f'configurations to carry out a calculation of.') |
| 1078 | 1083 |
|
Formats disponibles : Unified diff