Révision 96d422c7
| b/modules/isolated.py | ||
|---|---|---|
| 163 | 163 |
logger.error(err_msg) |
| 164 | 164 |
raise ValueError(err_msg) |
| 165 | 165 |
run_calc('isolated', inp_vars, ase_atms_list)
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| 166 |
finished_calcs, failed_calcs = check_finished_calcs('isolated',
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| 166 |
logger.info("Finished the procedures for the isolated molecule section. ")
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| 167 |
if inp_vars["batch_q_sys"]: |
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| 168 |
finished_calcs, failed_calcs = check_finished_calcs('isolated',
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| 167 | 169 |
inp_vars['code']) |
| 168 |
conf_list = collect_confs(finished_calcs, inp_vars['code'], 'isolated', |
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| 170 |
conf_list = collect_confs(finished_calcs, inp_vars['code'], 'isolated',
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| 169 | 171 |
inp_vars['special_atoms']) |
| 170 |
most_stable_conf = select_stable_confs(conf_list, 0)[0] |
|
| 171 |
logger.info("Finished the procedures for the isolated molecule section. "
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| 172 |
f"Most stable conformers is {most_stable_conf.info['id']}, "
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| 173 |
f"with a total energy of {most_stable_conf.info['energy']} eV.")
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| 172 |
most_stable_conf = select_stable_confs(conf_list, 0)[0] |
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| 173 |
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| 174 |
logger.info(f"Most stable conformers is {most_stable_conf.info['iso']},"
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f" with a total energy of {most_stable_conf.info['energy']}"
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| 176 |
f" eV.") |
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| b/modules/refinement.py | ||
|---|---|---|
| 60 | 60 |
selected_confs = select_stable_confs(conf_list, inp_vars['energy_cutoff']) |
| 61 | 61 |
logger.info(f"Selected {len(selected_confs)} structures to carry out the"
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| 62 | 62 |
f" refinement") |
| 63 |
# run_calc('refinement', inp_vars, selected_confs)
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| 64 |
finished_calcs, failed_calcs = check_finished_calcs('refinement',
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| 65 |
inp_vars['code']) |
|
| 66 |
conf_list = collect_confs(finished_calcs, inp_vars['code'], 'refinement', |
|
| 67 |
inp_vars['special_atoms']) |
|
| 68 |
sorted_confs = select_stable_confs(conf_list, np.inf) |
|
| 63 |
run_calc('refinement', inp_vars, selected_confs)
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| 69 | 64 |
logger.info("Finished the procedures for the refinement of "
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| 70 | 65 |
"adsorbate-surface structures section. ") |
| 71 |
logger.info("Most stable structure "
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| 72 |
f"is {sorted_confs[0].info['ref']} with a total energy of "
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| 73 |
f"{sorted_confs[0].info['energy']} eV.")
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| 74 |
confs_str = "\n".join([" ".join((str(conf.info['ref']), 'E =', |
|
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str(conf.info['energy'] - |
|
| 66 |
if inp_vars["batch_q_sys"]: |
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| 67 |
finished_calcs, failed_calcs = check_finished_calcs('refinement',
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| 68 |
inp_vars['code']) |
|
| 69 |
conf_list = collect_confs(finished_calcs, inp_vars['code'], |
|
| 70 |
'refinement', inp_vars['special_atoms']) |
|
| 71 |
sorted_confs = select_stable_confs(conf_list, np.inf) |
|
| 72 |
logger.info(f"Most stable structure is {sorted_confs[0].info['ref']} "
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| 73 |
f"with a total energy of {sorted_confs[0].info['energy']} "
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| 74 |
f"eV.") |
|
| 75 |
confs_str = "\n".join([" ".join((str(conf.info['ref']), 'E =', |
|
| 76 |
str(conf.info['energy'] - |
|
| 76 | 77 |
sorted_confs[0].info['energy']), |
| 77 |
'eV')) |
|
| 78 |
for conf in sorted_confs]) |
|
| 79 |
logger.info("The relative energies, of all structures obtained at the "
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| 80 |
"refinement stage, respect the most stable one " |
|
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f"({sorted_confs[0].info['ref']}) are:\n{confs_str}")
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| 78 |
'eV')) |
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| 79 |
for conf in sorted_confs]) |
|
| 80 |
logger.info("The relative energies, of all structures obtained at the "
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| 81 |
"refinement stage, respect the most stable one " |
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| 82 |
f"({sorted_confs[0].info['ref']}) are:\n{confs_str}")
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