Révision a5d76bfb
| b/modules/dos_input.py | ||
|---|---|---|
| 265 | 265 |
|
| 266 | 266 |
|
| 267 | 267 |
def get_pbc_cell(): |
| 268 |
from ase.atoms import Cell |
|
| 268 | 269 |
err_msg = "'pbc_cell' must be either 3 vectors of size 3 or False." |
| 269 | 270 |
pbc_cell_str = dos_inp.get('Global', 'pbc_cell', fallback="False")
|
| 270 | 271 |
if pbc_cell_str.lower() in turn_false_answers: |
| ... | ... | |
| 279 | 280 |
err_msg = "The volume of the defined cell is 0" |
| 280 | 281 |
logger.error(err_msg) |
| 281 | 282 |
raise ValueError(err_msg) |
| 282 |
return pbc_cell
|
|
| 283 |
return Cell(pbc_cell)
|
|
| 283 | 284 |
|
| 284 | 285 |
|
| 285 | 286 |
def get_subm_script(): |
| ... | ... | |
| 871 | 872 |
inp_vars['special_atoms']) |
| 872 | 873 |
if inp_vars['code'] == 'vasp' and np.linalg.det(atms.cell) == 0.0 \ |
| 873 | 874 |
and inp_vars['pbc_cell'] is False: |
| 874 |
err_msg = "When running calculations with 'VASP', the PBC cell" \ |
|
| 875 |
err_msg = "When running calculations with 'VASP', the PBC cell " \
|
|
| 875 | 876 |
"should be provided either implicitely inside " \ |
| 876 | 877 |
"'molec_file' or by setting the 'pbc_cell' option." |
| 877 | 878 |
logger.error(err_msg) |
| 878 | 879 |
raise ValueError(err_msg) |
| 879 |
elif np.allclose(inp_vars['pbc_cell'], atms.cell): |
|
| 880 |
elif inp_vars['pbc_cell'] is False and np.linalg.det(atms.cell) != 0.0: |
|
| 881 |
inp_vars['pbc_cell'] = atms.cell |
|
| 882 |
logger.info(f"Obtained pbc_cell from '{inp_vars['molec_file']}' "
|
|
| 883 |
f"file.") |
|
| 884 |
elif (atms.cell != 0).any() and not np.allclose(inp_vars['pbc_cell'], |
|
| 885 |
atms.cell): |
|
| 880 | 886 |
logger.warning("'molec_file' has an implicit cell defined "
|
| 881 |
f"different than 'pbc_cell' ('molec_file'="
|
|
| 882 |
f"{atms.cell}, 'pbc_cell'= {inp_vars['pbc_cell']}). "
|
|
| 883 |
f"'pbc_cell' value will be used.") |
|
| 887 |
f"different than 'pbc_cell'.\n" |
|
| 888 |
f"'molec_file' = {atms.cell}.\n"
|
|
| 889 |
f"'pbc_cell' = {inp_vars['pbc_cell']}).\n"
|
|
| 890 |
"'pbc_cell' value will be used.") |
|
| 884 | 891 |
|
| 885 | 892 |
# Facultative options (Default/Fallback value present) |
| 886 | 893 |
inp_vars['num_conformers'] = get_num_conformers() |
| ... | ... | |
| 905 | 912 |
inp_vars['molec_ctrs'] = get_molec_ctrs() |
| 906 | 913 |
|
| 907 | 914 |
# Checks for PBC |
| 915 |
# Checks for PBC |
|
| 908 | 916 |
atms = adapt_format('ase', inp_vars['surf_file'],
|
| 909 | 917 |
inp_vars['special_atoms']) |
| 910 | 918 |
if inp_vars['code'] == 'vasp' and np.linalg.det(atms.cell) == 0.0 \ |
| 911 | 919 |
and inp_vars['pbc_cell'] is False: |
| 912 |
err_msg = "When running calculations with 'VASP', the PBC cell" \ |
|
| 920 |
err_msg = "When running calculations with 'VASP', the PBC cell " \
|
|
| 913 | 921 |
"should be provided either implicitely inside " \ |
| 914 |
"'molec_file' or by setting the 'pbc_cell' option."
|
|
| 922 |
"'surf_file' or by setting the 'pbc_cell' option."
|
|
| 915 | 923 |
logger.error(err_msg) |
| 916 | 924 |
raise ValueError(err_msg) |
| 917 |
elif np.allclose(inp_vars['pbc_cell'], atms.cell): |
|
| 918 |
logger.warning("'molec_file' has an implicit cell defined, "
|
|
| 919 |
"different than 'pbc_cell' ('molec_file'="
|
|
| 920 |
f"{atms.cell}, 'pbc_cell'={inp_vars['pbc_cell']}). "
|
|
| 925 |
elif inp_vars['pbc_cell'] is False and np.linalg.det(atms.cell) != 0.0: |
|
| 926 |
inp_vars['pbc_cell'] = atms.cell |
|
| 927 |
logger.info(f"Obtained pbc_cell from '{inp_vars['surf_file']}' "
|
|
| 928 |
f"file.") |
|
| 929 |
elif (atms.cell != 0).any() and not np.allclose(inp_vars['pbc_cell'], |
|
| 930 |
atms.cell): |
|
| 931 |
logger.warning("'surf_file' has an implicit cell defined "
|
|
| 932 |
f"different than 'pbc_cell'.\n" |
|
| 933 |
f"'surf_file' = {atms.cell}.\n"
|
|
| 934 |
f"'pbc_cell' = {inp_vars['pbc_cell']}).\n"
|
|
| 921 | 935 |
"'pbc_cell' value will be used.") |
| 922 | 936 |
|
| 923 | 937 |
# Facultative options (Default value present) |
Formats disponibles : Unified diff