Révision 7d37379d modules/dos_input.py
| b/modules/dos_input.py | ||
|---|---|---|
| 159 | 159 |
return True |
| 160 | 160 |
|
| 161 | 161 |
|
| 162 |
def check_inp_files(inp_files, code, potcar_dir): |
|
| 162 |
def check_inp_files(inp_files, code, potcar_dir=None):
|
|
| 163 | 163 |
if code == 'cp2k': |
| 164 | 164 |
from pycp2k import CP2K |
| 165 | 165 |
if not isinstance(inp_files, str): |
| ... | ... | |
| 403 | 403 |
|
| 404 | 404 |
# Isolated |
| 405 | 405 |
|
| 406 |
def get_isol_inp_file(code, potcar_dir): # TODO allow spaces in path names |
|
| 406 |
def get_isol_inp_file(code, potcar_dir=None): # TODO allow spaces in path names
|
|
| 407 | 407 |
inp_file_lst = dos_inp.get('Isolated', 'isol_inp_file').split()
|
| 408 | 408 |
check_inp_files(inp_file_lst[0] if len(inp_file_lst) == 1 else inp_file_lst, |
| 409 | 409 |
code, potcar_dir) |
| ... | ... | |
| 440 | 440 |
|
| 441 | 441 |
# Screening |
| 442 | 442 |
|
| 443 |
def get_screen_inp_file(code, potcar_dir): # TODO allow spaces in path names |
|
| 443 |
def get_screen_inp_file(code, |
|
| 444 |
potcar_dir=None): # TODO allow spaces in path names |
|
| 444 | 445 |
inp_file_lst = dos_inp.get('Screening', 'screen_inp_file').split()
|
| 445 | 446 |
check_inp_files(inp_file_lst[0] if len(inp_file_lst) == 1 else inp_file_lst, |
| 446 | 447 |
code, potcar_dir) |
| ... | ... | |
| 731 | 732 |
|
| 732 | 733 |
def get_H_donor(spec_atoms): |
| 733 | 734 |
from ase.data import chemical_symbols |
| 734 |
err_msg = "The value of 'h_donor' must be either False, a chemical symbol "\ |
|
| 735 |
err_msg = "The value of 'h_donor' must be either False, a chemical symbol " \
|
|
| 735 | 736 |
"or an atom index" |
| 736 | 737 |
h_donor_str = dos_inp.get('Screening', 'h_donor', fallback="False")
|
| 737 | 738 |
h_donor = [] |
| ... | ... | |
| 793 | 794 |
|
| 794 | 795 |
# Refinement |
| 795 | 796 |
|
| 796 |
def get_refine_inp_file(code, potcar_dir): |
|
| 797 |
def get_refine_inp_file(code, potcar_dir=None):
|
|
| 797 | 798 |
inp_file_lst = dos_inp.get('Refinement', 'refine_inp_file').split()
|
| 798 | 799 |
check_inp_files(inp_file_lst[0] if len(inp_file_lst) == 1 else inp_file_lst, |
| 799 | 800 |
code, potcar_dir) |
| ... | ... | |
| 887 | 888 |
if not dos_inp.has_option('Isolated', opt):
|
| 888 | 889 |
logger.error(no_opt_err % (opt, 'Isolated')) |
| 889 | 890 |
raise NoOptionError(opt, 'Isolated') |
| 890 |
inp_vars['isol_inp_file'] = get_isol_inp_file(inp_vars['code'], |
|
| 891 |
inp_vars['potcar_dir']) |
|
| 891 |
if 'potcar_dir' in inp_vars: |
|
| 892 |
inp_vars['isol_inp_file'] = get_isol_inp_file(inp_vars['code'], |
|
| 893 |
inp_vars[ |
|
| 894 |
'potcar_dir']) |
|
| 895 |
else: |
|
| 896 |
inp_vars['isol_inp_file'] = get_isol_inp_file(inp_vars['code']) |
|
| 892 | 897 |
inp_vars['molec_file'] = get_molec_file() |
| 893 | 898 |
|
| 894 | 899 |
# Checks for PBC |
| ... | ... | |
| 930 | 935 |
if not dos_inp.has_option('Screening', opt):
|
| 931 | 936 |
logger.error(no_opt_err % (opt, 'Screening')) |
| 932 | 937 |
raise NoOptionError(opt, 'Screening') |
| 933 |
inp_vars['screen_inp_file'] = get_screen_inp_file(inp_vars['code'], |
|
| 934 |
inp_vars[ |
|
| 935 |
'potcar_dir']) |
|
| 938 |
if 'potcar_dir' in inp_vars: |
|
| 939 |
inp_vars['screen_inp_file'] = get_screen_inp_file(inp_vars['code'], |
|
| 940 |
inp_vars[ |
|
| 941 |
'potcar_dir']) |
|
| 942 |
else: |
|
| 943 |
inp_vars['screen_inp_file'] = get_screen_inp_file(inp_vars['code']) |
|
| 936 | 944 |
inp_vars['surf_file'] = get_surf_file() |
| 937 | 945 |
inp_vars['sites'] = get_sites() |
| 938 | 946 |
inp_vars['molec_ctrs'] = get_molec_ctrs() |
| ... | ... | |
| 1017 | 1025 |
if not dos_inp.has_option('Refinement', opt):
|
| 1018 | 1026 |
logger.error(no_opt_err % (opt, 'Refinement')) |
| 1019 | 1027 |
raise NoOptionError(opt, 'Refinement') |
| 1020 |
inp_vars['refine_inp_file'] = get_refine_inp_file(inp_vars['code'], |
|
| 1021 |
inp_vars[ |
|
| 1022 |
'potcar_dir']) |
|
| 1028 |
if 'potcar_dir' in inp_vars: |
|
| 1029 |
inp_vars['refine_inp_file'] = get_refine_inp_file(inp_vars['code'], |
|
| 1030 |
inp_vars[ |
|
| 1031 |
'potcar_dir']) |
|
| 1032 |
else: |
|
| 1033 |
inp_vars['refine_inp_file'] = get_refine_inp_file(inp_vars['code']) |
|
| 1023 | 1034 |
|
| 1024 | 1035 |
# Facultative options (Default value present) |
| 1025 | 1036 |
inp_vars['energy_cutoff'] = get_energy_cutoff() |
Formats disponibles : Unified diff