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276 add bandstructure support for qe #279

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276 add bandstructure support for qe #279

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540555d
bump mypy version nomad
Feb 28, 2025
4a5766b
Apply ruff formatting
Feb 28, 2025
2c1d7e6
Fix mypy error
Feb 28, 2025
f4c2801
First design bandstructur extraction
Feb 27, 2025
25f0d9f
- Resolve direct runtime errors
Mar 4, 2025
41dca99
- Fix regex macthing
Mar 4, 2025
18d5c8d
- Fix extraction and reshaping of band structure
Mar 6, 2025
3c3225d
- Add support reciprocal cell
Mar 6, 2025
c2be740
Correct instantiation band structure, energies, and gap
Mar 28, 2025
425e3d2
Fix parser matching symmetry groups
Mar 28, 2025
6bcb71e
Extract Fermi energy from other calculation
Apr 23, 2025
e0d4c54
- Fix band structure plotting:
Apr 23, 2025
748e147
Add selective matching for bandstructure
Apr 24, 2025
c946ccd
- Separate bandstructure parsing from file reading
Apr 24, 2025
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2 changes: 1 addition & 1 deletion electronicparsers/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -41,7 +41,7 @@ class EntryPoint(ParserEntryPoint):
metadata: Optional[dict] = Field(
None,
description="""
Metadata passed to the UI. Deprecated. """
Metadata passed to the UI. Deprecated. """,
)

def load(self):
Expand Down
9 changes: 5 additions & 4 deletions electronicparsers/abacus/parser.py
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Expand Up @@ -315,7 +315,7 @@ def extract_data(val_in, nks):
data = []
for i in range(nks):
kx, ky, kz, npws = re.search(
rf'{i+1}/{nks} kpoint \(Cartesian\)\s*=\s*({re_float})\s*({re_float})\s*({re_float})\s*\((\d+)\s*pws\)',
rf'{i + 1}/{nks} kpoint \(Cartesian\)\s*=\s*({re_float})\s*({re_float})\s*({re_float})\s*\((\d+)\s*pws\)',
val_in,
).groups()
# TODO pylinit error, unbalanced-tuple-unpacking
Expand All @@ -324,7 +324,7 @@ def extract_data(val_in, nks):
map(
lambda x: x.strip().split(),
re.search(
rf'{i+1}/{nks} kpoint \(Cartesian\)\s*=.*\n([\s\S]+?)\n\n',
rf'{i + 1}/{nks} kpoint \(Cartesian\)\s*=.*\n([\s\S]+?)\n\n',
val_in,
)
.group(1)
Expand Down Expand Up @@ -368,15 +368,16 @@ def extract_data(val_in, nks):
data = []
for i in range(nks):
kx, ky, kz = re.search(
rf'k\-points{i+1}\(\d+\):\s*({re_float})\s*({re_float})\s*({re_float})',
rf'k\-points{i + 1}\(\d+\):\s*({re_float})\s*({re_float})\s*({re_float})',
val_in,
).groups()
res = np.array(
list(
map(
lambda x: x.strip().split(),
re.search(
rf'k\-points{i+1}\(\d+\):.*\n([\s\S]+?)\n\n', val_in
rf'k\-points{i + 1}\(\d+\):.*\n([\s\S]+?)\n\n',
val_in,
)
.group(1)
.split('\n'),
Expand Down
8 changes: 4 additions & 4 deletions electronicparsers/edmft/parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -848,8 +848,8 @@ def parse(self, filepath: str, archive: EntryArchive, logger):
if params_files:
if len(params_files) > 1:
self.logger.warning(
'Multiple *params.dat files found; we will parse the last one.',
data={'files': params_files},
f'Multiple *params.dat files found: {params_files};',
'we will parse the last one.',
)
self.params_parser.mainfile = params_files[-1]

Expand All @@ -875,8 +875,8 @@ def parse(self, filepath: str, archive: EntryArchive, logger):
if indmfl_files:
if len(indmfl_files) > 1:
self.logger.warning(
'Multiple *.indmfl files found; we will parse the last one.',
data={'files': indmfl_files},
f'Multiple *.indmfl files found ({indmfl_files});',
'we will parse the last one.',
)
self.indmfl_parser.mainfile = indmfl_files[-1]
if self.general_parameters and self.impurity_parameters:
Expand Down
2 changes: 1 addition & 1 deletion electronicparsers/exciting/parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3254,7 +3254,7 @@ def parse_configuration(section):
volume_index = 1
while True:
info_volume = get_files(
f"run_dir{str(volume_index).rjust(2, '0')}/INFO.OUT",
f'run_dir{str(volume_index).rjust(2, "0")}/INFO.OUT',
self.filepath,
'INFO.OUT',
)
Expand Down
29 changes: 14 additions & 15 deletions electronicparsers/magres/parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -105,7 +105,7 @@ def init_quantities(self):
),
Quantity(
'kpoint_mp_offset',
rf'calc\_kpoint\_mp\_offset({re_float*3})$',
rf'calc\_kpoint\_mp\_offset({re_float * 3})$',
),
]
),
Expand All @@ -115,11 +115,11 @@ def init_quantities(self):
r'([\[\<]*atoms[\>\]]*[\s\S]+?)(?:[\[\<]*\/atoms[\>\]]*)',
sub_parser=TextParser(
quantities=[
Quantity('lattice', rf'lattice({re_float*9})'),
Quantity('lattice', rf'lattice({re_float * 9})'),
Quantity('symmetry', r'symmetry *([\w\-\+\,]+)', repeats=True),
Quantity(
'atom',
rf'atom *([a-zA-Z]+) *[a-zA-Z\d]* *([\d]+) *({re_float*3})',
rf'atom *([a-zA-Z]+) *[a-zA-Z\d]* *([\d]+) *({re_float * 3})',
repeats=True,
),
]
Expand All @@ -131,47 +131,47 @@ def init_quantities(self):
sub_parser=TextParser(
quantities=[
Quantity(
'ms', rf'ms *(\w+) *(\d+)({re_float*9})', repeats=True
'ms', rf'ms *(\w+) *(\d+)({re_float * 9})', repeats=True
),
Quantity(
'efg', rf'efg *(\w+) *(\d+)({re_float*9})', repeats=True
'efg', rf'efg *(\w+) *(\d+)({re_float * 9})', repeats=True
),
Quantity(
'efg_local',
rf'efg_local *(\w+) *(\d+)({re_float*9})',
rf'efg_local *(\w+) *(\d+)({re_float * 9})',
repeats=True,
),
Quantity(
'efg_nonlocal',
rf'efg_nonlocal *(\w+) *(\d+)({re_float*9})',
rf'efg_nonlocal *(\w+) *(\d+)({re_float * 9})',
repeats=True,
),
Quantity(
'isc',
rf'isc *(\w+) *(\d+) *(\w+) *(\d+)({re_float*9})',
rf'isc *(\w+) *(\d+) *(\w+) *(\d+)({re_float * 9})',
repeats=True,
),
Quantity(
'isc_fc',
rf'isc_fc *(\w+) *(\d+) *(\w+) *(\d+)({re_float*9})',
rf'isc_fc *(\w+) *(\d+) *(\w+) *(\d+)({re_float * 9})',
repeats=True,
),
Quantity(
'isc_orbital_p',
rf'isc_orbital_p *(\w+) *(\d+) *(\w+) *(\d+)({re_float*9})',
rf'isc_orbital_p *(\w+) *(\d+) *(\w+) *(\d+)({re_float * 9})',
repeats=True,
),
Quantity(
'isc_orbital_d',
rf'isc_orbital_d *(\w+) *(\d+) *(\w+) *(\d+)({re_float*9})',
rf'isc_orbital_d *(\w+) *(\d+) *(\w+) *(\d+)({re_float * 9})',
repeats=True,
),
Quantity(
'isc_spin',
rf'isc_spin *(\w+) *(\d+) *(\w+) *(\d+)({re_float*9})',
rf'isc_spin *(\w+) *(\d+) *(\w+) *(\d+)({re_float * 9})',
repeats=True,
),
Quantity('sus', rf'sus *({re_float*9})', repeats=True),
Quantity('sus', rf'sus *({re_float * 9})', repeats=True),
]
),
),
Expand Down Expand Up @@ -443,8 +443,7 @@ def parse(self, filepath, archive, logger):
program_name = calculation_params.get('code', '')
if program_name != 'CASTEP':
self.logger.error(
'Only CASTEP-based NMR simulations are supported by the '
'magres parser.'
'Only CASTEP-based NMR simulations are supported by the magres parser.'
)
return
sec_run.program = Program(
Expand Down
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