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Update hdf5 references #214

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merged 4 commits into from
Apr 19, 2024
Merged

Update hdf5 references #214

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354232b
Update writing of vasp charge density
ladinesa Apr 18, 2024
308f976
Update hdf5 reference in soliddmft
ladinesa Apr 18, 2024
1d0b3f9
Update hdf5 ref in w2dynamics
ladinesa Apr 18, 2024
91cb972
Try to fix gh actions
ladinesa Apr 18, 2024
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4 changes: 2 additions & 2 deletions .github/workflows/python-actions.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -12,11 +12,11 @@ jobs:
- name: Install dependencies
run: |
pip install --upgrade pip
# we need the latest nomad version for testing
pip install nomad-lab[infrastructure]@git+https://github.com/nomad-coe/nomad.git@develop
pip install '.[dev]' --index-url https://gitlab.mpcdf.mpg.de/api/v4/projects/2187/packages/pypi/simple
pip install coverage coveralls
pip install types-PyYAML
# we need the latest nomad version for testing
pip install nomad-lab[infrastructure]@git+https://github.com/nomad-coe/nomad.git@develop
- name: mypy
run: |
python -m mypy --ignore-missing-imports --follow-imports=silent --no-strict-optional *parsers tests
Expand Down
2 changes: 1 addition & 1 deletion electronicparsers/soliddmft/metainfo/soliddmft.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,8 +25,8 @@
Section,
SubSection,
JSON,
HDF5Reference,
)
from nomad.datamodel.hdf5 import HDF5Reference
import runschema.run # pylint: disable=unused-import
import runschema.calculation # pylint: disable=unused-import
import runschema.method # pylint: disable=unused-import
Expand Down
100 changes: 44 additions & 56 deletions electronicparsers/soliddmft/parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,6 @@
)
from runschema.system import System, Atoms
from .metainfo.soliddmft import x_soliddmft_observables_parameters
from nomad.parsing.parser import to_hdf5
from ..utils import numpy_type_to_json_serializable


Expand Down Expand Up @@ -423,9 +422,9 @@ def parse_scf(
val = self.extract_groups_datasets(
value.get(n_imp)[f'{i_scf}']
)
conv_obs[
f'{key}_imp{n_imp}'
] = numpy_type_to_json_serializable(val)
conv_obs[f'{key}_imp{n_imp}'] = (
numpy_type_to_json_serializable(val)
)
sec_scf.x_soliddmft_convergence_obs = conv_obs

# Energy per scf iteration step
Expand Down Expand Up @@ -454,58 +453,47 @@ def parse_scf(

# Observables per scf iteration step
scf_iteration = self.dmft_results.get(f'it_{i_scf + 1}')
if self.archive.m_context:
with self.archive.m_context.raw_file(filename, farg) as file:
for n in range(n_impurities):
n_imp = str(n_imp)
sec_obs_scf = x_soliddmft_observables_parameters()
sec_scf.x_soliddmft_observables.append(sec_obs_scf)
for gf_iteration in self.iteration_gfs:
if f'{gf_iteration}_{n_imp}' not in scf_iteration.keys():
continue
value_per_spin_orbital = scf_iteration.get(
f'{gf_iteration}_{n_imp}'
)
value_tot = []
for spin_orb in value_per_spin_orbital.keys():
if spin_orb == 'block_names':
continue
value = value_per_spin_orbital.get(spin_orb).get('data')
value = to_hdf5(
value,
file,
f'DMFT_results/it_{i_scf + 1}/{gf_iteration}_{n_imp}/{spin_orb}/data',
)
value_tot.append(value)
sec_obs_scf.m_set(
sec_obs_scf.m_get_quantity_definition(
f'x_soliddmft_{gf_iteration}'
),
value_tot,
)
for gf_observable in self.observable_gfs:
if gf_observable not in observables.keys():
continue
value_per_spin_orbital = observables.get(gf_observable).get(
f'{n_imp}'
)
value_tot = []
for spin_orb in value_per_spin_orbital.keys():
value = value_per_spin_orbital.get(spin_orb).get(
f'{i_scf + 1}'
)
value = to_hdf5(
value,
file,
f'DMFT_results/observables/{gf_observable}/{n_imp}/{spin_orb}/{i_scf + 1}',
)
value_tot.append(value)
sec_obs_scf.m_set(
sec_obs_scf.m_get_quantity_definition(
f'x_soliddmft_{gf_observable}'
),
value_tot,
)
for n in range(n_impurities):
n_imp = str(n_imp)
sec_obs_scf = x_soliddmft_observables_parameters()
sec_scf.x_soliddmft_observables.append(sec_obs_scf)
h5_base = f'{os.path.basename(self.mainfile)}#/DMFT_results'
for gf_iteration in self.iteration_gfs:
if f'{gf_iteration}_{n_imp}' not in scf_iteration.keys():
continue
value_per_spin_orbital = scf_iteration.get(
f'{gf_iteration}_{n_imp}'
)
value_tot = []
for spin_orb in value_per_spin_orbital.keys():
if spin_orb == 'block_names':
continue
value_tot.append(
f'{h5_base}/it_{i_scf + 1}/{gf_iteration}_{n_imp}/{spin_orb}/data'
)
sec_obs_scf.m_set(
sec_obs_scf.m_get_quantity_definition(
f'x_soliddmft_{gf_iteration}'
),
value_tot,
)
for gf_observable in self.observable_gfs:
if gf_observable not in observables.keys():
continue
value_per_spin_orbital = observables.get(gf_observable).get(
f'{n_imp}'
)
value_tot = []
for spin_orb in value_per_spin_orbital.keys():
value_tot.append(
f'{h5_base}/observables/{gf_observable}/{n_imp}/{spin_orb}/{i_scf + 1}'
)
sec_obs_scf.m_set(
sec_obs_scf.m_get_quantity_definition(
f'x_soliddmft_{gf_observable}'
),
value_tot,
)

def parse_gfs(sec_scc: Calculation, n_impurities: int):
"""Parses Green's functions quantities.
Expand Down
51 changes: 11 additions & 40 deletions electronicparsers/vasp/parser.py
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Expand Up @@ -1293,9 +1293,9 @@ def kpoints_info(self):
# initialize parsing of k_points
method = self._get_key_values('/modeling[0]/kpoints[0]/generation[0]/param')
if method:
self._kpoints_info[
'sampling_method'
] = RunContentParser.sampling_method_mapping[method['param']]
self._kpoints_info['sampling_method'] = (
RunContentParser.sampling_method_mapping[method['param']]
)
divisions = self._get_key_values(
'/modeling[0]/kpoints[0]/generation[0]/v[@name="divisions"]'
)
Expand Down Expand Up @@ -1844,9 +1844,9 @@ def parse_method(self):
if len(sec_xc_functional.hybrid):
if not sec_xc_functional.hybrid[-1].parameters:
sec_xc_functional.hybrid[-1].parameters = dict()
sec_xc_functional.hybrid[-1].parameters[
'exact_exchange_mixing_factor'
] = aexx
sec_xc_functional.hybrid[-1].parameters['exact_exchange_mixing_factor'] = (
aexx
)
sec_xc_functional.normalize_hybrid()

# convergence thresholds
Expand Down Expand Up @@ -2257,40 +2257,11 @@ def parse_dos(n_calc):
elif len(charge_density) < n_points:
charge_density.extend([float(v) for v in line.strip().split()])
if charge_density and len(charge_density) == n_points:
# TODO remove temporary fix
if hasattr(Density, 'value_hdf5'):
from nomad.parsing.parser import to_hdf5

filename = os.path.join(
os.path.dirname(self.filepath.split('/raw/')[-1]),
f'{os.path.basename(self.filepath)}.archive.hdf5',
)
farg = (
'r+b'
if os.path.isfile(
os.path.join(os.path.dirname(self.filepath), filename)
)
else 'wb'
)
sec_density = Density()
sec_scc.density_charge.append(sec_density)
if self.archive.m_context:
with self.archive.m_context.raw_file(filename, farg) as f:
sec_density.value_hdf5 = to_hdf5(
np.reshape(
np.array(charge_density, np.float64), grid
),
f,
f'{sec_density.m_path()}/value_hdf5',
)
else:
sec_scc.density_charge.append(
Density(
value=np.reshape(
np.array(charge_density, np.float64), grid
)
)
)
sec_density = Density()
sec_density.value_hdf5 = np.reshape(
np.array(charge_density, np.float64), grid
)
sec_scc.density_charge.append(sec_density)
grid = []
n_points = 0
charge_density = []
Expand Down
2 changes: 1 addition & 1 deletion electronicparsers/w2dynamics/metainfo/w2dynamics.py
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Original file line number Diff line number Diff line change
Expand Up @@ -25,8 +25,8 @@
Section,
SubSection,
JSON,
HDF5Reference,
)
from nomad.datamodel.hdf5 import HDF5Reference
import runschema.run # pylint: disable=unused-import
import runschema.calculation # pylint: disable=unused-import
import runschema.method # pylint: disable=unused-import
Expand Down
7 changes: 2 additions & 5 deletions electronicparsers/w2dynamics/parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,6 @@
x_w2dynamics_config_atoms_parameters,
)
from ..wannier90.parser import WOutParser, HrParser
from nomad.parsing.parser import to_hdf5

# For automatic workflows
from ..utils import get_files, BeyondDFTWorkflowsParser
Expand Down Expand Up @@ -435,7 +434,7 @@ def parse_scc(self):
sec_energy.fermi = np.float64(value) * ureg.eV
elif subkey not in ineq_keys:
value = parameter.get('value')[:]
value = to_hdf5(value, f, f'{key}/{subkey}/value')
value = f'{os.path.basename(self.mainfile)}#/{key}/{subkey}/value'
name = self._re_namesafe.sub('_', subkey)
setattr(sec_scf_iteration, f'x_w2dynamics_{name}', value)
else:
Expand All @@ -451,9 +450,7 @@ def parse_scc(self):
value = value.get('value')
if not isinstance(value, h5py.Dataset):
continue
value = to_hdf5(
value, f, f'{key}/{subkey}/{name}/value'
)
value = f'{os.path.basename(self.mainfile)}#/{key}/{subkey}/{name}/value'
name = self._re_namesafe.sub('_', name)
setattr(sec_ineq, f'x_w2dynamics_{name}', value)

Expand Down
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