def _read_gf_element(file, index):
"""
Read the information needed for a given Green's function element form a ``greensf.hdf``
file
:param file: filepath or handle to be read
:param index: integer index of the element to read in (indexing starts at 1)
:returns: tuple of the information containing the :py:class:`GreensfElement` for the element
and the datasets and attributes dict produced by the corresponding
:py:class:`~masci_tools.io.parsers.hdf5.HDF5Reader`
"""
with HDF5Reader(file) as h5reader:
gf_element = _read_element_header(h5reader._h5_file, index)
group_name = _get_greensf_group_name(h5reader._h5_file)
if gf_element.sphavg:
recipe = _get_sphavg_recipe(group_name, index, gf_element.contour)
else:
recipe = _get_radial_recipe(group_name,
index,
gf_element.contour,
nlo=gf_element.nLO)
data, attributes = h5reader.read(recipe=recipe)
return gf_element, data, attributes
def create_aiida_bands_data(fleurinp, retrieved):
"""
Creates :py:class:`aiida.orm.BandsData` object containing the kpoints and eigenvalues
from the `banddos.hdf` file of the calculation
:param fleurinp: :py:class:`~aiida_fleur.data.fleurinp.FleurinpData` for the calculation
:param retrieved: :py:class:`aiida.orm.FolderData` for the bandstructure calculation
:returns: :py:class:`aiida.orm.BandsData` for the bandstructure calculation
:raises: ExitCode 300, banddos.hdf file is missing
:raises: ExitCode 310, banddos.hdf reading failed
:raises: ExitCode 320, reading kpointsdata from Fleurinp failed
"""
from masci_tools.io.parsers.hdf5 import HDF5Reader, HDF5TransformationError
from masci_tools.io.parsers.hdf5.recipes import FleurSimpleBands #no projections only eigenvalues for now
from aiida.engine import ExitCode
try:
kpoints = fleurinp.get_kpointsdata_ncf(only_used=True)
except ValueError as exc:
return ExitCode(
320,
message=f'Retrieving kpoints data from fleurinp failed with: {exc}'
)
if 'banddos.hdf' in retrieved.list_object_names():
try:
with retrieved.open('banddos.hdf', 'rb') as f:
with HDF5Reader(f) as reader:
data, attributes = reader.read(recipe=FleurSimpleBands)
except (HDF5TransformationError, ValueError) as exc:
return ExitCode(310,
message=f'banddos.hdf reading failed with: {exc}')
else:
return ExitCode(300,
message='banddos.hdf file not in the retrieved files')
bands = BandsData()
bands.set_kpointsdata(kpoints)
nkpts, nbands = attributes['nkpts'], attributes['nbands']
eigenvalues = data['eigenvalues_up'].reshape((nkpts, nbands))
if 'eigenvalues_down' in data:
eigenvalues_dn = data['eigenvalues_down'].reshape((nkpts, nbands))
eigenvalues = [eigenvalues, eigenvalues_dn]
bands.set_bands(eigenvalues, units='eV')
bands.label = 'output_banddos_wc_bands'
bands.description = (
'Contains BandsData for the bandstructure calculation')
return bands
def test_plot_bands_weighted_spinpol_mpl():
from masci_tools.io.parsers.hdf5 import HDF5Reader
from masci_tools.io.parsers.hdf5.recipes import FleurBands
from masci_tools.vis.fleur import plot_fleur_bands
TEST_BANDDOS_FILE = os.path.join(HDFTEST_DIR, 'banddos_spinpol_bands.hdf')
with HDF5Reader(TEST_BANDDOS_FILE) as h5reader:
data, attributes = h5reader.read(recipe=FleurBands)
gcf().clear()
plot_fleur_bands(data, attributes, show=False, weight='MT:1d')
return gcf()
def test_plot_spinpol_dos_defaults_mpl():
from masci_tools.io.parsers.hdf5 import HDF5Reader
from masci_tools.io.parsers.hdf5.recipes import FleurDOS
from masci_tools.vis.fleur import plot_fleur_dos
TEST_BANDDOS_FILE = os.path.join(HDFTEST_DIR, 'banddos_spinpol_dos.hdf')
with HDF5Reader(TEST_BANDDOS_FILE) as h5reader:
data, attributes = h5reader.read(recipe=FleurDOS)
gcf().clear()
plot_fleur_dos(data, attributes, show=False)
return gcf()
def test_hdf5_reader_jdos(data_regression):
"""
Tests of the dos recipe (also pass opened file handle)
"""
from masci_tools.io.parsers.hdf5 import HDF5Reader
from masci_tools.io.parsers.hdf5.recipes import FleurJDOS
TEST_BANDDOS_FILE = os.path.join(HDFTEST_DIR, 'banddos_spinpol_dos.hdf')
with HDF5Reader(TEST_BANDDOS_FILE) as reader:
data, attrs = reader.read(recipe=FleurJDOS)
data_regression.check({
'datasets': convert_to_pystd(data),
'attributes': convert_to_pystd(attrs)
})
def test_hdf5_reader_bands(data_regression):
"""
Tests of the bands recipe
"""
from masci_tools.io.parsers.hdf5 import HDF5Reader
from masci_tools.io.parsers.hdf5.recipes import FleurBands
TEST_BANDDOS_FILE = os.path.join(HDFTEST_DIR, 'banddos_bands.hdf')
with HDF5Reader(TEST_BANDDOS_FILE) as reader:
data, attrs = reader.read(recipe=FleurBands)
data_regression.check({
'datasets': convert_to_pystd(data),
'attributes': convert_to_pystd(attrs)
})
def test_plot_dos_param_change_by_label_mpl():
from masci_tools.io.parsers.hdf5 import HDF5Reader
from masci_tools.io.parsers.hdf5.recipes import FleurDOS
from masci_tools.vis.fleur import plot_fleur_dos
TEST_BANDDOS_FILE = os.path.join(HDFTEST_DIR, 'banddos_dos.hdf')
with HDF5Reader(TEST_BANDDOS_FILE) as h5reader:
data, attributes = h5reader.read(recipe=FleurDOS)
gcf().clear()
plot_fleur_dos(data,
attributes,
show=False,
color={'MT:1_up': 'red'},
linewidth={'Total_up': 6})
return gcf()
def create_aiida_dos_data(retrieved):
"""
Creates :py:class:`aiida.orm.XyData` object containing the standard DOS components
from the `banddos.hdf` file of the calculation
:param retrieved: :py:class:`aiida.orm.FolderData` for the DOS calculation
:returns: :py:class:`aiida.orm.XyData` containing all standard DOS components
:raises: ExitCode 300, banddos.hdf file is missing
:raises: ExitCode 310, banddos.hdf reading failed
"""
from masci_tools.io.parsers.hdf5 import HDF5Reader, HDF5TransformationError
from masci_tools.io.parsers.hdf5.recipes import FleurDOS #only standard DOS for now
from aiida.engine import ExitCode
if 'banddos.hdf' in retrieved.list_object_names():
try:
with retrieved.open('banddos.hdf', 'rb') as f:
with HDF5Reader(f) as reader:
data, attributes = reader.read(recipe=FleurDOS)
except (HDF5TransformationError, ValueError) as exc:
return ExitCode(310,
message=f'banddos.hdf reading failed with: {exc}')
else:
return ExitCode(300,
message='banddos.hdf file not in the retrieved files')
dos = XyData()
dos.set_x(data['energy_grid'], 'energy', x_units='eV')
names = [key for key in data if key != 'energy_grid']
arrays = [entry for key, entry in data.items() if key != 'energy_grid']
units = ['1/eV'] * len(names)
dos.set_y(arrays, names, y_units=units)
dos.label = 'output_banddos_wc_dos'
dos.description = (
'Contains XyData for the density of states calculation with total, interstitial, atom and orbital weights'
)
return dos
def test_plot_bands_characterize_mpl():
from masci_tools.io.parsers.hdf5 import HDF5Reader
from masci_tools.io.parsers.hdf5.recipes import FleurBands
from masci_tools.vis.fleur import plot_fleur_bands_characterize
TEST_BANDDOS_FILE = os.path.join(HDFTEST_DIR, 'banddos_spinpol_bands.hdf')
with HDF5Reader(TEST_BANDDOS_FILE) as h5reader:
data, attributes = h5reader.read(recipe=FleurBands)
gcf().clear()
plot_fleur_bands_characterize(
data,
attributes, ['MT:1s', 'MT:1p', 'MT:1d', 'MT:1f'],
['darkblue', 'darkred', 'darkgreen', 'darkorange'],
show=False,
markersize=30,
only_spin='up')
return gcf()
def test_plot_dos_selection_mpl():
from masci_tools.io.parsers.hdf5 import HDF5Reader
from masci_tools.io.parsers.hdf5.recipes import FleurDOS
from masci_tools.vis.fleur import plot_fleur_dos
TEST_BANDDOS_FILE = os.path.join(HDFTEST_DIR, 'banddos_dos.hdf')
with HDF5Reader(TEST_BANDDOS_FILE) as h5reader:
data, attributes = h5reader.read(recipe=FleurDOS)
gcf().clear()
plot_fleur_dos(data,
attributes,
show=False,
show_total=False,
show_interstitial=False,
show_atoms=1,
show_lresolved=2,
plot_keys='MT:1p')
return gcf()