diff --git a/nomad/config.py b/nomad/config.py
index 23116806251b58d09dfcd349ea9ded696b593f67..ab87be0f89684a90bbfbf903f6fab892087acaee 100644
--- a/nomad/config.py
+++ b/nomad/config.py
@@ -239,8 +239,8 @@ normalize = NomadConfig(
# The threshold for point equality in k-space. Unit: 1/m.
k_space_precision=150e6,
# The energy threshold for how much a band can be on top or below the fermi
- # level in order to detect a gap. k_B x T at room temperature. Unit: Joule
- band_structure_energy_tolerance=300 * 1.38064852E-23,
+ # level in order to detect a gap. Unit: Joule.
+ band_structure_energy_tolerance=1.6022e-20, # 0.1 eV
springer_db_path=os.path.join(
os.path.dirname(os.path.abspath(__file__)),
'normalizing/data/springer.msg'
diff --git a/nomad/datamodel/metainfo/public.py b/nomad/datamodel/metainfo/public.py
index d1e4292c1442ff65705dcc7d6bb02b8ee78088e8..056b16322fe756690c012c58513064001161a517 100644
--- a/nomad/datamodel/metainfo/public.py
+++ b/nomad/datamodel/metainfo/public.py
@@ -1264,10 +1264,17 @@ class section_dos(MSection):
shape=['number_of_dos_values'],
unit='joule',
description='''
- Array containing the set of discrete energy values with respect to the top of the
- valence band for the density (electronic-energy) of states (DOS). This is the
- total DOS, see atom_projected_dos_energies and species_projected_dos_energies for
+ Array containing the set of discrete energy values with respect to the
+ highest occupied energy level. This is the total DOS, see
+ atom_projected_dos_energies and species_projected_dos_energies for
partial density of states.
+
+ If not available through energy_reference_highest_occupied, the highest
+ occupied energy level is detected by searching for a non-zero DOS value
+ below (or nearby) the reported energy_reference_fermi. In case the
+ highest occupied energy level cannot be detected accurately, the
+ normalized values are not reported. For calculations with multiple
+ spin-channels, the normalization is determined by the first channel.
''',
a_legacy=LegacyDefinition(name='dos_energies_normalized'))
diff --git a/nomad/normalizing/dos.py b/nomad/normalizing/dos.py
index 10b0633e547f91a6856dda5735d3eb2d5f71e5cc..c8e8809e63ee0af58450f92e3da70066ad4f1522 100644
--- a/nomad/normalizing/dos.py
+++ b/nomad/normalizing/dos.py
@@ -47,7 +47,8 @@ class DosNormalizer(Normalizer):
dos_values = dos.dos_values
dos_energies = dos.dos_energies
energy_reference_fermi = scc.energy_reference_fermi
- if dos_energies is None or dos_values is None or energy_reference_fermi is None:
+ energy_reference_highest_occupied = scc.energy_reference_highest_occupied
+ if dos_energies is None or dos_values is None or (energy_reference_fermi is None and energy_reference_highest_occupied is None):
continue
# Normalize DOS values to be 1/J/atom/m^3
@@ -68,75 +69,90 @@ class DosNormalizer(Normalizer):
dos_values_normalized = dos_values / (number_of_atoms * unit_cell_volume)
# Normalize energies so that they are normalized to HOMO.
- i_channel = 0
- fermi_energy = energy_reference_fermi[i_channel]
- fermi_idx = (np.abs(dos_energies - fermi_energy)).argmin()
- energy_threshold = config.normalize.band_structure_energy_tolerance
- value_threshold = 1e-8 # The DOS value that is considered to be zero
- homo_found = False
- zero_found = False
- energy_reference = fermi_energy
-
- # Walk through the energies in descencing direction to see if a
- # gap is nearby (see energy_threshold). If gap found, continue
- # until HOMO found
- idx = fermi_idx
- while True:
- try:
- value = dos_values_normalized[i_channel, idx]
- energy_distance = fermi_energy - dos_energies[idx]
- except IndexError:
- break
- if energy_distance.magnitude > energy_threshold and not zero_found:
- break
- if value <= value_threshold:
- zero_found = True
- if zero_found and value > value_threshold:
- energy_reference = dos_energies[idx + 1]
- homo_found = True
- break
- idx -= 1
- # If gap was not found in descending direction, check the
- # ascending direction for a nearby (see energy_threshold) HOMO
- # value
- if not homo_found:
- idx = fermi_idx + 1
- while True:
- try:
- value = dos_values_normalized[i_channel, idx]
- energy_distance = dos_energies[idx] - fermi_energy
- except IndexError:
- break
- if energy_distance.magnitude > energy_threshold:
- break
- if value <= value_threshold:
- energy_reference = dos_energies[idx]
- break
- idx += 1
-
- dos_energies_normalized = dos_energies - energy_reference
-
- # Data for DOS fingerprint
- dos_fingerprint = None
- try:
- dos_fingerprint = DOSFingerprint().calculate(
- dos_energies_normalized.magnitude,
- dos_values_normalized,
- n_atoms=number_of_atoms
- )
- except Exception as e:
- self.logger.error('could not generate dos fingerprint', exc_info=e)
+ dos_energies_normalized = None
+
+ # Primarily normalize to the HOMO level reported by the parser.
+ # The first channel is used.
+ energy_reference = None
+ if energy_reference_highest_occupied is not None:
+ energy_reference = energy_reference_highest_occupied[0]
+ # If HOMO is not reported, search for it in the DOS values
+ else:
+ i_channel = 0
+ fermi_energy = energy_reference_fermi[i_channel]
+ fermi_idx = (np.abs(dos_energies - fermi_energy)).argmin()
+ energy_threshold = config.normalize.band_structure_energy_tolerance
+ value_threshold = 1e-8 # The DOS value that is considered to be zero
+ homo_found = False
+ zero_found = False
+ energy_reference = fermi_energy
+
+ # First check that the closest dos energy to fermi_energy is not too
+ # far away. If it is very far away, the normalization may be very
+ # inaccurate and we do not report it.
+ fermi_energy_closest = dos_energies[fermi_idx]
+ distance = np.abs(fermi_energy_closest - fermi_energy)
+ if distance.magnitude <= energy_threshold:
+
+ # Walk through the energies in descencing direction to see if a
+ # gap is nearby (see energy_threshold). If gap found, continue
+ # until HOMO found
+ idx = fermi_idx
+ while True:
+ try:
+ value = dos_values_normalized[i_channel, idx]
+ energy_distance = fermi_energy_closest - dos_energies[idx]
+ except IndexError:
+ break
+ if energy_distance.magnitude > energy_threshold and not zero_found:
+ break
+ if value <= value_threshold:
+ zero_found = True
+ if zero_found and value > value_threshold:
+ energy_reference = dos_energies[idx + 1]
+ homo_found = True
+ break
+ idx -= 1
+ # If gap was not found in descending direction, check the
+ # ascending direction for a nearby (see energy_threshold) HOMO
+ # value
+ if not homo_found:
+ idx = fermi_idx + 1
+ while True:
+ try:
+ value = dos_values_normalized[i_channel, idx]
+ energy_distance = dos_energies[idx] - fermi_energy
+ except IndexError:
+ break
+ if energy_distance.magnitude > energy_threshold:
+ break
+ if value <= value_threshold:
+ energy_reference = dos_energies[idx]
+ break
+ idx += 1
# Add quantities to NOMAD's Metainfo
scc_url = '/section_run/0/section_single_configuration_calculation/%d/section_dos/0' % scc.m_parent_index
self._backend.openContext(scc_url)
dos.dos_values_normalized = dos_values_normalized
- dos.dos_energies_normalized = dos_energies_normalized
- if dos_fingerprint is not None:
- sec_dos_fingerprint = dos.m_create(section_dos_fingerprint)
- sec_dos_fingerprint.bins = dos_fingerprint.bins
- sec_dos_fingerprint.indices = dos_fingerprint.indices
- sec_dos_fingerprint.stepsize = dos_fingerprint.stepsize
- sec_dos_fingerprint.grid_id = dos_fingerprint.grid_id
- sec_dos_fingerprint.filling_factor = dos_fingerprint.filling_factor
+
+ # Data for DOS fingerprint
+ if energy_reference is not None:
+ dos_energies_normalized = dos_energies - energy_reference
+ dos.dos_energies_normalized = dos_energies_normalized
+ try:
+ dos_fingerprint = DOSFingerprint().calculate(
+ dos_energies_normalized.magnitude,
+ dos_values_normalized,
+ n_atoms=number_of_atoms
+ )
+ except Exception as e:
+ self.logger.error('could not generate dos fingerprint', exc_info=e)
+ else:
+ sec_dos_fingerprint = dos.m_create(section_dos_fingerprint)
+ sec_dos_fingerprint.bins = dos_fingerprint.bins
+ sec_dos_fingerprint.indices = dos_fingerprint.indices
+ sec_dos_fingerprint.stepsize = dos_fingerprint.stepsize
+ sec_dos_fingerprint.grid_id = dos_fingerprint.grid_id
+ sec_dos_fingerprint.filling_factor = dos_fingerprint.filling_factor
self._backend.closeContext(scc_url)
diff --git a/tests/normalizing/test_dos.py b/tests/normalizing/test_dos.py
index f0d91edf862cf303ca63bf493f4dfd0cb719903f..1fdb73b14173fe4eb0d12a6db1e5f60b2cd4721f 100644
--- a/tests/normalizing/test_dos.py
+++ b/tests/normalizing/test_dos.py
@@ -40,19 +40,19 @@ def test_fingerprint(dos_si_vasp):
# def test_dos_energies(dos_si_vasp: Backend, dos_si_exciting: Backend, dos_si_fhiaims: Backend):
-# """For debugging.
-# """
-# x_exciting = dos_si_exciting.get_value('dos_energies_normalized', 0)
-# y_exciting = dos_si_exciting.get_value('dos_values_normalized', 0)
-# x_vasp = dos_si_vasp.get_value('dos_energies_normalized', 0)
-# y_vasp = dos_si_vasp.get_value('dos_values_normalized', 0)
-# x_fhiaims = dos_si_fhiaims.get_value('dos_energies_normalized', 0)
-# y_fhiaims = dos_si_fhiaims.get_value('dos_values_normalized', 0)
-# mpl.plot(x_vasp, y_vasp[0], label="VASP")
-# mpl.plot(x_exciting, y_exciting[0], label="exciting")
-# mpl.plot(x_fhiaims, y_fhiaims[0], label="FHI-aims")
-# mpl.legend()
-# mpl.show()
+# """For debugging.
+# """
+# x_exciting = dos_si_exciting.get_value('dos_energies_normalized', 0)
+# y_exciting = dos_si_exciting.get_value('dos_values_normalized', 0)
+# x_vasp = dos_si_vasp.get_value('dos_energies_normalized', 0)
+# y_vasp = dos_si_vasp.get_value('dos_values_normalized', 0)
+# x_fhiaims = dos_si_fhiaims.get_value('dos_energies_normalized', 0)
+# y_fhiaims = dos_si_fhiaims.get_value('dos_values_normalized', 0)
+# mpl.plot(x_vasp, y_vasp[0], label="VASP", marker=".")
+# mpl.plot(x_exciting, y_exciting[0], label="exciting", marker=".")
+# mpl.plot(x_fhiaims, y_fhiaims[0], label="FHI-aims", marker=".")
+# mpl.legend()
+# mpl.show()
def test_dos_magnitude(dos_si_vasp: Backend, dos_si_exciting: Backend, dos_si_fhiaims: Backend):