diff --git a/nomad/normalizing/data/aflow_prototypes.py b/nomad/aflow_prototypes.py
similarity index 100%
rename from nomad/normalizing/data/aflow_prototypes.py
rename to nomad/aflow_prototypes.py
diff --git a/nomad/atomutils.py b/nomad/atomutils.py
index 14035ada1a89fdcd40f1e7fe0ae1ba6468858280..6ec85c0ccab7d7ba76b940bea8d7a530e85a58cb 100644
--- a/nomad/atomutils.py
+++ b/nomad/atomutils.py
@@ -23,7 +23,7 @@ import numpy as np
from scipy.spatial import Voronoi # pylint: disable=no-name-in-module
from matid.symmetry import WyckoffSet
-from nomad.normalizing.data.aflow_prototypes import aflow_prototypes
+from nomad.aflow_prototypes import aflow_prototypes
from nomad.constants import atomic_masses
diff --git a/nomad/cli/admin/admin.py b/nomad/cli/admin/admin.py
index fe493794cc19c6c680533b28e4dde321e7042017..9b970bec458269a479028cabe482f7cd63ade781 100644
--- a/nomad/cli/admin/admin.py
+++ b/nomad/cli/admin/admin.py
@@ -409,7 +409,7 @@ def write_prototype_data_file(aflow_prototypes: dict, filepath) -> None:
def prototypes_update(ctx, filepath, matches_only):
if matches_only:
- from nomad.normalizing.data.aflow_prototypes import aflow_prototypes
+ from nomad.aflow_prototypes import aflow_prototypes
else:
# The basic AFLOW prototype data is available in a Javascript file. Here we
# retrieve it and read only the prototype list from it.
diff --git a/nomad/datamodel/metainfo/public.py b/nomad/datamodel/metainfo/public.py
index 99426480983d89d27289d575ce624282b0417cd3..19243a4f7c4d7358e894c30dc8029b4970f810d2 100644
--- a/nomad/datamodel/metainfo/public.py
+++ b/nomad/datamodel/metainfo/public.py
@@ -2,9 +2,10 @@ import numpy as np # pylint: disable=unused-import
import typing # pylint: disable=unused-import
from nomad.metainfo import ( # pylint: disable=unused-import
MSection, MCategory, Category, Package, Quantity, Section, SubSection, SectionProxy,
- Reference, MEnum
+ Reference, MEnum, derived
)
from nomad.metainfo.legacy import LegacyDefinition
+import nomad.atomutils
m_package = Package(
@@ -5157,6 +5158,30 @@ class section_thermodynamical_properties(MSection):
''',
a_legacy=LegacyDefinition(name='thermodynamical_property_heat_capacity_C_v'))
+ @derived(
+ type=np.dtype(np.float64),
+ shape=['number_of_thermodynamical_property_values'],
+ unit='joule / kelvin * kilogram',
+ description='''
+ Stores the specific heat capacity at constant volume.
+ ''',
+ a_legacy=LegacyDefinition(name='specific_heat_capacity'),
+ cached=True
+ )
+ def specific_heat_capacity(self) -> np.array:
+ """Returns the specific heat capacity by dividing the heat capacity per
+ cell with the mass of the atoms in the cell.
+ """
+ s_frame_sequence = self.m_parent
+ first_frame = s_frame_sequence.frame_sequence_local_frames_ref[0]
+ system = first_frame.single_configuration_calculation_to_system_ref
+ atomic_numbers = system.atom_species
+ mass_per_unit_cell = nomad.atomutils.get_summed_atomic_mass(atomic_numbers)
+ heat_capacity = self.thermodynamical_property_heat_capacity_C_v
+ specific_heat_capacity = heat_capacity / mass_per_unit_cell
+
+ return specific_heat_capacity
+
thermodynamical_property_temperature = Quantity(
type=np.dtype(np.float64),
shape=['number_of_thermodynamical_property_values'],
diff --git a/nomad/metainfo/encyclopedia.py b/nomad/metainfo/encyclopedia.py
index 1553793d43bc2ae663d031ea2c66f4d406e8c67c..aed7e9c183e22137f20e45546537f9088feac730 100644
--- a/nomad/metainfo/encyclopedia.py
+++ b/nomad/metainfo/encyclopedia.py
@@ -1,7 +1,7 @@
import numpy as np
from elasticsearch_dsl import InnerDoc
from nomad.metainfo import MSection, Section, SubSection, Quantity, MEnum, Reference
-from nomad.datamodel.metainfo.public import section_k_band, section_dos
+from nomad.datamodel.metainfo.public import section_k_band, section_dos, section_thermodynamical_properties
class WyckoffVariables(MSection):
@@ -452,6 +452,27 @@ class Properties(MSection):
Reference to an electronic density of states.
"""
)
+ phonon_band_structure = Quantity(
+ type=Reference(section_k_band.m_def),
+ shape=[],
+ description="""
+ Reference to a phonon band structure.
+ """
+ )
+ phonon_dos = Quantity(
+ type=Reference(section_dos.m_def),
+ shape=[],
+ description="""
+ Reference to a phonon density of states.
+ """
+ )
+ thermodynamical_properties = Quantity(
+ type=Reference(section_thermodynamical_properties.m_def),
+ shape=[],
+ description="""
+ Reference to a specific heat capacity.
+ """
+ )
class section_encyclopedia(MSection):
diff --git a/nomad/normalizing/data/__init__.py b/nomad/normalizing/data/__init__.py
deleted file mode 100644
index 355a267cc43cb62fc063f74c37d50632d442372c..0000000000000000000000000000000000000000
--- a/nomad/normalizing/data/__init__.py
+++ /dev/null
@@ -1,13 +0,0 @@
-# Copyright 2018 Markus Scheidgen
-#
-# Licensed under the Apache License, Version 2.0 (the "License");
-# you may not use this file except in compliance with the License.
-# You may obtain a copy of the License at
-#
-# http://www.apache.org/licenses/LICENSE-2.0
-#
-# Unless required by applicable law or agreed to in writing, software
-# distributed under the License is distributed on an"AS IS" BASIS,
-# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-# See the License for the specific language governing permissions and
-# limitations under the License.
diff --git a/nomad/normalizing/encyclopedia/encyclopedia.py b/nomad/normalizing/encyclopedia/encyclopedia.py
index 786cb0d4147926057b3a12e4f1c526183162d205..37ce29152fce21092d6e8b170f81646c9b70d84e 100644
--- a/nomad/normalizing/encyclopedia/encyclopedia.py
+++ b/nomad/normalizing/encyclopedia/encyclopedia.py
@@ -279,14 +279,9 @@ class EncyclopediaNormalizer(Normalizer):
)
return
- # Get the method type, stop if unknown
+ # Get the method type. For now, we allow unknown method type.
+ # Mostly to allow phonon calculations through.
representative_method, method_type = self.method_type(method, calc_type)
- if method_type == config.services.unavailable_value:
- self.logger.info(
- "Unsupported method type for encyclopedia, encyclopedia metainfo not created.",
- enc_status="unsupported_method_type",
- )
- return
# Get representative scc
try:
diff --git a/nomad/normalizing/encyclopedia/properties.py b/nomad/normalizing/encyclopedia/properties.py
index d13ebebd120d6e5e9572ec18cfdd051afec0aecb..501c8bb829ec90d9db894f688c79109eb76f0f92 100644
--- a/nomad/normalizing/encyclopedia/properties.py
+++ b/nomad/normalizing/encyclopedia/properties.py
@@ -102,20 +102,51 @@ class PropertiesNormalizer():
def has_fermi_surface(self) -> None:
pass
- def has_thermal_properties(self) -> None:
- pass
-
- def phonon_dispersion(self) -> None:
- pass
-
- def phonon_dos(self) -> None:
- pass
-
- def specific_heat_cv(self) -> None:
- pass
+ def thermodynamical_properties(self, properties: Properties) -> None:
+ """Tries to resolve a reference to a representative set of
+ thermodynamical properties. Will not store any data if it cannot be
+ resolved unambiguously.
+ """
+ try:
+ resolved_section = None
+ frame_sequences = self.backend.entry_archive.section_run[0].section_frame_sequence
+ for frame_sequence in frame_sequences:
+ thermodynamical_props = frame_sequence.section_thermodynamical_properties
+ for thermodynamical_prop in thermodynamical_props:
+ if resolved_section is None:
+ resolved_section = thermodynamical_prop
+ else:
+ self.logger("Could not unambiguously select data to display for specific heat.")
+ return
+ except Exception:
+ return
+ if resolved_section is not None:
+ properties.thermodynamical_properties = resolved_section
- def helmholtz_free_energy(self) -> None:
- pass
+ def phonon_band_structure(self, properties: Properties, context: Context) -> None:
+ """Tries to resolve a reference to a representative phonon band
+ structure. Will not store any data if it cannot be resolved
+ unambiguously.
+ """
+ try:
+ representative_scc = context.representative_scc
+ bands = representative_scc.section_k_band
+ if bands is None:
+ return
+
+ representative_phonon_band = None
+ for band in bands:
+ if band.band_structure_kind == "vibrational":
+ if representative_phonon_band is None:
+ representative_phonon_band = band
+ else:
+ self.logger("Could not unambiguously select data to display for a phonon band structure.")
+ return
+
+ except Exception:
+ return
+ if representative_phonon_band is not None:
+ properties.phonon_band_structure = representative_phonon_band
def energies(self, properties: Properties, gcd: int, representative_scc: Section) -> None:
energy_dict = {}
@@ -152,3 +183,8 @@ class PropertiesNormalizer():
# Save metainfo
self.electronic_band_structure(properties, calc_type, material_type, context, sec_system)
self.energies(properties, gcd, representative_scc)
+
+ # Phonon calculations have a specific set of properties to extract
+ if context.calc_type == Calculation.calculation_type.type.phonon_calculation:
+ self.thermodynamical_properties(properties)
+ self.phonon_band_structure(properties, context)
diff --git a/tests/normalizing/test_encyclopedia.py b/tests/normalizing/test_encyclopedia.py
index d60de2c32a6044b3afaf098d9ee8fd061819470b..c80cb50fc13bfe67ab403ba5d66f2d3ce34546b0 100644
--- a/tests/normalizing/test_encyclopedia.py
+++ b/tests/normalizing/test_encyclopedia.py
@@ -54,15 +54,6 @@ def test_molecular_dynamics(molecular_dynamics: EntryArchive):
assert calc_type == "molecular dynamics"
-# Disabled until the method information can be retrieved
-# def test_phonon(phonon: EntryArchive):
- # """Tests that geometry optimizations are correctly processed."
- # """
- # enc = phonon.get_mi2_section(Encyclopedia.m_def)
- # calc_type = enc.calc_type.calc_type
- # assert calc_type == "phonon calculation"
-
-
def test_1d_metainfo(one_d: EntryArchive):
"""Tests that metainfo for 1D systems is correctly processed.
"""
@@ -476,3 +467,29 @@ def test_hashes_undefined(hash_vasp):
# not really need the method to be accurately defined.
assert method_hash is None
assert group_eos_hash is None
+
+
+def test_phonon(phonon: EntryArchive):
+ """Tests that phonon calculations are correctly processed.
+ """
+ enc = phonon.entry_archive.section_encyclopedia
+ calc_type = enc.calculation.calculation_type
+ prop = enc.properties
+ band = prop.phonon_band_structure
+ thermo_props = prop.thermodynamical_properties
+ assert calc_type == "phonon calculation"
+
+ # Check band structure
+ assert band is not None
+ assert band.band_structure_kind == "vibrational"
+ for segment in band.section_k_band_segment:
+ assert segment.band_energies is not None
+ assert segment.band_k_points is not None
+ assert segment.band_segm_labels is not None
+
+ # Check thermodynamical properties
+ assert thermo_props is not None
+ assert thermo_props.thermodynamical_property_heat_capacity_C_v is not None
+ assert thermo_props.specific_heat_capacity is not None
+ assert thermo_props.thermodynamical_property_temperature is not None
+ assert thermo_props.vibrational_free_energy_at_constant_volume is not None