diff --git a/nomad/config.py b/nomad/config.py
index 25f2306373e676f0e85da6f61b072b55688762b6..3698a866a6a4084ee1aaf835f9c0fe179bb01530 100644
--- a/nomad/config.py
+++ b/nomad/config.py
@@ -192,6 +192,8 @@ normalize = NomadConfig(
# The distance tolerance between atoms for grouping them into the same
# cluster. Used in detecting system type.
cluster_threshold=3.1,
+ # Defines the "bin size" for rounding cell angles for the material hash
+ angle_rounding = float(10.0) # unit: degree
)
client = NomadConfig(
diff --git a/nomad/metainfo/encyclopedia.py b/nomad/metainfo/encyclopedia.py
index a73946a9b714e552339a4bdf01f38769fcbdad3a..1aa594a270554e2a9ee44a9e0bea4f723209db88 100644
--- a/nomad/metainfo/encyclopedia.py
+++ b/nomad/metainfo/encyclopedia.py
@@ -75,6 +75,20 @@ class Material(MSection):
F = All faces centred
"""
)
+ cell_normalized = Quantity(
+ type=np.dtype('f8'),
+ shape=[3, 3],
+ description="""
+ Unit cell in normalized form, meaning the bravais cell.
+ """
+ )
+ periodicity = Quantity(
+ type=np.dtype('i1'),
+ shape=["1..*"],
+ description="""
+ The indices of the periodic dimensions.
+ """
+ )
class Calculation(MSection):
@@ -109,6 +123,19 @@ class Calculation(MSection):
Atomic density of the material (atoms/volume)."
"""
)
+ cell_angles_string = Quantity(
+ type=str,
+ description="""
+ A summary of the cell angles, part of material definition.
+ """
+ )
+ lattice_parameters = Quantity(
+ type=np.dtype('f8'),
+ shape=[6],
+ description="""
+ Lattice parameters of the normalized cell of a specific calculation.
+ """
+ )
class Encyclopedia(MSection):
diff --git a/nomad/normalizing/encyclopedia.py b/nomad/normalizing/encyclopedia.py
index adf002ecbee9cd792a6fefd2f78d5bae72513260..9a1e314a58de68f945dbfbab1a80b1aaa4d18524 100644
--- a/nomad/normalizing/encyclopedia.py
+++ b/nomad/normalizing/encyclopedia.py
@@ -14,11 +14,14 @@
from hashlib import sha512
from typing import Dict
+from abc import abstractmethod
+import math
import ase
+import numpy as np
from nomad.normalizing.normalizer import Normalizer, s_scc, s_system, s_frame_sequence, r_frame_sequence_to_sampling, s_sampling_method, r_frame_sequence_local_frames, r_scc_to_system
from nomad.metainfo.encyclopedia import Encyclopedia, Material, Calculation
-from nomad.normalizing import symmetry
+from nomad.normalizing import structure
from nomad import config
@@ -32,274 +35,182 @@ class EncyclopediaNormalizer(Normalizer):
def __init__(self, backend):
super().__init__(backend)
- # NOTE: Enc specific visualization
- def get_atom_labels(self, material: Material, std_atoms: ase.Atoms) -> None:
- material.atom_labels = std_atoms.get_chemical_symbols()
-
- # NOTE: Enc specific visualization
- def get_atom_positions(self, material: Material, std_atoms: ase.Atoms) -> None:
- material.atom_positions = std_atoms.get_scaled_positions(wrap=False)
-
- # NOTE: System normalizer
- def get_atomic_density(self, calculation: Calculation, repr_system: ase.Atoms) -> None:
- orig_n_atoms = len(repr_system)
- orig_volume = repr_system.get_volume() * (1e-10)**3
- calculation.atomic_density = float(orig_n_atoms / orig_volume)
-
- # NOTE: Does not exist?
- def get_atomistic_structure(self) -> None:
- pass
-
# NOTE: Band structure normalizer
- def get_band_gap(self) -> None:
+ def band_gap(self) -> None:
pass
# NOTE: Band structure normalizer
- def get_band_gap_position(self) -> None:
+ def band_gap_position(self) -> None:
pass
# NOTE: Band structure normalizer
- def get_band_gap_type(self) -> None:
+ def band_gap_type(self) -> None:
pass
# NOTE: Band structure normalizer
- def get_band_structure(self) -> None:
+ def band_structure(self) -> None:
pass
# NOTE: Method normalizer
- def get_basis_set_short_name(self) -> None:
+ def basis_set_short_name(self) -> None:
pass
# NOTE: Method normalizer
- def get_basis_set_type(self) -> None:
+ def basis_set_type(self) -> None:
pass
- # NOTE: System normalizer
- def get_bravais_lattice(self, material: Material, section_system: Dict) -> None:
- bravais_lattice = section_system["section_symmetry"][0]["bravais_lattice"]
- material.bravais_lattice = bravais_lattice
-
# NOTE: Band structure normalizer
- def get_brillouin_zone(self) -> None:
+ def brillouin_zone(self) -> None:
pass
# NOTE: Band structure normalizer
- def get_brillouin_zone_viewer(self) -> None:
+ def brillouin_zone_viewer(self) -> None:
pass
- def get_calculation(self) -> None:
+ def calculation(self) -> None:
pass
- def get_calculation_pid(self) -> None:
- pass
-
- # NOTE: Enc specific visualization
- def get_cell_angles(self) -> None:
- pass
-
- # NOTE: System normalizer
- def get_cell_normalized(self) -> None:
- pass
-
- # NOTE: System normalizer
- def get_cell_primitive(self) -> None:
- pass
-
- # NOTE: System normalizer
- def get_cell_volume(self) -> None:
+ def calculation_pid(self) -> None:
pass
# NOTE: Parser
- def get_code_name(self) -> None:
+ def code_name(self) -> None:
pass
# NOTE: Parser
- def get_code_version(self) -> None:
+ def code_version(self) -> None:
pass
# NOTE: Repo
- def get_contributor_first_name(self) -> None:
+ def contributor_first_name(self) -> None:
pass
# NOTE: Repo
- def get_contributor_last_name(self) -> None:
+ def contributor_last_name(self) -> None:
pass
# NOTE: Repo
- def get_contributor_type(self) -> None:
+ def contributor_type(self) -> None:
pass
# NOTE: Repo
- def get_contributors(self) -> None:
+ def contributors(self) -> None:
pass
# NOTE: Method normalizer
- def get_core_electron_treatment(self) -> None:
- pass
-
- # NOTE: System normalizer
- def get_crystal_system(self) -> None:
+ def core_electron_treatment(self) -> None:
pass
# NOTE: Band structure normalizer
- def get_dos(self) -> None:
+ def dos(self) -> None:
pass
# NOTE: Elastic properties normalizer
- def get_elastic_constants_matrix(self) -> None:
+ def elastic_constants_matrix(self) -> None:
pass
# NOTE: Elastic properties normalizer
- def get_elastic_deformation_energies(self) -> None:
+ def elastic_deformation_energies(self) -> None:
pass
# NOTE: Elastic properties normalizer
- def get_elastic_fitting_parameters(self) -> None:
+ def elastic_fitting_parameters(self) -> None:
pass
# NOTE: Elastic properties normalizer
- def get_elastic_moduli(self) -> None:
+ def elastic_moduli(self) -> None:
pass
# NOTE: Elastic properties normalizer
- def get_elastic_properties(self) -> None:
+ def elastic_properties(self) -> None:
pass
- def get_energies(self) -> None:
+ def energies(self) -> None:
pass
# NOTE: Band structure normalizer
- def get_fermi_surface(self) -> None:
- pass
-
- # NOTE: System normalizer
- def get_formula(self) -> None:
- pass
-
- # NOTE: System normalizer
- def get_formula_cell(self) -> None:
- pass
-
- # NOTE: System normalizer
- def get_formula_reduced(self) -> None:
- pass
-
- # NOTE: System normalizer
- def get_free_wyckoff_parameters(self) -> None:
+ def fermi_surface(self) -> None:
pass
# NOTE: Method normalizer
- def get_functional_long_name(self) -> None:
+ def functional_long_name(self) -> None:
pass
# NOTE: Method normalizer
- def get_functional_type(self) -> None:
+ def functional_type(self) -> None:
pass
# TODO: ??
- def get_group_e_min(self) -> None:
+ def group_e_min(self) -> None:
pass
# TODO: ??
- def get_group_type(self) -> None:
+ def group_type(self) -> None:
pass
# TODO: Method normalizer
- def get_gw_starting_point(self) -> None:
+ def gw_starting_point(self) -> None:
pass
# TODO: Method normalizer
- def get_gw_type(self) -> None:
+ def gw_type(self) -> None:
pass
# NOTE: Enc specific
- def get_has_bs(self) -> None:
+ def has_bs(self) -> None:
pass
# NOTE: Enc specific
- def get_has_dos(self) -> None:
+ def has_dos(self) -> None:
pass
# NOTE: Enc specific
- def get_has_fermi_surface(self) -> None:
+ def has_fermi_surface(self) -> None:
pass
# NOTE: Enc specific
- def get_has_thermal_properties(self) -> None:
- pass
-
- def get_helmholtz_free_energy(self) -> None:
- pass
-
- def get_k_point_grid_description(self) -> None:
- pass
-
- def get_lattice_parameters(self) -> None:
+ def has_thermal_properties(self) -> None:
pass
- def get_mainfile_uri(self) -> None:
+ def helmholtz_free_energy(self) -> None:
pass
- # NOTE: System normalizer
- def get_mass_density(self) -> None:
+ def k_point_grid_description(self) -> None:
pass
- def get_material_hash(self, material: Material, section_system: Dict) -> None:
- # Get symmetry information from the section
- section_symmetry = section_system["section_symmetry"][0]
- space_group_number = section_symmetry["space_group_number"]
- section_std_system = section_symmetry["section_std_system"][0]
- wyckoff_sets = section_std_system.tmp["wyckoff_sets"]
-
- # Create and store hash based on SHA512
- norm_hash_string = symmetry.create_symmetry_string(space_group_number, wyckoff_sets)
- material.material_hash = sha512(norm_hash_string.encode('utf-8')).hexdigest()
-
- def get_material_name(self) -> None:
+ def mainfile_uri(self) -> None:
pass
- # NOTE: System normalizer
- def get_number_of_atoms(self, material: Material, std_atoms: ase.Atoms) -> None:
- material.number_of_atoms = len(std_atoms)
-
# NOTE: Postprocessing
- def get_number_of_calculation(self) -> None:
- pass
-
- # NOTE: System normalizer
- def get_periodic_dimensions(self) -> None:
+ def number_of_calculation(self) -> None:
pass
# NOTE: Phonon normalizer
- def get_phonon_dispersion(self) -> None:
+ def phonon_dispersion(self) -> None:
pass
# NOTE: Phonon normalizer
- def get_phonon_dos(self) -> None:
- pass
-
- # NOTE: System normalizer
- def get_point_group(self) -> None:
+ def phonon_dos(self) -> None:
pass
# NOTE: Method normalizer
- def get_pseudopotential_type(self) -> None:
+ def pseudopotential_type(self) -> None:
pass
# NOTE: Repo
- def get_repository_dowload_uri(self) -> None:
+ def repository_dowload_uri(self) -> None:
pass
# NOTE: Repo
- def get_repository_upload_comment(self) -> None:
+ def repository_upload_comment(self) -> None:
pass
# NOTE: Repo
- def get_repository_uri(self) -> None:
+ def repository_uri(self) -> None:
pass
# NOTE: Enc specific
- def get_run_type(self, calculation) -> str:
+ def run_type(self, calculation) -> str:
"""Decides what type of calculation this is: single_point, md,
geometry_optimization, etc.
"""
@@ -367,63 +278,63 @@ class EncyclopediaNormalizer(Normalizer):
calculation.run_type = run_type
return run_type
- def get_scf_threshold(self) -> None:
+ def scf_threshold(self) -> None:
pass
# NOTE: Enc specific
- def get_similar_materials(self) -> None:
+ def similar_materials(self) -> None:
pass
# NOTE: Method normalizer
- def get_smearing_kind(self) -> None:
+ def smearing_kind(self) -> None:
pass
# NOTE: Method normalizer
- def get_smearing_parameters(self) -> None:
+ def smearing_parameters(self) -> None:
pass
# NOTE: System normalizer
- def get_space_group(self) -> None:
+ def space_group(self) -> None:
pass
# NOTE: System normalizer
- def get_space_group_international_short_symbol(self) -> None:
+ def space_group_international_short_symbol(self) -> None:
pass
# NOTE: System normalizer
- def get_space_group_number(self) -> None:
+ def space_group_number(self) -> None:
pass
# NOTE: Phonon normalizer
- def get_specific_heat_cv(self) -> None:
+ def specific_heat_cv(self) -> None:
pass
# NOTE: System normalizer
- def get_springer_classification(self) -> None:
+ def springer_classification(self) -> None:
pass
# NOTE: System normalizer
- def get_springer_compound_class(self) -> None:
+ def springer_compound_class(self) -> None:
pass
# NOTE: System normalizer
- def get_springer_prototype(self) -> None:
+ def springer_prototype(self) -> None:
pass
# NOTE: System normalizer
- def get_structure_prototype(self) -> None:
+ def structure_prototype(self) -> None:
pass
# NOTE: System normalizer
- def get_structure_type(self) -> None:
+ def structure_type(self) -> None:
pass
# NOTE: System normalizer
- def get_strukturbericht_designation(self) -> None:
+ def strukturbericht_designation(self) -> None:
pass
# NOTE: System normalizer
- def get_system_type(self, material: Material, calculation: Calculation) -> tuple:
+ def system_type(self, material: Material, calculation: Calculation) -> tuple:
# Select the representative system from which system type is retrieved.
# For geometry optimizations system type is analyzed from last relaxed
# frame. For phonon calculations system type is analyzed from first
@@ -468,13 +379,19 @@ class EncyclopediaNormalizer(Normalizer):
material.system_type = system_type
return system, system_type
- def get_template(self) -> None:
+ def template(self) -> None:
pass
# NOTE: System normalizer
- def get_wyckoff_groups(self) -> None:
+ def wyckoff_groups(self) -> None:
pass
+ def fill(self, run_type, system_type, representative_system):
+ # Fill structure related meta
+ if system_type == Material.system_type.type.bulk:
+ system_worker = StructureBulk()
+ system_worker.fill(self._backend, representative_system)
+
def normalize(self, logger=None) -> None:
super().normalize(logger)
system_enums = Material.system_type.type
@@ -485,25 +402,175 @@ class EncyclopediaNormalizer(Normalizer):
calculation = sec_enc.m_create(Calculation)
# Determine run type, stop if unknown
- run_type = self.get_run_type(calculation)
+ run_type = self.run_type(calculation)
if run_type == config.services.unavailable_value:
self.logger.info("unknown run type for encyclopedia")
return
# Get the system type, stop if unknown
- system, system_type = self.get_system_type(material, calculation)
+ representative_system, system_type = self.system_type(material, calculation)
if system_type != system_enums.bulk and system_type != system_enums.two_d and system_type != system_enums.one_d:
self.logger.info("unknown system type for encyclopedia")
return
- # Proceed to fill rest of data
- std_atoms = system["section_symmetry"][0]["section_std_system"][0].tmp["std_atoms"] # Temporary value stored by SystemNormalizer
- repr_atoms = system["section_symmetry"][0]["section_original_system"][0].tmp["orig_atoms"] # Temporary value stored by SystemNormalizer
- self.get_material_hash(material, system)
- self.get_number_of_atoms(material, std_atoms)
- self.get_atom_labels(material, std_atoms)
- self.get_atomic_density(calculation, repr_atoms)
- self.get_bravais_lattice(material, system)
+ # Get the method type, stop if unknown
+ # TODO
# Put the encyclopedia section into backend
self._backend.add_mi2_section(sec_enc)
+ self.fill(run_type, system_type, representative_system)
+
+
+class Structure():
+ """A base class that is used for processing structure related information
+ in the Encylopedia.
+ """
+ @abstractmethod
+ def atom_labels(self, material: Material, std_atoms: ase.Atoms) -> None:
+ pass
+
+ @abstractmethod
+ def atom_positions(self, material: Material, std_atoms: ase.Atoms) -> None:
+ pass
+
+ @abstractmethod
+ def atomic_density(self, calculation: Calculation, repr_system: ase.Atoms) -> None:
+ pass
+
+ # NOTE: Does not exist?
+ # def atomistic_structure(self) -> None:
+ # pass
+
+ @abstractmethod
+ def bravais_lattice(self, material: Material, section_system: Dict) -> None:
+ pass
+
+ @abstractmethod
+ def cell_angles_string(self, calculation: Calculation) -> None:
+ pass
+
+ @abstractmethod
+ def cell_normalized(self, material: Material, std_atoms: ase.Atoms) -> None:
+ pass
+
+ # def cell_primitive(self) -> None:
+ # pass
+
+ # def cell_volume(self) -> None:
+ # pass
+
+ # def crystal_system(self) -> None:
+ # pass
+
+ # def formula(self) -> None:
+ # pass
+
+ # def formula_cell(self) -> None:
+ # pass
+
+ # def formula_reduced(self) -> None:
+ # pass
+
+ # def free_wyckoff_parameters(self) -> None:
+ # pass
+
+ @abstractmethod
+ def lattice_parameters(self, calculation: Calculation, std_atoms: ase.Atoms) -> None:
+ pass
+
+ # def mass_density(self) -> None:
+ # pass
+
+ @abstractmethod
+ def material_hash(self, material: Material, section_system: Dict) -> None:
+ pass
+
+ # def material_name(self) -> None:
+ # pass
+
+ @abstractmethod
+ def number_of_atoms(self, material: Material, std_atoms: ase.Atoms) -> None:
+ pass
+
+ @abstractmethod
+ def periodicity(self, material: Material) -> None:
+ pass
+
+ # def point_group(self) -> None:
+ # pass
+
+ def fill(self, backend, representative_system: Dict) -> None:
+ # Fetch resources
+ sec_enc = backend.get_mi2_section(Encyclopedia.m_def)
+ material = sec_enc.material
+ calculation = sec_enc.calculation
+ repr_system = representative_system
+ std_atoms = repr_system["section_symmetry"][0]["section_std_system"][0].tmp["std_atoms"] # Temporary value stored by SystemNormalizer
+ repr_atoms = repr_system["section_symmetry"][0]["section_original_system"][0].tmp["orig_atoms"] # Temporary value stored by SystemNormalizer
+
+ self.material_hash(material, repr_system)
+ self.number_of_atoms(material, std_atoms)
+ self.atom_labels(material, std_atoms)
+ self.atomic_density(calculation, repr_atoms)
+ self.bravais_lattice(material, repr_system)
+ self.cell_normalized(material, std_atoms)
+ self.lattice_parameters(calculation, std_atoms)
+ self.cell_angles_string(calculation)
+ self.periodicity(material)
+
+
+class StructureBulk(Structure):
+ """Processes structure related metainfo for Encyclopedia bulk structures.
+ """
+ def atom_labels(self, material: Material, std_atoms: ase.Atoms) -> None:
+ material.atom_labels = std_atoms.get_chemical_symbols()
+
+ def atom_positions(self, material: Material, std_atoms: ase.Atoms) -> None:
+ material.atom_positions = std_atoms.get_scaled_positions(wrap=False)
+
+ def atomic_density(self, calculation: Calculation, repr_system: ase.Atoms) -> None:
+ orig_n_atoms = len(repr_system)
+ orig_volume = repr_system.get_volume() * (1e-10)**3
+ calculation.atomic_density = float(orig_n_atoms / orig_volume)
+
+ def material_hash(self, material: Material, section_system: Dict) -> None:
+ # Get symmetry information from the section
+ section_symmetry = section_system["section_symmetry"][0]
+ space_group_number = section_symmetry["space_group_number"]
+ section_std_system = section_symmetry["section_std_system"][0]
+ wyckoff_sets = section_std_system.tmp["wyckoff_sets"]
+
+ # Create and store hash based on SHA512
+ norm_hash_string = structure.create_symmetry_string(space_group_number, wyckoff_sets)
+ material.material_hash = sha512(norm_hash_string.encode('utf-8')).hexdigest()
+
+ def number_of_atoms(self, material: Material, std_atoms: ase.Atoms) -> None:
+ material.number_of_atoms = len(std_atoms)
+
+ # NOTE: System normalizer
+ def bravais_lattice(self, material: Material, section_system: Dict) -> None:
+ bravais_lattice = section_system["section_symmetry"][0]["bravais_lattice"]
+ material.bravais_lattice = bravais_lattice
+
+ # NOTE: Enc specific visualization
+ def cell_angles_string(self, calculation: Calculation) -> None:
+ angles = calculation.lattice_parameters[3:6]
+ angles_rounded = []
+ for angle in angles:
+ angle_deg = math.degrees(angle)
+ angles_rounded.append(
+ round(angle_deg / config.normalize.angle_rounding) * config.normalize.angle_rounding)
+ calculation.cell_angles_string = "/".join([str(angle) for angle in angles_rounded])
+
+ # NOTE: System normalizer
+ def cell_normalized(self, material: Material, std_atoms: ase.Atoms) -> None:
+ cell_normalized = std_atoms.get_cell()
+ cell_normalized *= 1e-10
+ material.cell_normalized = cell_normalized
+
+ def lattice_parameters(self, calculation: Calculation, std_atoms: ase.Atoms) -> None:
+ cell_normalized = std_atoms.get_cell()
+ calculation.lattice_parameters = structure.get_lattice_parameters(cell_normalized)
+
+ def periodicity(self, material: Material) -> None:
+ material.periodicity = np.array([0, 1, 2], dtype=np.int8)
diff --git a/nomad/normalizing/symmetry.py b/nomad/normalizing/structure.py
similarity index 56%
rename from nomad/normalizing/symmetry.py
rename to nomad/normalizing/structure.py
index e9fb3e79d057bd0e9f1c82cdfb87e33a0bf571d2..0d36029738875132a65c2147ea1f34b57b8d31b8 100644
--- a/nomad/normalizing/symmetry.py
+++ b/nomad/normalizing/structure.py
@@ -13,6 +13,7 @@
# limitations under the License.
from typing import Dict
+import numpy as np
def create_symmetry_string(space_group: int, wyckoff_sets: Dict) -> str:
@@ -40,3 +41,43 @@ def create_symmetry_string(space_group: int, wyckoff_sets: Dict) -> str:
string = "{} {}".format(space_group, wyckoff_string)
return string
+
+
+def get_lattice_parameters(normalized_cell):
+ """Calculate the lattice parameters for the normalized cell.
+
+ :param normalized_cell: The normalized cell as a 2D array. Each row is a
+ basis vector.
+ :type normalized_cell: numpy.array
+
+ :return: Six parameters a, b, c, alpha, beta, gamma (in this order) as a
+ list. Here is an explanation of each parameter:
+
+ #. a = length of first basis vector
+ #. b = length of second basis vector
+ #. c = length of third basis vector
+ #. alpha = angle between b and c
+ #. beta = angle between a and c
+ #. gamma = angle between a and b
+
+ :rtype: numpy.array
+ """
+ if normalized_cell is None:
+ return None
+
+ # Lengths
+ lengths = np.linalg.norm(normalized_cell, axis=1)
+ a, b, c = lengths
+
+ # Angles
+ angles = np.zeros(3)
+ for i in range(3):
+ j = (i + 1) % 3
+ k = (i + 2) % 3
+ angles[i] = np.dot(
+ normalized_cell[j],
+ normalized_cell[k]) / (lengths[j] * lengths[k])
+ angles = np.clip(angles, -1.0, 1.0)
+ alpha, beta, gamma = np.arccos(angles)
+
+ return [a, b, c, alpha, beta, gamma]
diff --git a/tests/normalizing/test_encyclopedia.py b/tests/normalizing/test_encyclopedia.py
index e4b9c1f462257e1dc7c03817a868949ca99df7b7..597f656907bf5d641a591303563d5d2bdb573e34 100644
--- a/tests/normalizing/test_encyclopedia.py
+++ b/tests/normalizing/test_encyclopedia.py
@@ -13,6 +13,7 @@
# limitations under the License.
import pytest
+import numpy as np
from nomad.metainfo.encyclopedia import Encyclopedia
from tests.normalizing.conftest import geometry_optimization, molecular_dynamics, phonon # pylint: disable=unused-import
@@ -55,3 +56,7 @@ def test_bulk_information(geometry_optimization: Encyclopedia):
assert go.material.atom_labels == ["Na", "Na", "Na", "Na"]
assert go.calculation.atomic_density == pytest.approx(4.0e+30, rel=0.000001, abs=None)
assert go.material.bravais_lattice == "cF"
+ assert go.material.cell_normalized is not None
+ assert go.calculation.lattice_parameters is not None
+ assert go.calculation.cell_angles_string is not None
+ assert np.array_equal(go.material.periodicity, [0, 1, 2])