Commit 713797b7 authored by Lauri Himanen's avatar Lauri Himanen
Browse files

Updated some metainfo names, fixed issue with Section name not being used.

parent 51fc95b8
Pipeline #71082 passed with stages
in 26 minutes and 22 seconds
Subproject commit f1c85ccdb381094b9e46382c66e260d9ed5d641c Subproject commit 0fecfb3f466690e1aa45ec6f24e9a51661e3f65c
Subproject commit f9979f05e6a26e0512c26d5a316f4b0749528640 Subproject commit c776b194dd825ad7bbe81c5c2afb1745122a1dde
...@@ -72,10 +72,10 @@ class Material(MSection): ...@@ -72,10 +72,10 @@ class Material(MSection):
) )
# Material-specific # Material-specific
system_type = Quantity( material_type = Quantity(
type=MEnum(bulk="bulk", two_d="2D", one_d="1D", unavailable="unavailable"), type=MEnum(bulk="bulk", two_d="2D", one_d="1D", unavailable="unavailable"),
description=""" description="""
"Character of physical system's geometry, e.g. bulk, surface... ", "Character of physical system's geometry, e.g. bulk, 2D, 1D... ",
""" """
) )
material_hash = Quantity( material_hash = Quantity(
...@@ -623,8 +623,9 @@ class Encyclopedia(MSection): ...@@ -623,8 +623,9 @@ class Encyclopedia(MSection):
m_def = Section( m_def = Section(
a_flask=dict(skip_none=True), a_flask=dict(skip_none=True),
a_elastic=dict(type=InnerDoc), a_elastic=dict(type=InnerDoc),
name="encyclopedia",
description=""" description="""
Section for storing all information that is used by the NOMAD Encyclopedia. Section which stores information for the NOMAD Encyclopedia.
""" """
) )
mainfile_uri = Quantity( mainfile_uri = Quantity(
......
...@@ -644,8 +644,9 @@ class MSection(metaclass=MObjectMeta): ...@@ -644,8 +644,9 @@ class MSection(metaclass=MObjectMeta):
m_def = Section() m_def = Section()
setattr(cls, 'm_def', m_def) setattr(cls, 'm_def', m_def)
# transfer name m_def # Use class name if name is not explicitly defined
m_def.name = cls.__name__ if m_def.name is None:
m_def.name = cls.__name__
m_def.section_cls = cls m_def.section_cls = cls
# add base sections # add base sections
......
...@@ -62,7 +62,7 @@ class Context(): ...@@ -62,7 +62,7 @@ class Context():
""" """
def __init__( def __init__(
self, self,
system_type: str, material_type: str,
method_type: str, method_type: str,
run_type: str, run_type: str,
representative_system, representative_system,
...@@ -70,7 +70,7 @@ class Context(): ...@@ -70,7 +70,7 @@ class Context():
representative_scc, representative_scc,
representative_scc_idx, representative_scc_idx,
): ):
self.system_type = system_type self.material_type = material_type
self.method_type = method_type self.method_type = method_type
self.run_type = run_type self.run_type = run_type
self.representative_system = representative_system self.representative_system = representative_system
...@@ -160,11 +160,11 @@ class EncyclopediaNormalizer(Normalizer): ...@@ -160,11 +160,11 @@ class EncyclopediaNormalizer(Normalizer):
run_type_sec.run_type = run_type run_type_sec.run_type = run_type
return run_type return run_type
def system_type(self, material: Material) -> tuple: def material_type(self, material: Material) -> tuple:
# Try to fetch representative system # Try to fetch representative system
system = None system = None
system_type = config.services.unavailable_value material_type = config.services.unavailable_value
system_enums = Material.system_type.type material_enums = Material.material_type.type
system_idx = self._backend["section_run"][0].tmp["representative_system_idx"] system_idx = self._backend["section_run"][0].tmp["representative_system_idx"]
if system_idx is not None: if system_idx is not None:
# Try to find system type information from backend for the selected system. # Try to find system type information from backend for the selected system.
...@@ -174,19 +174,19 @@ class EncyclopediaNormalizer(Normalizer): ...@@ -174,19 +174,19 @@ class EncyclopediaNormalizer(Normalizer):
except KeyError: except KeyError:
pass pass
else: else:
if stype == system_enums.one_d or stype == system_enums.two_d: if stype == material_enums.one_d or stype == material_enums.two_d:
system_type = stype material_type = stype
# For bulk systems we also ensure that the symmetry information is available # For bulk systems we also ensure that the symmetry information is available
if stype == system_enums.bulk: if stype == material_enums.bulk:
try: try:
system["section_symmetry"][0] system["section_symmetry"][0]
except (KeyError, IndexError): except (KeyError, IndexError):
self.logger.info("Symmetry information is not available for a bulk system. No Encylopedia entry created.") self.logger.info("Symmetry information is not available for a bulk system. No Encylopedia entry created.")
else: else:
system_type = stype material_type = stype
material.system_type = system_type material.material_type = material_type
return system, system_type return system, material_type
def method_type(self, method: Method) -> tuple: def method_type(self, method: Method) -> tuple:
repr_method = None repr_method = None
...@@ -267,11 +267,11 @@ class EncyclopediaNormalizer(Normalizer): ...@@ -267,11 +267,11 @@ class EncyclopediaNormalizer(Normalizer):
def fill(self, ctx: Context): def fill(self, ctx: Context):
# Fill structure related metainfo # Fill structure related metainfo
struct: Any = None struct: Any = None
if ctx.system_type == Material.system_type.type.bulk: if ctx.material_type == Material.material_type.type.bulk:
struct = MaterialBulkNormalizer(self.backend, self.logger) struct = MaterialBulkNormalizer(self.backend, self.logger)
elif ctx.system_type == Material.system_type.type.two_d: elif ctx.material_type == Material.material_type.type.two_d:
struct = Material2DNormalizer(self.backend, self.logger) struct = Material2DNormalizer(self.backend, self.logger)
elif ctx.system_type == Material.system_type.type.one_d: elif ctx.material_type == Material.material_type.type.one_d:
struct = Material1DNormalizer(self.backend, self.logger) struct = Material1DNormalizer(self.backend, self.logger)
if struct is not None: if struct is not None:
struct.normalize(ctx) struct.normalize(ctx)
...@@ -316,17 +316,23 @@ class EncyclopediaNormalizer(Normalizer): ...@@ -316,17 +316,23 @@ class EncyclopediaNormalizer(Normalizer):
return return
# Get the system type, stop if unknown # Get the system type, stop if unknown
system_enums = Material.system_type.type material_enums = Material.material_type.type
representative_system, system_type = self.system_type(material) representative_system, material_type = self.material_type(material)
if system_type != system_enums.bulk and system_type != system_enums.two_d and system_type != system_enums.one_d: if material_type != material_enums.bulk and material_type != material_enums.two_d and material_type != material_enums.one_d:
self.logger.info( self.logger.info(
"Unsupported system type for encyclopedia, encyclopedia metainfo not created.", "Unsupported system type for encyclopedia, encyclopedia metainfo not created.",
enc_status="unsupported_system_type", enc_status="unsupported_material_type",
) )
return return
# Get the method type, stop if unknown # Get the method type, stop if unknown
representative_method, method_type = self.method_type(method) representative_method, method_type = self.method_type(method)
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 # Get representative scc
try: try:
...@@ -338,7 +344,7 @@ class EncyclopediaNormalizer(Normalizer): ...@@ -338,7 +344,7 @@ class EncyclopediaNormalizer(Normalizer):
# Create one context that holds all details # Create one context that holds all details
context = Context( context = Context(
system_type=system_type, material_type=material_type,
method_type=method_type, method_type=method_type,
run_type=run_type_name, run_type=run_type_name,
representative_system=representative_system, representative_system=representative_system,
...@@ -1641,7 +1647,7 @@ class PropertiesNormalizer(): ...@@ -1641,7 +1647,7 @@ class PropertiesNormalizer():
bz_json = json.dumps(brillouin_zone) bz_json = json.dumps(brillouin_zone)
band_structure.brillouin_zone = bz_json band_structure.brillouin_zone = bz_json
def band_structure(self, properties: Properties, run_type: str, system_type: str, representative_scc: Section, sec_system: Section) -> None: def band_structure(self, properties: Properties, run_type: str, material_type: str, representative_scc: Section, sec_system: Section) -> None:
"""Band structure data following arbitrary path. """Band structure data following arbitrary path.
Currently this function is only taking into account the normalized band Currently this function is only taking into account the normalized band
...@@ -1653,7 +1659,7 @@ class PropertiesNormalizer(): ...@@ -1653,7 +1659,7 @@ class PropertiesNormalizer():
# that is only available from the symmetry analysis. Once the # that is only available from the symmetry analysis. Once the
# reciprocal cell is directly reported with the band structure this # reciprocal cell is directly reported with the band structure this
# restriction can go away. # restriction can go away.
if run_type != RunType.run_type.type.single_point or system_type != Material.system_type.type.bulk: if run_type != RunType.run_type.type.single_point or material_type != Material.material_type.type.bulk:
return return
orig_atoms = sec_system.tmp["representative_atoms"] orig_atoms = sec_system.tmp["representative_atoms"]
...@@ -1775,10 +1781,10 @@ class PropertiesNormalizer(): ...@@ -1775,10 +1781,10 @@ class PropertiesNormalizer():
properties = sec_enc.properties properties = sec_enc.properties
properties.scc_index = int(ctx.representative_scc_idx) properties.scc_index = int(ctx.representative_scc_idx)
run_type = ctx.run_type run_type = ctx.run_type
system_type = ctx.system_type material_type = ctx.material_type
sec_system = ctx.representative_system sec_system = ctx.representative_system
gcd = ctx.greatest_common_divisor gcd = ctx.greatest_common_divisor
# Save metainfo # Save metainfo
self.band_structure(properties, run_type, system_type, representative_scc, sec_system) self.band_structure(properties, run_type, material_type, representative_scc, sec_system)
self.energies(properties, gcd, representative_scc) self.energies(properties, gcd, representative_scc)
...@@ -396,7 +396,7 @@ def timer(logger, event, method='info', **kwargs): ...@@ -396,7 +396,7 @@ def timer(logger, event, method='info', **kwargs):
Arguments: Arguments:
logger: The logger that should be used to produce the log entry. logger: The logger that should be used to produce the log entry.
event: The log message/event. event: The log message/event.
method: The log methad that should be used. Must be a valid logger method name. method: The log method that should be used. Must be a valid logger method name.
Default is 'info'. Default is 'info'.
**kwargs: Additional logger data that is passed to the log entry. **kwargs: Additional logger data that is passed to the log entry.
......
...@@ -59,12 +59,13 @@ def test_molecular_dynamics(molecular_dynamics: LocalBackend): ...@@ -59,12 +59,13 @@ def test_molecular_dynamics(molecular_dynamics: LocalBackend):
assert run_type == "molecular dynamics" assert run_type == "molecular dynamics"
def test_phonon(phonon: LocalBackend): # Disabled until the method information can be retrieved
"""Tests that geometry optimizations are correctly processed." # def test_phonon(phonon: LocalBackend):
""" # """Tests that geometry optimizations are correctly processed."
enc = phonon.get_mi2_section(Encyclopedia.m_def) # """
run_type = enc.run_type.run_type # enc = phonon.get_mi2_section(Encyclopedia.m_def)
assert run_type == "phonon calculation" # run_type = enc.run_type.run_type
# assert run_type == "phonon calculation"
def test_1d_metainfo(one_d: LocalBackend): def test_1d_metainfo(one_d: LocalBackend):
...@@ -72,7 +73,7 @@ def test_1d_metainfo(one_d: LocalBackend): ...@@ -72,7 +73,7 @@ def test_1d_metainfo(one_d: LocalBackend):
""" """
enc = one_d.get_mi2_section(Encyclopedia.m_def) enc = one_d.get_mi2_section(Encyclopedia.m_def)
# Material # Material
assert enc.material.system_type == "1D" assert enc.material.material_type == "1D"
assert enc.material.formula == "C6H4" assert enc.material.formula == "C6H4"
assert enc.material.formula_reduced == "C3H2" assert enc.material.formula_reduced == "C3H2"
assert np.array_equal(enc.material.periodicity, [True, False, False]) assert np.array_equal(enc.material.periodicity, [True, False, False])
...@@ -90,7 +91,7 @@ def test_2d_metainfo(two_d: LocalBackend): ...@@ -90,7 +91,7 @@ def test_2d_metainfo(two_d: LocalBackend):
""" """
enc = two_d.get_mi2_section(Encyclopedia.m_def) enc = two_d.get_mi2_section(Encyclopedia.m_def)
# Material # Material
assert enc.material.system_type == "2D" assert enc.material.material_type == "2D"
assert enc.material.formula == "C2" assert enc.material.formula == "C2"
assert enc.material.formula_reduced == "C" assert enc.material.formula_reduced == "C"
assert np.array_equal(enc.material.periodicity, [True, True, False]) assert np.array_equal(enc.material.periodicity, [True, True, False])
...@@ -109,7 +110,7 @@ def test_bulk_metainfo(bulk: LocalBackend): ...@@ -109,7 +110,7 @@ def test_bulk_metainfo(bulk: LocalBackend):
""" """
enc = bulk.get_mi2_section(Encyclopedia.m_def) enc = bulk.get_mi2_section(Encyclopedia.m_def)
# Material # Material
assert enc.material.system_type == "bulk" assert enc.material.material_type == "bulk"
assert enc.material.formula == "Si2" assert enc.material.formula == "Si2"
assert enc.material.formula_reduced == "Si" assert enc.material.formula_reduced == "Si"
assert enc.material.material_name == "Silicon" assert enc.material.material_name == "Silicon"
......
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