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fix: raise="ignore" default let to invalid prototypes being returned.
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@CompRhys
CompRhys committed Jul 19, 2024
1 parent ebc1f6e commit 94fba8c
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Showing 3 changed files with 239 additions and 91 deletions.
175 changes: 85 additions & 90 deletions aviary/wren/utils.py
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,6 @@
from os.path import abspath, dirname, join
from shutil import which
from string import ascii_uppercase, digits
from typing import Literal

from monty.fractions import gcd
from pymatgen.core import Composition, Structure
Expand Down Expand Up @@ -97,7 +96,7 @@ def count_values_for_wyckoff(
def get_aflow_label_from_aflow(
struct: Structure,
aflow_executable: str | None = None,
errors: Literal["raise", "annotate", "ignore"] = "raise",
raise_errors: bool = False,
) -> str:
"""Get Aflow prototype label for a pymatgen Structure. Make sure you're running a
recent version of the aflow CLI as there's been several breaking changes. This code
Expand All @@ -111,16 +110,12 @@ def get_aflow_label_from_aflow(
Args:
struct (Structure): pymatgen Structure
aflow_executable (str): path to aflow executable. Defaults to which("aflow").
errors ('raise' | 'annotate' | 'ignore']): How to handle errors. 'raise' and
'ignore' are self-explanatory. 'annotate' prefixes problematic Aflow labels
with 'invalid <reason>: '.
Raises:
ValueError: if errors='raise' and Wyckoff multiplicities do not add up to
expected composition.
raise_errors (bool): Whether to raise errors or annotate them. Defaults to
False.
Returns:
str: Aflow prototype label
str: AFLOW prototype label or explanation of failure if symmetry detection
failed and raise_errors is False.
"""
if aflow_executable is None:
aflow_executable = which("aflow")
Expand All @@ -144,12 +139,13 @@ def get_aflow_label_from_aflow(
aflow_proto = json.loads(output.stdout)

aflow_label = aflow_proto["aflow_prototype_label"]
chem_sys = struct.composition.chemical_system
full_label = f"{aflow_label}:{chem_sys}"

# check that multiplicities satisfy original composition
_, _, spg_num, *wyckoff_letters = aflow_label.split("_")
elements = sorted(el.symbol for el in struct.composition)
elem_dict = {}
for elem, wyk_letters_per_elem in zip(elements, wyckoff_letters):
for elem, wyk_letters_per_elem in zip(chem_sys.split("-"), wyckoff_letters):
# normalize Wyckoff letters to start with 1 if missing digit
wyk_letters_normalized = re.sub(
RE_WYCKOFF_NO_PREFIX, RE_SUBST_ONE_PREFIX, wyk_letters_per_elem
Expand All @@ -162,91 +158,35 @@ def get_aflow_label_from_aflow(
wyckoff_multiplicity_dict,
)

full_label = f"{aflow_label}:{'-'.join(elements)}"

observed_formula = Composition(elem_dict).reduced_formula
expected_formula = struct.composition.reduced_formula
if observed_formula != expected_formula:
if errors == "raise":
raise ValueError(
f"invalid WP multiplicities - {aflow_label}, expected "
f"{observed_formula} to be {expected_formula}"
)
if errors == "annotate":
return f"invalid multiplicities: {full_label}"

return full_label


def get_aflow_label_from_spglib(
struct: Structure,
errors: Literal["raise", "annotate", "ignore"] = "ignore",
init_symprec: float = 0.1,
fallback_symprec: float = 1e-5,
) -> str | None:
"""Get AFLOW prototype label for pymatgen Structure.
Args:
struct (Structure): pymatgen Structure object.
errors ('raise' | 'annotate' | 'ignore']): How to handle errors. 'raise' and
'ignore' are self-explanatory. 'annotate' prefixes problematic Aflow labels
with 'invalid <reason>: '.
init_symprec (float): Initial symmetry precision for spglib. Defaults to 0.1.
fallback_symprec (float): Fallback symmetry precision for spglib if first
symmetry detection failed. Defaults to 1e-5.
Returns:
str: AFLOW prototype label or None if errors='ignore' and symmetry detection
failed.
"""
try:
spg_analyzer = SpacegroupAnalyzer(
struct, symprec=init_symprec, angle_tolerance=5
)
aflow_label_with_chemsys = get_aflow_label_from_spg_analyzer(
spg_analyzer, errors
err_msg = (
f"Invalid WP multiplicities - {full_label}, expected "
f"{observed_formula} to be {expected_formula}"
)
if raise_errors:
raise ValueError(err_msg)

# try again with refined structure if it initially fails
# NOTE structures with magmoms fail unless all have same magnetic moment
if "invalid" in aflow_label_with_chemsys:
spg_analyzer = SpacegroupAnalyzer(
spg_analyzer.get_refined_structure(),
symprec=fallback_symprec,
angle_tolerance=-1,
)
aflow_label_with_chemsys = get_aflow_label_from_spg_analyzer(
spg_analyzer, errors
)
return aflow_label_with_chemsys
return err_msg

except ValueError as exc:
if errors == "annotate":
return f"invalid spglib: {exc}"
raise # we only get here if errors == "raise"
return full_label


def get_aflow_label_from_spg_analyzer(
spg_analyzer: SpacegroupAnalyzer,
errors: Literal["raise", "annotate", "ignore"] = "raise",
raise_errors: bool = False,
) -> str:
"""Get AFLOW prototype label for pymatgen SpacegroupAnalyzer.
Args:
spg_analyzer (SpacegroupAnalyzer): pymatgen SpacegroupAnalyzer object.
errors ('raise' | 'annotate' | 'ignore']): How to handle errors. 'raise' and
'ignore' are self-explanatory. 'annotate' prefixes problematic Aflow labels
with 'invalid <reason>: '.
Raises:
ValueError: if errors='raise' and Wyckoff multiplicities do not add up to
expected composition.
Raises:
ValueError: if Wyckoff multiplicities do not add up to expected composition.
raise_errors (bool): Whether to raise errors or annotate them. Defaults to
False.
Returns:
str: AFLOW prototype labels
str: AFLOW prototype label or explanation of failure if symmetry detection
failed and raise_errors is False.
"""
spg_num = spg_analyzer.get_space_group_number()
sym_struct = spg_analyzer.get_symmetrized_structure()
Expand Down Expand Up @@ -288,22 +228,77 @@ def get_aflow_label_from_spg_analyzer(
prototype_form = prototype_formula(sym_struct.composition)

chem_sys = sym_struct.composition.chemical_system
aflow_label_with_chemsys = (
f"{prototype_form}_{pearson_symbol}_{spg_num}_{canonical}:{chem_sys}"
)
full_label = f"{prototype_form}_{pearson_symbol}_{spg_num}_{canonical}:{chem_sys}"

observed_formula = Composition(elem_dict).reduced_formula
expected_formula = sym_struct.composition.reduced_formula
if observed_formula != expected_formula:
if errors == "raise":
raise ValueError(
f"Invalid WP multiplicities - {aflow_label_with_chemsys}, expected "
f"{observed_formula} to be {expected_formula}"
err_msg = (
f"Invalid WP multiplicities - {full_label}, expected "
f"{observed_formula} to be {expected_formula}"
)
if raise_errors:
raise ValueError(err_msg)

return err_msg

return full_label


def get_aflow_label_from_spglib(
struct: Structure,
raise_errors: bool = False,
init_symprec: float = 0.1,
fallback_symprec: float | None = 1e-5,
) -> str | None:
"""Get AFLOW prototype label for pymatgen Structure.
Args:
struct (Structure): pymatgen Structure object.
raise_errors (bool): Whether to raise errors or annotate them. Defaults to
False.
init_symprec (float): Initial symmetry precision for spglib. Defaults to 0.1.
fallback_symprec (float): Fallback symmetry precision for spglib if first
symmetry detection failed. Defaults to 1e-5.
Returns:
str: AFLOW prototype label or explanation of failure if symmetry detection
failed and raise_errors is False.
"""
attempt_to_recover = False
try:
spg_analyzer = SpacegroupAnalyzer(
struct, symprec=init_symprec, angle_tolerance=5
)
try:
aflow_label_with_chemsys = get_aflow_label_from_spg_analyzer(
spg_analyzer, raise_errors
)
if errors == "annotate":
return f"invalid multiplicities: {aflow_label_with_chemsys}"

return aflow_label_with_chemsys
if ("Invalid" in aflow_label_with_chemsys) and fallback_symprec is not None:
attempt_to_recover = True
except ValueError as exc:
if fallback_symprec is None:
raise exc
attempt_to_recover = True

# try again with refined structure if it initially fails
# NOTE structures with magmoms fail unless all have same magnetic moment
if attempt_to_recover:
spg_analyzer = SpacegroupAnalyzer(
spg_analyzer.get_refined_structure(),
symprec=fallback_symprec,
angle_tolerance=-1,
)
aflow_label_with_chemsys = get_aflow_label_from_spg_analyzer(
spg_analyzer, raise_errors
)
return aflow_label_with_chemsys

except ValueError as exc:
if not raise_errors:
return str(exc)
raise


def canonicalize_elem_wyks(elem_wyks: str, spg_num: int | str) -> str:
Expand Down
107 changes: 107 additions & 0 deletions tests/data/U2Pa4Tc6.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,107 @@
{
"@module": "pymatgen.core.structure",
"@class": "Structure",
"charge": 0,
"lattice": {
"matrix": [
[5.989671, 0.00015953, 7.795e-05],
[0.00021958, 8.25008569, -0.03720131],
[-2.99487801, -4.14847393, 5.20632921]
],
"pbc": [true, true, true],
"a": 5.9896710026317,
"b": 8.250169566622487,
"c": 7.299657121096198,
"alpha": 124.85712587044729,
"beta": 114.22257511338135,
"gamma": 89.99695241219993,
"volume": 256.349880211745
},
"properties": {},
"sites": [
{
"species": [{"element": "U", "occu": 1}],
"abc": [0.49997316, 0.25000333, 0.50000537],
"xyz": [1.4972745454666476, -0.011630586301441285, 2.5939310845153174],
"properties": {},
"label": "U"
},
{
"species": [{"element": "U", "occu": 1}],
"abc": [0.50002684, 0.74999667, 0.49999463],
"xyz": [1.497738024533353, 4.113401876301443, 2.5752747654846826],
"properties": {},
"label": "U"
},
{
"species": [{"element": "Pa", "occu": 1}],
"abc": [0.16664895, 0.91662717, 0.83327202],
"xyz": [-1.4971743930568415, 4.105472032220753, 4.304201716381764],
"properties": {},
"label": "Pa"
},
{
"species": [{"element": "Pa", "occu": 1}],
"abc": [0.16662875, 0.41663202, 0.83327108],
"xyz": [-1.4974023581607492, -0.019526903520663105, 4.322797295431363],
"properties": {},
"label": "Pa"
},
{
"species": [{"element": "Pa", "occu": 1}],
"abc": [0.83337125, 0.58336798, 0.16672892],
"xyz": [4.492414928160749, 4.121298193520663, 0.8464085545686368],
"properties": {},
"label": "Pa"
},
{
"species": [{"element": "Pa", "occu": 1}],
"abc": [0.83335105, 0.08337283, 0.16672798],
"xyz": [4.4921869630568425, -0.003700742220752091, 0.8650041336182359],
"properties": {},
"label": "Pa"
},
{
"species": [{"element": "Tc", "occu": 1}],
"abc": [5.1e-07, 0.74999811, 0.99999918],
"xyz": [-2.994707814882828, 2.03907814666803, 5.178424028660278],
"properties": {},
"label": "Tc"
},
{
"species": [{"element": "Tc", "occu": 1}],
"abc": [0.99999949, 0.25000189, 8.2e-07],
"xyz": [5.989720384882829, 2.062693143331971, -0.0092181786602782],
"properties": {},
"label": "Tc"
},
{
"species": [{"element": "Tc", "occu": 1}],
"abc": [0.49999907, 0.74998284, 0.99999871],
"xyz": [0.00012046423061040414, 2.0390338824125678, 5.1784611246373045],
"properties": {},
"label": "Tc"
},
{
"species": [{"element": "Tc", "occu": 1}],
"abc": [0.0, 0.0, 0.5],
"xyz": [-1.497439005, -2.074236965, 2.603164605],
"properties": {},
"label": "Tc"
},
{
"species": [{"element": "Tc", "occu": 1}],
"abc": [0.0, 0.5, 0.5],
"xyz": [-1.497329215, 2.0508058800000004, 2.5845639499999997],
"properties": {},
"label": "Tc"
},
{
"species": [{"element": "Tc", "occu": 1}],
"abc": [0.50000093, 0.25001716, 1.29e-06],
"xyz": [2.9948921057693902, 2.062737407587434, -0.0092552746373052],
"properties": {},
"label": "Tc"
}
]
}
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