Skip to content

Commit

Permalink
doc: adopt protostructure naming
Browse files Browse the repository at this point in the history
  • Loading branch information
@CompRhys
CompRhys committed Jul 18, 2024
1 parent 3e06cd8 commit ae65204
Show file tree
Hide file tree
Showing 8 changed files with 152 additions and 124 deletions.
152 changes: 77 additions & 75 deletions aviary/wren/utils.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -94,14 +94,15 @@ def count_values_for_wyckoff(
return sum(int(n) * lookup_dict[spg][k] for n, k in zip(multiplicity, wyckoff))


def get_aflow_label_from_aflow(
def get_protostructure_label_from_aflow(
struct: Structure,
aflow_executable: str | None = None,
errors: Literal["raise", "annotate", "ignore"] = "raise",
) -> str:
"""Get Aflow prototype label for a pymatgen Structure. Make sure you're running a
"""Get protostructure 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
was tested under v3.2.12.
was tested under v3.2.12. The protostructure label is constructed as
`aflow_label:chemsys`.
Install guide: https://aflow.org/install-aflow/#install_aflow
http://aflow.org/install-aflow/install-aflow.sh -o install-aflow.sh
Expand All @@ -112,15 +113,15 @@ def get_aflow_label_from_aflow(
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
'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.
Returns:
str: Aflow prototype label
str | None: protostructure_label which is constructed as `aflow_label:chemsys`.
"""
if aflow_executable is None:
aflow_executable = which("aflow")
Expand Down Expand Up @@ -162,80 +163,80 @@ def get_aflow_label_from_aflow(
wyckoff_multiplicity_dict,
)

full_label = f"{aflow_label}:{'-'.join(elements)}"
protostructure_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}"
f"Invalid WP multiplicities - {aflow_label}, expected "
f"{observed_formula} to be {expected_formula}."
)
if errors == "annotate":
return f"invalid multiplicities: {full_label}"
return f"Invalid multiplicities: {protostructure_label}"

return full_label
return protostructure_label


def get_aflow_label_from_spglib(
def get_protostructure_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.
) -> str:
"""Get protostructure 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
'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.
str: protostructure_label which is constructed as `aflow_label:chemsys` or a
a str explaining the reason for failure if errors = "annotate".
"""
try:
spg_analyzer = SpacegroupAnalyzer(
struct, symprec=init_symprec, angle_tolerance=5
)
aflow_label_with_chemsys = get_aflow_label_from_spg_analyzer(
protostructure_label = get_protostructure_label_from_spg_analyzer(
spg_analyzer, errors
)

# 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:
if "invalid" in protostructure_label:
spg_analyzer = SpacegroupAnalyzer(
spg_analyzer.get_refined_structure(),
symprec=fallback_symprec,
angle_tolerance=-1,
)
aflow_label_with_chemsys = get_aflow_label_from_spg_analyzer(
protostructure_label = get_protostructure_label_from_spg_analyzer(
spg_analyzer, errors
)
return aflow_label_with_chemsys
return protostructure_label

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


def get_aflow_label_from_spg_analyzer(
def get_protostructure_label_from_spg_analyzer(
spg_analyzer: SpacegroupAnalyzer,
errors: Literal["raise", "annotate", "ignore"] = "raise",
) -> str:
"""Get AFLOW prototype label for pymatgen SpacegroupAnalyzer.
"""Get protostructure 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
'ignore' are self-explanatory. 'annotate' prefixes problematic AFLOW labels
with 'invalid <reason>: '.
Raises:
Expand All @@ -246,7 +247,7 @@ def get_aflow_label_from_spg_analyzer(
ValueError: if Wyckoff multiplicities do not add up to expected composition.
Returns:
str: AFLOW prototype labels
str: protostructure_label which is constructed as `aflow_label:chemsys`.
"""
spg_num = spg_analyzer.get_space_group_number()
sym_struct = spg_analyzer.get_symmetrized_structure()
Expand Down Expand Up @@ -288,7 +289,7 @@ 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 = (
protostructure_label = (
f"{prototype_form}_{pearson_symbol}_{spg_num}_{canonical}:{chem_sys}"
)

Expand All @@ -297,13 +298,13 @@ def get_aflow_label_from_spg_analyzer(
if observed_formula != expected_formula:
if errors == "raise":
raise ValueError(
f"Invalid WP multiplicities - {aflow_label_with_chemsys}, expected "
f"Invalid WP multiplicities - {protostructure_label}, expected "
f"{observed_formula} to be {expected_formula}"
)
if errors == "annotate":
return f"invalid multiplicities: {aflow_label_with_chemsys}"
return f"invalid multiplicities: {protostructure_label}"

return aflow_label_with_chemsys
return protostructure_label


def canonicalize_elem_wyks(elem_wyks: str, spg_num: int | str) -> str:
Expand Down Expand Up @@ -336,7 +337,7 @@ def canonicalize_elem_wyks(elem_wyks: str, spg_num: int | str) -> str:


def sort_and_score_wyks(wyks: str) -> tuple[str, int]:
"""Determines the order or Wyckoff positions when canonicalizing Aflow labels.
"""Determines the order or Wyckoff positions when canonicalizing AFLOW labels.
Args:
wyks (str): Wyckoff position substring from AFLOW-style prototype label
Expand Down Expand Up @@ -413,16 +414,16 @@ def get_anom_formula_from_prototype_formula(prototype_formula: str) -> str:
)


def count_wyckoff_positions(aflow_label: str) -> int:
"""Count number of Wyckoff positions in Wyckoff representation.
def count_wyckoff_positions(protostructure_label: str) -> int:
"""Count number of Wyckoff positions in protostructure_label.
Args:
aflow_label (str): AFLOW-style prototype label with appended chemical system
protostructure_label (str): label constructed as `aflow_label:chemsys`
Returns:
int: number of distinct Wyckoff positions
"""
aflow_label, _ = aflow_label.split(":") # remove chemical system
aflow_label, _ = protostructure_label.split(":") # remove chemical system
# discard prototype formula and spg symbol and spg number
wyk_letters = aflow_label.split("_", maxsplit=3)[-1]
# throw Wyckoff positions for all elements together
Expand All @@ -433,20 +434,20 @@ def count_wyckoff_positions(aflow_label: str) -> int:
return sum(1 if len(x) == 0 else int(x) for x in wyk_list)


def count_crystal_dof(aflow_label: str) -> int:
"""Count number of free parameters in coarse-grained Wyckoff representation: how
many degrees of freedom would remain to optimize during a crystal structure
relaxation.
def count_crystal_dof(protostructure_label: str) -> int:
"""Count number of free parameters in coarse-grained protostructure_label
representation: how many degrees of freedom would remain to optimize during
a crystal structure relaxation.
Args:
aflow_label (str): AFLOW-style prototype label with appended chemical system
protostructure_label (str): label constructed as `aflow_label:chemsys`
Returns:
int: Number of free-parameters in given prototype
"""
n_params = 0

aflow_label, _ = aflow_label.split(":") # chop off chemical system
aflow_label, _ = protostructure_label.split(":") # chop off chemical system
_, pearson, spg, *wyks = aflow_label.split("_")

n_params += cry_param_dict[pearson[0]]
Expand All @@ -467,18 +468,18 @@ def count_crystal_dof(aflow_label: str) -> int:
return n_params


def count_crystal_sites(aflow_label: str) -> int:
"""Count number of sites from Wyckoff representation.
def count_crystal_sites(protostructure_label: str) -> int:
"""Count number of sites from protostructure_label.
Args:
aflow_label (str): AFLOW-style prototype label with appended chemical system
protostructure_label (str): label constructed as `aflow_label:chemsys`
Returns:
int: Number of free-parameters in given prototype
"""
n_params = 0

aflow_label, _ = aflow_label.split(":") # chop off chemical system
aflow_label, _ = protostructure_label.split(":") # chop off chemical system
_, pearson, spg, *wyks = aflow_label.split("_")

for wyk_letters_per_elem in wyks:
Expand All @@ -497,16 +498,25 @@ def count_crystal_sites(aflow_label: str) -> int:
return int(n_params)


def get_isopointal_proto_from_aflow(aflow_label: str) -> str:
"""Get a canonicalized string for the prototype.
def count_distinct_wyckoff_letters(protostructure_label: str) -> int:
"""Count number of distinct Wyckoff letters in protostructure_label."""
aflow_label, _ = protostructure_label.split(":") # drop chemical system
_, _, _, wyckoff_letters = aflow_label.split("_", 3) # drop prototype, Pearson, spg
wyckoff_letters = wyckoff_letters.translate(remove_digits).replace("_", "")
return len(set(wyckoff_letters)) # number of distinct Wyckoff letters


def get_prototype_from_protostructure(protostructure_label: str) -> str:
"""Get a canonicalized string for the prototype. This prototype should be
the same for all isopointal protostructures.
Args:
aflow_label (str): AFLOW-style prototype label with appended chemical system
protostructure_label (str): label constructed as `aflow_label:chemsys`
Returns:
str: Canonicalized AFLOW-style prototype label with appended chemical system
str: Canonicalized AFLOW-style prototype label
"""
aflow_label, _ = aflow_label.split(":")
aflow_label, _ = protostructure_label.split(":")
anonymous_formula, pearson, spg, *wyckoffs = aflow_label.split("_")

anonymous_formula = re.sub(
Expand Down Expand Up @@ -614,26 +624,20 @@ def backtrack(translation, index):
return backtrack({}, 0)


def get_aflow_strs_from_iso_and_composition(
isopointal_proto: str, composition: Composition
def get_protostructures_from_aflow_label_and_composition(
aflow_label: str, composition: Composition
) -> list[str]:
"""Get a canonicalized string for the prototype.
Args:
isopointal_proto (str): AFLOW-style Canonicalized prototype label
aflow_label (str): AFLOW-style prototype label
composition (Composition): pymatgen Composition object
Returns:
list[str]: List of possible AFLOW-style prototype labels with appended
chemical systems that can be generated from combinations of the
input isopointal_proto and composition.
list[str]: List of possible protostructure labels that can be generated
from combinations of the input aflow_label and composition.
"""
if not isinstance(isopointal_proto, str):
raise TypeError(
f"Invalid isopointal_proto: {isopointal_proto} ({type(isopointal_proto)})"
)

anonymous_formula, pearson, spg, *wyckoffs = isopointal_proto.split("_")
anonymous_formula, pearson, spg, *wyckoffs = aflow_label.split("_")

ele_amt_dict = composition.get_el_amt_dict()
proto_formula = prototype_formula(composition)
Expand All @@ -643,7 +647,7 @@ def get_aflow_strs_from_iso_and_composition(
anom_ele_to_wyk = dict(zip(anom_amt_dict.keys(), wyckoffs))
anonymous_formula = RE_ANONYMOUS.sub(RE_SUBST_ONE_PREFIX, anonymous_formula)

result = []
protostructures = []
for t in translations:
wyckoff_part = "_".join(
RE_WYCKOFF.sub(RE_SUBST_ONE_PREFIX, anom_ele_to_wyk[t[elem]])
Expand All @@ -652,32 +656,30 @@ def get_aflow_strs_from_iso_and_composition(
canonicalized_wyckoff = canonicalize_elem_wyks(wyckoff_part, spg)
chemical_system = "-".join(sorted(t.keys()))

aflow_str = (
protostructure_label = (
f"{proto_formula}_{pearson}_{spg}_{canonicalized_wyckoff}:{chemical_system}"
)
result.append(aflow_str)

return result

protostructures.append(protostructure_label)

def count_distinct_wyckoff_letters(aflow_str: str) -> int:
"""Count number of distinct Wyckoff letters in Wyckoff representation."""
aflow_str, _ = aflow_str.split(":") # drop chemical system
_, _, _, wyckoff_letters = aflow_str.split("_", 3) # drop prototype, Pearson, spg
wyckoff_letters = wyckoff_letters.translate(remove_digits).replace("_", "")
return len(set(wyckoff_letters)) # number of distinct Wyckoff letters
return protostructures


def get_random_structure_for_protostructure(protostructure: str, **kwargs) -> Structure:
def get_random_structure_for_protostructure(
protostructure_label: str, **kwargs
) -> Structure:
"""Generate a random structure for a given prototype structure.
NOTE that due to the random nature of the generation, the output structure
may be higher symmetry than the requested prototype structure.
Args:
protostructure_label (str): label constructed as `aflow_label:chemsys`
**kwargs: Keyword arguments to pass to pyxtal().from_random()
"""
if pyxtal is None:
raise ImportError("pyxtal is required for this function")

aflow_label, chemsys = protostructure.split(":")
aflow_label, chemsys = protostructure_label.split(":")
_, _, spg, *wyckoffs = aflow_label.split("_")

wyckoffs = [re.sub(RE_WYCKOFF_NO_PREFIX, RE_SUBST_ONE_PREFIX, w) for w in wyckoffs]
Expand Down
7 changes: 5 additions & 2 deletions examples/inputs/poscar_to_df.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,10 @@
from pymatgen.core import Composition, Structure
from tqdm import tqdm

from aviary.wren.utils import count_wyckoff_positions, get_aflow_label_from_spglib
from aviary.wren.utils import (
count_wyckoff_positions,
get_protostructure_label_from_spglib,
)

tqdm.pandas() # prime progress_map functionality

Expand Down Expand Up @@ -62,7 +65,7 @@
print(f"Number of points in dataset: {len(df)}")

# takes ~ 15mins
df["wyckoff"] = df.final_structure.progress_map(get_aflow_label_from_spglib)
df["wyckoff"] = df.final_structure.progress_map(get_protostructure_label_from_spglib)

# lattice, sites = zip(*df.final_structure.progress_map(get_cgcnn_input))

Expand Down
Loading

0 comments on commit ae65204

Please sign in to comment.