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from typing import Dict, Optional
import numpy as np
from pydantic import model_validator, Field
from pymatgen.analysis.diffraction.xrd import (
WAVELENGTHS,
DiffractionPattern,
XRDCalculator,
)
from pymatgen.core import Structure
from pymatgen.core.periodic_table import Element
from emmet.core.mpid import MPID
from emmet.core.spectrum import SpectrumDoc
from emmet.core.utils import ValueEnum
class Edge(ValueEnum):
K_Alpha = "Ka"
K_Alpha1 = "Ka1"
K_Alpha2 = "Ka2"
K_Beta = "Kb"
K_Beta1 = "Kb1"
K_Beta2 = "Kb2"
class XRDDoc(SpectrumDoc):
"""
Document describing a XRD Diffraction Pattern
"""
spectrum_name: str = "XRD"
spectrum: DiffractionPattern
min_two_theta: float
max_two_theta: float
wavelength: float = Field(..., description="Wavelength for the diffraction source.")
target: Optional[Element] = Field(
None, description="Target element for the diffraction source."
)
edge: Optional[Edge] = Field(
None, description="Atomic edge for the diffraction source."
)
@model_validator(mode="before")
@classmethod
def get_target_and_edge(cls, values: Dict):
print("Validations")
# Only do this if neither target not edge is defined
if "target" not in values and "edge" not in values:
try:
pymatgen_wavelength = next(
k
for k, v in WAVELENGTHS.items()
if np.allclose(values["wavelength"], v)
)
values["target"] = pymatgen_wavelength[:2]
values["edge"] = pymatgen_wavelength[2:]
except Exception:
return values
return values
@classmethod
def from_structure( # type: ignore[override]
cls,
material_id: MPID,
spectrum_id: str,
structure: Structure,
wavelength: float,
min_two_theta=0,
max_two_theta=180,
symprec=0.1,
**kwargs,
) -> "XRDDoc":
calc = XRDCalculator(wavelength=wavelength, symprec=symprec)
pattern = calc.get_pattern(
structure, two_theta_range=(min_two_theta, max_two_theta)
)
return super().from_structure(
material_id=material_id,
spectrum_id=spectrum_id,
meta_structure=structure,
spectrum=pattern,
wavelength=wavelength,
min_two_theta=min_two_theta,
max_two_theta=max_two_theta,
**kwargs,
)
@classmethod
def from_target(
cls,
material_id: MPID,
structure: Structure,
target: Element,
edge: Edge,
min_two_theta=0,
max_two_theta=180,
symprec=0.1,
**kwargs,
) -> "XRDDoc":
if f"{target}{edge}" not in WAVELENGTHS:
raise ValueError(f"{target}{edge} not in pymatgen wavelenghts dictionarty")
wavelength = WAVELENGTHS[f"{target}{edge}"]
spectrum_id = f"{material_id}-{target}{edge}"
return cls.from_structure(
material_id=material_id,
spectrum_id=spectrum_id,
structure=structure,
wavelength=wavelength,
target=target,
edge=edge,
min_two_theta=min_two_theta,
max_two_theta=max_two_theta,
**kwargs,
)
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