Pysimxrd 1.0.0

Physical simulation of powder X-ray diffraction patterns

Pysimxrd

Physical simulation of powder X-ray diffraction patterns.

Pysimxrd provides high-level utilities for generating simulated powder XRD profiles from crystal structures stored in ASE database files. It includes a pymatgen-backed simulation path and a WPEM path for diffraction conditions, systematic extinction, multiplicity, structure factors, peak broadening, background, and noise.

Bin Cao, PhD of HKUST(Guangzhou), https://bin-cao.github.io
URL: https://github.com/Bin-Cao/SimXRD

Features

• Simulate powder XRD patterns from ASE database entries.
• Support 2-theta output and d-spacing output.
• Include peak broadening from crystallite size and instrumental effects.
• Add preferred-orientation variation, thermal vibration, background, and noise.
• Provide a WPEM path with symmetry-based extinction and multiplicity handling.
• Support optional random lattice deformation for data augmentation.

Installation

Install from PyPI:

pip install Pysimxrd

Install from the project root:

pip install .

For editable development:

pip install -e .

Quick Start

from ase.db import connect
from Pysimxrd import generator

database = connect("sim/demo_mp.db")
x, y = generator.parser(database, entry_id=1)

print(len(x), len(y))
print(x[:5], y[:5])

Use the WPEM simulation path:

from ase.db import connect
from Pysimxrd import generator

database = connect("sim/demo_mp.db")
x, y = generator.parser(database, entry_id=1, sim_model="WPEM")

Use d-spacing output instead of 2-theta:

x_d, intensity = generator.parser(
    database,
    entry_id=1,
    sim_model="WPEM",
    xrd="real",
)

Main API

Pysimxrd.generator.parser

parser(
    database,
    entry_id,
    grainsize=20,
    prefect_orientation=[0.1, 0.1],
    thermo_vibration=0.1,
    zero_shift=0.1,
    dis_detector2sample=500,
    half_height_slit_detector=5,
    half_height_sample=2.5,
    deformation=False,
    sim_model=None,
    xrd="reciprocal",
    background_order=6,
    background_ratio=0.05,
    mixture_noise_ratio=0.02,
    lattice_extinction_ratio=0.01,
    lattice_torsion_ratio=0.01,
    verbose=False,
)

Important arguments:

• database: an open ASE database connection.
• entry_id: row id in the ASE database.
• sim_model: set to "WPEM" for the WPEM simulation path; use None for the pymatgen-backed default path.
• xrd: "reciprocal" returns 2-theta; "real" returns d-spacing.
• deformation: applies random lattice deformation for peak-position augmentation.
• lattice_extinction_ratio: random stretching/compression ratio used when deformation=True.
• lattice_torsion_ratio: random shear ratio used when deformation=True.
• verbose: prints package and run metadata before simulation.

Returns:

x, y

where x is the simulated x-axis and y is the normalized intensity profile.

WPEM Deformation Behavior

For sim_model="WPEM" with deformation=True, symmetry information is taken from the undeformed conventional cell:

• space group
• centering symbol
• crystal system
• atom coordinates

The deformed lattice constants are then used for peak position and d-spacing calculation. This keeps the symmetry/extinction logic tied to the original crystal while allowing peak shifts from lattice perturbation.

Package Layout

src/Pysimxrd/
  __init__.py
  generator.py
  CGCNN_atom_emb.json
  utils/
    MatgenKit.py
    WPEMsim.py
    funs.py

Development Checks

Run a simple import and smoke test from the repository root:

python -c "from ase.db import connect; from Pysimxrd import generator; db=connect('sim/demo_mp.db'); x,y=generator.parser(db,1); print(len(x), len(y))"

Build a source distribution and wheel:

python setup.py sdist bdist_wheel

Citation

If this package or the associated SimXRD dataset is useful in your work, please cite the related project and repository:

SimXRD / Pysimxrd
Cao Bin
https://github.com/Bin-Cao/SimXRD

License

This project is released under the MIT License. See LICENSE for details.