moyopy

0.7.9 · active · verified Thu Apr 16

moyopy is a Python binding for the moyo library, a fast and robust crystal symmetry finder written in Rust. It provides functionalities for crystallographic analysis, including space group determination and primitive cell finding. The library is actively maintained, with a current version of 0.7.9, and requires Python 3.10 or newer. New releases appear with an active cadence.

Common errors

```
ModuleNotFoundError: No module named 'moyopy'
```
cause The moyopy library is not installed in the current Python environment.

fix Run `pip install moyopy` to install the package.
```
AttributeError: module 'moyopy' has no attribute 'Moyo' (or 'SpaceGroupAnalyzer')
```
cause Attempting to import a non-existent class or accessing functionality through an incorrect path. `moyopy` directly exposes functions like `get_symmetry_dataset` at its top level, rather than through a main class like `Moyo` or `SpaceGroupAnalyzer` as seen in other libraries.

fix Import the relevant function directly, e.g., `from moyopy import get_symmetry_dataset`.
```
ValueError: Invalid cell format. The cell must be a tuple of (lattice, positions, numbers).
```
cause The input structure `cell` passed to `get_symmetry_dataset` (or similar functions) does not adhere to the expected `(lattice, positions, numbers)` tuple format.

fix Ensure that `cell` is a tuple where `lattice` is a 3x3 array (float), `positions` is an Nx3 array (float, fractional coordinates), and `numbers` is a list of N integers.

Warnings

breaking moyopy versions 0.6.1 and later dropped support for Python 3.9. Users on Python 3.9 must upgrade their Python environment to 3.10 or newer.
Fix: Upgrade Python to 3.10 or a later supported version (e.g., `pyenv install 3.10.10`, `conda install python=3.10`).
breaking The default setting for crystal standardization in moyo-core (which moyopy binds to) changed to International Tables for Crystallography (ITA) standard. This may affect the output of standardized cells compared to previous versions.
Fix: Review your code for any assumptions about the standardization output. If specific standardization behavior is required, consult moyopy documentation for available flags or methods to control standardization.
gotcha There can be differences in lattice vector ordering between the underlying Rust moyo-core and its Python bindings (moyopy), which may lead to discrepancies in `prim_std_cell.basis` results compared to other symmetry libraries like spglib. This often necessitates additional explicit ordering constraints for consistent results in downstream applications.
Fix: If relying on `prim_std_cell.basis` or comparing results with `spglib`, implement explicit checks or re-ordering of lattice vectors. Consider applying constraints like a < b < c for cell parameters if needed for a specific standardization convention.

Install

pip install moyopy Basic installation
pip install moyopy[interface] With Pymatgen/ASE interfaces

Imports

get_symmetry_dataset
wrong:
```
import moyopy.moyo
```
correct:
```
from moyopy import get_symmetry_dataset
```
The primary symmetry analysis function `get_symmetry_dataset` is exposed directly under the top-level `moyopy` package, not in a nested `moyo` submodule.

Quickstart

This quickstart demonstrates how to define a simple crystal structure and use `moyopy.get_symmetry_dataset` to obtain its symmetry properties, including the space group number, international symbol, and Hall symbol. The structure is provided as a tuple `(lattice, positions, numbers)`.

import numpy as np
from moyopy import get_symmetry_dataset

# Define crystal structure (lattice, positions, numbers)
# Example: Diamond cubic silicon
lattice = np.array([
    [0, 2.735, 2.735],
    [2.735, 0, 2.735],
    [2.735, 2.735, 0]
])
positions = np.array([
    [0.0, 0.0, 0.0],
    [0.25, 0.25, 0.25]
])
numbers = [14, 14] # Atomic numbers for Si

cell = (lattice, positions, numbers)

symprec = 1e-5 # Symmetry precision in Angstrom
angle_tolerance = 1.0 # Angle tolerance in degrees

dataset = get_symmetry_dataset(cell, symprec=symprec, angle_tolerance=angle_tolerance)

print(f"Space group number: {dataset['number']}")
print(f"International symbol: {dataset['international']}")
print(f"Hall symbol: {dataset['hall']}")
# print(f"Rotations: {dataset['rotations']}")
# print(f"Translations: {dataset['translations']}")

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