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pyscal — python Structural Environment Calculator

Complete documentation with examples available here.

What changed in version 4

pyscal grew over the years from a small wrapper around a few C++ routines into a full structural-analysis toolkit. With each addition the original System / Atoms object model became more rigid: every new descriptor had to be threaded through the same class hierarchy, neighbor lists were tied to a particular System instance, and interoperating with the rest of the atomistic-simulation Python ecosystem (ASE, pymatgen, OVITO, LAMMPS dump readers) required converting back and forth between formats.

Version 4 is a ground-up rewrite around two ideas:

  • ASE Atoms is the data structure. pyscal no longer ships its own atoms class. Any ase.Atoms object — read from a LAMMPS dump, a POSCAR, a CIF, an XYZ, built with ase.build.bulk, or constructed by hand — can be passed directly to a pyscal function. Results are written back as atoms.arrays["pyscal_*"] for per-atom quantities and atoms.info["pyscal_*"] for global ones, so they travel with the atoms object and remain accessible to the rest of the ASE ecosystem.

  • Functional API. Every descriptor is a top-level function in pyscal that takes an Atoms object as its first argument. Neighbor lists are computed once with pyscal.find_neighbors(atoms, ...) and reused by every subsequent descriptor. There is no system state to keep in sync, no method-chaining order to remember, and no class to subclass when adding a new descriptor.

The C++ core is unchanged in spirit — voro++ for tessellation, hand-written kernels for Steinhardt-type invariants, pybind11 bindings — but is now exposed through a much thinner Python layer.

A typical session looks like:

import pyscal
from ase.build import bulk

atoms = bulk("Cu", "fcc", cubic=True).repeat(4)
pyscal.find_neighbors(atoms, method="cutoff", cutoff=0)   # adaptive
q4, q6 = pyscal.steinhardt_parameter(atoms, l=[4, 6])
labels, names = pyscal.identify_ackland_jones(atoms)

print(atoms.arrays["pyscal_q6"].mean())   # ≈ 0.57 for fcc

What is included

This release consolidates a number of new descriptors alongside the existing ones:

  • Neighbors — fixed cutoff, adaptive cutoff, SANN, Voronoi
  • Steinhardt $q_l$ and averaged $\bar{q}_l$
  • Wigner $W_l$ — third-order rotational invariants for distinguishing cubic structures
  • Minkowski structure metrics — Voronoi-area-weighted, parameter-free $q_l$
  • Solid/liquid classification and clustering
  • Disorder parameter
  • Angular and $\chi$ parameters; Ackland-Jones structural classifier
  • Coordination measures — coordination number, effective coordination, generalised coordination, local density
  • Angular distribution function and bond-length distribution function
  • Voronoi tessellation — structural vector and Voronoi volume
  • Centrosymmetry parameter
  • Common neighbor analysis (CNA, adaptive CNA, diamond variants)
  • Entropy parameter (Piaggi–Parrinello)
  • Warren–Cowley short-range order
  • Atomic deformation — strain tensor, von Mises invariant, $D^2_{\min}$, slip vector
  • Wigner–Seitz defect analysis — vacancies, interstitials, antisites against a reference
  • Atomic Cluster Expansion (ACE) descriptors up to body order four

A complete list with mathematical definitions and example notebooks is available in the documentation.

Installation

pyscal is distributed on PyPI and conda-forge as pyscal3 (the name pyscal on PyPI refers to a separate, unrelated package). After installation, both import pyscal and import pyscal3 work.

From conda-forge:

conda install -c conda-forge pyscal3

or from PyPI:

pip install pyscal3

To build from source:

git clone https://github.com/pyscal/pyscal3.git
cd pyscal3
pip install .

A C++ compiler with C++17 support is required when building from source.

Citing the work

If you use pyscal in your work, please cite the following article:

Sarath Menon, Grisell Díaz Leines and Jutta Rogal (2019). pyscal: A python module for structural analysis of atomic environments. Journal of Open Source Software 4(43), 1824. https://doi.org/10.21105/joss.01824

Works using pyscal

For a list of publications that used pyscal, see here.

Metadata

Release files for pyscal3 4.0.0

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Source distribution for pyscal3 4.0.0
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Built distributions (wheels)

Table of built distributions (wheels) for pyscal3 4.0.0
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pyscal3-4.0.0-cp314-cp314-win_amd64.whl CPython 3.14 CPython 3.14 Windows x86-64 Details
pyscal3-4.0.0-cp314-cp314-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl CPython 3.14 CPython 3.14 Linux glibc 2.28+ x86-64, Linux glibc 2.24+ x86-64 Details
pyscal3-4.0.0-cp314-cp314-macosx_11_0_arm64.whl CPython 3.14 CPython 3.14 macOS 11.0+ ARM64 Details
pyscal3-4.0.0-cp314-cp314-macosx_10_15_x86_64.whl CPython 3.14 CPython 3.14 macOS 10.15+ x86-64 Details
pyscal3-4.0.0-cp313-cp313-win_amd64.whl CPython 3.13 CPython 3.13 Windows x86-64 Details
pyscal3-4.0.0-cp313-cp313-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl CPython 3.13 CPython 3.13 Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64 Details
pyscal3-4.0.0-cp313-cp313-macosx_11_0_arm64.whl CPython 3.13 CPython 3.13 macOS 11.0+ ARM64 Details
pyscal3-4.0.0-cp313-cp313-macosx_10_13_x86_64.whl CPython 3.13 CPython 3.13 macOS 10.13+ x86-64 Details
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pyscal3-4.0.0-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl CPython 3.12 CPython 3.12 Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64 Details
pyscal3-4.0.0-cp312-cp312-macosx_11_0_arm64.whl CPython 3.12 CPython 3.12 macOS 11.0+ ARM64 Details
pyscal3-4.0.0-cp312-cp312-macosx_10_13_x86_64.whl CPython 3.12 CPython 3.12 macOS 10.13+ x86-64 Details
pyscal3-4.0.0-cp311-cp311-win_amd64.whl CPython 3.11 CPython 3.11 Windows x86-64 Details
pyscal3-4.0.0-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl CPython 3.11 CPython 3.11 Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64 Details
pyscal3-4.0.0-cp311-cp311-macosx_11_0_arm64.whl CPython 3.11 CPython 3.11 macOS 11.0+ ARM64 Details
pyscal3-4.0.0-cp311-cp311-macosx_10_9_x86_64.whl CPython 3.11 CPython 3.11 macOS 10.9+ x86-64 Details
pyscal3-4.0.0-cp310-cp310-win_amd64.whl CPython 3.10 CPython 3.10 Windows x86-64 Details
pyscal3-4.0.0-cp310-cp310-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl CPython 3.10 CPython 3.10 Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64 Details
pyscal3-4.0.0-cp310-cp310-macosx_11_0_arm64.whl CPython 3.10 CPython 3.10 macOS 11.0+ ARM64 Details
pyscal3-4.0.0-cp310-cp310-macosx_10_9_x86_64.whl CPython 3.10 CPython 3.10 macOS 10.9+ x86-64 Details

Total release size: 8.4 MB

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Release files / pyscal3-4.0.0-cp311-cp311-macosx_10_9_x86_64.whl

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Release files / pyscal3-4.0.0-cp310-cp310-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl

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