cg-pytools 0.1.0

Crystal-shape / coarse-grained morphology analysis library

cg-pytools

A small library for analysing crystal morphology from CrystoGen (formerly CrystalGrower) - crystal growth simulations: shape characterisation (Zingg ratios, aspect ratios, surface area / volume), Wulff and surface processing, energy-network parsing, and plotting utilities. It also ships example SGE / SLURM job scripts for running CrystoGen + OCC workflows (solvent screens, growth rates, growth modifiers, …) on HPC clusters.

For a full, GUI-driven workflow, see CGAspects — CrystoGen's official (PySide6) data-analysis tool for CrystoGen output. cg-pytools is a stripped-down, lightweight alternative: a scriptable library and command-line utilities for the same kind of analysis, without the GUI. It is currently limited in scope, and may in future grow to contain the core of CGAspects.

Installation

pip install cg-pytools

Or, for local development:

git clone https://github.com/CrystoGenLtd/cg-pytools.git
cd cg-pytools
pip install -e .

Usage

from cgpytools import CrystalShape, ShapeAnalyser

crystal = CrystalShape.from_file("crystal.xyz")

analyser = ShapeAnalyser(zingg_method="svd")
analyser.analyse_crystal(crystal)
metrics = analyser.get_all_frame_metrics()

Modules

Module	Purpose
crystal_io	Read crystal shapes / frames (CrystalShape)
shape_analysis	Morphology metrics, Zingg classification (ShapeAnalyser)
surfaces	Wulff construction and surface/size-file processing
cg_net	Interaction-energy network parsing (CGNet)
plot	Shared plotting theme and styling helpers
log	Logging configuration

Scripts

Command-line tools live in scripts/python/:

Script	Depends on	Description
screen.py	cgpytools	Main crystal-shape analysis tool (general / solvent / size / movie / CDA modes). See scripts/python/README.md.
growth_kinetics.py	numpy, pandas, matplotlib, scipy	Standalone: time-evolution plots of size data from simulation subfolders.
growth_rates.py	numpy, pandas, matplotlib	Standalone: growth-rate-vs-supersaturation summaries from size.csv files.

screen.py imports cgpytools, so install the package first. The two growth_* scripts are single-file and have no dependency on cgpytools — they can be copied and run on their own.

HPC job scripts

Example SGE and SLURM job scripts for the CrystoGen + OCC workflows live under scripts/HPC/ organised by use case (solvent screens, growth rates, etc.). Each folder has a README.txt describing the inputs it needs.

Copy the scripts to a folder containing a CIF or other inputs, depending on which job type is to be submitted.

License

MIT — see LICENSE.