pylattica 0.1.3

pylattica is a package for fast prototyping of lattice models for chemistry and materials science

pylattica - A Framework for Lattice and Cellular Automata Simulation

pylattica is a Python library for prototyping and constructing cellular automaton and lattice models. The core features of these models are:

• There is a simulation state that evolves over time by repeatedly applying some unchanging rule
• The state of the simulation has a topology defined by a network of sites (i.e. each site has an unchanging set of neighbor sites)
• Each site has a state value associated with it that could change at each simulation step
• The future state of a site is determined by the state of its neighbor sites

These rules capture many common models in chemistry and materials science. For instance, in the Ising Model, spins are updated with probabilities related to the neighboring spins. In a Lattice Gas Automaton, the velocities of particles are determined collisions with neighboring particles. In lattice Monte Carlo simulations of surface catalysis, adsorption, desorption, and surface diffusion are dependent on the occupancy of neighboring sites.

pylattica aims to provide a general framework for prototyping these types of lattice simulations. It prioritizes providing a straightforward method for experimenting with different interaction rules and interaction neighborhoods. It provides some simple utilities for analyzing simulation states, and in the case of square grid systems, it provides visualization tools for the system state itself. Additionally, since this tool is focused on materials science, there is functionality for mapping system states to CIF files (for use in crystal lattice simulations).

Installation

pylattica can be installed from the PyPi source by running:

pip install pylattica

It can also be installed by cloning this repository, then running the following in the root of the repository:

pip install .

Documentation

Detailed documentation for this library can be found here.

Jupyter Notebook Examples

Example notebooks are included in docs/guides.

Note about Windows

pylattica makes use of Python's fork functionality in the multiprocessing library. This functionality is not available on windows, so certain features (the parallel keyword for the SynchronousRunner) will not be available on Windows platforms.

Development

Installation for development

To install pylattica for development purposes, use the standard editable installation command:

pip install -e .

from the root of the repository.

Running tests

After you have installed the repository, ensure that pytest is installed, then run:

pytest

from the root of the repository.

Building Documentation

The docs for this project are built using mkdocs. To build the documentation

pip install '.[docs]'
mkdocs build

To run the documentation server locally:

mkdocs serve

Linting

This project uses the black package for style and formatting, and prospector for type checking and other lint warnings. These packages are not listed as dependencies of this project, so you can install them manually. This is partially because this project doesn't rely on specific versions of them, and we expect developers to have their own installations already. You can run them as follows:

To assess the changes that will happen if you run the black linter, run the following:

black --check src

To automatically make the changes, remove the --check flag:

black src

To run all other linters with prospector, use this:

prospector

In the top of this repository.