LAMMPSKit Documentation

LAMMPSKit is a Python toolkit for running, post-processing, and analyzing molecular dynamics (MD) simulations with LAMMPS. It provides a collection of functions and scripts to streamline simulation workflows and automate analysis of LAMMPS output data.

Features

Modular architecture with separate I/O, plotting, and analysis components
Comprehensive data processing for LAMMPS trajectory and displacement files
Advanced visualization tools including timeseries plotting with font customization
Atomic-scale analysis functions for distributions, charges, displacements, and clusters
Filament evolution tracking for electrochemical simulation analysis
Configuration management with centralized settings and validation
Complete example workflows demonstrating real-world usage patterns
Extensive test coverage with visual regression testing for plots

Installation

Install from PyPI:

pip install lammpskit

For development:

pip install .[dev]

Quick Start

Basic workflow for electrochemical analysis:

import lammpskit as lk
from lammpskit.config import DEFAULT_COLUMNS_TO_READ

# Load trajectory data
file_list = ['trajectory1.lammpstrj', 'trajectory2.lammpstrj']
coords, timesteps, total_atoms, xlo, xhi, ylo, yhi, zlo, zhi = lk.io.read_coordinates(
    file_list, skip_rows=9, columns_to_read=DEFAULT_COLUMNS_TO_READ)

# Perform cluster analysis
from lammpskit.ecellmodel.filament_layer_analysis import analyze_clusters
analyze_clusters('trajectory1.lammpstrj')

Package Structure

LAMMPSKit features a modular architecture:

lammpskit.io - Data reading and I/O operations
lammpskit.plotting - Visualization utilities and timeseries plots
lammpskit.ecellmodel - Electrochemical analysis functions
lammpskit.config - Centralized configuration management

Target Applications

Electrochemical memory device simulations (ReRAM, memristors)
Ion transport and defect migration studies
Phase transition analysis in oxide materials
General LAMMPS trajectory post-processing

API Reference

API Documentation: