SurfCat

A Python library for analyzing surface science and electrocatalysis molecular dynamics simulations.

Features

• Species Identification: Automatic identification of OH⁻, H₂O, H₃O⁺ based on bonding topology
• Spatial Analysis: Define interface/surface regions for localized analysis
• Density Profiles: Calculate 1D distributions along any dimension
• Dynamic Properties: MSD, displacement correlations, residence times

Quick Start

import surfcat as sc

# Load trajectory
system = sc.System('trajectory.xyz')

# Define interface region
system.define_region('interface', method='z_slice', z_min=10, z_max=15)

# Identify species
oh_atoms = system.find_species('hydroxide')
water_atoms = system.find_species('water')

# Calculate density profile
density_data = sc.analysis.profiles.calculate_density_profile(
    system, selection='name O', region=system.regions['interface']
)

# Plot results
fig, ax = sc.plotting.profiles.plot_density_profile(density_data)

Installation

pip install -e .

Requirements

• Python ≥ 3.8
• MDAnalysis ≥ 2.0.0
• NumPy, Matplotlib, Pandas, SciPy

Testing

python run_tests.py basic

License

MIT License