Python wrapper for the Zacros kinetic Monte Carlo (KMC) code

This repository contains a Python library for a wrapper for the Zacros kinetic Monte Carlo (KMC) code, which can be found at http://zacros.org/. For users familiar with the Zacros software, our package offers ease-of-use as well as additional analysis functionality. Modified source files for Zacros are included which produce additional output files that are used by the wrapper.

• Documentation available at http://vlachosgroup.github.io/Zacros-Wrapper/
• Download or clone source code from the Github repository

Key features

• Run KMC simulations with parallel processing
• Rescale rate constants of fast, equilibrated reactions to accelerate simulation
• Perform parameteric sensitivity analysis using the likelihood ratio method

Developers

• Marcel Nunez (mpnunez@udel.edu)
• Taylor Robie
• Gerhard Wittreich, P.E.

Related Publications

• M. Nunez, T.A. Robie, D.G. Vlachos, J. Chem. Phys. 147, 164103 (2017).

Dependencies

• mpi4py : Used for parallelization of multiple trajectories.
• Atomic simualtion environment : Used to convert ab initio data to input parameters.

Getting Started

1. Obtain modified Zacros executable. See Separate page.
2. Add the Zacros-Wrapper repository to your Python path.
3. Configure input in demo file and run.

Documentation

• Examples
  • Converting DFT data to Zacros input files
  • Analyzing a single trajectory
  • Running and analyzing multiple trajectories
  • Rate constant rescaling and steady state detection
• Compiling modified Zacros executable
  • Installation instructions
  • Additional Zacros output files
  • Compiling on Farber

Code

• Single trajectory
• Multiple trajectories
• Rate Constant Rescaling
• Thermodynamics calculator
• KMC lattice
• Reading/writing Zacros input/output

Indices and tables

• Index
• Module Index
• Search Page