ptc-cmc / pore-builder

mBuild recipe for building slit-pores.

Pore-Builder

Overview

Pore-Builder is an mBuild recipe to build carbon slit pores and surfaces. Recipes are designed to be add-ons, allowing users to develop routines to initialize specific chemistries using mBuild.

Disclaimer

Continuous integration pipelines on Azure are currently not working. The Azure organization for this project may have been inadvertently flagged due to attempts to cut down on abuse, such as crypto mining, in recent months. See: https://devblogs.microsoft.com/devops/change-in-azure-pipelines-grant-for-public-projects/. A ticket has been submitted to resolve this issue.

Installation

To install Pore-Builder, its dependencies must first be installed. It is recommended to do so through Conda by running the following commands:

# Create conda environment
conda create -n pore37 python=3.7
# Add channels
conda config --add channels conda-forge
# Install packages
conda install --file requirements.txt

Once the dependencies have been installed, Pore-Builder can be installed from the package root directory: pip install -e .. To check the package has been correctly installed, we can run Python and attempt to import the package via mBuild:

>>> import mbuild
>>> mbuild.recipes.GraphenePore()
<GraphenePore 2688 particles, periodicity: [3.9296     2.675      2.97774175], 0 bonds, id: 140234327632848>
>>> 

Docker

A docker image is available on DockerHub to try out Pore-Builder.

Publications using Pore-Builder

• https://www.tandfonline.com/doi/abs/10.1080/00268976.2020.1742938
• https://www.authorea.com/users/311036/articles/496195-open-source-molecular-modeling-software-in-chemical-engineering-focusing-on-the-molecular-simulation-design-framework?commit=bed95fe98da6c2ed7360a8ef4442e0b35ed82b63