MDSYN2019 / nanoparticle_optimization

NanoOpt: Deriving potentials for coarse-grained nanoparticles via potential-matching

NanoOpt: Deriving potentials for coarse-grained nanoparticles via potential-matching

Installation

NanoOpt is centered around the mBuild package which is easiest to install using the Anaconda package manager. The recommended installation instructions are as follows:

NOTE

For the version of mbuild used in this paper and study, use environment.yml. For a newer version of the packages with improved mBuild features, use environment-dev.yml.

1. Clone NanoOpt:

git clone https://github.com/summeraz/nanoparticle_optimization
cd nanoparticle_optimization

2. Determine what version you want to use: Refer to the note above

• If you want to emulate the study and paper:

git checkout bdaa8b8
conda env create -f environment.yml
conda activate nanoopt-binder
pip install .

• If you want to use newer package versions

conda env create -f environment.yml
conda activate nanoopt-binder
pip install .

Tutorials

The tutorials directory contains several tutorials in the form of Jupyter notebooks that provide examples of the optimization code. These can be accessed online via Binder: However, these are best run locally as several of the code blocks can take a considerable amount of time to run on Binder.