The Hetero2d package leverages well known computational tools: pymatgen, MPInterfaces, atomate, fireworks, and custodian to perform high-throughput ab-initio calculations. Hetero2d is tailored to addressing scientific questions regarding the stability of 2D-substrate hetero-structured materials using an all-in-one workflow approach to model the hetero-structures formed by arbitrary 2D materials and substrates. The workflow creates, computes, analyzes and stores all relevant simulation parameters and results in a queryable MongoDB database that can be accessed through our API. Check out our documentation or the paper!
The 2D-substrate hetero-structure workflow takes a given 2D material, 3D phase (bulk) of the 2D material, and a substrate, relaxes the structures using vdW-corrected DFT and creates hetero-structures subject to user constraints. The workflow analyzes and stores energetic stability information of various 2D hetero-structured materials to predict the feasibility of a substrate stabilizing a meta-stable 2D material
Hetero2d provides automated routines for the generation of low-lattice mismatched hetero-structures for arbitrary 2D materials and substrate surfaces, the creation of van der Waals corrected density-functional theory (DFT) input files, the submission and monitoring of simulations on computing resources, the post-processing of the key parameters to compute (a) the interface interaction energy of 2D-substrate hetero-structures, (b) the identification of substrate-induced changes in interfacial structure, and (c) charge doping of the 2D material.
IMPORTANT NOTE: Atomate and FireWorks do not run on Windows OS. You need a unix-based OS (Mac or Linux) in order for these packages to run. As such, all setup instructions are given for Unix systems.
- Download the repo using one of the following methods:
gh repo clone cmdlab/Hetero2d(gh must be installed)git clone https://github.com/cmdlab/Hetero2d.gitgit clone git@github.com:cmdlab/Hetero2d.git
- Install Hetero2d in a clean python enviromnent using python>=3.9. I suggest using Anaconda3 to manange environments.
conda create --name hetero2d python=3.9
- Activate the Hetero2d virtual environment and install the package from the Hetero2d directory:
pip install -r requirements.txt
- After installation, Hetero2d needs to be added to your python path. This can be done by running the first line below OR by adding the 2nd line listed below to your .bashrc file. Only necessary if python cannot find the package or the setup.py failed for some reason.
python setup.py developorpython setup.py installexport PYTHONPATH="$HOME/path_to_package/Hetero2d:$PYTHONPATH"
- If this is your first time installing the package dependencies listed below, please ensure you have followed the respective setup instructions:
- To run jupyter notebooks on various resources the ipykernel has to be installed. Sometimes this isn't enough and you need explicitly add the kernel to the list of environments. Via the command line:
- Activate your environment
conda activate hetero2d python -m ipykernel install --user --name hetero2d
The Hetero2d package dependancies have a lot of documentation to look over. I will highlight the essential documentation to get started as quickly as possible.
- atomate requires the most set up. Mainly, creating a directory scaffold and writing the 5 required files to connect to the database and run jobs. (MongoDB or free Atlas MongoDB is required)
- pymatgen has a command line tool installed to set up default directory paths called pmg. There are 2 essential commands you have to run to use Hetero2d on any system.
- Reference directory for the VASP POTCARs. You need to have the POTCARs from VASP yourself.
pmg config -p <EXTRACTED_VASP_POTCAR> <MY_PSP>
- Default pseudopotential files from VASP
pmg config --add PMG_DEFAULT_FUNCTIONAL PBE_54
To get started using Hetero2d, various tutorials and examples have been created using Jupyter Notebooks. These notebooks demonstrate the basic functionality of Hetero2d to enable users to quickly learn how to use the various modules within this package. These can be found under Hetero2d/examples.
- If you have a new install you likely do not have the gcc compiler that pymatgen requires. In that case run
sudo apt install build-essentialsudo apt-get install manpages-dev
If you use Hetero2d in your research, please consider citing the paper!
Tara M. Boland, Arunima K. Singh. Computational synthesis of 2D materials: A high-throughput approach to materials design. Computational Materials Science, 2022, 207, 111238. doi:10.1016/j.commatsci.2022.111238