structureREST

structureREST is a library of wrapper functions and a RESTful server for calculating basic structure descriptors of bulk crystalline materials. It also has support for some methods which compare but do not describe structures, like the pymatgen StructureMatcher.

Features

• Descriptors:
  • Matminer CrystalNNFingerprint
  • STRUCTURE TIDY spacegroup/wyckoff
  • SOAP
• Comparitors:
  • Matminer CrystalNNFingerprint
  • pymatgen StructureMatcher
  • SOAP
    • Average Distance Kernel w/ similarity cutoff
• Continuous Distance Metrics:
  • Matminer CrystalNNFingerprint
  • SOAP
    • Average Distance Kernel

Installation

Dependencies:

• pymatgen
• ase
• matminer
• QUIP with GAP
• quippy
• glosim2
  • tqdm
  • psutil
• flask
• flask_restful
• numpy
• scipy

1. Clone the repository

   git clone https://github.com/zooks97/structureREST ~/structureREST

2. Install python dependencies

   pip install numpy scipy pymatgen ase matminer flask flask_restful

3. Install QUIP / GAP / quippy

   a. One option is to use the precompiled Docker image libatoms/quip. This image is a bit bloated (3 compilations of QUIP, LAMMPS included, etc.).

   docker pull libatomsquip/quip

   b. A more lightweight option is to compile the Dockerfile in docker/

   From docker/:

    . build.sh
    . run.sh
   

   c. If you're feeling adventurous, you could try to locally compile QUIP, GAP, and quippy following the instructions in the libAtoms/QUIP repository.

4. Install glosim2

In the same environment where QUIP / GAP / quippy are installed (docker image or locally), do the following to get glosim2:

git clone https://github.com/cosmo-epfl/glosim2
pip install tqdm psutil

To use structureREST libraries, use sys.path.insert(0, 'path/to/structureREST/lib) followed by import [filename] to import all functions / classes / etc. from structureREST/lib/[filename].py.

To run the RESTful server, point your favorite webserver to script/rest/structurerest.py. Documentation for the RESTful interface can be found in docs/. If you wish to use SOAP through the restful interface, the current method is to install a small RESTful server script/rest/soaprest.py wherever quippy is available. Make sure to also download glosim2 and modify script/rest/soaprest.py so that glosim is added to the path.