Python Materials Discovery Framework

PyChemia is a open-source Python Library for materials structural search. The purpose of the initiative is to create a method agnostic framework for materials discovery and design using a variety of methods from Minima Hoping to Soft-computing based methods. PyChemia is also a library for data-mining, using several methods to discover interesting candidates among the materials already processed.

The core of the library is the Structure python class, it is able to describe periodic and non-periodic structures. As the focus of this library is structural search the class defines extensive capabilities to modify atomic structures.

The library includes capability to read and write in several ab-initio codes. At the level of DFT, PyChemia support VASP, ABINIT and Octopus. At Tight-binding level development is in process to support DFTB+ and Fireball. This allows the library to compute electronic-structure properties using state-of-the-art ab-initio software packages and extract properties from those calculations.

Before installing PyChemia, you may need to first install a few critical dependencies

1. Python >= 2.7.x or Python >= 3.1.x The library is tested for the current version of Python

2. Numpy >= 1.5 NumPy is a fundamental package for any Python scientific library. Numpy arrays are essential for efficient array manipulation.

3. SciPy >= 0.9 SciPy is used for many linear algebra and FFT calls

1. Pandas Library for Data Analysis used by the datamining modules

2. PyMC PyMC is a python module that implements Bayesian statistical models and fitting algorithms Important for the datamining capabilities of PyChemia

3. Matplotlib >= 1.2 Used to plot band structures, densities of states and other 2D plots

4. Mayavi >= 4.1 Some basic visualization tools are incorporated using this library

5. ScientificPython >2.6 This library is used for reading and writing NetCDF files

6. pymatgen >= 2.9 pymatgen is an excellent library for materials analysis

7. ASE Atomic Simulation Environment is another good library for ab-initio calculations. Quite impressive for the number of ab-initio packages supported

8. qmpy The Python library behind the Open Quantum Materials Database. The OQMD is a database of DFT calculated structures. For the time being the database contains more than 300000 structures, with more than 90% of them with the electronic ground-state computed.

The best way to install PyChemia is from its GitHub repository

git clone https://github.com/MaterialsDiscovery/PyChemia.git

Once the repository is downloaded, you can install it using

cd PyChemia
python setup.py built
sudo python setup.py install