Clinamen 0.2.0a3
Clinamen: a Python package for the first-principles systematic discovery of low-energy configurations in defective systems.
License: Apache License 2.0
Requires Python: >=3.8

Clinamen
********

Purpose
=======
**Clinamen**: Covariance-matrix-adaptation evolution strategy for Localized
Impurities with unsupervised Machine learning Exploration of Non-elementary
structures.


**Clinamen** is a software package developed in order to assist in the discovery of low-energy defective configurations
in first-principles atomistic calculations.

The approach is based on a modified version of the covariance-matrix-adaptation evolution-strategy (CMA-ES), a state-of-the-art
evolutionary algorithm for continuous-parameter multimodal optimization.
In addition, the approach employs an unsupervised machine learning model for identifying additional local minima explored
during the run of the evolutionary algorithm. A supervised Gaussian-process regressor trained on-the-fly during the evolutionary
process can also be used in order to reduce the number of first-principles calculations.

**Clinamen** is written mostly in Python and employs Cython and C extension modules for an increased computational speed.

Installation
============

The code is available on the PyPi index.
The easiest way to install **Clinamen** is through `pip`:

::
    
    pip install clinamen

We suggest to create a virtual environment in which the **Clinamen** code can be installed.

The requirements for a successful installation are:

 - `Python` version 3.8 or newer;
 - `NumPy <https://www.numpy.org>`_ version  1.18 or newer;
 - `SciPy <https://www.scipy.org>`_ version 1.5 or newer;
 - `Pandas <https://pandas.pydata.org/>`_ version 1.0 or newer;
 - `scikit-learn <https://scikit-learn.org/>`_ version 0.23 or newer;
 - `Cython <https://cython.org/>`_ version 0.29 or newer;
 - `mpi4py <https://mpi4py.readthedocs.io/>`_ version 3.0 or newer;
 - `h5py <https://www.h5py.org/>`_ version 2.10 or newer;
 - `Atomic Simulation Environment <https://wiki.fysik.dtu.dk/ase>`_ version 3.19 or newer;
 - `PyTorch <https://pytorch.org/>`_ version 1.7 or newer;
 - `GPyTorch <https://gpytorch.ai/>`_ version 1.3 or newer;
 - `DScribe <https://singroup.github.io/dscribe/latest/>`_ version 0.4 or newer. 

It might be that some packages cannot be installed directly with the **Clinamen** package using `pip`
(for example `PyTorch` installation could fail in this way). For this reason these packages have to
be installed manually before installing **Clinamen** with `pip`. 


Authors
-------
 - Marco Arrigoni - marco.arrigoni@outlook.de, marco.arrigoni@tuwien.ac.at


Contacts
--------
  - Marco Arrigoni - marco.arrigoni@tuwien.ac.at
  - Georg K. H. Madsen - georg.madsen@tuwien.ac.at


The meaning of the word `clinamen`
----------------------------------
`Clinamen` is the name that the Roman philosopher and poet Titus Lucretius Carus gave to the
random deviations in the rectilinear motion of atoms, which, according to the Epicurean atomistic theory,
are responsible for their collisions and aggregation into objects.

In the `De Rerum Natura`, Lucretius also presents a theory of natural selection based on the random
generation, by the Earth, of creatures of any sort, among which only the most fit ones are able to survive and reproduce.

The importance of the random generation of individuals and of fitness-based selection in the doctrine of Lucretius, together
with the fact that `clinamen` can be used as an acronym describing the main ingredients of the method 
implemented in this package, are the main reasons for the choice of this name.