Machine Learning Methods For Material Sciences

Software Setup

Python

Python is a popular language for research computing and general-purpose programming. Installing all research packages individually can be challenging, so we recommend Anaconda, an all-in-one installer.

• Please install Python version 3.x (e.g., 3.9 is fine).
• We will use the IPython notebook, a programming environment running in a web browser. Use an up-to-date browser such as Chrome, Safari, or Firefox. Older browsers, like Internet Explorer 9 or earlier, are not supported (details here).

Windows

Video Tutorial

1. Open http://continuum.io/downloads in your web browser.
2. Download the Python 3 installer for Windows.
3. Install Python 3 using all the default settings, except check Make Anaconda the default Python.

Mac OS X

Video Tutorial

1. Open http://continuum.io/downloads in your web browser.
2. Download the Python 3 installer for OS X.
3. Install Python 3 using all the default settings.

Linux

1. Open http://continuum.io/downloads in your web browser.
2. Download the Python 3 installer for Linux.
   (Installation requires using the shell. If you’re not comfortable, request help at the workshop.)
3. Open a terminal window.
4. Type bash Anaconda3- and press tab. The downloaded file name should appear. If not, navigate to the folder where you downloaded the file using, for example

   cd Downloads

Then try again.

1. Press enter and follow the prompts. Use the space key to scroll through text. Approve the license by typing yes and pressing enter. Accept the default file location by pressing enter. Type yes and press enter to prepend Anaconda to your PATH (this makes Anaconda the default Python).
2. Close the terminal window.

Enumlib

Enumeration library for generating derivative structures. To compile the code manually, clone the repository with the –recursive flag:

git clone --recursive https://github.com/msg-byu/enumlib.git

We need to compile the symlib submodule before compiling enumlib. Go to the enumlib/symlib/src directory:

cd enumlib/symlib/src

Set an environment variable to identify your fortran compiler: [in the bash shell, gfortran compiler] export F90=gfortran [the Makefile also recognizes ifort]

Then compile using the Makefile:

make

(Alternatively, instead of setting the F90 environmental variable first, you may just specify the variable during the make:

$ make F90=gfortran.)

Next, make the enumeration library itself

$ cd ../../src
$ make

Finally, to make a stand-alone executable for enumeration:

make enum.x

It is possible to compile enumlib using conda on OSX and Linux. To do so use the command:

$ conda install conda-forge::enumlib

Alternatively you would like to use the enumeration capabilities powered by Gus Hart’s enumlib or perform Bader charge analysis powered by the Bader analysis code of the Henkelmann group, please try installing these from source using the pmg command line tool as follows::

$ pmg config --install enumlib
$ pmg config --install blader 

icet

icet is another Enumeration library tool for generating derivative structures for the construction and sampling of alloy cluster expansions. A detailed description of the functionality provided as well as an extensive tutorial can be found in the user guide.

pip install icet

HyDGL

pip install git+https://github.com/hkneiding/HyDGL

which installs HyDGL as a library to your Python installation or virtual environment.

Afterwards you can import the library with:

import HyDGL

{: .python