ASE2SPRKKR

ASE2SPRKKR package provide an interface that allow use of the SPR-KKR package to electronic structure calculation within Atomic Simulation Environment (abbreviated as ASE) — Python tool that integrates the various tools for electronic structure calculation.

Installation of the package using package managers

The simplest way how to install and use the package is to install them using package managers: either pip

pip install ase2sprkkr

or conda

conda install -c ase2sprkkr ase2sprkkr

I reccomend to install beta version: there can be some bugs, but mostly it has more bugs repaired than introduced, moreover, you can enjoy new properties. The beta versions are available only through pip:

pip install --pre ase2sprkkr

To use bleading edge sources (the newest features, but you risk to encounter bugs), you can install the packages from github:

pip install git+https://github.com/ase2sprkkr/ase2sprkkr.git@develop

Further notes

In some systems, the pip utility for python3 is called pip3. It may be possible, that pip is installed, but it is not in PATH. In such case, the pip utility can be runned using python -m pip or python3 -m pip3.

If pip is not installed, you can install it using the linux distribution package manager, e.g. in Debian/Ubuntu

apt install pip3

or

zypper install pip

For the conda installation instructions, see the Anaconda documentation https://docs.anaconda.com/anaconda/install/linux/ however, for the users unexperienced with conda, the (simpler) pip way is recommended.

Install the packages from GIT (and/or source codes)

If you do not want to use public package managers as pip or conda, or you want to contribute to development, you can use GIT to obtain the package sources.

Requirements

  • Python >= 3.8

  • SPR-KKR (not checked by the installer)

  • Python packages: see the the pypoject.toml file

  • Git (to obtain the sources)

Obtaining the package using GIT

git clone https://github.com/ase2sprkkr/ase2sprkkr.git
git checkout release

The first line fetches the code of the package. The second one checks out the stable (production) version of the code.

If you want to obtain the current version of the (earlier-downloaded) code, run

git fetch
git checkout release

Alternatively, you can checkout master branch

git checkout master

to obtain a newer (not thorougly tested yet) version or develop`

git checkout develop

to obtain the bleeding edge version (feel free to try it, test it and report the bugs).

Using the package (without installing the pip/conda packages)

You can install the package from the obtained sources using

pip install .

Or, if you want to develop ase2sprkkr, it is better idea to do an editable installation, where the package will see the changes made.

pip install --no-build-isolation --editable .

You can add --no-deps switch for a faster rebuild.

The known issues of the editable build

1. Unfortunatelly, pip is not able to install the build requirements. So if they are not installed, the previous command will fail. You can either install the dependencies manually, copying them out from pyproject.toml:

pip install scikit-build cmake ninja cython

or (which will be usefull if I add a build requirement and forgot to update this help) run the following snippet to install all the build-dependencies mentioned in pyproject.toml:

pip install tomllib
pip install --no-build-isolation $(python -c "import tomllib; print(' '.join(tomllib.load(open('pyproject.toml','rb'))['build-system']['requires']))")

2. The limitation of the editable install is, that it won’t see newly created files automatically: you need run the command above again to make it notice it.

3. If the build process fail, try to remove the build directory created by the previous build (if it exists). Mostly, it happens if the --no-build-isolation switch is ommited.

Documentation of the package

The documentation is published online at https://ase2sprkkr.github.io/ase2sprkkr/

If you are using Git cloned sources, you can run

open docs/index.html

to see the (offline version of the) documentation. The documentation contains parts, that are generated from the docstrings in the source code. You can regenerate these by

make docs

Sphinx and sphinx-toolbox python packages (installable e.g. using pip) and pandoc (for generating README.md) are needed for the build.

However, the official build of Sphinx miss some attributes when it is used to build the documentation. So, till the pullrequest that corrects the Sphinx behavior will be merged into Sphinx, please use the following fork for building the documentation. https://github.com/lokik/sphinx.git

How to contribute or to report a bug

Please feel free to make a pull-request or post an issue at: https://github.com/ase2sprkkr/ase2sprkkr