Skip to content

Preparations

Webinar Participants

For the participants of the hands-on session on AWS, there is no need to follow these preparations, everything will be available on the cluster for you. Please consult the README.md that will be in your home directory for further details.

1. Download the tutorial material

You can download all of the tutorial material either as a tarball, or, if you are familiar with git, with the following command:

git clone git@gitlab.com:FHI-aims-club/tutorials/finding-transition-states-with-aimschain.git

2. Install FHI-aims

Info

This tutorial has been tested with FHI-aims version 240920.

The installation of FHI-aims follow the instructions

  1. on this page: https://fhi-aims-club.gitlab.io/tutorials/cmake-tutorial/,
  2. or on our wiki (with several templates for different architectures): https://aims-git.rz-berlin.mpg.de/aims/FHIaims/-/wikis/CMake%20Tutorial,
  3. or, alternatively, download and read the manual.

3. Install aimsChain

Info

Starting from Python 3.11, pip does not allow the user to install packages in a system-wide environment by default. They should be installed in a virtual environment. There are several ways of creating it (Python's venv module, conda/forge package manager, uv etc). Please use whatever you know and find convenient.

If you are new to the concept of Python's virtual environments, the easiest way of creating the environment would be standard venv module. Assuming that python can be called as python at your command line, run 

python -m venv env
source env/bin/activate
to create and activate a virtual environment called env. Note that some installations will not provide the vanilla python command - they may require you to use a command that specifies the version, e.g., python3.12.

Install aims-chain and clims into the activated environment.

Newer python versions than 3.10 will also require you to pip3 install setuptools, which is needed by aims-chain.

Once you are finished working in the virtual environment, you can leave the environment by typing deactivate.

Please also go through the Python venv tutorial to get more details on the topic.

aims-chain is package for finding minimum energy path and transition state, for FHI-aims. You can simply install it from Python Package Index to a virtual environment via:

pip3 install aims-chain

Info

If you wish to find the source and/or contribute to the development of the aims-chain package, you can access the repository via git clone https://gitlab.com/FHI-aims-club/aims-chain. Also, the source code for the package is available in utilities/aimsChain folder within FHI-aims source as a git subproject. If you want to use it and find the directory empty (this may happen if you work with the FHI-aims git repository), you need to update FHI-aims git submodules. For this run in the FHI-aims directory: 

git submodule init
git submodule update
After this the directory should be populated.

To install the Python project from a source directory, change into this directory and issue the following command: 

pip3 install .

The source code can also be installed in editable mode by changing into the source code directory and issuing 

pip3 install -e .
This way you will have on-the-fly access to the files being run and be able to alter them to your own needs.

4. Install clims

clims is a command-line interface for materials simulations for FHI-aims. It simplifies and streamlines the generation of input files. clims requires at least Python 3.9. You can simply install it into the same environment via:

pip3 install clims

More information can be found in the README of clims.