SAMPLE

Surface Adsorbate Polymorph Prediction with Little Effort

A tool for efficient structure search on surfaces. For details see https://www.sciencedirect.com/science/article/pii/S0010465519301973

Setup

1. Cloning

You can clone this repository by using

git clone git@gitlab.tugraz.at:othgroup/sample.git
git clone git@gitlab.tugraz.at:othgroup/tools.git

in the command line. This clones the SAMPLE code base and the tools library (AIMSTools, VASPTools, QETools). You need to setup SSH keys in your gitlab settings to succesfully clone the repositories.

2. Build C libraries

Next step is to build the CWrapper library of SAMPLE and AIMSTools. For that you need to execute the script in build.sh in sample/C and in tools/AIMSTools/C. If successful you should find a libCUtil.so file in the Release folder.

3. Set PYTHONPATH

Now one need to add sample and the tools library to the PYTHONPATH so that all import statements in the sample package are working. You can add these lines to your .bashrc file

export PYTHONPATH=${PYTHONPATH}:<sample-repo-directory>
export PYTHONPATH=${PYTHONPATH}:<tools-repo-directory>
export PYTHONPATH=${PYTHONPATH}:<tools-repo-directory>/AIMSTools
export PYTHONPATH=${PYTHONPATH}:<tools-repo-directory>/VASPTools
export PYTHONPATH=${PYTHONPATH}:<tools-repo-directory>/QETools

You need to exchange <sample-repo-directory> and <tool-repo-directory> with the path to your sample repository

4. install required python packages

sample needs several external python packages which can be easily installed via pip. Just run the following install command at the root folder of the sample repository.

pip install -r requirements.txt

For anaconda one can use

conda install --file requirements.txt

5. Run unittests

To test if everything is set up correctly run the unittests inside the tests folder in the sample repo and in the tools library.

python3 TestAll.py