Phono3py Installations on Tetralith & Sigma

Phono3py "calculates phonon-phonon interaction and related properties using the supercell approach."

Documentation and further information can be found here

How to use

At the moment, we recommend that you install phono3py in your own account. Here, we will outline how you can do this, following the recommendations from here and here. This is a recipe for how to install phonopy and phono3py using Anaconda Python on Tetralith/Sigma. Since phono3py needs to use phonopy, we recommend to install it at the same time.

First, load a suitable new Anaconda Python module on Tetralith, e.g.:

module load Python/2.7.14-anaconda-5.0.1-nsc1

The idea is to create a virtual environment installation which you control.

The virtual environments by default ends up in a folder .conda in your home directory. We would recommend to move this folder to your project space, since it may grow quite much, especially if you create several virtual environments. After moving the folder, you can create a link to it in your home folder:

mv .conda /proj/your/project/space
ln -s /proj/your/project/space/.conda .conda

If it doesn’t exist already, you might create the folder first and then the link. If it exists, moving it might take some time if it’s large.

Create a virtual environment called e.g. “allphonopy”:

conda create -n allphonopy python=2.7

To use it, it needs to be activated:

source activate allphonopy

Now install phonopy with:

conda install -c conda-forge phonopy h5py
conda install hdf5=1.8.18

and install phono3py:

conda install -c atztogo phono3py

as long as the virtual environment “allphonopy” is activated, it can be used. To switch it off, type:

source deactivate

To list the installed packages:

conda list

e.g. you can find that it has its own version of ASE, so all dependencies are taken care of from within the virtual environment.

While everything seems to be installed, you might need to check that it works as expected.

To summarize, when you want to use phonopy/phono3py from the example:

module load Python/2.7.14-anaconda-5.0.1-nsc1
source activate allphonopy

OBS: it’s typically not a good idea to load the Anaconda Python module directly in .bashrc

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