In the case of Ubuntu, the installation has be made as follows:
% sudo apt-get install python-dev python-numpy python-yaml python-paramiko python-h5py python-pip
% pip install spur --user
* pip install phonopy --user
* pip install phono3py --user
spur.py is an interface for ssh communication necessary to connect to computer clusters. spur.py uses python-paramiko as its ssh kernel.
For the automation of phonon related calculations, phonopy (https://atztogo.github.io/phonopy/) and phono3py (https://atztogo.github.io/phono3py/) have to be installed on a local machine where a cogue script is executed.
Cogue automation system controls computer clusters via queueing system. It is supported that the following software are installed on your computer cluster:
* Grid-engine queueing system
* VASP (http://vasp.at)
PBE-like queueing system is not yet prepared.
If you want to run everything on a local machine, see the following contents for how to set-up the grid-engine queueing system:
crystalView requires mayavi (http://docs.enthought.com/mayavi/mayavi/).
% sudo apt-get install mayavi2
Download Cogue from https://github.com/atztogo/cogue/tags .
Move into cogue directory and run setup.py script as follows:
python setup.py install --home=.
When using with VASP, location of pseudopotentials has to be told to
Cogue using the environment variable COGUE_POTCAR_PATH. The
details are given in the following sections.
For automatic generation of POTCAR files, directory of VASP
pseudopotentails has to be informed to cogue by setting environment
variable of COGUE_POTCAR_PATH. This is specified by setting the
following line in your shell configuration file, e.g., .bashrc or .zshenv.
COGUE_POTCAR_PATH=$DIR_PREFIX/cogue_potcar_dir
where $DIR_PREFIX is the directory prefix, for instance home
directory, /home/your_unix_name.
All the POTCAR files for every atom and electronic configuration
have to be extracted to plane text files. the filenames of the
extracted files are used to notify pseudopotential files used in
cogue through python dictionary.
For example, POTCAR files of GGA-PBE may be prepared by running
the following command in potpaw_PBE directory using zsh:
for i in `/bin/ls -d *(/)`;do zcat $i/POTCAR.Z > cogue_potcar_dir/"$i_PBE";done
In this example, the PAW potential files are created in
cogue_potcar_dir. Then a dictionary is used to pass this filename
to a VASP task using the keyword pseudo_potential_map like:
pseudo_potential_map = { 'Si': 'Si_PBE', 'O': 'O_PBE' }