Conda is a software package management system. Once the conda system is set-up (see miniforge), the installation of phonopy is super easy for any of Linux, MacOSX, and Windows. Phonopy is installed using conda by
% conda install -c conda-forge phonopy
This phonopy’s conda package is prepared and maintained by Paweł T. Jochym at conda-forge channel (please be aware that this is not a trivial job).
In the following procedure, conda’s environment (see miniforge) is used not to interfere existing environment (mainly python environment).
% conda create -n phonopy -c conda-forge % conda activate phonopy % conda install -c conda-forge phonopy
To exit from this conda’s environment:
% conda deactivate
To use this phonopy, entering this environment is necessary like below.
% conda activate phonopy (phonopy) % phonopy _ _ __ | |__ ___ _ __ ___ _ __ _ _ | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | | | |_) | | | | (_) | | | | (_) || |_) | |_| | | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, | |_| |_| |___/ 2.12.0 Python version 3.9.6 Spglib version 1.16.2 Supercell matrix (DIM or --dim) was not explicitly specified. By this reason, phonopy_yaml mode was invoked. But "phonopy_params.yaml", "phonopy_disp.yaml" and "phonopy.yaml" could not be found. ___ _ __ _ __ ___ _ __ / _ \ '__| '__/ _ \| '__| | __/ | | | | (_) | | \___|_| |_| \___/|_|
Recent hdf5 versions just as installed may not work on NFS mounted file systems. In this case, setting the following environment variable may solve the problem:
The procedure to setup phonopy is explained in this section. It is supposed that phonopy is installed on the recent linux distribution like Ubuntu or Fedora with Python version 3.7 or later. Mac OS X users may use conda (conda-forge channel) packages. Windows users should use conda (conda-forge channel) packages as well.
Prepare the following Python libraries:
Python (>=3.7) and its header files
It is recommended to install seekpath to plot phonon band structure:
Scipy is optional because most of features of phonopy can work without scipy, but scipy is needed for fitting to equations of states for quasi-harmonic phonon calculation.
For the CP2K interface, the following package will be needed to install:
The python libraries can be installed using conda. Conda packages are
distributed in binary. Minimum setup of conda envrironment is done by miniforge,
which is downloaded at https://github.com/conda-forge/miniforge. It is strongly
recommended to create conda’s virtual environment by
conda create -n <venvname> as written above. The installation of necessary
libraries is done as follows:
% conda install -c conda-forge numpy scipy h5py pyyaml matplotlib-base seekpath spglib
A libblas library installed can be chosen among
[openblas, mkl, blis, netlib].
If specific one is expected, it is installed by (e.g.
% conda install -c conda-forge "libblas=*=*openblas"
If you need a compiler,
% conda install -c conda-forge complilers
If package installation is not possible or you want to compile with special
compiler or special options, phonopy is built using
setup.py. In this case,
manual modification of
setup.py may be needed.
Get the source code from github
% git clone https://github.com/phonopy/phonopy.git % cd phonopy % git checkout master
% python setup.py build % pip install -e .
Sometimes previous installations of phonopy prevent from loading newly installed phonopy. In this case, it is recommended to uninstall all the older phonopy packages by
pip uninstall phonopyas many times as no phonopy packages will be found. Error message may be shown, but don’t mind it. Similarly do
conda uninstall phonopy.
There may still exist litter of phonopy packages. So it is also recommend to remove them if it is found, e.g.:
% rm -fr ~/.local/lib/python*/site-packages/phonopy*
Set correct environment variables
PYTHONPATH play important roles. Of course the
information about them can be easily found in internet (e.g.
https://en.wikipedia.org/wiki/PATH_(variable)), so you really have to find
information by yourself and read them. Even if you can’t understand them, first
you must ask to your colleagues or people before sending this unnecessary
question (as a researcher using computer simulation) to the mailing list.
The problem appears when phonopy execution and library paths are set multiple times in those environment variable. It is easy to check current environment variables by:
% echo $PATH
% echo $PYTHONPATH
When multiple different phonopy paths are found, remove all except for what you really need. Then logout from the current shell (terminal) and open new shell (terminal) to confirm that the modification is activated.
LDSHARED="icc -shared" may be of help. See this github issues,