From phonopy v2.7.0, spglib has to be installed separately.
Conda is an open source package management system. Once the conda system is set-up (see details about conda setting up), the installation of phonopy is super easy for any of Linux, MacOSX, and Windows. To install:
% 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). Installation of h5py is optional. When using hdf5 files from NFS mouted location, the latest h5py may not work. In this case, installation of an older version is recommended:
% conda install hdf5=1.8.18
In the following procedure, conda’s environment (see details at conda web site) is used not to interfere existing environment (mainly python environment).
% conda create -n phonopy -c conda-forge python=3 % 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 _ __ | |__ ___ _ __ ___ _ __ _ _ | '_ \| '_ \ / _ \| '_ \ / _ \ | '_ \| | | | | |_) | | | | (_) | | | | (_) || |_) | |_| | | .__/|_| |_|\___/|_| |_|\___(_) .__/ \__, | |_| |_| |___/ 2.7.0 Python version 3.7.6 Spglib version 1.14.1 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. ___ _ __ _ __ ___ _ __ / _ \ '__| '__/ _ \| '__| | __/ | | | | (_) | | \___|_| |_| \___/|_|
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 2.7 or later. Python version 3.4 or later is expected to work. 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 and its header files
And optionally the following:
cp2k-input-tools, for the CP2K force calculator backend
The python libraries can be installed using conda. Conda packages are
distributed in binary. Minimum setup of conda envrironment is done by
miniconda, which is downloaded at https://conda.io/miniconda.html. 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 spglib
If you need a compiler, for usual 64-bit linux system:
% conda install -c conda-forge gcc_linux-64
% conda install -c conda-forge clang_osx-64
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
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*
When using conda environment, this information is not applicable.
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.
dviping packages may be required
to install on your system, if you see something like the following
messages when ploting:
! I can't find file `pncr7t'.
! LaTeX Error: File `type1cm.sty' not found.
LDSHARED="icc -shared" may be of help. See this github issues,