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 2.6 or later. Python version 3.4 or later is expected to work. Mac OS X users may use conda packages and also find some more information at. Windows users should use conda packages as well. Prepare the following Python libraries:.
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PyCharm provides methods for installing, uninstalling, and upgrading Python. To manage Python packages for the project interpreter, select the Project.
Python and its header files. numpy. matplotlib. python-yaml (pyyaml). python-h5py (h5py).
Two kinds of multithreadings can be used in phonopy. Multithreaded BLAS linked numpy Phonopy uses numpy to run singular value decomposition in the calculation of force constants and diagonalizaion of dynamical matrices. For these, numpy internally calls the LAPACK routines. Therefore if a user installs a numpy that is linked with multithreaded BLAS, these parts are multithreaded. For example, MKL linked numpy is easily installed using conda. OpenMP support in phonopy and spglib OpenMP are applied in the symmetry finding of spglib and the distribution of symmetry reduced force constants elements to full force constants elements in phonopy. When a chosen supercell is very large and there are many cores on a computer, these parts may work well to reduce the computational time.
In the default phonopy setting, this is not activated. To enable this, it is necessary to build phonopy using modified setup.py in which withopenmp = False must be changed to withopenmp = True. For this, currently only gcc is supported. In phonopy, PATH and PYTHONPATH play important roles.
Of course the information about them can be easily found in internet (e.g. )), 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.
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