pymuon-suite

Collection of scripts and utilities for muon spectroscopy.

Installation

Requires Python 3.8+. Install with pip or conda:

pip install pymuonsuite

conda install pymuonsuite

If you plan to read CASTEP .phonon files, you will also need to install Euphonic:

pip install euphonic

conda install euphonic

Help with Euphonic installation can be found in the Euphonic documentation.

spglib build failed during pip install

On some platforms, additional tools are needed to build the spglib Python module when installing via pip. On Windows, you may need to install Microsoft C++ Build Tools; on Linux you may need to apt-get install python-dev or yum install python-devel according to your distribution. This should not be necessary if installing via conda, and so we recommend using conda if you want to avoid installing these tools.

Further help with Spglib installation can be found in the Spglib documentation.

Command line scripts

The following is a list of currently supported command line scripts. For any of them, use <script> --help to see usage information.

• pm-muairss: generates a number of random muon structures for AIRSS optimisation using Poisson spheres distribution and different calculators, as well as carries out their clustering analysis after the calculations have been done. Usage is pm-muairss <structure file> <parameter file>, with the additional option -t w when one desires to generate the structures instead of analysing the results. This is done to help avoid overwriting one's results by mistake;
• pm-muairss-gen: alias for pm-muairss with the -t w option on;
• pm-uep-opt: Unperturbed Electrostatic Potential optimisation for a single muon in a unit cell; it's used as pm-uep-opt <parameter file>;
• pm-uep-plot: Unperturbed Electrostatic Potential plotting for a given unit cell and specific lines or planes along it; it's used as pm-uep-plot <parameter file>;
• pm-symmetry: analyses the symmetry of a structure with spglib and identifies the Wyckoff points, which ones are occupied, and which ones can be uniquely identified as being extrema rather than saddle points, thus providing some candidates for stopping sites in crystals; it's used as pm-symmetry <structure file>;
• pm-asephonons: compute phonons for the given structure using ASE and DFTB+;
• pm-nq: generates input files for quantum effects using a phonon approximation or analyses the results (work in progress)

For more in-depth information about each tool and their usage, check the Wiki.