phaseshifts 0.1.5-dev

Python-based version of the Barbieri/Van Hove phase shift calculation package for LEED/XPD modelling

This package is a Python-based implementation of the Barbieri/Van Hove phase shift (a.k.a. phshift) calculation package needed to produce phase shifts for various LEED packages (including CLEED), as well as for certain XPD packages. To quote the original authors’ site:

“The phase shift calculation is performed in several steps:

1. Calculation of the radial charge density for a free atom.

2. Calculation of the radial muffin-tin potential for atoms embedded in a surface defined by the user (the surface is represented by a slab that is periodically repeated in 3 dimensions, within vacuum between the repeated slabs); various approximations to the exchange potential are available; relativistic effects are taken into account.

3. Calculation of phase shifts from the muffin-tin potential.

4. Elimination of pi-jumps in the energy dependence of the phase shifts.”

Note

You can get the original Fortran source (& learn more about the phshift programs) from:

http://www.icts.hkbu.edu.hk/surfstructinfo/SurfStrucInfo_files/leed/leedpack.html

The phsh.py script aims to simplify these steps with a single command. For more information please read the documentation at http://pythonhosted.org//phaseshifts/

Install

The phaseshifts package requires CPython 2.6 or later and also uses the numpy, scipy and periodictable packages. Currently, it has only been tested extensively with Python 2.7 on Windows, so there are no guarantees with other platforms. To perform a setup follow the steps below.

1. Install the numpy, scipy and periodictable packages.

   On systems compatible with PyPI this can be done using the command:

   pip install numpy scipy periodictable

   Or if you have the easy_install package:

   easy_install install numpy scipy periodictable

   Older versions of numpy & scipy did not allow simultaneous installation - if you experience problems then try first installing numpy before attempting to install scipy.

   The periodictable package allows lookup of the most common crystal structure for a given element and is instrumental in many of the convenience functions contained in the model module.

   Alternatively download and install these packages manually following the instructions provided for the respective packages.

2. To install the phaseshifts package:

   python setup.py install

   With any luck the package has been installed successfully. A set of test scripts are provided, however a few simple checks may suffice using the command and an interactive session of the python interpreter:

   phsh.py --help
   python
   >>> import phaseshifts
   >>> from phaseshifts.lib import libphsh  # compiled FORTRAN .pyd or .so using f2py
   >>> libphsh.hartfock
   <fortran object>
   >>> exit(0) # okay if no errors found above

   If these execute without errors then it is likely that all is well, but in case of problems or bugs please use the contact provided below and I will do my best to address the problem quickly.

Tip

On Windows systems it may be easier to install a scientific python distibution rather than install the dependencies from source - Python(x,y) with mingw (gcc & gfortran) installed is highly recommended.

Ubuntu

On Ubuntu (14.04 LTS) some dependencies were needed, which can be installed using the following bash commands:

$ sudo apt-get install python-pip python-numpy python-scipy python-dev libblas-dev gfortran # should install f2py as a dependency of numpy/scipy
$ sudo pip install phaseshifts==0.1.5-dev | tee phaseshifts.log # explicit version needed
$ sudo ln -s /usr/bin/python2.7 /usr/bin/python # can skip if only a single version of python is installed

You may need to verifiy whether the phsh.py script is installed on the system $PATH and therefore please check by typing:

$ python /usr/local/bin/phsh.py --help # should work okay
$ phsh.py --help # may not work: phsh.py should be on the $PATH and executable

Note

You may need to specify an explicit version of python when trying the above commands e.g. python2.7

About the code

The example source codes provided in this package are intended to be instructional in calculating phase shifts. While it is not recommended to use the example code in production, the code should be sufficient to explain the general use of the library.

If you aren’t familiar with the phase shift calculation process, you can read further information in doc/ folder:

• phshift2007.rst - a brief user guide/documentation concerning the input files (& details of the original fortran phshift package).

• phaseshifts.pdf - a more detailed overview of the library functions and how to calculate phase shifts using the convenience functions in this package. This is not yet finished and so the reader is referred to the above document for the time being.

For those wanting a crash course of the Van Hove / Tong programs, I advise reading the phsh2007.txt document. See the examples/ directory to get an idea of the structure of the input files (for a random selection of models & elements). In particular see the cluster_Ni.i file for helpful comments regarding each line of input.

Those of you who are eager to generate phase shifts - first look at the example cluster files for a bulk and slab calculation, noting that the atoms in the model are in fractional units of the a basis vector for the unitcell (SPA units). Next, after creating a bulk and slab model in the cluster.i format, simply use the following python code:

>>> from phaseshifts.phsh import Wrapper as phsh
>>> phsh.autogen_from_inputs(bulk_file, slab_file)

This will hopefully produce the desired phase shift output files (at least for simple models) and works by assessing the two models to determine what output to produce. For more detailed documentation and function use refer to the pdf manual.

Tip

A standalone command line utility phsh.py is provided as a way of automating the generation of phase shifts as part of a script. For more information use:

phsh.py --help

Note

The leed.py module provides a conversion class for CLEED .inp and .bul files. This is included as part of the phsh.py module, however the file extension is important (needs .inp, .pmin, .bul, or .bmin) and error checking is limited. There are also plans to include a validator to check the files for malformatted input at some point in the future.

Development

For those wishing to see the latest code, please visit: https://bitbucket.org/Liam_Deacon/phaseshifts/overview

Disclaimer: The latest code is actively developed and may potentially be bug ridden… It is recommended that you use it with caution and a great deal of skepticism!

Acknowledgements

As with all scientific progress, we stand on the shoulders of giants. If this package is of use to you in publishing papers then please acknowledge the following people who have made this package a reality:

• A. Barbieri and M.A. Van Hove - who developed most of the original fortran code. Use A. Barbieri and M.A. Van Hove, private communication. (see doc/phsh2007.txt for further details).

• E.L. Shirley - who developed part of the fortran code during work towards his PhD thesis (refer to the thesis: E.L. Shirley, “Quasiparticle calculations in atoms and many-body core-valence partitioning”, University of Illinois, Urbana, 1991).

• Christoph Gohlke - who developed the elements.py module used extensively throughout for the modelling convenience functions (see ‘elements.py’ for license details).

I would also be grateful if you acknowledge this python package (phaseshifts) as: L.M. Deacon, private communication.

Thanks

I wish to personally add a heart-felt thanks to both Eric Shirley and Michel Van Hove who have kindly allowed the use of their code in the libphsh.f file needed for the underlying low-level functions in this package.

Contact

This package is developed/maintained in my spare time so any bug reports, patches, or other feedback are very welcome and should be sent to: [e-mail]

The project is in the early developmental stages and so anyone who wishes to get involved are most welcome (simply contact me using the email above).

To do

1. Documentation - the manual has been started, but is not complete and thus is a high priority. The current aim is to use sphinx to generate html and latex documents for semi-automated generation of both the tutorial and supporting website. If you have the phaseshifts source and the sphinx and the numpydoc PyPi packages then you can try making html or latex manuals using make html or make latexpdf commands from the doc/ directory.

2. Test suit to verify the package is working as expected.

3. GUI frontend (Qt ui files are provided in the gui/ directory for anyone wishing to undertake this challenge). Other frontends are welcome (I use Qt due to familiarity/experience). For those wishing a sneak preview, try executing main.pyw

See TODO.rst for more information.

Author list

• Liam Deacon - current maintainer