6. Scripts

6.1. phsh.py

6.1.1. Command line usage

The phsh.py script is placed into the system PATH during installation of the phaseshifts package. It can then be used from the command line, e.g. phsh.py --help will produce a list of command line options:

usage: phsh.py [-h] -b <bulk_file> -i <slab_file> [-t <temp_dir>] [-l <lmax>]
             [-r <start_energy> <final_energy> <step>] [-f <format>]
             [-S <subdir>] [-v] [-V]


phsh - quickly generate phase shifts

      Created by Liam Deacon on 2013-11-15.
      Copyright 2013-2014 Liam Deacon. All rights reserved.

      Licensed under the MIT license (see LICENSE file for details)

      Please send your feedback, including bugs notifications
      and fixes, to: liam.deacon@diamond.ac.uk

    usage:-

  optional arguments:
  -h, --help            show this help message and exit
  -b <bulk_file>, --bulk <bulk_file>
                        path to MTZ bulk or CLEED *.bul input file
  -i <slab_file>, --slab <slab_file>
                        path to MTZ slab or CLEED *.inp input file
  -t <temp_dir>, --tmpdir <temp_dir>
                        temporary directory for intermediate file generation
  -l <lmax>, --lmax <lmax>
                        Maximum angular momentum quantum number. [default: 10]
  -f <format>, --format <format>
                        Use specific phase shift format i.e. 'cleed', 'curve'
                        or 'none'. Choose 'curve' if you wish to produce
                        XYY... data for easy plotting. <format> is case
                        in-sensitive. [default: 'cleed']
  -r <energy> [<energy> ...], --range <energy> [<energy> ...]
                        Energy range in eV with the format:
                        '<start> <stop> [<step>]', where the <step> value is
                        optional.  Valid for relativistic calculations
                        only. [default: (20, 600, 5)]
  -S <subdir>, --store <subdir>
                        Keep intermediate files in subdir when done
  -v, --verbose         set verbosity level [default: None].
  -V, --version         show program's version number and exit

6.1.2. CLEED compatibility

It is possible to use this script to generate phase shift files iteratively during a geometry search for the CLEED package. In this manner phase shifts will be generated at the beginning of each cycle of the search.

For this to work, the environment variable CSEARCH_LEED must point to the phsh.py script, which will invoke the LEED program in PHASESHIFT_LEED after execution. When operating in this mode, the following assumptions are made:

  1. -b <bulk_file> option is not needed and the filename is assumed by changing the file extension of <slab_file> to ‘.bul’

  2. -f CLEED format is implied.

  3. The generated phase shifts are stored in the directory set by the CLEED_PHASE environment variable, however a named copy with the iteration number (read from the matching ‘.log’ file) will be placed in the same directory as the <slab_file>.

  4. <lmax> is equal to 10, unless additional parameter syntax is given in the CLEED *.inp file. To use phase shift specific lmax values, then add a new line with:

    lmax:  <phase_shift> <lmax>

    for each phase shift you wish to have a different lmax to that of the default.

  5. The element and oxidation of each atom in a model is guessed by reading the phase shift tag from the CLEED input file. For example:

    po:  O_2-_COOH ...

    will be interpreted as a Oxygen with a -2 oxidation state and with a unique name tag of “O_2-_COOH” to show it is in a carboxylic group. Note the ‘-’ may be at the beginning or the end of the oxidation sub-string. If no oxidation state is given then the atom is assumed to have zero charge.

  6. The muffin-tin radius of the phase shift species is guessed from lines with:

    rm:  <phase_shift> <radius>

    However, if no value is found the radius is guessed from the ELEMENTS dictionary within phaseshifts.elements depending on the valency of the given phase shift element.

A full list of additional syntax to customise the generation of the phase shifts when using CLEED input files can be found in phaseshifts.leed.Converter.import_CLEED().

Note

If the PHASESHIFT_LEED environment variable is not found, but CLEED_PHASE is, however, found then the program will place the generated files in this directory unless a specific -S <subdir> is provided.