Metadata-Version: 1.1
Name: phaseshifts
Version: 0.1.2-dev
Summary: Python-based version of the Barbieri/Van Hove phase shift calculation package for LEED/XPD modelling
Home-page: https://pypi.python.org/pypi/phaseshifts
Author: Liam Deacon
Author-email: liam.deacon@diamond.ac.uk
License: MIT License
Description: ===================
        PHASESHIFTS PACKAGE
        ===================
        
        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
        
        Install
        =======
        
        The `phaseshifts <http://https://pypi.python.org/pypi/phaseshifts/>`_ package 
        requires CPython 2.6 or later and also uses the `numpy 
        <http://www.scipy.org/scipylib/download.html>`_, `scipy 
        <http://www.scipy.org/scipylib/download.html>`_ and `periodictable 
        <http://https://pypi.python.org/pypi/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 simple check may suffice using an interactive session of 
            the python interpreter:
        
              >>> import phaseshifts
              >>> from phaseshifts.lib import libphsh  # compiled FORTRAN .pyd or .so using f2py
        
            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) 
                 <http://code.google.com/p/pythonxy>`_ with mingw (gcc & gfortran) 
                 installed is highly recommended.
        
        
        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:
                 
                 .. code:: bash
                    
                    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, .bul, or .bmin) 
                  and error checking is limited There are also plans to include a 
                  validator to check the files for malformatted input.
                 
        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 heartfelt 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: liam.deacon@diamond.ac.uk
        
        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 <https://pypi.python.org/pypi/Sphinx>`_ 
            and the `numpydoc <https://pypi.python.org/pypi/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*
Keywords: phaseshifts atomic scattering muffin-tin diffraction
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Environment :: X11 Applications :: Qt
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Physics
