Metadata-Version: 1.1
Name: phenum
Version: 2.0.0
Summary: Enumeration of symmetrically unique derivative superstructures of crystals.
Home-page: https://github.com/wsmorgan/phonon-enumeration
Author: Wiley S Morgan
Author-email: wiley.s.morgan@gmail.com
License: MIT
Description: [![PyPI](https://img.shields.io/pypi/v/phenum.svg)](https://pypi.python.org/pypi/phenum/) [![Build Status](https://travis-ci.org/wsmorgan/phonon-enumeration.svg?branch=master)](https://travis-ci.org/wsmorgan/phonon-enumeration)[![Coverage Status](https://coveralls.io/repos/github/wsmorgan/phonon-enumeration/badge.svg?branch=phenum-dev)](https://coveralls.io/github/wsmorgan/phonon-enumeration?branch=phenum-dev)
        
        # phonon-enumeration
        
        This code is used to enumerate all the derivative structures of a
        system within a crystalographic system within specified concentration
        and cell size ranges. The code uses a newly developed group theoretic
        approach that is extremely efficient and can include the enumeration
        of displacement directions, or arrow directions, within a system.
        
        Full API Documentation available at: [github pages](https://wsmorgan.github.io/phenum/).
        
        ## Prerequisites
        
        The code currently requires a modified version of the previous
        enumeration code, available at https://github.com/msg-byu/enumlib, to
        run. To make this modified code do the following, get the symlib library:
        
        ```
        git clone https://github.com/msg-byu/symlib.git
        cd symlib/src/
        make F90=(your compiler, gfortran or ifort)
        cd ../../
        ```
        
        Then get a copy of enumlib:
        
        ```
        git clone https://github.com/msg-byu/enumlib.git
        ```
        
        Now copy the Makefile, derivative_structure_generator.f90, and
        wrapper.f90 from the phonon-enumeration/support directory to the
        enumlib/src/ directory. Now we can make the enum.x executable and
        place it in our path:
        
        ```
        cd enumlib/src/
        make F90=(your compiler) enum.x
        cp enum.x /bin/.
        ```
        
        In order for enum.x to run you will need to have its input folder
        struct_enum.in, an example of which can be found in the input folder,
        for the system you desire to model. You may then choose to run enum.x
        yourself to generate the needed input files by typing:
        
        ```
        enum.x
        ```
        
        This will now generate a number of files titled cell_# where # is the
        cell size. These files contain the information needed to run the new
        enumeration code. If you do not run enum.x the enumeration.py code
        will execute it for you as long as its in your path. The input files
        are setup so that each HNF with it's SNF and left transform (as
        described in http://msg.byu.edu/papers/multi.pdf and
        http://msg.byu.edu/papers/GLWHart_enumeration.pdf) are listed in a
        file titeled matrices:
        
        ```
          #n	SNF		   HNF			          left transform
           1  1  1  4    1  0  1  0  0  4      1    0    0    0    1    0    0    0    1
           1  1  1  4    1  0  1  0  1  4      1    0    0    0    1    0    0   -1    1   
        ```
        
        The first digit indicates which of the group.n files contains the
        symmetry group for that system. As can be seen only the diagonals of
        the SNF and lower traingular entries of the HNF should be included in
        this file. The group.n files contain the permutations of the sites on
        the lattice that constitute the symmtery group.
        
        ## Installing the code
        
        To install the code use the following command in the
        phonon-enumeration directory:
        
        ```
        python setup.py install
        ```
        
        ## Running the code
        
        # Enumerating a system
        
        You now have everything you need to run the new enumeration code. The
        work flow for this code is as follows. Samples of all input files can
        be found in the input folder. First find the polya distribution for the
        system described in your lattice.in file:
        
        ```
        enumeration.py -polya
        ```
        
        Next we need to build an enum.in file. You may either build this by
        hand or have the code build it for you using the `-distribution`
        option which takes two arguments, the type of distribution and the
        number of structures we want in the results.
        
        ```
        enumeration.py -distribution all all
        enumeration.py -distribution all 100
        ```
        
        If any option other than 'all' is passed into the first argument then
        the code will not produce an enum.in file that will be useful for the
        actual enumeration. The options of 'HNF', 'shape', and 'conc' are
        simply for the user's viewing purposes.
        
        Once an enum.in file has been constructed we can enumerate the entire
        set of unique configurations:
        
        ```
        enumeration.py -enum
        ```
        
        This will make an enum.out file listing the unique configurations.
        
        # Making POSCARS
        
        Phenum contains a second executable for making POSCARS. To make a
        POSCAR first select a structure number, or range of structures, for
        the POSCARs to be constructed for from the enum.out file. Then run:
        
        ```
        makeStr.py 10
        ```
        
        This would make the POSCAR for the 10th structure. For a range of
        structures use:
        
        ```
        makeStr.py 20 30
        ```
        
        To make POSCARs for the 20th to 30th structures. The POSCARS are saved
        as vasp.* files. To have the code calculate the lattice parameter as
        well use:
        
        ```
        makeStr.py 10 -species Al Ni
        ```
        
        Where the Al and Ni are replaced with the elements in the system being
        modeled.
        
        # Visualization
        
        At times it is useful to construct the distribution based off the
        shapes of the supercells. For the non-expert user an option has been
        added to the code to make pictures of the supercells. To do this first
        we need to make a distribution of only the supercells:
        
        ```
        enumeration.py -distribution shape all -savedist
        ```
        
        This created an enum.in file that lists only the supercells and the
        number of unique arrangements within each supercell. We can now
        visualize each of the supercells:
        
        ```
        enumeration.py -visualize -shape
        ```
        
        This creates a pdf file for each of the supercells. The `-shape`
        option forces the code to include the lines that define the cell in
        the pdfs.
        
        ## Python Packages Used
        
        The enumeration.py code require the following python packages to run:
        
        - numpy
        
        - pyparsing
        
        - termcolor
        
        - matplotlib
        
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: MacOS
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Topic :: Scientific/Engineering :: Physics
