Metadata-Version: 2.0
Name: phenum
Version: 1.4.2
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
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
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: Topic :: Scientific/Engineering :: Physics
Requires-Dist: numpy
Requires-Dist: pyparsing
Requires-Dist: termcolor

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.

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
----------------

You now have everything you need to run the new enumeration code. You
have two options for how to proceed. First the algorithm can use the
burnside polya algorithm to predict the number of unique structures that
exist for each HNF and symmetry group produced. This mode is run as
follows:

::

    enumeration.py -polya

and expects a file called lattice.in an example of which can be found in
the input folder. This mode produces a file for each cell size that
lists the number of unique configurations for each HNF at every possible
concentration range for the cell size. This data can be very useful when
modeling large systems as it will allow the user to select an
appropriate distribution of structures to use given the number of each
type available.

The second option is the actual enumeration of derivative structures.
This mode is run using:

::

    enumeration.py -enum

and expects a file called enum.in which can also be found in the input
folder. The enum.in folder should contain a list of the desired HNFs,
their concentration ranges, and the number of arrangements for the HNF
concetrtaion range pair the user would like. For example:

::

    # HNF                           Conc.       Number
      1 0 1 0 2 11                  8 3         2
      1 0 1 3 4 8                   4 4         1
      1 0 1 1 4 11                  6 5         3
      1 0 1 0 0 10                  6 4         2
      1 0 1 1 5 10                  8 2         1
      1 0 1 1 2 10                  7 3         1
      1 0 1 0 3 11                  7 4         3
      1 0 1 0 2 9                   5 4         2

Python Packages Used
--------------------

The enumeration.py code require the following python packages to run:

-  numpy

-  pyparsing

-  termcolor


