phenum 2.2.0

Description:

phenum 2.2.0

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.

Installing the code
To install the code use the following command in the phonon-enumeration
directory:
pip intsall phenum
Alternatively you can clone this repository and use:
python setup.py install
from within the phonon-enumeration directory.


Running the code

Complete enumeration of a system.
If you want to enumerate every possible structure specified in your
‘struct_enum.in’ file, a sample of which can be found in the input
folder, then use the commend:
enumeration-py -enum


Enumerating a subset
If the total number of arrangements in your system is huge you may not
want to enumerate them all. In that case it is possible to enumerate a
subset of the system as follows. Examples of all input files can be
found in the input folder. First have the code 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