Derivative structure enumeration library
Switch branches/tags
Nothing to show
Clone or download
Latest commit 400f6d3 Sep 15, 2018

README.md

BRIEF DESCRIPTION

This code generates the derivative superstructures of a parent lattice. It works for general lattices, including "multilattices," like HCP, which have more than one lattice point in the unit cell. The code can enumerate over all concentrations or in a restricted concentration range.

As of Dec. 2011, both modes (all concentrations vs. restricted conc. range) can also be used with site restrictions---some atomic types can be disallowed on some sites in the parent lattice. In other words, the possible occupation of sites by different atoms does not have to be the same on each parent lattice site. You could have two sites in the parent lattice and one could be populated by A or B atoms and the second site could be populated by B and C atoms, for example. (But see Ex. 5 in the EXAMPLES file for some caveats.)

As of Oct. 2016 the concentration restricted enumeration can also include displacement directions in the enumeration (the user may specify to displace any number of each atomic species from the lattice).

A discussion of the algorithm and its applications can be found in the following publications. If you use this code in a publication, we would appreciate it if you would cite the appropriate paper below. Thank you.

Gus L. W. Hart and Rodney W. Forcade, "Algorithm for generating derivative structures," Phys. Rev. B 77 224115, (26 June 2008)

Gus L. W. Hart and Rodney W. Forcade, "Generating derivative structures from multilattices: Application to hcp alloys," Phys. Rev. B 80 014120 (July 2009)

Gus L. W. Hart, Lance J. Nelson, and Rodney W. Forcade, "Generating derivative structures at a fixed concentration," Comp. Mat. Sci. 59 101-107 (March 2012)

If you download this code, please send me an email so I can let you know about bugs/improvements/etc.

COMPILING THE CODE

To compile the code manually, clone the repository with the --recursive flag:

git clone --recursive https://github.com/msg-byu/enumlib.git

We need to compile the symlib submodule before compiling enumlib.
Go to the enumlib/symlib/src directory:
cd enumlib/symlib/src

Set an environment variable to identify your fortran compiler:
[in the bash shell, gfortran compiler]
export F90=gfortran
[the Makefile also recognizes ifort]

Then compile using the Makefile:
make

(Alternatively, instead of setting the F90 environmental variable first, you may just specify the variable during the make: make F90=gfortran.)

Next, make the enumeration library
cd ../../enumlib/src
make

Finally, to make a stand-alone executable for enumeration:
make enum.x

It is possible to compile enumlib using conda on OSX and Linux. To do so use the command:

conda install --channel matsci enumlib

If you have trouble compiling, please send me a note and I'll try and assist you. gus.hart@gmail.com, 801-422-7444

HOW TO USE THE CODE:

Example input files are in the input ('enumlib/support/input') directory.

To include displacement directions in the enumeration, it is also neccessary to provide an arrows.in file examples of which can also be found in the ('enumlib/support/input') directory.

Detailed directions on how to run the code for several of the example input files can be found in the enumlib/support/EXAMPLES file.

There are also helper programs in the aux_src directory for making VASP POSCARs, pictures of 2-D enumerations, etc.

makeStr.py <-- Makes POSCARS for the desired enumerated structures. (makeStr.x from the fortran code has been superceded by this python script.) make 2Dplot.x <-- To make a program that plots 2D enumeration results. make polya.x <-- To make a program that predicts the maximum number of unique structures for the system (this program gives an upper bound on the number of solutions the user should expect because the polya algorithm counts the superperiodic structures but enum.x does not).

makeStr.py is a python code which can be accessed by typing python makeStr.py [struct#] -flags into the terminal where struct# an integer specifying the desired structure number from the struct_enum.out file. Additional options for the script include:

-elements [element list] <-- This option uses Vegard's law to make an initial guess at the lattice parameter for the cell. If using this option, list the elements in the system in a space-delimited list such as Al Cu Ni.

-displace [distance] <-- This option displaces atoms by the given fraction of the lattice parameter. This will only work if displacement directions were included in the enumeration. When using this option, express the desired displacement amount as a fraction of the lattice parameter.

-rattle [amount] <-- Adjusts the displacements of the atoms by a random distribution of the maximum fraction of the displacement specified by the displace flag.

If you have questions, email or call: gus.hart@gmail.com, 801-422-7444