CDW Unit Cell Generator

Copyright (C) 2016-2019 David C. Miller

Code written by David C. Miller (mill2723 at msu dot edu) Michigan State University Department of Physics and Astronomy

Quick Install:

Try the following:

• ./configure
• make
• make install

Other options:

• make debug
  • runs make with '-O0' optimization flag and '-pg -g3' debug flags
• make optim
  • runs make with '-O3' optimization flag
• make uninstall
  • removes binary files from install directory

You may need to run any of the above as root depending on local folder privileges. Additonally, see ./configure --help for more options.

Information

Description

This project is developed to generate a VASP coordinate file for a transition metal dichalcogenide (TMD) structure. Given a choice of metal and chalcogen atoms, the lattice parameters, and the super cell size in additional to information regarding the phase and layers of the material.

Current Functionality

Currently the only options for layers are bulk and monolayer systems. In the future I hope to add functionallity to have an arbitrary number of layer (i.e. 0 for bulk, 1 for monolayer, 2 for bilayer, etc.).

Currently there is a test functionallity (-t command line option) which will generate some sample files for monolayer with and without uniaxial and biaxial strain and some bulk structures. Currently there is no verification code for this so files need to be verified manually. This full testing functionallity is planned for a future release.

Use

Use of this program involves calling the binary and giving it all the arguments necessary for output. The order and style of inputs is given in the help for the program (just call the binary without any arguments). They are also given below:

All of the options in the first section below must be specified in the following order:

   1. Lattice parameter a (in Angstroms)
   2. Lattice parameter c (in Angstroms)
   3. Super cell length a'
   4. Super cell length a''
   5. Super cell length b'
   6. Super cell length b''
   7. Layers (Bulk = 0, Monolayer = 1)
   8. 1T (T) or 2H (F)
   9. Randomize coordinates (T/F)
   10. Element M (use atomic number)
   11. Element X (use atomic number)

The following options are not required but allow generation of additional unit cells with strain added along different axes:

  12. Logical for Strain (T/F)
  13. Strain a axis (T/F)
  14. Strain b axis (T/F)
  15. Strain c axis (T/F)

In addition to those options above, the following four options can be added after to specify the amount of strain:

  16. Absolute/Relative Strain (T/F)
  17. Strain Value (Ang or %)
  18. Minimum strain (#)
  19. Maximum strain (#)

The a', a'', b', and b'' parameters are the two-vectors that specify the super-cell size. These describe how the super-cell is constructed in terms of the original a and b lattice parameters (where b is at 120 degrees to a for the hexagonal primitive cell). This allows for not only typical super cells. For example a 3x3 super cell would be (3,0) x (0,3). More complex cells like the Star of David distortion in TaS2 are also possible where the $\sqrt{13}x\sqrt{13}$ cell is given by (4,1) x (-1,3) which results in the proper angle between the super cell and the primitive cell.

Compiling and Installing

This program was designed to be compiled with the GNU C Compiler (gcc) and GNU Make. Additionally It can also use the clang processor. It also uses some simple bash commands. It should work on any Linux/UNIX system that can meet these requirements but I can offer no guarantees. I suspect (but have not tested) that this could be compiled on Cygwin or any other system with a C compiler if one so desired. If another C compiler is used it is very likely that the current compiler options will need to be changed. This program does not use any special libraries so it should suffice to pass the include and source directories (./src and ./inc).

Currently I have used this on Ubuntu 16.04, Ubuntu 18.04, Ubuntu 16.04, and CentOS 6.6, CentOS 7, and ArchLinux.

Dependencies (with earliest tested version):

• GNU gcc 4.6.4
• GNU Make 3.81
• GNU bash 4.1.2
• GNU automake 1.11.1
• GNU autoconf 2.63

Also, this does compile with the C99 ISO standards. This includes using the gcc -std=c99 option. If you wish to compile without this dependency there should be no problems. This is mostly to ensure better portability. Additionally, one may wish to remove the WARN_FLAG variable from the makefile when compiling.

Also, the code was written on an x64 system but there shouldn't be many dependencies if any. If you do compile and run this code on a widely different system (or perhaps just a very popular system) than what has been described please let me know so I can add it to this document.

It should be possible to compile this code with older version of gcc or with Clang by removing certain warning flags.

To install:

1. Run ./configure with any additonal options (see ./configure --help for details). Use --prefix=/path/to/install/root to change the root directory for the install. By default make install will install the binary file to '/usr/local/bin'.
2. Run make
3. Assuming everything went smoothly run make install (you may need to run this as root or use sudo depending on the installation directory).

To uninstall simply run make uninstall

Other: make mostlyclean will delete any extraneous files while make clean will remove all files generated by make

Git repository

This code is available at: repository

For releases see: releases

-For other information go to: cdw-unit-cell-generator

Bug Reports

Please reports all bugs in the GitHub Issues section. This way others can view the bugs. If there is no response there you can try sending me an email with the subject "Bug - CDW Unit Cell Generator" along with a thorough description of the bug. Please include the following:

• output files
• full printout of stdout and stderr
• version
• any other potentially useful information
• description of what you expected and what went wrong

I will try to take a look at it as soon as possible and get back to you with a fix or a patch.

Disclaimer

I wrote this to be a useful program for computational work done with VASP. There are other tools out there as well and I cannot promise compatability with them or that my code will produce identical results. Please verify the results and output on your own. Additionally, this project is partially done in my free time so I make no guarantees about the time line for fixes or additional features. Likely the best way to fix something is to modify the code yourself and make a pull request.

License

This code is licensed under LGPLv3. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE for details.