Transire generates and manipulates crystalline interface structures built on the Atomic Simulation Environment (ASE). A number of search methods are available to minimize the interface energy, including a random walk Markov Chain search and rotations of one slab relative to the other.
Energy calculations are performed using CP2K or LAMMPS, and any method available in either can be used for calculating the interface energy. The electron transport properties across the interface can be calculated using the non-equilibrium Green's function (NEGF) method implemented in ASE (requires CP2K calculation).

Transire is Latin for "to cross over" in reference to transport across the interface.

Requirements

Python 2.7

ASE 3.12 or newer

pycp2k (if using cp2k)

    available from project page: https://github.com/SINGROUP/pycp2k

cp2k 4.1 or newer (optional)

    If not using cp2k, make sure all energy related flags are set to
    False in the input file 

LAMMPS (26 Jan 2017) or newer (optional)

    install serial version with mode=shlib and install-python options

lammpslib

    https://svn.fysik.dtu.dk/projects/ase-extra/trunk/ase/calculators
    
    copy the file into your local library folder, usually
    ~/.local/lib/python2.7/site-packages which is where python installs
    the other libraries

Installation

Installation performed using setup.py in the main directory:

>>>  python setup.py install

To install into the local user space:

>>>  python setup.py install --user

If transire is installed in local space, ensure that the path environmental variables are set. The $PYTHONPATH variable needs to include ~/.local/lib/pythonX/site-packages where pythonX is the version of python on your system. The $PATH variable needs to include ~/.local/bin. Example commands to set environment variables (cshell):

>>>  setenv PYTHONPATH $(PYTHONPATH):~/.local/lib/pythonX/site-packages
>>>  setenv PATH $(PATH):~/.local/bin

To test for successful installation use:

>>>  transire.py -h

or

>>>  python -m transire.py -h

If installed correctly, the help description of input options for transire will be printed.

Documentation

Documentation is designed for sphinx v1.7.0 and can be compiled by running:

make html

in the 'doc' directory. Documentation output defaults to 'doc/html/'.

Citations

If you find ARL Transire useful, please cite its

Legal

Transire is available under the GNU Lesser General Public License (LGPL). A copy of the LGPL is provided in the LICENSE file.

Copyright (2018) Caleb Carlin.