https://github.com/usarmyresearchlab/arl_transire
https://github.com/usarmyresearchlab/arl_transire
Last synced: about 1 year ago
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- Host: GitHub
- URL: https://github.com/usarmyresearchlab/arl_transire
- Owner: USArmyResearchLab
- License: other
- Created: 2019-01-08T14:26:22.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2019-10-18T13:32:28.000Z (over 6 years ago)
- Last Synced: 2025-03-24T04:23:59.060Z (about 1 year ago)
- Language: Python
- Size: 262 KB
- Stars: 3
- Watchers: 5
- Forks: 3
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
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README
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 [](https://zenodo.org/badge/latestdoi/164665839)
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.