Work with thirdorder

Work with thirdorder#

thirdorder was originally developed based on Python2.
Some of its contents have become less compatible with Python3.
Tepkit provides some ways to make thirdorder more suitable for the current environment.

Installation#

The original installation script (setup.py) of thirdorder needs the distutils package to work. However, distutils has been deprecated since Python 3.10 and been removed since Python 3.12. [1]

Tepkit provides a new setup.py file which uses the more modern setuptools package to compile and install the thirdorder package.
You can find the scripts at Tepkit/tools/thirdorder_tools/*.

In addition, our script can automatically obtain the pathes of the spglib libraries installed by python. You no longer need to find and fill the pathes in the script by yourself anymore.

How to use the scripts:

  1. Download the lastest released version of thirdorder from the release page, and extract it. Or clone the repository (git clone https://bitbucket.org/sousaw/thirdorder.git) to your local machine.

  2. Replace the original setup.py and cthirdorder_core.pxd file with the ones by Tepkit.

  3. Install the required packages of thirdorder by the command pip install -r requirements.txt.

  4. Install thirdorder by the command python setup.py install.

  5. The thirdorder package will be installed as thirdorder_core in the python site-packages directory.

  6. Try the following code to test if the installation is successful.

For Windows:

import spglib
import os
spglib_dll_dir = os.path.dirname(spglib.__file__)
os.add_dll_directory(spglib_dll_dir)
import thirdorder_core

For Linux:

import spglib
import os
import ctypes
libsymspg_so_path = os.path.join(os.path.dirname(spglib.__file__), "lib", "libsymspg.so.2")
ctypes.cdll.LoadLibrary(libsymspg_so_path)
import thirdorder_core

You can also manually add the path of the required file [2] to the environment variables,

For linux:

export LD_LIBRARY_PATH=/path/to/spglib/lib:$LD_LIBRARY_PATH

For Windows:

  • TODO

So that you can import thirdorder_core directly:

import thirdorder_core

Run#

Step 1 - Generate Poscars#

Original command:

python thirdorder_vasp.py sow 3 3 1 -3

Tepkit command:

tepkit thirdorder vasp_sow -a 3 3 1 -3

Step 2 - Set Job Folders#

Original command:

workdir="./jobs"
cp INCAR KPOINTS POTCAR ${workdir}
for i in 3RD.POSCAR.*
do
    d=${workdir}/job-${i##*.}
    mkdir $d
    mv $i $d/POSCAR
    ln -s ../INCAR ../KPOINTS ../POTCAR $d
done

Tepkit command:

tepkit thirdorder set_jobs --to ./jobs

Step 3 - Check Duplicate Jobs#

tepkit thirdorder check_dupl --dir jobs

Step 4 - Run Jobs#

TODO

Step 5 - Get Results#

Original command:

find job* -name vasprun.xml | sort -n | python thirdorder_vasp.py reap 3 3 1 -3

Tepkit command:

tepkit thirdorder vasp_reap -a 3 3 1 -3 --pattern job*