GitGreg228 / qe-scripts

Scripts for several tasks in Computational Materials Science

Quantum Espresso scripts

input.opt generator

Currently, several QE input generators are available on the Internet (for example, https://www.materialscloud.org/work/tools/qeinputgenerator). However, for some reason, they are not capable in detecting crystal symmetry, which can crucially affect the calculation speed. qe_sc.py is used to set up the vc-relax calculation for given structure. It generates input.opt and script1.sh files basing on given POSCAR and (optionally) system.json file.

• input.opt contains parameters of calculation and crystal structure geometry. Only inequvalently placed atoms are written in this file. The space_group parameter defines the symmetry, and the A, B, C, cosAB, cosAC, cosBC define the unit cell shape and volume.
• script1.sh is a script for Slurm Workload Manager

Usage

For input.opt generation, run the

python qe_sc.py

in a folder containing POSCAR

User can choose the tolerance running

python qe_sc.py --tol=%desired_tolerance%

Default tolerance is 0.2.

The pressure can also be set up by

python qe_sc.py --press=%desired_pressure_in_kbar%

Default pressure is 2000.

If the POSCAR placed in another path (for example, in ~/QE/H3S) and named differently (for example, CONTCAR), user can run

python qe_sc.py --path=~/QE/H3S --poscar=CONTCAR

Multiple pressures

The program qe_sc.py allows to create multiple folders for each given pressure. To set up multiple calculations, run

python qe_sc.py --press %P1% %P2% %P3% ... %Pn% 

As result, corresponding folders will appear in the folder next to POSCAR file.

Symmetry analyzer

Symmetry analyzer analyze.py code allows to conveniently analyze symmetry of relaxed structures. It looks for output.opt. files next to POSCAR (or in subdirectories next to POSCAR, which could be created by qe_sc.py). When output.opt. is found, final lattice and atomic coordinates are parsed. Then the CONTCAR and the symmetrized .cif file are generated in the folder. The summary of all found symmetries are placed in symm.json file in the directory in which analyze.py was launched. The algorithm of symmetry analysis is the same as in symmetrize.py

Usage

In a directory containing output.opt. or containing subdirectories with output.opt., run

python analyze.py

You can choose range of tolerances in which the structure will be analyzed.

python analyze.py --tol_step=%desired_tolerance_step% --tol_max=%desired_max_tolerance%

Default --tol_step and --tol_max are 0.01 and 0.5 accordingly. You can disable creation of .cif files running analyze.py with tag:

python analyze.py --save_cif=False