Collection of generic pre- and post- processing tools using the Atomic Simulation Environment. Developed while working with Walsh Materials Design, kept on as a personal toolkit and developed further while at Scanlon Materials Theory Group.
The recommended way of installing is to clone the repository and make a local installation using pip:
git clone https://github.com/ajjackson/mctools.git
cd mctools
pip install --user -e .To run unit tests, install pytest and run with
python -m pytestUse Spglib to analyse the symmetry of a
crystal structure file over a range of distance thresholds. This can
be useful for identifying when numerical noise or limited convergence
has resulted in a lower-symmetry spacegroup, as well as for quickly
checking the identity of an unknown structure. Call with -h flag for
usage information.
# EXAMPLE
bash> get_spacegroup.py -i geometry.in.next_step
| Threshold / Å | Space group |
|---------------|-------------------|
| 0.00001 | P-1 (2) |
| 0.00010 | P-1 (2) |
| 0.00050 | C2/m (12) |
| 0.00100 | C2/m (12) |
| 0.00500 | P-3m1 (164) |
| 0.01000 | P-3m1 (164) |
| 0.05000 | P-3m1 (164) |
| 0.10000 | P-3m1 (164) |
Use ASE to import a trajectory, typically a vasprun.xml or OUTCAR file from a structure relaxation. Find the step with lowest energy and write it out to a file. This is useful for salvaging optimisation calculations that get 'lost'.
Use Spglib to generate a primitive cell
from/to any ASE-supported structure file format. It can be helpful to
use get_spacegroup.py first in order to identify an appropriate
symmetry threshold. Call with -h flag for usage information.
This is an alternative plotter to the GNUplot scripts generated by the Chemical Potential Limits Analysis Program (CPLAP). (website, paper) Specifically it deals with analysis of ternary systems where one phase is set as the dependent variable. All of the necessary data is read from the grid.dat and 2Dplot.txt output files, including the elements and compound formulae. The chemical potential of the dependent element is displayed as a colour map on the stability region. The plotter makes use of various matplotlib features (choice of file formats, appearance customisation with style sheets) to generate publication/presentation-quality graphics.
Copy the current directory to a specified remote server. The server accounts must be set up in sendto.conf. This is a convenience tool for copying files around, and does not submit to a queue.
Read a "bestsqs.out" file as generated by the ATAT mcsqs tool. Print to standard output, optionally write file or open ASE GUI.
Computing the unfolded band structure of a disordered or alloy material requires a reference primitive cell, but it makes no sense to compute such a cell. This tool will generate a "dummy" primitive cell from a relaxed supercell, given the supercell matrix.
WORK IN PROGRESS
Report the number of electrons in a proposed vasp calculation (NELECT). The name refers to an intended feature (specify system charge). At the moment there is no real user interface.
Uses the VASP_PP_PATH environment variable; if you use ASE for VASP calculations this should be set up. Otherwise it will not work.
Report lattice vectors in a, b, c, alpha, beta, gamma format. This is
useful for comparing structures and makes for more compact and
intuitive reporting. Call with -h flag for usage information.
# EXAMPLE
bash> vectors.py geometry.in
a b c alpha beta gamma
11.451 3.856 6.193 90.00 103.21 90.00
Optimal k-point meshes with a single convergence parameter
Rapid volume optimisation with an auxiliary equation of state