CASTEP ELNES Parser

A simple python script for parsing CASTEP output files especially for ELNES calculations.

Overview

This includes some functions for reading .cell, .castep, .bands, and .eels_mat files, calculating excitation energy, and forming core-loss spectra with Gaussian smearing.

Requirements

• python (=>3)
• numpy

Install

Clone this repository and run pip install:

git clone https://github.com/nmdl-mizo/castep_elnes_parser.git
cd castep_elne_parser
pip intall .

or directry run pip install:

pip install git+https://github.com/nmdl-mizo/castep_elnes_parser

Usage

This simple script contains several primitive functions for dealing with CASTEP files.

Get energies from castep files and calculate excitation energy

This script can extract energies and calculate the excitation energies from a pair of {seed_name}.castep files for the ground state (gs) and excited state (ex). The label of the site of interest can be specified by element and suffix.

>>> !ls . # prepare two {seed_name}.castep files for ground state and excitated state
case_gs.castep    case.castep
>>> import ceparser as cep
>>> # extract energies and calculate excitation energy for a site labelled as "C:ex"
>>> energies = cep.get_energies(filename_gs="./case_gs.castep", filename_ex="./case.castep", element="C", suffix=":ex")

Form spectra from eigen values and transition matrix elements

This script can form spectra from a pair of {seed_name}.bands and {seed_name}.eels_mat files.

>>> !ls . # prepare {seed_name}.bands and {seed_name}.eels_mat
case_elnes.bands    case_elnes.eels_mat
>>> import numpy as np
>>> import matplotlib.pyplot as plt
>>> import ceparser as cep
>>> # calculate gaussian smeared spectra of Gaussian sigma 0.3 eV
>>> energies = np.arange(-4.999, 30.002, 0.001) # make an array for energies with a desired range and resolution
>>> sp = cep.get_smeared_spectrum(energies=energies, sigma=0.3, calc_dir=".", seed_name="case_elnes") # parse and make spectra by gaussian smearing with sigma
>>> fig, ax = plt.subplots(1)
>>> ax.set_xlabel("Energy (eV)")
>>> ax.set_ylabel("Intensity (arb. u.)")
>>> ax.plot(energies, sp[0, 0], label="x") # plot a spectrum for x component of the 1st core projection
>>> ax.plot(energies, sp[0, 1], label="y") # plot a spectrum for y component of the 1st core projection
>>> ax.plot(energies, sp[0, 2], label="z") # plot a spectrum for z component of the 1st core projection
>>> ax.plot(energies, np.mean(sp[0], axis=0), label="total") # plot a total spectrum of the 1st core projection

Note

This script is tested on input and output files of CASTEP version 8 and may not be incompatible to other versions.

Reference

This code is citable through Zenodo with the following DOI:

In all papers using the CASTEP code, you should cite:

"First principles methods using CASTEP", Zeitschrift fuer Kristallographie 220(5-6) pp. 567-570 (2005) S. J. Clark, M. D. Segall, C. J. Pickard, P. J. Hasnip, M. J. Probert, K. Refson, M. C. Payne

If you use get_energies() for calculating excitation energy, please consider to cite:

Mizoguchi, T.; Tanaka, I.; Gao, S.-P.; Pickard, C. J. "First-Principles Calculation of Spectral Features, Chemical Shift and Absolute Threshold of ELNES and XANES Using a Plane Wave Pseudopotential Method."
J. Phys. Condens. Matter 2009, 21 (10), 104204.

Documentation

Documentation generated by Sphinx is available.

Author

• Kiyou
• Mizoguchi Lab.

Licence

The source code is licensed MIT.