plot-mb

A Python 3 script for (hassle-free) plotting of Mößbauer (MB) spectra from parameter files (text files) or from ORCA output files.

In case of ORCA output files, the script calculates the isomeric shift δ from ρ(0) according to the equation δ = ɑ*(ρ(0) - C) + β, ΔE_Q is taken from the ORCA output. The parameters ɑ, C and β can be changed in the script or from the command line.

The script can also read δ, ΔE_Q, line width (fwhm, optional) and the ratio (optional) of components from a text file and plot the Mößbauer (MB) spectra (have a look at mb-param.txt and Example 3).

The Mößbauer spectrum is calculated as a summation of Lorentz functions. The script can plot and also export single or multiple spectra.

External modules

numpy matplotlib

Quick start

Start the script with:

python3 plot-mb.py filename

it will save the plot as PNG: filename-mb.png

Command-line options

• filename , required: filename
• -s , optional: shows the matplotlib window
• -n , optional: do not save the spectrum
• -e , optional: export the line spectrum or spectra in a csv-like fashion; filename of the export is the atom or compound label + ".dat" for each atom or compound and "all.dat" for the whole spectrum
• -w N , optional: line width (fwhm) of the Lorentzian (default is N = 0.2) - ignored if 'fwhm' is specified in a text file with MB parameters
• -xmin N , optional: start spectrum at N mm/s (automatic scaling if not specified)
• -xmax N , optional: end spectrum at N mm/s (automatic scaling if not specified)
• -a N, optional: ɑ for δ = ɑ*(ρ(0) - C) + β (if not specified, ɑ is taken from the script) - ignored in the case of MB parameters from a text file
• -b N, optional: β for δ = ɑ*(ρ(0) - C) + β (if not specified, β is taken from the script) - ignored in the case of MB parameters from a text file
• -c N, optional: C for δ = ɑ*(ρ(0) - C) + β (if not specified, C is taken from the script) - ignored in the case of MB parameters from a text file
• -sh N, optional: shift δ by +/- N mm/s

Script options

There are numerous ways to configure the spectrum in the script: Check # plot config section - configure here in the script.

The delimiter for the line spectrum export can be changed by changing the value of export_delim =.

Code options

Colors, line thickness, line styles and more can be changed in the code directly.

Remarks

The PNG file will be replaced everytime you start the script with the same output file. If you want to keep the file, you have to rename it.

The script can only handle singlets and doublets.

The key for the calculation of the isomeric shift ist the equation δ = ɑ*(ρ(0) - C) + β. You should adjust ɑ, β and C according to functional and basis to achieve reasonable results.

For MB parameters from a text file, have a look at mb-param.txt and Example 3.

Examples

Example 1:

python3 plot-mb.py test.out -w 0.6 -s

Open the ORCA output file test.out, select a line width of 0.6 (-w 0.6), show the spectrum (-s). A PNG of the spectrum is saved as test-mb.png. Output:

=============================================================
δ = ɑ(ρ(0) - C) + β (+ shift)
ɑ = -0.366 C = 11810 β = 2.852 shift = 0
=============================================================
0Fe: δ = 0.47 mm/s ΔEQ = 3.45 mm/s ρ(0)=11816.51263 a.u.⁻³
1Fe: δ = 0.27 mm/s ΔEQ = 1.96 mm/s ρ(0)=11817.06310 a.u.⁻³
=============================================================

Example 2:

python3 plot-mb.py test.out -s -e

Open the ORCA output file test.out, show the spectrum (-s), export the data (-e). The files 0Fe.dat, 1Fe.dat, 4Fe.dat and all.dat containing the data of the doublets and the entire spectrum are saved. A PNG of the spectrum is saved as test-mb.png. Output:

=============================================================
δ = ɑ(ρ(0) - C) + β (+ shift)
ɑ = -0.366 C = 11810 β = 2.852 shift = 0
=============================================================
0Fe: δ = 0.61 mm/s ΔEQ = 2.37 mm/s ρ(0)=11816.13420 a.u.⁻³
1Fe: δ = 0.88 mm/s ΔEQ = -2.89 mm/s ρ(0)=11815.37543 a.u.⁻³
4Fe: δ = 1.74 mm/s ΔEQ = -2.90 mm/s ρ(0)=11813.03611 a.u.⁻³
=============================================================

Example 3:

python3 plot-mb.py mb-param.txt -xmin -6 -xmax 6 -s

Open the text file with MB paramters mb-param.txt, start the spectrum at -6 mm/s and end at +6 mm/s (-xmin -6 -xmax 6), show the spectrum (-s). A PNG of the spectrum is saved as mb-param-mb.png. Output:

This file does not contain MB parameters from an ORCA calculation.
Trying to read MB parameters directly.
=============================================================
L1Fe: δ = 0.24 mm/s ΔEQ = 1.51 mm/s fwhm = 0.33 ratio = 0.40
L2Fe: δ = 0.25 mm/s ΔEQ = 3.12 mm/s fwhm = 0.39 ratio = 0.35
L3Fe: δ =-0.03 mm/s ΔEQ = 1.24 mm/s fwhm = 0.44 ratio = 0.12
L4Fe: δ =-0.06 mm/s ΔEQ = 0.61 mm/s fwhm = 0.37 ratio = 0.13
=============================================================

Example 4:

python3 plot-mb.py test.out -w 0.6 -s

python3 plot-mb.py mb-param.txt -s -xmin -6 -xmax 6