Tips

This page collects small workflow tips for running pySED more efficiently.

Use a Run Script

For repeated calculations, it is convenient to use a small shell script to switch input_SED.in between compute mode and plot/fitting mode. This is especially useful on clusters, where the same folder may be submitted several times while tuning plotting and Lorentzian fitting parameters.

The older silicon example contains a simple script: run_SED.sh. The idea is:

1. set plot_SED = 0 and run pySED once to compute .SED, .Qpts, and .THz files;

2. set plot_SED = 1 and run pySED again to plot the existing SED data;

3. repeat plot/fitting mode while tuning peak_height, peak_prominence, lorentz_fit_cutoff, and related parameters.

A more robust Bash version is:

#!/usr/bin/env bash
set -euo pipefail

input_file="input_SED.in"

set_param() {
    local key="$1"
    local value="$2"
    sed -i -E "s|^(${key}[[:space:]]*=[[:space:]]*).*|\\1${value}|" "${input_file}"
}

# First run: compute SED from the trajectory.
set_param plot_SED 0
pysed "${input_file}"

# Second run: read existing SED data and plot or fit.
set_param plot_SED 1
pysed "${input_file}"

This avoids changing a fixed line number. It is safer when comments or new parameters are added to input_SED.in.

On Windows PowerShell, the same idea can be written as:

$inputFile = "input_SED.in"

function Set-SedParam($key, $value) {
    $content = Get-Content $inputFile
    $content = $content -replace "^($key\s*=\s*).*", "`${1}$value"
    Set-Content -Path $inputFile -Value $content
}

Set-SedParam "plot_SED" "0"
pysed $inputFile

Set-SedParam "plot_SED" "1"
pysed $inputFile

Keep Compute and Plot Modes Separate

Use plot_SED = 0 only when the trajectory, basis.in, q-path, and cell settings are ready. After SED files are written, use plot_SED = 1 for plotting and fitting. This avoids recompressing large trajectories each time you only want to tune figure or fitting parameters.

Sync Documentation to ReadTheDocs

The online manual is built from the files under docs/source. The repository also contains .readthedocs.yml, so ReadTheDocs rebuilds the manual after the documentation changes are pushed to GitHub.

Recommended update workflow:

python -m sphinx -b html docs/source docs/_build/html
git add README.md docs/source example publications .readthedocs.yml
git commit -m "Update pySED documentation"
git push

For the publication list, edit only publications/readme.md. During each Sphinx build, pySED copies that file into the manual as the Publications page, so the online page stays synchronized after ReadTheDocs rebuilds.