Input Parameters

pySED reads a plain-text control file. The default file name is input_SED.in, but another file name can be passed on the command line. Each active line has the form

parameter_name = value

Blank lines and text after # are ignored. If no input file is passed on the command line, pySED reads input_SED.in in the current directory:

pysed
pysed input_SED.in
pySED input_SED.in

The table below lists the parameters accepted by the pySED input file. Each parameter has its own page with the parameter name as the title, plus syntax, meaning, defaults, examples, practical notes, and related parameters.

Parameter pages

Parameter	Group	Purpose
num_atoms	MD simulation	Number of atoms in the MD trajectory.
total_num_steps	MD simulation	Number of MD steps used for the production trajectory.
time_step	MD simulation	MD time step in fs.
output_data_stride	MD simulation	Trajectory output interval; controls the maximum resolvable frequency.
num_splits	Averaging	Number of trajectory blocks used for averaging.
compress	Averaging	Compress trajectory data to HDF5 before SED.
out_files_name	Files	Prefix for pySED output files.
basis_lattice_file	Files	Path to basis.in.
file_format	Files	Select GPUMD or LAMMPS trajectory reader.
dump_xyz_file	Files	GPUMD extended XYZ trajectory path.
pos_file	Files	LAMMPS position trajectory path.
vels_file	Files	LAMMPS velocity trajectory path.
lammps_unit	Files	LAMMPS unit style for velocity conversion.
output_hdf5	Files	Compressed trajectory database name.
output_partial	Files	Write atom-type and direction-resolved SED files.
use_parallel	Parallelization	Enable multiprocessing over q-points.
max_cores	Parallelization	Maximum number of worker processes.
prim_unitcell	Crystal structure	Primitive lattice vectors.
prim_axis	Crystal structure	Primitive-axis transformation.
supercell_dim	Crystal structure	Supercell repeats; controls q-point resolution.
rescale_prim	Crystal structure	Reconstruct the primitive cell from the trajectory cell.
num_qpaths	Q-path	Number of high-symmetry path segments.
q_path_name	Q-path	Labels for high-symmetry points.
q_path	Q-path	High-symmetry q-points in reduced coordinates.
plot_SED	Plotting	Select compute mode or plot/fitting mode.
plot_cutoff_freq	Plotting	Maximum plotted frequency in THz.
plot_interval	Plotting	Frequency tick interval.
plot_color	Plotting	Matplotlib colormap.
colorbar_min	Plotting	Lower log-scale colorbar limit.
colorbar_max	Plotting	Upper log-scale colorbar limit.
use_contourf	Plotting	Use contour-style SED plotting.
qpoint_slice_index	Plotting	Zero-based q-point index for slice plots and fitting.
plot_slice	Plotting	Plot one q-point spectrum.
plot_partial_SED	Plotting	Plot one atom-type or direction-resolved partial SED.
if_show_figures	Plotting	Show figures interactively.
lorentz	Lorentzian fitting	Enable Lorentzian peak fitting.
peak_height	Lorentzian fitting	Minimum detected peak height.
peak_prominence	Lorentzian fitting	Minimum detected peak prominence.
initial_guess_hwhm	Lorentzian fitting	Initial HWHM guess.
peak_max_hwhm	Lorentzian fitting	Maximum fitted HWHM.
lorentz_fit_cutoff	Lorentzian fitting	Maximum fitting frequency in THz.
modulate_factor	Lorentzian fitting	Shrink fitting windows around detected peaks.
lorentz_fit_all_qpoint	Lorentzian fitting	Fit peaks at all q-points.
re_output_total_freq_lifetime	Lorentzian fitting	Rebuild total frequency-lifetime output after refitting.
with_eigs	Reserved	Reserved for eigenvector-related development.