A repository to store output from Ab2tds/OClimax/Euphonic, to validate Euphonic's phonon frequency and inelastic neutron scattering intensity calculations
The cut directories are organised by material -> cut -> software
e.g. the quartz -> 2ph_m4_0_qe -> oclimax directory contains
OClimax input/output files for the quartz cut named 2ph_m4_0_qe.
cut -> CASTEP directory
This only applies for the quartz, Nb and LZO materials. Contains a
material.cell CASTEP input file and material.phonon CASTEP output
file for the q-points contained in the cut.
cut -> Phonopy directory
Only applies for the Al material. Contains an cut_band.yaml Phonopy
output file containing the q-points, frequencies and eigenvectors for
the cut.
cut -> ab2tds directory
This contains the input files for Abt2ds for a particular cut
(intensity_map_input.py, resolution.txt), the output intensities
at 300K (res_300K.dat), the output mode-resolved structure factors
with Bose factor applied at the mode frequencies (alongthelineF_300K.dat)
and a short script to run ab2tds with the input files (run_ab2tds.sh). The
ab2tds_sqw_300K.json file is the data in alongthelineF_300K.dat which has
been transformed to a Euphonic Spectrum2D object via binning with the
shared/generate_compare_data/ab2tds_to_sqw.py script.
cut -> Oclimax directory
This contains the input files for OClimax for a particular cut, both
quartz.params.copy and quartz.params to prevent quartz.params
from being overwritten by OClimax. material.oclimax contains the
q-points, frequencies and eigenvectors for the q-points in that cut
in Oclimax format, created by running oclimax convert on the corresponding
material\cut\castep\material.phonon file. material_2Dmesh_scqw_TK.csv
are the OClimax output intensities at T K. oclimax_sqw_TK.json is the
data in material_2Dmesh_scqw_TK.csv which has been transformed to a
Euphonic Spectrum2D object via binning with the
shared/generate_compare_data/oclimax_to_sqw.py script. The run_oclimax.sh
script will run OClimax with the relevant input files.
cut -> Euphonic directory
This contains output Euphonic files. euphonic_sf_fc_TK.json contains the
Euphonic structure factors calculated for the q-points in that cut at T K,
produced by the shared/generate_compare_data/generate_euphonic_sf.py script,
calculated from Euphonic frequencies calculated from the force constants. The
euphonic_sf_phonons_TK.json is the same as euphonic_sf_fc_TK.json but the
structure factors have been calculated from phonon frequencies read from the
material.phonon file (using the --freqs argument to generate_euphonic_sf.py).
The euphonic_sqw_fc/phonons_TK.json file contains the Euphonic intensities,
calculated by binning the contents of the corresponding
euphonic_sf_fc/phonons_TK.json with the
shared/generate_compare_data/generate_euphonic_sqw.py script. There are
also some files with reduced in the name e.g.
euphonic_sf_fc_reduced_300K.json, these have been created with a
symmetry-reduced (rather than full unfolded) Debye-Waller grid.
The grid q-point data and Debye-Waller files (for each software as
applicable) are in the material -> shared -> software directory.
e.g. the quartz -> shared -> castep directory contains CASTEP
input/output files for gridded data for quartz.
shared -> CASTEP directory
This only applies for the quartz, Nb and LZO materials.
Contains a material.castep_bin, material.param and
material.cell CASTEP input files and material.phonon
CASTEP output file for a q-point grid for that material
shared -> Phonopy directory
Only applies for the Al material. Contains a Phonopy
material.yaml input file (containing the structure
and force constants) and a material_mesh.yaml output
file containing the q-points, frequencies and
eigenvectors for the Debye-Waller grid.
shared -> ab2tds directory
Contains the input files for the Ab2tds Debye-Waller calculation (dw_input
and symmetry_input), a script to run the Ab2tds DW calculation
(run_ab2tds.sh) and the output HDF5 file (material.md5_code) storing the
Debye-Waller data.
shared -> Oclimax directory
material.oclimax contains the q-points, frequencies and eigenvectors for
the q-point grid in Oclimax format, created by running oclimax convert
on the corresponding material\shared\castep\material.phonon file.
shared -> Euphonic directory
Contains output Euphonic files. The euphonic_dw_fc/phonons_NNN_TK.json
file contains a Euphonic DebyeWaller object calculated at T K on a
NxNxN grid, using frequencies calculated from force constants (fc) or
read from a CASTEP .phonon file (phonon), produced with the
shared/generate_compare_data/generate_euphonic_dw.py script.
These are contained in the shared -> generate_compare_data directory.
What each script does is described in the docstring in the script.