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Added several examples (#23)
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* Added several examples:
- diamond
- graphite
- GaAs => bands are still a bit not good
- Al

* Adding Miki Bonacci to the contributors in the README file.

* Bands for GaAs now are good

* fixing the q-path for the new examples.
fixed back the convert-to-json script, and added also some custom qpts and reps
dict for the new cases.

* New qpath

* performed a more converged calculation for Aluminum, and added more q points for U|K->G path,
to have a better interpolation (there is a crossing point just outside U|K).

Added specific path for FCC examples that I added: Diamond, Aluminum and GaAs.

* disabling the tooltip (problematic selection if we have bands which are close)

* Fixed names for the files and the convert-to-json file
mikibonacci authored Jun 6, 2024
1 parent 3a9aa7b commit 818df1e
Showing 45 changed files with 27,505 additions and 5 deletions.
1 change: 1 addition & 0 deletions README.rst
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@@ -17,6 +17,7 @@ Contributors
- Henrique Miranda (UCL, Belgium) [development of the original phonon visualizer]
- Thibault Sohier (EPFL) [support on the python code and on the examples]
- Chara Cignarella (EPFL) [bug reporting and fixing]
- Miki Bonacci (PSI) [support on the examples]

=======
License
12 changes: 12 additions & 0 deletions config.yaml
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@@ -37,6 +37,12 @@ data:
C:
title: "Graphene"
filename: C.json
C4:
title: "Graphite"
filename: graphite.json
C2:
title: "Diamond"
filename: diamond.json
PbI2:
title: "PbI<sub>2</sub>"
filename: PbI2.json
@@ -52,3 +58,9 @@ data:
AgNO2:
title: "AgNO<sub>2</sub>"
filename: AgNO2.json
Al:
title: "Aluminum"
filename: aluminum.json
GaAs:
title: "GaAs"
filename: GaAs.json
30 changes: 26 additions & 4 deletions convert-to-json.py
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@@ -22,17 +22,39 @@
with open(os.path.join(folder_name, "matdyn.modes")) as fhandle:
matdyn_modes = fhandle.read()

pretty_name_dict = {"BaTiO_3": "BaTiO<sub>3</sub>"}
# pretty_name_dict only contains the names which should be rewritten with HTML (subscripts and other effects)
pretty_name_dict = {
"PbI2": "PbI<sub>2</sub>",
"MoS2": "MoS<sub>2</sub>",
"AgNO2": "AgNO<sub>2</sub>",
"BaTiO_3": "BaTiO<sub>3</sub>",
}

highsym_qpts_default = [[0, "Γ"], [20, "M"], [40, "K"], [60, "Γ"]]
highsym_qpts_dict = {
"BaTiO_3": [[0, "X"], [20, "Γ"], [40, "M"], [60, "Γ"], [100, "R"]],
system: [
[0, "Γ"],
[20, "X"],
[40, "U|K"],
[70, "Γ"],
[90, "L"],
[110, "W"],
[130, "X"],
]
for system in ["GaAs", "diamond", "Aluminum"]
}

starting_reps_default = (5, 5, 1)
starting_reps_dict = {"BaTiO_3": (3, 3, 3)}
highsym_qpts_dict["BaTiO_3"] = (
[[0, "X"], [20, "Γ"], [40, "M"], [60, "Γ"], [100, "R"]],
)

# supercell.
starting_reps_default = (5, 5, 1) # for the 2D systems we use this default
starting_reps_dict = {
system: (3, 3, 3) for system in ["BaTiO_3", "GaAs", "diamond", "Aluminum"]
}

print(system_name)
phonons = QePhononQetools(
scf_input=scf_input,
scf_output=scf_output,
1 change: 1 addition & 0 deletions user_static/data/GaAs.json

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17 changes: 17 additions & 0 deletions user_static/data/GaAs/matdyn.in
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&INPUT
asr = 'simple'
flfrc = 'GaAs.fc'
flfrq = 'GaAs.freq'
flvec = 'GaAs.modes'
! loto_2d = .true.
q_in_cryst_coord = .true.
q_in_band_form = .true.
/
7
0.000 0.000 0.000 20 ! G
0.5000000000 0.0000000000 0.5000000000 20 ! X
0.6250000000 0.2500000000 0.6250000000 30 ! K
1 1 1 20 ! G
0.5000000000 0.5000000000 0.5000000000 20 ! L
0.5000000000 0.2500000000 0.7500000000 20 ! W
0.5000000000 0.0000000000 0.5000000000 1 ! X
3,013 changes: 3,013 additions & 0 deletions user_static/data/GaAs/matdyn.modes

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31 changes: 31 additions & 0 deletions user_static/data/GaAs/matdyn.out
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Program MATDYN v.7.1 starts on 4Jun2024 at 0:57:44

This program is part of the open-source Quantum ESPRESSO suite
for quantum simulation of materials; please cite
"P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);
"P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);
"P. Giannozzi et al., J. Chem. Phys. 152 154105 (2020);
URL http://www.quantum-espresso.org",
in publications or presentations arising from this work. More details at
http://www.quantum-espresso.org/quote

Parallel version (MPI & OpenMP), running on 12 processor cores
Number of MPI processes: 12
Threads/MPI process: 1

MPI processes distributed on 1 nodes
R & G space division: proc/nbgrp/npool/nimage = 12
238142 MiB available memory on the printing compute node when the environment starts

mass for atomic type 1 not given; uses mass from file GaAs.fc
mass for atomic type 2 not given; uses mass from file GaAs.fc

MATDYN : 0.04s CPU 0.04s WALL


This run was terminated on: 0:57:44 4Jun2024

=------------------------------------------------------------------------------=
JOB DONE.
=------------------------------------------------------------------------------=
17 changes: 17 additions & 0 deletions user_static/data/GaAs/ph.in
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GaAs
&inputph
outdir='/home/bonacc_m/Documents/phonons/GaAs/TMP'
prefix='GaAs'
fildyn='GaAs.dyn',
tr2_ph=1d-13,
epsil=.true.,
asr=.true.,
!lraman=.true.,
!elop=.true.,
!zeu=.true.,
!zue=.true.,
ldisp=.true.
nq1=4
nq2=4
nq3=4
/
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