Added several examples (#23)

* 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

README.rst

@@ -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

config.yaml

@@ -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

convert-to-json.py

@@ -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,

user_static/data/GaAs/matdyn.in

@@ -0,0 +1,17 @@
+&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

user_static/data/GaAs/matdyn.out

@@ -0,0 +1,31 @@
+
+     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.
+=------------------------------------------------------------------------------=

user_static/data/GaAs/ph.in

@@ -0,0 +1,17 @@
+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
+/