To read the json.bz2 files you can use the following code in python:
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#!/usr/bin/env python
import json, bz2
from pymatgen.entries.computed_entries import ComputedStructureEntry
with bz2.open("garnets.json.bz2") as fh:
data = json.loads(fh.read().decode('utf-8'))
entries = [ComputedStructureEntry.from_dict(i) for i in data["entries"]]
print("Found " + str(len(entries)) + " entries")
print("\nEntry:\n", entries[0])
print("\nStructure:\n", entries[0].structure)
------------------------------------
Output:
Found 15742 entries
Entry: None ComputedStructureEntry - Ac48 Ag12 H20 (Ac12Ag3H5)
Energy (Uncorrected) = -312.1258 eV (-3.9016 eV/atom)
Correction = -0.0000 eV (-0.0000 eV/atom)
Energy (Final) = -312.1259 eV (-3.9016 eV/atom)
Energy Adjustments:
Manual energy adjustment: -0.0000 eV (-0.0000 eV/atom)
Parameters:
Data:
mat_id = agm001254430
prototype_id = A3B5C12_37_spg230
location = cgat_prot/A3B5C12_prot1_spg230/runs/batch-002/H/H5Ag3Ac12/xxx_02p-00_agm001254430_spg230
formula = Ac12Ag3H5
elements = ['Ag', 'H', 'Ac']
spg = 230
nsites = 80
stress = [[2.0345, 0.0, 0.0], [0.0, 2.0345, 0.0], [0.0, 0.0, 2.0345]]
energy_total = -312.12584145
total_mag = -0.0003234
band_gap_ind = 0.0131
band_gap_dir = 0.0865
dos_ef = 78.46667
energy_corrected = -312.12585
e_above_hull = 0.13003096
e_form = -0.19915126
e_phase_separation = 0.13003096
decomposition = AcAg Ac AcH2
Structure: Full Formula (Ac48 Ag12 H20)
Reduced Formula: Ac12Ag3H5
abc : 14.778497 14.778497 14.778497
angles: 109.471221 109.471221 109.471221
Sites (80)
# SP a b c charge forces magmom
--- ---- -------- -------- -------- -------- --------------------------------------- --------
0 Ag 0.75 0.375 0.125 9.538 [-0.0, -0.0, 0.0] -0
1 Ag 0.875 0.75 0.125 9.538 [-0.0, -0.0, 0.0] -0
2 Ag 0.375 0.75 0.625 9.538 [-0.0, -0.0, 0.0] -0
3 Ag 0.25 0.125 0.375 9.538 [-0.0, -0.0, 0.0] -0
4 Ag 0.875 0.125 0.25 9.538 [-0.0, -0.0, 0.0] -0
5 Ag 0.375 0.625 0.25 9.538 [-0.0, -0.0, 0.0] -0
6 Ag 0.625 0.375 0.75 9.538 [-0.0, -0.0, 0.0] -0
7 Ag 0.125 0.875 0.75 9.538 [-0.0, -0.0, 0.0] -0
8 Ag 0.75 0.875 0.625 9.538 [-0.0, -0.0, 0.0] -0
9 Ag 0.625 0.25 0.375 9.538 [-0.0, -0.0, 0.0] -0
10 Ag 0.125 0.25 0.875 9.538 [-0.0, -0.0, 0.0] -0
11 Ag 0.25 0.625 0.875 9.538 [-0.0, -0.0, 0.0] -0
12 H 0.125 0.375 0.25 0.565 [-0.0, -0.0, 0.0] 0
13 H 0 0.5 0 0.488 [-0.0, -0.0, 0.0] 0
14 H 0 0 0 0.488 [-0.0, -0.0, 0.0] 0
15 H 0.375 0.25 0.125 0.565 [-0.0, -0.0, 0.0] 0
16 H 0.5 0 0.5 0.488 [-0.0, -0.0, 0.0] 0
17 H 0.5 0.5 0 0.488 [-0.0, -0.0, 0.0] 0
18 H 0.125 0.75 0.375 0.565 [-0.0, -0.0, 0.0] 0
19 H 0.75 0.125 0.875 0.565 [-0.0, -0.0, 0.0] 0
20 H 0.75 0.625 0.375 0.565 [-0.0, -0.0, 0.0] 0
21 H 0.375 0.125 0.75 0.565 [-0.0, -0.0, 0.0] 0
22 H 0.625 0.875 0.25 0.565 [-0.0, -0.0, 0.0] 0
23 H 0.5 0.5 0.5 0.488 [-0.0, -0.0, 0.0] 0
24 H 0.5 0 0 0.488 [-0.0, -0.0, 0.0] 0
25 H 0 0 0.5 0.488 [-0.0, -0.0, 0.0] 0
26 H 0.25 0.375 0.625 0.565 [-0.0, -0.0, 0.0] 0
27 H 0.25 0.875 0.125 0.565 [-0.0, -0.0, 0.0] 0
28 H 0 0.5 0.5 0.488 [-0.0, -0.0, 0.0] 0
29 H 0.875 0.25 0.625 0.565 [-0.0, -0.0, 0.0] 0
30 H 0.625 0.75 0.875 0.565 [-0.0, -0.0, 0.0] 0
31 H 0.875 0.625 0.75 0.565 [-0.0, -0.0, 0.0] 0
32 Ac 0.710271 0.113014 0.018819 8.27 [0.00106111, 0.00508306, -0.00889708] -0
33 Ac 0.308548 0.518819 0.405805 8.27 [-0.00106111, -0.00516357, -0.0088506] -0
34 Ac 0.981181 0.386986 0.289729 8.27 [0.01001432, -0.00116731, 0.00211479] -0
35 Ac 0.518819 0.210271 0.113014 8.27 [-0.01001432, -0.00241512, -4.648e-05] -0
36 Ac 0.597257 0.710271 0.691452 8.27 [-0.00443866, -0.00635771, 0.00678229] -0
37 Ac 0.981181 0.594195 0.191452 8.27 [0.00451455, 0.00630404, 0.00678229] -0
38 Ac 0.308548 0.789729 0.402743 8.27 [-0.01001432, 0.00124781, 0.00206832] -0
39 Ac 0.094195 0.902743 0.113014 8.27 [0.01001432, 0.00241512, -4.648e-05] -0
40 Ac 0.594195 0.981181 0.691452 8.27 [0.00443866, 0.00635771, 0.00678229] -0
41 Ac 0.710271 0.597257 0.191452 8.27 [-0.00451455, -0.00630404, 0.00678229] -0
42 Ac 0.789729 0.481181 0.386986 8.27 [-0.00106111, 0.01024663, 4.648e-05] -0
43 Ac 0.808548 0.905805 0.018819 8.27 [-0.00106111, -0.00508306, -0.00889708] -0
44 Ac 0.113014 0.710271 0.518819 8.27 [0.00443866, 0.00269478, -0.00889708] -0
45 Ac 0.386986 0.405805 0.097257 8.27 [0.00451455, -0.00902565, -0.00206832] -0
46 Ac 0.097257 0.905805 0.386986 8.27 [0.00106111, -0.01024663, 4.648e-05] -0
47 Ac 0.402743 0.113014 0.594195 8.27 [-0.00106111, -0.00516357, 0.0088506] -0
48 Ac 0.097257 0.191452 0.210271 8.27 [-0.00443866, 0.00905249, -0.00211479] -0
49 Ac 0.481181 0.691452 0.094195 8.27 [0.00451455, 0.00272161, 0.0088506] -0
50 Ac 0.808548 0.902743 0.289729 8.27 [-0.01001432, 0.00116731, 0.00211479] -0
51 Ac 0.113014 0.402743 0.094195 8.27 [-0.00451455, -0.00272161, 0.0088506] -0
52 Ac 0.386986 0.981181 0.789729 8.27 [-0.00443866, 0.00905249, 0.00211479] -0
53 Ac 0.594195 0.613014 0.402743 8.27 [0.01001432, -0.00124781, 0.00206832] -0
54 Ac 0.905805 0.808548 0.518819 8.27 [-0.00443866, -0.00269478, -0.00889708] -0
55 Ac 0.789729 0.308548 0.902743 8.27 [0.00451455, -0.00902565, 0.00206832] -0
56 Ac 0.405805 0.386986 0.597257 8.27 [-0.01001432, 0.00124781, -0.00206832] -0
57 Ac 0.094195 0.191452 0.481181 8.27 [0.00443866, 0.00269478, 0.00889708] -0
58 Ac 0.210271 0.691452 0.097257 8.27 [-0.00451455, 0.00902565, -0.00206832] -0
59 Ac 0.191452 0.097257 0.710271 8.27 [0.01001432, -0.00116731, -0.00211479] -0
60 Ac 0.613014 0.018819 0.210271 8.27 [0.00443866, -0.00905249, -0.00211479] -0
61 Ac 0.886986 0.597257 0.905805 8.27 [0.00451455, 0.00272161, -0.0088506] -0
62 Ac 0.518819 0.308548 0.905805 8.27 [-0.00451455, -0.00272161, -0.0088506] -0
63 Ac 0.597257 0.886986 0.405805 8.27 [0.00106111, 0.00516357, -0.0088506] -0
64 Ac 0.902743 0.808548 0.789729 8.27 [0.00443866, -0.00905249, 0.00211479] -0
65 Ac 0.902743 0.094195 0.613014 8.27 [-0.00106111, 0.01024663, -4.648e-05] -0
66 Ac 0.886986 0.289729 0.481181 8.27 [-0.00443866, -0.00269478, 0.00889708] -0
67 Ac 0.191452 0.094195 0.981181 8.27 [0.00106111, 0.00508306, 0.00889708] -0
68 Ac 0.613014 0.594195 0.902743 8.27 [-0.00451455, 0.00902565, 0.00206832] -0
69 Ac 0.405805 0.018819 0.308548 8.27 [-0.00443866, -0.00635771, -0.00678229] -0
70 Ac 0.289729 0.402743 0.808548 8.27 [0.00451455, 0.00630404, -0.00678229] -0
71 Ac 0.210271 0.518819 0.613014 8.27 [0.00106111, -0.01024663, -4.648e-05] -0
72 Ac 0.905805 0.097257 0.886986 8.27 [-0.01001432, -0.00241512, 4.648e-05] -0
73 Ac 0.691452 0.210271 0.597257 8.27 [0.01001432, -0.00124781, -0.00206832] -0
74 Ac 0.481181 0.789729 0.886986 8.27 [0.01001432, 0.00241512, 4.648e-05] -0
75 Ac 0.018819 0.405805 0.808548 8.27 [-0.00451455, -0.00630404, -0.00678229] -0
76 Ac 0.402743 0.289729 0.308548 8.27 [0.00443866, 0.00635771, -0.00678229] -0
77 Ac 0.018819 0.613014 0.710271 8.27 [-0.01001432, 0.00116731, -0.00211479] -0
78 Ac 0.691452 0.481181 0.594195 8.27 [0.00106111, 0.00516357, 0.0088506] -0
79 Ac 0.289729 0.886986 0.981181 8.27 [-0.00106111, -0.00508306, 0.00889708] -0
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List of POTCARs used:
Ac: PAW_PBE Ac 06Sep2000
Ag: PAW_PBE Ag 06Sep2000
Al: PAW_PBE Al 04Jan2001
As: PAW_PBE As 06Sep2000
Au: PAW_PBE Au 06Sep2000
B: PAW_PBE B 06Sep2000
Ba: PAW_PBE Ba_sv 06Sep2000
Be: PAW_PBE Be_sv 06Sep2000
Bi: PAW_PBE Bi 08Apr2002
Br: PAW_PBE Br 06Sep2000
C: PAW_PBE C 08Apr2002
Ca: PAW_PBE Ca_sv 06Sep2000
Cd: PAW_PBE Cd 06Sep2000
Ce: PAW_PBE Ce 28Sep2000
Cl: PAW_PBE Cl 17Jan2003
Co: PAW_PBE Co 06Sep2000
Cr: PAW_PBE Cr_pv 07Sep2000
Cs: PAW_PBE Cs_sv 08Apr2002
Cu: PAW_PBE Cu_pv 06Sep2000
Dy: PAW_PBE Dy_3 06Sep2000
Er: PAW_PBE Er_3 06Sep2000
Eu: PAW_PBE Eu 08Apr2002
F: PAW_PBE F 08Apr2002
Fe: PAW_PBE Fe_pv 06Sep2000
Ga: PAW_PBE Ga_d 06Sep2000
Gd: PAW_PBE Gd 08Apr2002
Ge: PAW_PBE Ge_d 06Sep2000
H: PAW_PBE H 15Jun2001
Hf: PAW_PBE Hf_pv 06Sep2000
Hg: PAW_PBE Hg 06Sep2000
Ho: PAW_PBE Ho_3 06Sep2000
I: PAW_PBE I 08Apr2002
In: PAW_PBE In_d 06Sep2000
Ir: PAW_PBE Ir 06Sep2000
K: PAW_PBE K_sv 06Sep2000
La: PAW_PBE La 06Sep2000
Li: PAW_PBE Li_sv 23Jan2001
Lu: PAW_PBE Lu_3 06Sep2000
Mg: PAW_PBE Mg_pv 06Sep2000
Mn: PAW_PBE Mn_pv 07Sep2000
Mo: PAW_PBE Mo_pv 08Apr2002
N: PAW_PBE N 08Apr2002
Na: PAW_PBE Na_pv 05Jan2001
Nb: PAW_PBE Nb_pv 08Apr2002
Nd: PAW_PBE Nd_3 06Sep2000
Ni: PAW_PBE Ni_pv 06Sep2000
Np: PAW_PBE Np 06Sep2000
O: PAW_PBE O 08Apr2002
Os: PAW_PBE Os_pv 20Jan2003
P: PAW_PBE P 17Jan2003
Pa: PAW_PBE Pa 07Sep2000
Pb: PAW_PBE Pb_d 06Sep2000
Pd: PAW_PBE Pd 05Jan2001
Pm: PAW_PBE Pm_3 07Sep2000
Pr: PAW_PBE Pr_3 07Sep2000
Pt: PAW_PBE Pt 05Jan2001
Pu: PAW_PBE Pu 06Sep2000
Rb: PAW_PBE Rb_sv 06Sep2000
Re: PAW_PBE Re_pv 06Sep2000
Rh: PAW_PBE Rh_pv 06Sep2000
Ru: PAW_PBE Ru_pv 06Sep2000
S: PAW_PBE S 17Jan2003
Sb: PAW_PBE Sb 06Sep2000
Sc: PAW_PBE Sc_sv 07Sep2000
Se: PAW_PBE Se 06Sep2000
Si: PAW_PBE Si 05Jan2001
Sm: PAW_PBE Sm_3 07Sep2000
Sn: PAW_PBE Sn_d 06Sep2000
Sr: PAW_PBE Sr_sv 07Sep2000
Ta: PAW_PBE Ta_pv 07Sep2000
Tb: PAW_PBE Tb_3 06Sep2000
Tc: PAW_PBE Tc_pv 06Sep2000
Te: PAW_PBE Te 08Apr2002
Th: PAW_PBE Th 07Sep2000
Ti: PAW_PBE Ti_pv 07Sep2000
Tl: PAW_PBE Tl_d 06Sep2000
Tm: PAW_PBE Tm_3 20Jan2003
U: PAW_PBE U 06Sep2000
V: PAW_PBE V_sv 07Sep2000
W: PAW_PBE W_pv 06Sep2000
Y: PAW_PBE Y_sv 06Sep2000
Yb: PAW_PBE Yb 24Feb2003
Zn: PAW_PBE Zn 06Sep2000
Zr: PAW_PBE Zr_sv 07Sep2000