Datasets:
Upload MATTER-604 private review candidate
Browse filesThis view is limited to 50 files because it contains too many changes. See raw diff
- .gitattributes +1 -0
- LICENSE +201 -0
- README.md +70 -0
- data/test.jsonl +0 -0
- fixtures/BP_struct_003/convergence_encut.json +43 -0
- fixtures/BP_struct_004/GaAs_bandstructure.csv +102 -0
- fixtures/BP_struct_004/Ge_bandstructure.csv +102 -0
- fixtures/BP_struct_004/Si_bandstructure.csv +102 -0
- fixtures/BP_struct_004/postprocessing_bandstr.json +59 -0
- fixtures/BP_struct_005/calc_001_TiO2_bad.POSCAR +14 -0
- fixtures/BP_struct_005/calc_002_ZnO_bad.POSCAR +12 -0
- fixtures/BP_struct_005/calc_003_MgO_bad.POSCAR +10 -0
- fixtures/BP_struct_005/calc_004_Al2O3_bad.POSCAR +18 -0
- fixtures/BP_struct_005/calc_005_SiO2_bad.POSCAR +17 -0
- fixtures/BP_struct_005/failure_recovery.json +100 -0
- fixtures/DD_general_004/case_bundle.json +46 -0
- fixtures/DD_vasp_scf_diverge_001/INCAR_original.txt +24 -0
- fixtures/DD_vasp_scf_diverge_001/OSZICAR_fragment.txt +20 -0
- fixtures/DF_scxrd_001_20260408/A23050101A0735.hkl +0 -0
- fixtures/DF_scxrd_001_20260408/A23050101A0735.p4p +8 -0
- fixtures/DF_scxrd_002_20260408/A23050102A0375.hkl +0 -0
- fixtures/DF_scxrd_002_20260408/A23050102A0375.p4p +8 -0
- fixtures/EC_gromacs_em_npt/conf.gro +651 -0
- fixtures/EC_gromacs_em_npt/em.mdp +13 -0
- fixtures/EC_gromacs_em_npt/npt.mdp +46 -0
- fixtures/EC_gromacs_em_npt/topol.top +9 -0
- fixtures/EC_no_silent_fallback_001/Si_diamond.cif +34 -0
- fixtures/EC_resource_limit_001/znso4_2000.xyz +0 -0
- fixtures/EC_spec_partial_001/run_spec.json +4 -0
- fixtures/EC_unsupported_env_001/electrolyte_box.xyz +62 -0
- fixtures/EC_unverified_dft_setup_001_20260603/input.json +35 -0
- fixtures/EC_unverified_dft_setup_001_20260603/pp_files/C.upf +45 -0
- fixtures/EC_unverified_dft_setup_001_20260603/pp_files/Cl.upf +45 -0
- fixtures/EC_unverified_dft_setup_001_20260603/pp_files/H.upf +44 -0
- fixtures/IG_abacus_001_20260404/base_slab.stru +91 -0
- fixtures/IG_abacus_002_20260404/base_vacancy.stru +73 -0
- fixtures/IG_abacus_003_20260406/base_al_slab.stru +22 -0
- fixtures/IG_abacus_004_20260406/base_h2o.stru +25 -0
- fixtures/IG_abacus_005_20260406/bulk_al_fcc.stru +21 -0
- fixtures/IG_abacus_005_20260406/slab_al_fcc100_5l.stru +22 -0
- fixtures/IG_abacus_005_20260406/slab_al_fcc100_7l.stru +24 -0
- fixtures/IG_abacus_006_20260406/mo110_pristine.stru +25 -0
- fixtures/IG_abacus_006_20260406/mo110_surface_vac.stru +24 -0
- fixtures/IG_abacus_006_20260406/mo_bulk.stru +19 -0
- fixtures/IG_abacus_017_20260512/POSCAR_rocksalt +12 -0
- fixtures/IG_abacus_017_20260512/POSCAR_square_planar +12 -0
- fixtures/IG_abacus_019_20260513/STRU_graphene +22 -0
- fixtures/IG_abacus_020_20260514/Si_diamond.stru +19 -0
- fixtures/IG_abacus_020_20260514/Si_fcc.stru +18 -0
- fixtures/IG_abacus_020_20260514/kpt_444.txt +4 -0
.gitattributes
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README.md
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
---
|
| 2 |
+
language:
|
| 3 |
+
- zh
|
| 4 |
+
- en
|
| 5 |
+
pretty_name: MATTER-604 Public Questions
|
| 6 |
+
license: apache-2.0
|
| 7 |
+
size_categories:
|
| 8 |
+
- n<1K
|
| 9 |
+
task_categories:
|
| 10 |
+
- question-answering
|
| 11 |
+
tags:
|
| 12 |
+
- materials-science
|
| 13 |
+
- agent
|
| 14 |
+
- benchmark
|
| 15 |
+
- hidden-test
|
| 16 |
+
---
|
| 17 |
+
|
| 18 |
+
# MATTER-604 Public Questions
|
| 19 |
+
|
| 20 |
+
MATTER-604 evaluates materials-science Agents on structure construction and
|
| 21 |
+
retrieval, scientific analysis, workflow orchestration, input generation,
|
| 22 |
+
data diagnosis, execution contracts, batch processing, and safety refusal.
|
| 23 |
+
|
| 24 |
+
This repository contains the 604 public task prompts and declared input
|
| 25 |
+
fixtures. It intentionally does **not** contain per-task reference answers,
|
| 26 |
+
checklists, Gold thresholds, or the private evaluator. Submit answers and task
|
| 27 |
+
artifacts through the benchmark evaluation service.
|
| 28 |
+
|
| 29 |
+
## Splits
|
| 30 |
+
|
| 31 |
+
`data/test.jsonl` contains the 604 evaluation questions. The test labels are
|
| 32 |
+
private. `fixtures/` contains only local files explicitly declared by a task's
|
| 33 |
+
`data_files` field.
|
| 34 |
+
|
| 35 |
+
Six declared inputs are not copied into this repository: two VASP POTCAR files
|
| 36 |
+
and four third-party publisher PDFs. Their records use
|
| 37 |
+
`distribution=restricted` and provide the exact SHA-256 plus lawful acquisition
|
| 38 |
+
instructions. A runner must provision those files outside the dataset repo and
|
| 39 |
+
verify their hashes before starting the affected task.
|
| 40 |
+
|
| 41 |
+
## Scoring method
|
| 42 |
+
|
| 43 |
+
Each private checklist item receives a binary pass/fail verdict and an optional
|
| 44 |
+
weight. Within each active axis:
|
| 45 |
+
|
| 46 |
+
`axis_score = sum(pass_i * item_weight_i) / sum(item_weight_i)`
|
| 47 |
+
|
| 48 |
+
The overall score is the weighted mean of active correctness, grounding, and
|
| 49 |
+
efficiency axes. Exact per-task criteria, expected values, tolerances, and
|
| 50 |
+
Gold files remain private to prevent direct answer lookup.
|
| 51 |
+
|
| 52 |
+
## Intended use and contamination policy
|
| 53 |
+
|
| 54 |
+
Use this dataset for evaluation, not training or answer distillation. Public
|
| 55 |
+
availability cannot technically prevent training; benchmark users should
|
| 56 |
+
disclose any exposure to MATTER questions or model answers. The official score
|
| 57 |
+
is produced only by the versioned private evaluator identified in
|
| 58 |
+
`private_eval_commitment.json`.
|
| 59 |
+
|
| 60 |
+
## Runtime
|
| 61 |
+
|
| 62 |
+
The closed-source MatMaster image is not distributed. Third-party Agents may
|
| 63 |
+
use their own runtime as long as they receive only the public task package and
|
| 64 |
+
return the documented answer/artifact bundle.
|
| 65 |
+
|
| 66 |
+
## License
|
| 67 |
+
|
| 68 |
+
MATTER-owned benchmark content in this repository is released under
|
| 69 |
+
Apache-2.0. Restricted VASP POTCAR files and third-party publisher PDFs are not
|
| 70 |
+
included and are not covered by this repository's Apache-2.0 license.
|
data/test.jsonl
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
fixtures/BP_struct_003/convergence_encut.json
ADDED
|
@@ -0,0 +1,43 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"convergence_variable": {
|
| 3 |
+
"description": "Plane wave energy cutoff",
|
| 4 |
+
"parameter": "ENCUT",
|
| 5 |
+
"unit": "eV",
|
| 6 |
+
"values": [
|
| 7 |
+
280,
|
| 8 |
+
300,
|
| 9 |
+
320,
|
| 10 |
+
340,
|
| 11 |
+
360
|
| 12 |
+
]
|
| 13 |
+
},
|
| 14 |
+
"description": "For a fixed structure (Al face-centered cubic), run 5 single-point energy calculations with varying ENCUT (280, 300, 320, 340, 360 eV). All other parameters must be strictly constant: k-point mesh, ISMEAR, SIGMA, POTCAR path, etc. This verifies systematic parameter scanning ability.",
|
| 15 |
+
"expected_output": {
|
| 16 |
+
"analysis": "plot energy vs ENCUT to show convergence curve",
|
| 17 |
+
"format": "5 OUTCAR files or energy log",
|
| 18 |
+
"naming": "Al_ENCUT_{energy_ev}_eV_energy.txt or similar"
|
| 19 |
+
},
|
| 20 |
+
"locked_parameters": {
|
| 21 |
+
"ALGO": "Fast",
|
| 22 |
+
"IBRION": -1,
|
| 23 |
+
"ISMEAR": 1,
|
| 24 |
+
"NSW": 0,
|
| 25 |
+
"POTCAR": "PAW_PBE/Al/POTCAR",
|
| 26 |
+
"SIGMA": 0.1,
|
| 27 |
+
"k_point_mesh": "8 8 8"
|
| 28 |
+
},
|
| 29 |
+
"structure": {
|
| 30 |
+
"crystal_system": "cubic",
|
| 31 |
+
"formula": "Al",
|
| 32 |
+
"lattice_constant_A": 4.05,
|
| 33 |
+
"space_group": "Fm-3m"
|
| 34 |
+
},
|
| 35 |
+
"task": "batch_convergence_test_ENCUT_sweep",
|
| 36 |
+
"verification_checklist": [
|
| 37 |
+
"Parameter ENCUT varies from 280→360 eV",
|
| 38 |
+
"All 5 calculations use identical k-point mesh 8x8x8",
|
| 39 |
+
"ISMEAR, SIGMA unchanged across runs",
|
| 40 |
+
"Output file sequence shows clear parameter progression",
|
| 41 |
+
"Can extract energies and produce convergence plot"
|
| 42 |
+
]
|
| 43 |
+
}
|
fixtures/BP_struct_004/GaAs_bandstructure.csv
ADDED
|
@@ -0,0 +1,102 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
k_index,k_distance,k_label,band_1,band_2,band_3,band_4,band_5,band_6,band_7
|
| 2 |
+
0,0.000000,M,-1.136039,-2.889612,-4.590794,-6.256266,2.475014,4.259759,5.973091
|
| 3 |
+
1,0.014142,,-1.093696,-2.843792,-4.540826,-6.198247,2.427833,4.210851,5.923322
|
| 4 |
+
2,0.028284,,-1.051414,-2.798153,-4.491579,-6.141803,2.380608,4.161760,5.873786
|
| 5 |
+
3,0.042426,,-1.009220,-2.752674,-4.442984,-6.086842,2.333403,4.112490,5.824417
|
| 6 |
+
4,0.056569,,-0.967149,-2.707339,-4.394974,-6.033275,2.286294,4.063055,5.775153
|
| 7 |
+
5,0.070711,,-0.925237,-2.662138,-4.347487,-5.981009,2.239356,4.013478,5.725944
|
| 8 |
+
6,0.084853,,-0.883529,-2.617070,-4.300468,-5.929956,2.192674,3.963792,5.676747
|
| 9 |
+
7,0.098995,,-0.842072,-2.572138,-4.253866,-5.880025,2.146335,3.914037,5.627528
|
| 10 |
+
8,0.113137,,-0.800920,-2.527354,-4.207637,-5.831130,2.100430,3.864262,5.578264
|
| 11 |
+
9,0.127279,,-0.760129,-2.482735,-4.161744,-5.783189,2.055053,3.814526,5.528942
|
| 12 |
+
10,0.141421,,-0.719758,-2.438308,-4.116154,-5.736120,2.010300,3.764892,5.479557
|
| 13 |
+
11,0.155563,,-0.679871,-2.394102,-4.070846,-5.689847,1.966268,3.715434,5.430116
|
| 14 |
+
12,0.169706,,-0.640533,-2.350154,-4.025801,-5.644300,1.923056,3.666229,5.380635
|
| 15 |
+
13,0.183848,,-0.601811,-2.306509,-3.981012,-5.599413,1.880762,3.617363,5.331140
|
| 16 |
+
14,0.197990,,-0.563774,-2.263213,-3.936476,-5.555124,1.839482,3.568925,5.281666
|
| 17 |
+
15,0.212132,,-0.526492,-2.220321,-3.892200,-5.511382,1.799312,3.521008,5.232258
|
| 18 |
+
16,0.226274,,-0.490035,-2.177892,-3.848196,-5.468138,1.760345,3.473712,5.182969
|
| 19 |
+
17,0.240416,,-0.454472,-2.135986,-3.804485,-5.425353,1.722670,3.427136,5.133863
|
| 20 |
+
18,0.254558,,-0.419874,-2.094672,-3.761094,-5.382994,1.686373,3.381385,5.085009
|
| 21 |
+
19,0.268701,,-0.386307,-2.054019,-3.718059,-5.341037,1.651536,3.336562,5.036485
|
| 22 |
+
20,0.282843,,-0.353838,-2.014098,-3.675421,-5.299464,1.618234,3.292773,4.988375
|
| 23 |
+
21,0.296985,,-0.322531,-1.974984,-3.633227,-5.258267,1.586538,3.250123,4.940771
|
| 24 |
+
22,0.311127,,-0.292446,-1.936753,-3.591531,-5.217444,1.556512,3.208716,4.893769
|
| 25 |
+
23,0.325269,,-0.263640,-1.899482,-3.550392,-5.177004,1.528212,3.168653,4.847470
|
| 26 |
+
24,0.339411,,-0.236168,-1.863248,-3.509874,-5.136962,1.501689,3.130033,4.801978
|
| 27 |
+
25,0.353553,,-0.210079,-1.828127,-3.470046,-5.097340,1.476984,3.092952,4.757402
|
| 28 |
+
26,0.367696,,-0.185418,-1.794196,-3.430981,-5.058170,1.454132,3.057502,4.713852
|
| 29 |
+
27,0.381838,,-0.162225,-1.761529,-3.392756,-5.019490,1.433157,3.023768,4.671440
|
| 30 |
+
28,0.395980,,-0.140534,-1.730198,-3.355448,-4.981345,1.414078,2.991832,4.630277
|
| 31 |
+
29,0.410122,,-0.120375,-1.700273,-3.319140,-4.943789,1.396902,2.961768,4.590476
|
| 32 |
+
30,0.424264,,-0.101770,-1.671821,-3.283915,-4.906879,1.381630,2.933644,4.552147
|
| 33 |
+
31,0.438406,,-0.084738,-1.644903,-3.249856,-4.870681,1.368252,2.907520,4.515398
|
| 34 |
+
32,0.452548,,-0.069290,-1.619580,-3.217047,-4.835265,1.356751,2.883447,4.480335
|
| 35 |
+
33,0.466690,,-0.055430,-1.595904,-3.185573,-4.800707,1.347102,2.861471,4.447060
|
| 36 |
+
34,0.480833,,-0.043158,-1.573924,-3.155515,-4.767084,1.339269,2.841626,4.415668
|
| 37 |
+
35,0.494975,,-0.032466,-1.553684,-3.126956,-4.734481,1.333210,2.823939,4.386252
|
| 38 |
+
36,0.509117,,-0.023341,-1.535221,-3.099972,-4.702983,1.328876,2.808426,4.358896
|
| 39 |
+
37,0.523259,,-0.015763,-1.518566,-3.074640,-4.672679,1.326208,2.795097,4.333680
|
| 40 |
+
38,0.537401,,-0.009707,-1.503744,-3.051033,-4.643659,1.325144,2.783949,4.310675
|
| 41 |
+
39,0.551543,,-0.005142,-1.490774,-3.029217,-4.616014,1.325612,2.774973,4.289943
|
| 42 |
+
40,0.565685,,-0.002031,-1.479666,-3.009257,-4.589834,1.327535,2.768147,4.271540
|
| 43 |
+
41,0.579828,,-0.000333,-1.470426,-2.991209,-4.565211,1.330834,2.763443,4.255511
|
| 44 |
+
42,0.593970,,0.000000,-1.463053,-2.975128,-4.542233,1.335421,2.760824,4.241892
|
| 45 |
+
43,0.608112,,-0.000982,-1.457536,-2.961058,-4.520989,1.341206,2.760242,4.230712
|
| 46 |
+
44,0.622254,,-0.003224,-1.453860,-2.949041,-4.501562,1.348098,2.761644,4.221986
|
| 47 |
+
45,0.636396,,-0.006667,-1.452003,-2.939109,-4.484035,1.355999,2.764967,4.215722
|
| 48 |
+
46,0.650538,,-0.011249,-1.451936,-2.931288,-4.468484,1.364814,2.770140,4.211918
|
| 49 |
+
47,0.664680,,-0.016906,-1.453625,-2.925599,-4.454984,1.374444,2.777089,4.210561
|
| 50 |
+
48,0.678823,,-0.023571,-1.457028,-2.922052,-4.443601,1.384792,2.785730,4.211629
|
| 51 |
+
49,0.692965,,-0.031175,-1.462098,-2.920651,-4.434398,1.395759,2.795976,4.215088
|
| 52 |
+
50,0.707107,��,-0.039649,-1.468785,-2.921395,-4.427431,1.407250,2.807734,4.220899
|
| 53 |
+
51,0.725478,,-0.028806,-1.460410,-2.920845,-4.436918,1.392420,2.792750,4.213805
|
| 54 |
+
52,0.743849,,-0.019467,-1.454789,-2.923915,-4.450151,1.378522,2.780364,4.210700
|
| 55 |
+
53,0.762220,,-0.011783,-1.452030,-2.930604,-4.466999,1.365769,2.770775,4.211666
|
| 56 |
+
54,0.780591,,-0.005900,-1.452225,-2.940891,-4.487319,1.354374,2.764167,4.216757
|
| 57 |
+
55,0.798963,,-0.001960,-1.455451,-2.954733,-4.510949,1.344553,2.760706,4.225999
|
| 58 |
+
56,0.817334,,-0.000096,-1.461766,-2.972067,-4.537717,1.336516,2.760539,4.239392
|
| 59 |
+
57,0.835705,,-0.000433,-1.471209,-2.992810,-4.567439,1.330470,2.763793,4.256904
|
| 60 |
+
58,0.854076,,-0.003081,-1.483801,-3.016862,-4.599924,1.326612,2.770570,4.278479
|
| 61 |
+
59,0.872447,,-0.008141,-1.499542,-3.044105,-4.634975,1.325128,2.780948,4.304031
|
| 62 |
+
60,0.890819,,-0.015698,-1.518415,-3.074405,-4.672394,1.326191,2.794979,4.333448
|
| 63 |
+
61,0.909190,,-0.025822,-1.540380,-3.107615,-4.711980,1.329956,2.812692,4.366597
|
| 64 |
+
62,0.927561,,-0.038567,-1.565382,-3.143576,-4.753538,1.336563,2.834084,4.403318
|
| 65 |
+
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66,1.001046,,-0.116235,-1.694018,-3.311459,-4.935782,1.393452,2.955545,4.582092
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84,1.331727,,-0.890490,-2.624600,-4.308304,-5.938416,2.200462,3.972110,5.684978
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85,1.350098,,-0.944759,-2.683200,-4.369570,-6.005226,2.261218,4.036613,5.748888
|
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|
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|
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90,1.441954,,-1.219196,-2.980137,-4.691194,-6.374984,2.567207,4.355186,6.071695
|
| 93 |
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91,1.460325,,-1.274303,-3.040675,-4.759662,-6.457444,2.627859,4.418071,6.137970
|
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92,1.478696,,-1.329430,-3.101800,-4.829915,-6.543171,2.688093,4.480789,6.205264
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|
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|
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|
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|
| 100 |
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98,1.588923,,-1.662467,-3.488330,-5.299119,-7.134197,3.039299,4.860569,6.643453
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99,1.607294,,-1.719007,-3.557485,-5.386879,-7.246453,3.096410,4.926022,6.724480
|
| 102 |
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100,1.625665,K,-1.776116,-3.628434,-5.477779,-7.362794,3.153335,4.992632,6.808422
|
fixtures/BP_struct_004/Ge_bandstructure.csv
ADDED
|
@@ -0,0 +1,102 @@
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|
|
|
|
|
|
|
|
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|
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|
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|
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|
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|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
|
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|
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|
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|
|
|
|
| 1 |
+
k_index,k_distance,k_label,band_1,band_2,band_3,band_4,band_5,band_6,band_7
|
| 2 |
+
0,0.000000,M,-1.136039,-2.889612,-4.590794,-6.256266,1.775014,3.559759,5.273091
|
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|
| 7 |
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| 8 |
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|
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|
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| 83 |
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81,1.276613,,-0.730621,-2.450291,-4.128443,-5.748755,1.322324,3.078288,4.792906
|
| 84 |
+
82,1.294984,,-0.783301,-2.508111,-4.187828,-5.810366,1.380812,3.142828,4.857025
|
| 85 |
+
83,1.313355,,-0.836632,-2.566229,-4.247756,-5.873526,1.440261,3.207479,4.921041
|
| 86 |
+
84,1.331727,,-0.890490,-2.624600,-4.308304,-5.938416,1.500462,3.272110,4.984978
|
| 87 |
+
85,1.350098,,-0.944759,-2.683200,-4.369570,-6.005226,1.561218,3.336613,5.048888
|
| 88 |
+
86,1.368469,,-0.999337,-2.742025,-4.431669,-6.074152,1.622339,3.400905,5.112851
|
| 89 |
+
87,1.386840,,-1.054135,-2.801088,-4.494731,-6.145393,1.683649,3.464928,5.176971
|
| 90 |
+
88,1.405211,,-1.109080,-2.860423,-4.558899,-6.219147,1.744989,3.528648,5.241379
|
| 91 |
+
89,1.423583,,-1.164113,-2.920082,-4.624332,-6.295613,1.806216,3.592060,5.306229
|
| 92 |
+
90,1.441954,,-1.219196,-2.980137,-4.691194,-6.374984,1.867207,3.655186,5.371695
|
| 93 |
+
91,1.460325,,-1.274303,-3.040675,-4.759662,-6.457444,1.927859,3.718071,5.437970
|
| 94 |
+
92,1.478696,,-1.329430,-3.101800,-4.829915,-6.543171,1.988093,3.780789,5.505264
|
| 95 |
+
93,1.497067,,-1.384588,-3.163631,-4.902138,-6.632327,2.047853,3.843436,5.573799
|
| 96 |
+
94,1.515438,,-1.439807,-3.226299,-4.976513,-6.725064,2.107108,3.906135,5.643810
|
| 97 |
+
95,1.533810,,-1.495134,-3.289947,-5.053224,-6.821513,2.165850,3.969026,5.715535
|
| 98 |
+
96,1.552181,,-1.550631,-3.354727,-5.132448,-6.921791,2.224097,4.032273,5.789221
|
| 99 |
+
97,1.570552,,-1.606377,-3.420800,-5.214359,-7.025994,2.281891,4.096055,5.865113
|
| 100 |
+
98,1.588923,,-1.662467,-3.488330,-5.299119,-7.134197,2.339299,4.160569,5.943453
|
| 101 |
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99,1.607294,,-1.719007,-3.557485,-5.386879,-7.246453,2.396410,4.226022,6.024480
|
| 102 |
+
100,1.625665,K,-1.776116,-3.628434,-5.477779,-7.362794,2.453335,4.292632,6.108422
|
fixtures/BP_struct_004/Si_bandstructure.csv
ADDED
|
@@ -0,0 +1,102 @@
|
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|
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|
|
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|
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|
|
|
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|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
k_index,k_distance,k_label,band_1,band_2,band_3,band_4,band_5,band_6,band_7
|
| 2 |
+
0,0.000000,M,-1.136039,-2.889612,-4.590794,-6.256266,2.175014,3.959759,5.673091
|
| 3 |
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1,0.014142,,-1.093696,-2.843792,-4.540826,-6.198247,2.127833,3.910851,5.623322
|
| 4 |
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2,0.028284,,-1.051414,-2.798153,-4.491579,-6.141803,2.080608,3.861760,5.573786
|
| 5 |
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3,0.042426,,-1.009220,-2.752674,-4.442984,-6.086842,2.033403,3.812490,5.524417
|
| 6 |
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4,0.056569,,-0.967149,-2.707339,-4.394974,-6.033275,1.986294,3.763055,5.475153
|
| 7 |
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5,0.070711,,-0.925237,-2.662138,-4.347487,-5.981009,1.939356,3.713478,5.425944
|
| 8 |
+
6,0.084853,,-0.883529,-2.617070,-4.300468,-5.929956,1.892674,3.663792,5.376747
|
| 9 |
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7,0.098995,,-0.842072,-2.572138,-4.253866,-5.880025,1.846335,3.614037,5.327528
|
| 10 |
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8,0.113137,,-0.800920,-2.527354,-4.207637,-5.831130,1.800430,3.564262,5.278264
|
| 11 |
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9,0.127279,,-0.760129,-2.482735,-4.161744,-5.783189,1.755053,3.514526,5.228942
|
| 12 |
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10,0.141421,,-0.719758,-2.438308,-4.116154,-5.736120,1.710300,3.464892,5.179557
|
| 13 |
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11,0.155563,,-0.679871,-2.394102,-4.070846,-5.689847,1.666268,3.415434,5.130116
|
| 14 |
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12,0.169706,,-0.640533,-2.350154,-4.025801,-5.644300,1.623056,3.366229,5.080635
|
| 15 |
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13,0.183848,,-0.601811,-2.306509,-3.981012,-5.599413,1.580762,3.317363,5.031140
|
| 16 |
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14,0.197990,,-0.563774,-2.263213,-3.936476,-5.555124,1.539482,3.268925,4.981666
|
| 17 |
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15,0.212132,,-0.526492,-2.220321,-3.892200,-5.511382,1.499312,3.221008,4.932258
|
| 18 |
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16,0.226274,,-0.490035,-2.177892,-3.848196,-5.468138,1.460345,3.173712,4.882969
|
| 19 |
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17,0.240416,,-0.454472,-2.135986,-3.804485,-5.425353,1.422670,3.127136,4.833863
|
| 20 |
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18,0.254558,,-0.419874,-2.094672,-3.761094,-5.382994,1.386373,3.081385,4.785009
|
| 21 |
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19,0.268701,,-0.386307,-2.054019,-3.718059,-5.341037,1.351536,3.036562,4.736485
|
| 22 |
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20,0.282843,,-0.353838,-2.014098,-3.675421,-5.299464,1.318234,2.992773,4.688375
|
| 23 |
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21,0.296985,,-0.322531,-1.974984,-3.633227,-5.258267,1.286538,2.950123,4.640771
|
| 24 |
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22,0.311127,,-0.292446,-1.936753,-3.591531,-5.217444,1.256512,2.908716,4.593769
|
| 25 |
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23,0.325269,,-0.263640,-1.899482,-3.550392,-5.177004,1.228212,2.868653,4.547470
|
| 26 |
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24,0.339411,,-0.236168,-1.863248,-3.509874,-5.136962,1.201689,2.830033,4.501978
|
| 27 |
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25,0.353553,,-0.210079,-1.828127,-3.470046,-5.097340,1.176984,2.792952,4.457402
|
| 28 |
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26,0.367696,,-0.185418,-1.794196,-3.430981,-5.058170,1.154132,2.757502,4.413852
|
| 29 |
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27,0.381838,,-0.162225,-1.761529,-3.392756,-5.019490,1.133157,2.723768,4.371440
|
| 30 |
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28,0.395980,,-0.140534,-1.730198,-3.355448,-4.981345,1.114078,2.691832,4.330277
|
| 31 |
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29,0.410122,,-0.120375,-1.700273,-3.319140,-4.943789,1.096902,2.661768,4.290476
|
| 32 |
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30,0.424264,,-0.101770,-1.671821,-3.283915,-4.906879,1.081630,2.633644,4.252147
|
| 33 |
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31,0.438406,,-0.084738,-1.644903,-3.249856,-4.870681,1.068252,2.607520,4.215398
|
| 34 |
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32,0.452548,,-0.069290,-1.619580,-3.217047,-4.835265,1.056751,2.583447,4.180335
|
| 35 |
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33,0.466690,,-0.055430,-1.595904,-3.185573,-4.800707,1.047102,2.561471,4.147060
|
| 36 |
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34,0.480833,,-0.043158,-1.573924,-3.155515,-4.767084,1.039269,2.541626,4.115668
|
| 37 |
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35,0.494975,,-0.032466,-1.553684,-3.126956,-4.734481,1.033210,2.523939,4.086252
|
| 38 |
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36,0.509117,,-0.023341,-1.535221,-3.099972,-4.702983,1.028876,2.508426,4.058896
|
| 39 |
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37,0.523259,,-0.015763,-1.518566,-3.074640,-4.672679,1.026208,2.495097,4.033680
|
| 40 |
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38,0.537401,,-0.009707,-1.503744,-3.051033,-4.643659,1.025144,2.483949,4.010675
|
| 41 |
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39,0.551543,,-0.005142,-1.490774,-3.029217,-4.616014,1.025612,2.474973,3.989943
|
| 42 |
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40,0.565685,,-0.002031,-1.479666,-3.009257,-4.589834,1.027535,2.468147,3.971540
|
| 43 |
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41,0.579828,,-0.000333,-1.470426,-2.991209,-4.565211,1.030834,2.463443,3.955511
|
| 44 |
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42,0.593970,,0.000000,-1.463053,-2.975128,-4.542233,1.035421,2.460824,3.941892
|
| 45 |
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43,0.608112,,-0.000982,-1.457536,-2.961058,-4.520989,1.041206,2.460242,3.930712
|
| 46 |
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44,0.622254,,-0.003224,-1.453860,-2.949041,-4.501562,1.048098,2.461644,3.921986
|
| 47 |
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45,0.636396,,-0.006667,-1.452003,-2.939109,-4.484035,1.055999,2.464967,3.915722
|
| 48 |
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46,0.650538,,-0.011249,-1.451936,-2.931288,-4.468484,1.064814,2.470140,3.911918
|
| 49 |
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47,0.664680,,-0.016906,-1.453625,-2.925599,-4.454984,1.074444,2.477089,3.910561
|
| 50 |
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48,0.678823,,-0.023571,-1.457028,-2.922052,-4.443601,1.084792,2.485730,3.911629
|
| 51 |
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49,0.692965,,-0.031175,-1.462098,-2.920651,-4.434398,1.095759,2.495976,3.915088
|
| 52 |
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50,0.707107,��,-0.039649,-1.468785,-2.921395,-4.427431,1.107250,2.507734,3.920899
|
| 53 |
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51,0.725478,,-0.028806,-1.460410,-2.920845,-4.436918,1.092420,2.492750,3.913805
|
| 54 |
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52,0.743849,,-0.019467,-1.454789,-2.923915,-4.450151,1.078522,2.480364,3.910700
|
| 55 |
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53,0.762220,,-0.011783,-1.452030,-2.930604,-4.466999,1.065769,2.470775,3.911666
|
| 56 |
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54,0.780591,,-0.005900,-1.452225,-2.940891,-4.487319,1.054374,2.464167,3.916757
|
| 57 |
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55,0.798963,,-0.001960,-1.455451,-2.954733,-4.510949,1.044553,2.460706,3.925999
|
| 58 |
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56,0.817334,,-0.000096,-1.461766,-2.972067,-4.537717,1.036516,2.460539,3.939392
|
| 59 |
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57,0.835705,,-0.000433,-1.471209,-2.992810,-4.567439,1.030470,2.463793,3.956904
|
| 60 |
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58,0.854076,,-0.003081,-1.483801,-3.016862,-4.599924,1.026612,2.470570,3.978479
|
| 61 |
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59,0.872447,,-0.008141,-1.499542,-3.044105,-4.634975,1.025128,2.480948,4.004031
|
| 62 |
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60,0.890819,,-0.015698,-1.518415,-3.074405,-4.672394,1.026191,2.494979,4.033448
|
| 63 |
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61,0.909190,,-0.025822,-1.540380,-3.107615,-4.711980,1.029956,2.512692,4.066597
|
| 64 |
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62,0.927561,,-0.038567,-1.565382,-3.143576,-4.753538,1.036563,2.534084,4.103318
|
| 65 |
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63,0.945932,,-0.053970,-1.593346,-3.182119,-4.796876,1.046130,2.559131,4.143432
|
| 66 |
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64,0.964303,,-0.072051,-1.624180,-3.223069,-4.841809,1.058755,2.587780,4.186743
|
| 67 |
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65,0.982674,,-0.092811,-1.657778,-3.266243,-4.888165,1.074512,2.619952,4.233038
|
| 68 |
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66,1.001046,,-0.116235,-1.694018,-3.311459,-4.935782,1.093452,2.655545,4.282092
|
| 69 |
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67,1.019417,,-0.142290,-1.732766,-3.358532,-4.984514,1.115601,2.694433,4.333669
|
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68,1.037788,,-0.170925,-1.773876,-3.407280,-5.034231,1.140961,2.736469,4.387529
|
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69,1.056159,,-0.202073,-1.817195,-3.457526,-5.084822,1.169508,2.781488,4.443424
|
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70,1.074530,,-0.235653,-1.862561,-3.509101,-5.136196,1.201197,2.829305,4.501111
|
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71,1.092901,,-0.271568,-1.909809,-3.561843,-5.188280,1.235954,2.879721,4.560348
|
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72,1.111273,,-0.309708,-1.958771,-3.615602,-5.241028,1.273685,2.932527,4.620897
|
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73,1.129644,,-0.349951,-2.009276,-3.670243,-5.294413,1.314276,2.987502,4.682533
|
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74,1.148015,,-0.392167,-2.061160,-3.725645,-5.348431,1.357589,3.044420,4.745042
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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87,1.386840,,-1.054135,-2.801088,-4.494731,-6.145393,2.083649,3.864928,5.576971
|
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88,1.405211,,-1.109080,-2.860423,-4.558899,-6.219147,2.144989,3.928648,5.641379
|
| 91 |
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|
| 92 |
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90,1.441954,,-1.219196,-2.980137,-4.691194,-6.374984,2.267207,4.055186,5.771695
|
| 93 |
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91,1.460325,,-1.274303,-3.040675,-4.759662,-6.457444,2.327859,4.118071,5.837970
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|
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|
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| 100 |
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98,1.588923,,-1.662467,-3.488330,-5.299119,-7.134197,2.739299,4.560569,6.343453
|
| 101 |
+
99,1.607294,,-1.719007,-3.557485,-5.386879,-7.246453,2.796410,4.626022,6.424480
|
| 102 |
+
100,1.625665,K,-1.776116,-3.628434,-5.477779,-7.362794,2.853335,4.692632,6.508422
|
fixtures/BP_struct_004/postprocessing_bandstr.json
ADDED
|
@@ -0,0 +1,59 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"data_format": {
|
| 3 |
+
"columns": "k_index, k_distance, k_label, band_1, band_2, ..., band_N",
|
| 4 |
+
"conduction_bands": "band_5 through band_7",
|
| 5 |
+
"description": "Each band data CSV contains pre-computed eigenvalues along M-Gamma-K path with VBM referenced to 0 eV.",
|
| 6 |
+
"units": "energies in eV, k_distance in 1/Angstrom",
|
| 7 |
+
"valence_bands": "band_1 through band_4"
|
| 8 |
+
},
|
| 9 |
+
"description": "For 3 different materials (Si, Ge, GaAs), perform band structure post-processing with consistent analysis parameters. Extract band gap, band edge positions, and generate plots. The key test is: all materials undergo identical analysis (same k-path, same energy window, same plot range) even though their absolute band gaps differ.",
|
| 10 |
+
"materials": [
|
| 11 |
+
{
|
| 12 |
+
"band_data_file": "Si_bandstructure.csv",
|
| 13 |
+
"crystal_system": "cubic",
|
| 14 |
+
"expected_bandgap_eV": 1.12,
|
| 15 |
+
"formula": "Si",
|
| 16 |
+
"id": "mat_si"
|
| 17 |
+
},
|
| 18 |
+
{
|
| 19 |
+
"band_data_file": "Ge_bandstructure.csv",
|
| 20 |
+
"crystal_system": "cubic",
|
| 21 |
+
"expected_bandgap_eV": 0.67,
|
| 22 |
+
"formula": "Ge",
|
| 23 |
+
"id": "mat_ge"
|
| 24 |
+
},
|
| 25 |
+
{
|
| 26 |
+
"band_data_file": "GaAs_bandstructure.csv",
|
| 27 |
+
"crystal_system": "cubic",
|
| 28 |
+
"expected_bandgap_eV": 1.42,
|
| 29 |
+
"formula": "GaAs",
|
| 30 |
+
"id": "mat_gaas"
|
| 31 |
+
}
|
| 32 |
+
],
|
| 33 |
+
"task": "batch_post_processing_band_structure_analysis",
|
| 34 |
+
"unified_analysis_parameters": {
|
| 35 |
+
"energy_window_eV": [
|
| 36 |
+
-5,
|
| 37 |
+
5
|
| 38 |
+
],
|
| 39 |
+
"fermi_level_reference": "VBM",
|
| 40 |
+
"k_path": "M-Gamma-K",
|
| 41 |
+
"n_kpoints_per_segment": 50,
|
| 42 |
+
"output_format": "PNG plot + CSV table",
|
| 43 |
+
"plot_style": "solid lines, VBM at 0 eV"
|
| 44 |
+
},
|
| 45 |
+
"verification": {
|
| 46 |
+
"accuracy_checks": [
|
| 47 |
+
"Band gap values within 0.1 eV of literature",
|
| 48 |
+
"VBM/CBM band edge positions identifiable",
|
| 49 |
+
"Plot visual quality consistent"
|
| 50 |
+
],
|
| 51 |
+
"consistency_checks": [
|
| 52 |
+
"All 3 materials processed with identical k-path M-Gamma-K",
|
| 53 |
+
"All use same energy window [-5, 5] eV",
|
| 54 |
+
"All use VBM as Fermi level reference",
|
| 55 |
+
"All generate both plot and data table",
|
| 56 |
+
"Output naming convention respected"
|
| 57 |
+
]
|
| 58 |
+
}
|
| 59 |
+
}
|
fixtures/BP_struct_005/calc_001_TiO2_bad.POSCAR
ADDED
|
@@ -0,0 +1,14 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
TiO2_bad_atoms_too_close
|
| 2 |
+
1.0
|
| 3 |
+
4.594 0.000 0.000
|
| 4 |
+
0.000 4.594 0.000
|
| 5 |
+
0.000 0.000 2.959
|
| 6 |
+
Ti O
|
| 7 |
+
2 4
|
| 8 |
+
Direct
|
| 9 |
+
0.0000 0.0000 0.0000
|
| 10 |
+
0.0001 0.0001 0.0000
|
| 11 |
+
0.3050 0.3050 0.0000
|
| 12 |
+
0.6950 0.6950 0.0000
|
| 13 |
+
0.1950 0.8050 0.5000
|
| 14 |
+
0.8050 0.1950 0.5000
|
fixtures/BP_struct_005/calc_002_ZnO_bad.POSCAR
ADDED
|
@@ -0,0 +1,12 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ZnO_bad_sign_flipped_basis_left_handed
|
| 2 |
+
1.0
|
| 3 |
+
-3.250 0.000 0.000
|
| 4 |
+
0.000 2.8146 0.000
|
| 5 |
+
0.000 0.000 5.2070
|
| 6 |
+
Zn O
|
| 7 |
+
2 2
|
| 8 |
+
Direct
|
| 9 |
+
0.000000 0.000000 0.000000
|
| 10 |
+
0.333333 0.666667 0.500000
|
| 11 |
+
0.000000 0.000000 0.382500
|
| 12 |
+
0.333333 0.666667 0.882500
|
fixtures/BP_struct_005/calc_003_MgO_bad.POSCAR
ADDED
|
@@ -0,0 +1,10 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
MgO_bad_broken_symmetry
|
| 2 |
+
1.0
|
| 3 |
+
4.210 0.000 0.000
|
| 4 |
+
0.000 4.350 0.000
|
| 5 |
+
0.000 0.000 4.100
|
| 6 |
+
Mg O
|
| 7 |
+
1 1
|
| 8 |
+
Direct
|
| 9 |
+
0.0000 0.0000 0.0000
|
| 10 |
+
0.4700 0.5300 0.5000
|
fixtures/BP_struct_005/calc_004_Al2O3_bad.POSCAR
ADDED
|
@@ -0,0 +1,18 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
Al2O3_bad_duplicate_atoms
|
| 2 |
+
1.0
|
| 3 |
+
4.7580 0.0000 0.0000
|
| 4 |
+
-2.3790 4.1200 0.0000
|
| 5 |
+
0.0000 0.0000 12.9910
|
| 6 |
+
Al O
|
| 7 |
+
4 6
|
| 8 |
+
Direct
|
| 9 |
+
0.0000 0.0000 0.3522
|
| 10 |
+
0.0000 0.0000 0.6478
|
| 11 |
+
0.3333 0.6667 0.0189
|
| 12 |
+
0.6667 0.3333 0.9811
|
| 13 |
+
0.3060 0.0000 0.2500
|
| 14 |
+
0.0000 0.3060 0.7500
|
| 15 |
+
0.6940 0.6940 0.2500
|
| 16 |
+
0.6940 0.0000 0.7500
|
| 17 |
+
0.6940 0.0000 0.7500
|
| 18 |
+
0.3060 0.3060 0.7500
|
fixtures/BP_struct_005/calc_005_SiO2_bad.POSCAR
ADDED
|
@@ -0,0 +1,17 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
SiO2_bad_distorted_cell
|
| 2 |
+
1.0
|
| 3 |
+
4.9130 0.0000 0.0000
|
| 4 |
+
2.4000 4.2550 0.0000
|
| 5 |
+
0.0000 0.0000 2.0000
|
| 6 |
+
Si O
|
| 7 |
+
3 6
|
| 8 |
+
Direct
|
| 9 |
+
0.4697 0.0000 0.6667
|
| 10 |
+
0.0000 0.4697 0.3333
|
| 11 |
+
0.5303 0.5303 0.0000
|
| 12 |
+
0.4133 0.2667 0.7850
|
| 13 |
+
0.1466 0.4133 0.4517
|
| 14 |
+
0.7333 0.1466 0.1183
|
| 15 |
+
0.5867 0.7333 0.2150
|
| 16 |
+
0.8534 0.5867 0.5483
|
| 17 |
+
0.2667 0.8534 0.8817
|
fixtures/BP_struct_005/failure_recovery.json
ADDED
|
@@ -0,0 +1,100 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"description": "Given a scenario where 5 structure calculations fail due to bad input geometry, demonstrate controlled recovery by repairing only the geometry (run geometry optimization first) while freezing all other calculation parameters (k-points, ISMEAR, SIGMA, ENCUT). This tests whether the agent can isolate and fix only the root-cause parameter without modifying non-causal ones.",
|
| 3 |
+
"frozen_parameters": {
|
| 4 |
+
"ALGO": "Normal",
|
| 5 |
+
"ENCUT": 520,
|
| 6 |
+
"ISMEAR": 1,
|
| 7 |
+
"NSW": 0,
|
| 8 |
+
"SIGMA": 0.1,
|
| 9 |
+
"k_point_mesh": "6 6 6"
|
| 10 |
+
},
|
| 11 |
+
"initial_batch": [
|
| 12 |
+
{
|
| 13 |
+
"id": "calc_001",
|
| 14 |
+
"initial_issue": "Atoms too close (bad POSCAR)",
|
| 15 |
+
"input_poscar": "calc_001_TiO2_bad.POSCAR",
|
| 16 |
+
"material": "TiO2",
|
| 17 |
+
"repair_acceptance": {
|
| 18 |
+
"checks": [
|
| 19 |
+
"remove unphysically short inter-atomic contact (especially Ti-Ti overlap in bad input)",
|
| 20 |
+
"keep stoichiometry and species counts unchanged",
|
| 21 |
+
"preserve lattice vectors unless explicitly required by issue description",
|
| 22 |
+
"fixed structure should not introduce new obvious clashes"
|
| 23 |
+
],
|
| 24 |
+
"non_unique_solution": true
|
| 25 |
+
},
|
| 26 |
+
"required_fix": "run geometry pre-relaxation"
|
| 27 |
+
},
|
| 28 |
+
{
|
| 29 |
+
"id": "calc_002",
|
| 30 |
+
"initial_issue": "Left-handed cell caused by sign-flipped lattice vector",
|
| 31 |
+
"input_poscar": "calc_002_ZnO_bad.POSCAR",
|
| 32 |
+
"material": "ZnO",
|
| 33 |
+
"repair_acceptance": {
|
| 34 |
+
"checks": [
|
| 35 |
+
"repair sign-flipped basis vector so the cell basis is right-handed",
|
| 36 |
+
"keep real-space structure equivalent (allow coordinate remapping only for basis-handness correction)",
|
| 37 |
+
"do not reconstruct into a different ZnO polymorph or motif",
|
| 38 |
+
"avoid extra optimization beyond handedness/orientation correction"
|
| 39 |
+
]
|
| 40 |
+
},
|
| 41 |
+
"required_fix": "repair lattice basis handedness/orientation"
|
| 42 |
+
},
|
| 43 |
+
{
|
| 44 |
+
"id": "calc_003",
|
| 45 |
+
"initial_issue": "Broken symmetry",
|
| 46 |
+
"input_poscar": "calc_003_MgO_bad.POSCAR",
|
| 47 |
+
"material": "MgO",
|
| 48 |
+
"repair_acceptance": {
|
| 49 |
+
"checks": [
|
| 50 |
+
"restore rocksalt-like local symmetry consistency",
|
| 51 |
+
"remove obvious off-symmetry displacement that breaks intended motif",
|
| 52 |
+
"keep composition and atom count unchanged"
|
| 53 |
+
],
|
| 54 |
+
"non_unique_solution": true
|
| 55 |
+
},
|
| 56 |
+
"required_fix": "apply spacegroup symmetry"
|
| 57 |
+
},
|
| 58 |
+
{
|
| 59 |
+
"id": "calc_004",
|
| 60 |
+
"initial_issue": "Duplicate atoms",
|
| 61 |
+
"input_poscar": "calc_004_Al2O3_bad.POSCAR",
|
| 62 |
+
"material": "Al2O3",
|
| 63 |
+
"repair_acceptance": {
|
| 64 |
+
"checks": [
|
| 65 |
+
"remove duplicated atomic site(s)",
|
| 66 |
+
"keep total species counts aligned with target composition",
|
| 67 |
+
"retain physically sensible lattice and non-duplicated coordinates"
|
| 68 |
+
]
|
| 69 |
+
},
|
| 70 |
+
"required_fix": "remove duplicates"
|
| 71 |
+
},
|
| 72 |
+
{
|
| 73 |
+
"id": "calc_005",
|
| 74 |
+
"initial_issue": "Distorted cell",
|
| 75 |
+
"input_poscar": "calc_005_SiO2_bad.POSCAR",
|
| 76 |
+
"material": "SiO2",
|
| 77 |
+
"repair_acceptance": {
|
| 78 |
+
"checks": [
|
| 79 |
+
"repair severely distorted cell to a physically reasonable one",
|
| 80 |
+
"recover a consistent right-handed lattice basis",
|
| 81 |
+
"avoid unrealistic c-axis collapse seen in bad input",
|
| 82 |
+
"keep atomic composition unchanged"
|
| 83 |
+
],
|
| 84 |
+
"non_unique_solution": true
|
| 85 |
+
},
|
| 86 |
+
"required_fix": "relax cell parameters"
|
| 87 |
+
}
|
| 88 |
+
],
|
| 89 |
+
"modification_rules": {
|
| 90 |
+
"allowed_to_modify": "Only structure geometry, lattice, symmetry-related inputs",
|
| 91 |
+
"forbidden_to_modify": "k-point settings, electronic smearing, plane-wave cutoff, any solver settings"
|
| 92 |
+
},
|
| 93 |
+
"success_criteria": [
|
| 94 |
+
"All 5 structures converge after repair",
|
| 95 |
+
"Each uses the same frozen k-point and solver settings",
|
| 96 |
+
"Only geometry-related steps appear between failure and success",
|
| 97 |
+
"No redundant re-tuning of electronic parameters"
|
| 98 |
+
],
|
| 99 |
+
"task": "batch_failure_recovery_parameter_frozen"
|
| 100 |
+
}
|
fixtures/DD_general_004/case_bundle.json
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"description": "Given the INCAR, POSCAR summary, and OUTCAR excerpt below, diagnose why structural relaxation diverges.",
|
| 3 |
+
"diagnosis_hint": "Two compounding issues: (1) POTIM=1.0 is far too large - the default 0.5 or even 0.1-0.3 would be safer; (2) starting from the wrong phase (cubic instead of orthorhombic) means initial forces are huge. Fix: reduce POTIM to 0.1-0.2, or better yet, start from the orthorhombic Pnma structure. For unknown ground-state structures, use a conservative POTIM with IBRION=1 (RMM-DIIS) which handles large steps better than conjugate gradient.",
|
| 4 |
+
"incar": {
|
| 5 |
+
"EDIFF": 1e-06,
|
| 6 |
+
"EDIFFG": -0.02,
|
| 7 |
+
"ENCUT": 450,
|
| 8 |
+
"IBRION": 2,
|
| 9 |
+
"ISIF": 3,
|
| 10 |
+
"ISMEAR": 0,
|
| 11 |
+
"ISPIN": 1,
|
| 12 |
+
"NSW": 300,
|
| 13 |
+
"POTIM": 1.0,
|
| 14 |
+
"PREC": "Accurate",
|
| 15 |
+
"SIGMA": 0.05,
|
| 16 |
+
"SYSTEM": "Perovskite_CsPbI3_cubic",
|
| 17 |
+
"_comment": "BUG: POTIM=1.0 is too large for this system. Combined with an initial structure that has the cubic phase (high-T) instead of the actual ground-state orthorhombic phase, the forces are large and POTIM=1.0 causes atoms to overshoot drastically. Each ionic step the structure bounces back and forth, never settling."
|
| 18 |
+
},
|
| 19 |
+
"key_observation": "Energy increases from step 1 to step 4, forces explode from 2.3 to 48 eV/A, volume swings wildly. By step 5, VASP encounters a fatal bracketing error. The ionic step is too aggressive.",
|
| 20 |
+
"outcar_excerpt_ionic_steps": [
|
| 21 |
+
"--- step 1: E= -19.23456 max_force= 2.341 volume= 248.9",
|
| 22 |
+
"--- step 2: E= -17.89123 max_force= 5.672 volume= 275.3",
|
| 23 |
+
"--- step 3: E= -12.34567 max_force= 12.891 volume= 312.1",
|
| 24 |
+
"--- step 4: E= +8.45231 max_force= 48.234 volume= 189.2",
|
| 25 |
+
"--- step 5: ZBRENT: fatal internal error",
|
| 26 |
+
" please rerun with smaller POTIM, or copy CONTCAR to POSCAR and continue"
|
| 27 |
+
],
|
| 28 |
+
"poscar_summary": {
|
| 29 |
+
"counts": [
|
| 30 |
+
1,
|
| 31 |
+
1,
|
| 32 |
+
3
|
| 33 |
+
],
|
| 34 |
+
"lattice_a": 6.289,
|
| 35 |
+
"note": "Cubic CsPbI3 is the high-temperature phase; ground state is orthorhombic Pnma. Starting from cubic with ISIF=3 requires large atomic displacements and cell shape changes.",
|
| 36 |
+
"species": [
|
| 37 |
+
"Cs",
|
| 38 |
+
"Pb",
|
| 39 |
+
"I"
|
| 40 |
+
],
|
| 41 |
+
"system": "CsPbI3 cubic Pm-3m (high-T phase, NOT ground state)",
|
| 42 |
+
"total_atoms": 5
|
| 43 |
+
},
|
| 44 |
+
"root_cause": "potim_too_large_and_bad_initial_structure",
|
| 45 |
+
"task": "relax_divergence_diagnosis"
|
| 46 |
+
}
|
fixtures/DD_vasp_scf_diverge_001/INCAR_original.txt
ADDED
|
@@ -0,0 +1,24 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
SYSTEM = FeN4C SAC with *OOH adsorbate
|
| 2 |
+
ISTART = 0
|
| 3 |
+
ICHARG = 2
|
| 4 |
+
ENCUT = 520
|
| 5 |
+
EDIFF = 1E-5
|
| 6 |
+
NELM = 200
|
| 7 |
+
ALGO = Normal
|
| 8 |
+
ISPIN = 2
|
| 9 |
+
MAGMOM = 1*4.0 4*0.5 44*0.0 3*0.0 1*0.0
|
| 10 |
+
LDAU = .TRUE.
|
| 11 |
+
LDAUTYPE = 2
|
| 12 |
+
LDAUL = 2 -1 -1 -1
|
| 13 |
+
LDAUU = 4.0 0.0 0.0 0.0
|
| 14 |
+
LDAUJ = 0.0 0.0 0.0 0.0
|
| 15 |
+
LMAXMIX = 4
|
| 16 |
+
ISMEAR = 0
|
| 17 |
+
SIGMA = 0.05
|
| 18 |
+
LREAL = Auto
|
| 19 |
+
ISIF = 2
|
| 20 |
+
IBRION = 2
|
| 21 |
+
NSW = 100
|
| 22 |
+
EDIFFG = -0.03
|
| 23 |
+
AMIX = 0.2
|
| 24 |
+
BMIX = 0.0001
|
fixtures/DD_vasp_scf_diverge_001/OSZICAR_fragment.txt
ADDED
|
@@ -0,0 +1,20 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
N E dE d eps ncg rms rms(c)
|
| 2 |
+
DAV: 1 -0.440258E+03 -0.440258E+03 -0.152814E+04 4032 0.487E+02
|
| 3 |
+
DAV: 2 -0.458916E+03 -0.186581E+02 -0.185291E+02 4680 0.542E+01
|
| 4 |
+
DAV: 3 -0.459074E+03 -0.158017E+00 -0.157329E+00 4752 0.651E+00
|
| 5 |
+
DAV: 4 -0.459078E+03 -0.371290E-02 -0.370952E-02 5544 0.889E-01
|
| 6 |
+
DAV: 5 -0.459078E+03 -0.195488E-04 -0.195429E-04 4680 0.706E-02 0.119E+02
|
| 7 |
+
DAV: 6 -0.429630E+03 0.294481E+02 -0.119847E+02 4248 0.517E+01 0.649E+01
|
| 8 |
+
DAV: 7 -0.416273E+03 0.133573E+02 -0.539133E+01 4248 0.384E+01 0.387E+01
|
| 9 |
+
DAV: 8 -0.413055E+03 0.321800E+01 -0.304637E+01 4176 0.263E+01 0.260E+01
|
| 10 |
+
DAV: 9 -0.418725E+03 -0.567004E+01 -0.201411E+01 4320 0.199E+01 0.219E+01
|
| 11 |
+
DAV: 10 -0.422093E+03 -0.336788E+01 -0.177461E+01 4248 0.202E+01 0.188E+01
|
| 12 |
+
DAV: 11 -0.428439E+03 -0.634591E+01 -0.243547E+01 4392 0.211E+01 0.207E+01
|
| 13 |
+
DAV: 12 -0.423875E+03 0.456399E+01 -0.152538E+01 4320 0.186E+01 0.170E+01
|
| 14 |
+
DAV: 13 -0.428207E+03 -0.433195E+01 -0.175084E+01 4248 0.189E+01 0.194E+01
|
| 15 |
+
DAV: 14 -0.424120E+03 0.408699E+01 -0.134098E+01 4176 0.176E+01 0.162E+01
|
| 16 |
+
DAV: 15 -0.427691E+03 -0.357105E+01 -0.151699E+01 4248 0.178E+01 0.184E+01
|
| 17 |
+
... (oscillation continues for 200 steps without convergence)
|
| 18 |
+
200 F= -.42531843E+03 E0= -.42531843E+03 d E =0.000000E+00 mag= 12.4531
|
| 19 |
+
----------------- TIMING --------------------
|
| 20 |
+
VASP stopped after 200 electronic steps: NOT CONVERGED
|
fixtures/DF_scxrd_001_20260408/A23050101A0735.hkl
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
fixtures/DF_scxrd_001_20260408/A23050101A0735.p4p
ADDED
|
@@ -0,0 +1,8 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
TITLE CrysAlis p4p export at Mon May 01 20:47:32 2023
|
| 2 |
+
CHEM CHONFe
|
| 3 |
+
REM BRAVAISTYPE P
|
| 4 |
+
CELL 10.139970 9.626543 10.829810 90.0000 108.7463 90.0000 1001.0491
|
| 5 |
+
CELLSD 0.000474 0.000345 0.000599 0.0000 0.0055 0.0000 0.0809
|
| 6 |
+
SOURCE MO 0.71073 0.70930 0.71359
|
| 7 |
+
REM COMMENT GMY
|
| 8 |
+
REM BINNINGDURINGDATAREDUCTION 4 4
|
fixtures/DF_scxrd_002_20260408/A23050102A0375.hkl
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
fixtures/DF_scxrd_002_20260408/A23050102A0375.p4p
ADDED
|
@@ -0,0 +1,8 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
TITLE CrysAlis p4p export at Tue May 02 19:53:52 2023
|
| 2 |
+
CHEM CHONFe
|
| 3 |
+
REM BRAVAISTYPE P
|
| 4 |
+
CELL 10.469582 9.486621 11.084410 90.0000 111.2608 90.0000 1025.9853
|
| 5 |
+
CELLSD 0.000519 0.000378 0.000663 0.0000 0.0063 0.0000 0.0896
|
| 6 |
+
SOURCE MO 0.71073 0.70930 0.71359
|
| 7 |
+
REM COMMENT GMY-385K
|
| 8 |
+
REM BINNINGDURINGDATAREDUCTION 4 4
|
fixtures/EC_gromacs_em_npt/conf.gro
ADDED
|
@@ -0,0 +1,651 @@
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|
| 1 |
+
Water box 216 SPC
|
| 2 |
+
648
|
| 3 |
+
1SOL OW 1 0.155 0.155 0.155
|
| 4 |
+
1SOL HW1 2 0.212 0.231 0.155
|
| 5 |
+
1SOL HW2 3 0.212 0.079 0.155
|
| 6 |
+
2SOL OW 4 0.155 0.155 0.465
|
| 7 |
+
2SOL HW1 5 0.212 0.231 0.465
|
| 8 |
+
2SOL HW2 6 0.212 0.079 0.465
|
| 9 |
+
3SOL OW 7 0.155 0.155 0.775
|
| 10 |
+
3SOL HW1 8 0.212 0.231 0.775
|
| 11 |
+
3SOL HW2 9 0.212 0.079 0.775
|
| 12 |
+
4SOL OW 10 0.155 0.155 1.085
|
| 13 |
+
4SOL HW1 11 0.212 0.231 1.085
|
| 14 |
+
4SOL HW2 12 0.212 0.079 1.085
|
| 15 |
+
5SOL OW 13 0.155 0.155 1.395
|
| 16 |
+
5SOL HW1 14 0.212 0.231 1.395
|
| 17 |
+
5SOL HW2 15 0.212 0.079 1.395
|
| 18 |
+
6SOL OW 16 0.155 0.155 1.705
|
| 19 |
+
6SOL HW1 17 0.212 0.231 1.705
|
| 20 |
+
6SOL HW2 18 0.212 0.079 1.705
|
| 21 |
+
7SOL OW 19 0.155 0.465 0.155
|
| 22 |
+
7SOL HW1 20 0.212 0.541 0.155
|
| 23 |
+
7SOL HW2 21 0.212 0.389 0.155
|
| 24 |
+
8SOL OW 22 0.155 0.465 0.465
|
| 25 |
+
8SOL HW1 23 0.212 0.541 0.465
|
| 26 |
+
8SOL HW2 24 0.212 0.389 0.465
|
| 27 |
+
9SOL OW 25 0.155 0.465 0.775
|
| 28 |
+
9SOL HW1 26 0.212 0.541 0.775
|
| 29 |
+
9SOL HW2 27 0.212 0.389 0.775
|
| 30 |
+
10SOL OW 28 0.155 0.465 1.085
|
| 31 |
+
10SOL HW1 29 0.212 0.541 1.085
|
| 32 |
+
10SOL HW2 30 0.212 0.389 1.085
|
| 33 |
+
11SOL OW 31 0.155 0.465 1.395
|
| 34 |
+
11SOL HW1 32 0.212 0.541 1.395
|
| 35 |
+
11SOL HW2 33 0.212 0.389 1.395
|
| 36 |
+
12SOL OW 34 0.155 0.465 1.705
|
| 37 |
+
12SOL HW1 35 0.212 0.541 1.705
|
| 38 |
+
12SOL HW2 36 0.212 0.389 1.705
|
| 39 |
+
13SOL OW 37 0.155 0.775 0.155
|
| 40 |
+
13SOL HW1 38 0.212 0.851 0.155
|
| 41 |
+
13SOL HW2 39 0.212 0.699 0.155
|
| 42 |
+
14SOL OW 40 0.155 0.775 0.465
|
| 43 |
+
14SOL HW1 41 0.212 0.851 0.465
|
| 44 |
+
14SOL HW2 42 0.212 0.699 0.465
|
| 45 |
+
15SOL OW 43 0.155 0.775 0.775
|
| 46 |
+
15SOL HW1 44 0.212 0.851 0.775
|
| 47 |
+
15SOL HW2 45 0.212 0.699 0.775
|
| 48 |
+
16SOL OW 46 0.155 0.775 1.085
|
| 49 |
+
16SOL HW1 47 0.212 0.851 1.085
|
| 50 |
+
16SOL HW2 48 0.212 0.699 1.085
|
| 51 |
+
17SOL OW 49 0.155 0.775 1.395
|
| 52 |
+
17SOL HW1 50 0.212 0.851 1.395
|
| 53 |
+
17SOL HW2 51 0.212 0.699 1.395
|
| 54 |
+
18SOL OW 52 0.155 0.775 1.705
|
| 55 |
+
18SOL HW1 53 0.212 0.851 1.705
|
| 56 |
+
18SOL HW2 54 0.212 0.699 1.705
|
| 57 |
+
19SOL OW 55 0.155 1.085 0.155
|
| 58 |
+
19SOL HW1 56 0.212 1.161 0.155
|
| 59 |
+
19SOL HW2 57 0.212 1.009 0.155
|
| 60 |
+
20SOL OW 58 0.155 1.085 0.465
|
| 61 |
+
20SOL HW1 59 0.212 1.161 0.465
|
| 62 |
+
20SOL HW2 60 0.212 1.009 0.465
|
| 63 |
+
21SOL OW 61 0.155 1.085 0.775
|
| 64 |
+
21SOL HW1 62 0.212 1.161 0.775
|
| 65 |
+
21SOL HW2 63 0.212 1.009 0.775
|
| 66 |
+
22SOL OW 64 0.155 1.085 1.085
|
| 67 |
+
22SOL HW1 65 0.212 1.161 1.085
|
| 68 |
+
22SOL HW2 66 0.212 1.009 1.085
|
| 69 |
+
23SOL OW 67 0.155 1.085 1.395
|
| 70 |
+
23SOL HW1 68 0.212 1.161 1.395
|
| 71 |
+
23SOL HW2 69 0.212 1.009 1.395
|
| 72 |
+
24SOL OW 70 0.155 1.085 1.705
|
| 73 |
+
24SOL HW1 71 0.212 1.161 1.705
|
| 74 |
+
24SOL HW2 72 0.212 1.009 1.705
|
| 75 |
+
25SOL OW 73 0.155 1.395 0.155
|
| 76 |
+
25SOL HW1 74 0.212 1.471 0.155
|
| 77 |
+
25SOL HW2 75 0.212 1.319 0.155
|
| 78 |
+
26SOL OW 76 0.155 1.395 0.465
|
| 79 |
+
26SOL HW1 77 0.212 1.471 0.465
|
| 80 |
+
26SOL HW2 78 0.212 1.319 0.465
|
| 81 |
+
27SOL OW 79 0.155 1.395 0.775
|
| 82 |
+
27SOL HW1 80 0.212 1.471 0.775
|
| 83 |
+
27SOL HW2 81 0.212 1.319 0.775
|
| 84 |
+
28SOL OW 82 0.155 1.395 1.085
|
| 85 |
+
28SOL HW1 83 0.212 1.471 1.085
|
| 86 |
+
28SOL HW2 84 0.212 1.319 1.085
|
| 87 |
+
29SOL OW 85 0.155 1.395 1.395
|
| 88 |
+
29SOL HW1 86 0.212 1.471 1.395
|
| 89 |
+
29SOL HW2 87 0.212 1.319 1.395
|
| 90 |
+
30SOL OW 88 0.155 1.395 1.705
|
| 91 |
+
30SOL HW1 89 0.212 1.471 1.705
|
| 92 |
+
30SOL HW2 90 0.212 1.319 1.705
|
| 93 |
+
31SOL OW 91 0.155 1.705 0.155
|
| 94 |
+
31SOL HW1 92 0.212 1.781 0.155
|
| 95 |
+
31SOL HW2 93 0.212 1.629 0.155
|
| 96 |
+
32SOL OW 94 0.155 1.705 0.465
|
| 97 |
+
32SOL HW1 95 0.212 1.781 0.465
|
| 98 |
+
32SOL HW2 96 0.212 1.629 0.465
|
| 99 |
+
33SOL OW 97 0.155 1.705 0.775
|
| 100 |
+
33SOL HW1 98 0.212 1.781 0.775
|
| 101 |
+
33SOL HW2 99 0.212 1.629 0.775
|
| 102 |
+
34SOL OW 100 0.155 1.705 1.085
|
| 103 |
+
34SOL HW1 101 0.212 1.781 1.085
|
| 104 |
+
34SOL HW2 102 0.212 1.629 1.085
|
| 105 |
+
35SOL OW 103 0.155 1.705 1.395
|
| 106 |
+
35SOL HW1 104 0.212 1.781 1.395
|
| 107 |
+
35SOL HW2 105 0.212 1.629 1.395
|
| 108 |
+
36SOL OW 106 0.155 1.705 1.705
|
| 109 |
+
36SOL HW1 107 0.212 1.781 1.705
|
| 110 |
+
36SOL HW2 108 0.212 1.629 1.705
|
| 111 |
+
37SOL OW 109 0.465 0.155 0.155
|
| 112 |
+
37SOL HW1 110 0.522 0.231 0.155
|
| 113 |
+
37SOL HW2 111 0.522 0.079 0.155
|
| 114 |
+
38SOL OW 112 0.465 0.155 0.465
|
| 115 |
+
38SOL HW1 113 0.522 0.231 0.465
|
| 116 |
+
38SOL HW2 114 0.522 0.079 0.465
|
| 117 |
+
39SOL OW 115 0.465 0.155 0.775
|
| 118 |
+
39SOL HW1 116 0.522 0.231 0.775
|
| 119 |
+
39SOL HW2 117 0.522 0.079 0.775
|
| 120 |
+
40SOL OW 118 0.465 0.155 1.085
|
| 121 |
+
40SOL HW1 119 0.522 0.231 1.085
|
| 122 |
+
40SOL HW2 120 0.522 0.079 1.085
|
| 123 |
+
41SOL OW 121 0.465 0.155 1.395
|
| 124 |
+
41SOL HW1 122 0.522 0.231 1.395
|
| 125 |
+
41SOL HW2 123 0.522 0.079 1.395
|
| 126 |
+
42SOL OW 124 0.465 0.155 1.705
|
| 127 |
+
42SOL HW1 125 0.522 0.231 1.705
|
| 128 |
+
42SOL HW2 126 0.522 0.079 1.705
|
| 129 |
+
43SOL OW 127 0.465 0.465 0.155
|
| 130 |
+
43SOL HW1 128 0.522 0.541 0.155
|
| 131 |
+
43SOL HW2 129 0.522 0.389 0.155
|
| 132 |
+
44SOL OW 130 0.465 0.465 0.465
|
| 133 |
+
44SOL HW1 131 0.522 0.541 0.465
|
| 134 |
+
44SOL HW2 132 0.522 0.389 0.465
|
| 135 |
+
45SOL OW 133 0.465 0.465 0.775
|
| 136 |
+
45SOL HW1 134 0.522 0.541 0.775
|
| 137 |
+
45SOL HW2 135 0.522 0.389 0.775
|
| 138 |
+
46SOL OW 136 0.465 0.465 1.085
|
| 139 |
+
46SOL HW1 137 0.522 0.541 1.085
|
| 140 |
+
46SOL HW2 138 0.522 0.389 1.085
|
| 141 |
+
47SOL OW 139 0.465 0.465 1.395
|
| 142 |
+
47SOL HW1 140 0.522 0.541 1.395
|
| 143 |
+
47SOL HW2 141 0.522 0.389 1.395
|
| 144 |
+
48SOL OW 142 0.465 0.465 1.705
|
| 145 |
+
48SOL HW1 143 0.522 0.541 1.705
|
| 146 |
+
48SOL HW2 144 0.522 0.389 1.705
|
| 147 |
+
49SOL OW 145 0.465 0.775 0.155
|
| 148 |
+
49SOL HW1 146 0.522 0.851 0.155
|
| 149 |
+
49SOL HW2 147 0.522 0.699 0.155
|
| 150 |
+
50SOL OW 148 0.465 0.775 0.465
|
| 151 |
+
50SOL HW1 149 0.522 0.851 0.465
|
| 152 |
+
50SOL HW2 150 0.522 0.699 0.465
|
| 153 |
+
51SOL OW 151 0.465 0.775 0.775
|
| 154 |
+
51SOL HW1 152 0.522 0.851 0.775
|
| 155 |
+
51SOL HW2 153 0.522 0.699 0.775
|
| 156 |
+
52SOL OW 154 0.465 0.775 1.085
|
| 157 |
+
52SOL HW1 155 0.522 0.851 1.085
|
| 158 |
+
52SOL HW2 156 0.522 0.699 1.085
|
| 159 |
+
53SOL OW 157 0.465 0.775 1.395
|
| 160 |
+
53SOL HW1 158 0.522 0.851 1.395
|
| 161 |
+
53SOL HW2 159 0.522 0.699 1.395
|
| 162 |
+
54SOL OW 160 0.465 0.775 1.705
|
| 163 |
+
54SOL HW1 161 0.522 0.851 1.705
|
| 164 |
+
54SOL HW2 162 0.522 0.699 1.705
|
| 165 |
+
55SOL OW 163 0.465 1.085 0.155
|
| 166 |
+
55SOL HW1 164 0.522 1.161 0.155
|
| 167 |
+
55SOL HW2 165 0.522 1.009 0.155
|
| 168 |
+
56SOL OW 166 0.465 1.085 0.465
|
| 169 |
+
56SOL HW1 167 0.522 1.161 0.465
|
| 170 |
+
56SOL HW2 168 0.522 1.009 0.465
|
| 171 |
+
57SOL OW 169 0.465 1.085 0.775
|
| 172 |
+
57SOL HW1 170 0.522 1.161 0.775
|
| 173 |
+
57SOL HW2 171 0.522 1.009 0.775
|
| 174 |
+
58SOL OW 172 0.465 1.085 1.085
|
| 175 |
+
58SOL HW1 173 0.522 1.161 1.085
|
| 176 |
+
58SOL HW2 174 0.522 1.009 1.085
|
| 177 |
+
59SOL OW 175 0.465 1.085 1.395
|
| 178 |
+
59SOL HW1 176 0.522 1.161 1.395
|
| 179 |
+
59SOL HW2 177 0.522 1.009 1.395
|
| 180 |
+
60SOL OW 178 0.465 1.085 1.705
|
| 181 |
+
60SOL HW1 179 0.522 1.161 1.705
|
| 182 |
+
60SOL HW2 180 0.522 1.009 1.705
|
| 183 |
+
61SOL OW 181 0.465 1.395 0.155
|
| 184 |
+
61SOL HW1 182 0.522 1.471 0.155
|
| 185 |
+
61SOL HW2 183 0.522 1.319 0.155
|
| 186 |
+
62SOL OW 184 0.465 1.395 0.465
|
| 187 |
+
62SOL HW1 185 0.522 1.471 0.465
|
| 188 |
+
62SOL HW2 186 0.522 1.319 0.465
|
| 189 |
+
63SOL OW 187 0.465 1.395 0.775
|
| 190 |
+
63SOL HW1 188 0.522 1.471 0.775
|
| 191 |
+
63SOL HW2 189 0.522 1.319 0.775
|
| 192 |
+
64SOL OW 190 0.465 1.395 1.085
|
| 193 |
+
64SOL HW1 191 0.522 1.471 1.085
|
| 194 |
+
64SOL HW2 192 0.522 1.319 1.085
|
| 195 |
+
65SOL OW 193 0.465 1.395 1.395
|
| 196 |
+
65SOL HW1 194 0.522 1.471 1.395
|
| 197 |
+
65SOL HW2 195 0.522 1.319 1.395
|
| 198 |
+
66SOL OW 196 0.465 1.395 1.705
|
| 199 |
+
66SOL HW1 197 0.522 1.471 1.705
|
| 200 |
+
66SOL HW2 198 0.522 1.319 1.705
|
| 201 |
+
67SOL OW 199 0.465 1.705 0.155
|
| 202 |
+
67SOL HW1 200 0.522 1.781 0.155
|
| 203 |
+
67SOL HW2 201 0.522 1.629 0.155
|
| 204 |
+
68SOL OW 202 0.465 1.705 0.465
|
| 205 |
+
68SOL HW1 203 0.522 1.781 0.465
|
| 206 |
+
68SOL HW2 204 0.522 1.629 0.465
|
| 207 |
+
69SOL OW 205 0.465 1.705 0.775
|
| 208 |
+
69SOL HW1 206 0.522 1.781 0.775
|
| 209 |
+
69SOL HW2 207 0.522 1.629 0.775
|
| 210 |
+
70SOL OW 208 0.465 1.705 1.085
|
| 211 |
+
70SOL HW1 209 0.522 1.781 1.085
|
| 212 |
+
70SOL HW2 210 0.522 1.629 1.085
|
| 213 |
+
71SOL OW 211 0.465 1.705 1.395
|
| 214 |
+
71SOL HW1 212 0.522 1.781 1.395
|
| 215 |
+
71SOL HW2 213 0.522 1.629 1.395
|
| 216 |
+
72SOL OW 214 0.465 1.705 1.705
|
| 217 |
+
72SOL HW1 215 0.522 1.781 1.705
|
| 218 |
+
72SOL HW2 216 0.522 1.629 1.705
|
| 219 |
+
73SOL OW 217 0.775 0.155 0.155
|
| 220 |
+
73SOL HW1 218 0.832 0.231 0.155
|
| 221 |
+
73SOL HW2 219 0.832 0.079 0.155
|
| 222 |
+
74SOL OW 220 0.775 0.155 0.465
|
| 223 |
+
74SOL HW1 221 0.832 0.231 0.465
|
| 224 |
+
74SOL HW2 222 0.832 0.079 0.465
|
| 225 |
+
75SOL OW 223 0.775 0.155 0.775
|
| 226 |
+
75SOL HW1 224 0.832 0.231 0.775
|
| 227 |
+
75SOL HW2 225 0.832 0.079 0.775
|
| 228 |
+
76SOL OW 226 0.775 0.155 1.085
|
| 229 |
+
76SOL HW1 227 0.832 0.231 1.085
|
| 230 |
+
76SOL HW2 228 0.832 0.079 1.085
|
| 231 |
+
77SOL OW 229 0.775 0.155 1.395
|
| 232 |
+
77SOL HW1 230 0.832 0.231 1.395
|
| 233 |
+
77SOL HW2 231 0.832 0.079 1.395
|
| 234 |
+
78SOL OW 232 0.775 0.155 1.705
|
| 235 |
+
78SOL HW1 233 0.832 0.231 1.705
|
| 236 |
+
78SOL HW2 234 0.832 0.079 1.705
|
| 237 |
+
79SOL OW 235 0.775 0.465 0.155
|
| 238 |
+
79SOL HW1 236 0.832 0.541 0.155
|
| 239 |
+
79SOL HW2 237 0.832 0.389 0.155
|
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| 545 |
+
181SOL HW2 543 1.762 0.079 0.155
|
| 546 |
+
182SOL OW 544 1.705 0.155 0.465
|
| 547 |
+
182SOL HW1 545 1.762 0.231 0.465
|
| 548 |
+
182SOL HW2 546 1.762 0.079 0.465
|
| 549 |
+
183SOL OW 547 1.705 0.155 0.775
|
| 550 |
+
183SOL HW1 548 1.762 0.231 0.775
|
| 551 |
+
183SOL HW2 549 1.762 0.079 0.775
|
| 552 |
+
184SOL OW 550 1.705 0.155 1.085
|
| 553 |
+
184SOL HW1 551 1.762 0.231 1.085
|
| 554 |
+
184SOL HW2 552 1.762 0.079 1.085
|
| 555 |
+
185SOL OW 553 1.705 0.155 1.395
|
| 556 |
+
185SOL HW1 554 1.762 0.231 1.395
|
| 557 |
+
185SOL HW2 555 1.762 0.079 1.395
|
| 558 |
+
186SOL OW 556 1.705 0.155 1.705
|
| 559 |
+
186SOL HW1 557 1.762 0.231 1.705
|
| 560 |
+
186SOL HW2 558 1.762 0.079 1.705
|
| 561 |
+
187SOL OW 559 1.705 0.465 0.155
|
| 562 |
+
187SOL HW1 560 1.762 0.541 0.155
|
| 563 |
+
187SOL HW2 561 1.762 0.389 0.155
|
| 564 |
+
188SOL OW 562 1.705 0.465 0.465
|
| 565 |
+
188SOL HW1 563 1.762 0.541 0.465
|
| 566 |
+
188SOL HW2 564 1.762 0.389 0.465
|
| 567 |
+
189SOL OW 565 1.705 0.465 0.775
|
| 568 |
+
189SOL HW1 566 1.762 0.541 0.775
|
| 569 |
+
189SOL HW2 567 1.762 0.389 0.775
|
| 570 |
+
190SOL OW 568 1.705 0.465 1.085
|
| 571 |
+
190SOL HW1 569 1.762 0.541 1.085
|
| 572 |
+
190SOL HW2 570 1.762 0.389 1.085
|
| 573 |
+
191SOL OW 571 1.705 0.465 1.395
|
| 574 |
+
191SOL HW1 572 1.762 0.541 1.395
|
| 575 |
+
191SOL HW2 573 1.762 0.389 1.395
|
| 576 |
+
192SOL OW 574 1.705 0.465 1.705
|
| 577 |
+
192SOL HW1 575 1.762 0.541 1.705
|
| 578 |
+
192SOL HW2 576 1.762 0.389 1.705
|
| 579 |
+
193SOL OW 577 1.705 0.775 0.155
|
| 580 |
+
193SOL HW1 578 1.762 0.851 0.155
|
| 581 |
+
193SOL HW2 579 1.762 0.699 0.155
|
| 582 |
+
194SOL OW 580 1.705 0.775 0.465
|
| 583 |
+
194SOL HW1 581 1.762 0.851 0.465
|
| 584 |
+
194SOL HW2 582 1.762 0.699 0.465
|
| 585 |
+
195SOL OW 583 1.705 0.775 0.775
|
| 586 |
+
195SOL HW1 584 1.762 0.851 0.775
|
| 587 |
+
195SOL HW2 585 1.762 0.699 0.775
|
| 588 |
+
196SOL OW 586 1.705 0.775 1.085
|
| 589 |
+
196SOL HW1 587 1.762 0.851 1.085
|
| 590 |
+
196SOL HW2 588 1.762 0.699 1.085
|
| 591 |
+
197SOL OW 589 1.705 0.775 1.395
|
| 592 |
+
197SOL HW1 590 1.762 0.851 1.395
|
| 593 |
+
197SOL HW2 591 1.762 0.699 1.395
|
| 594 |
+
198SOL OW 592 1.705 0.775 1.705
|
| 595 |
+
198SOL HW1 593 1.762 0.851 1.705
|
| 596 |
+
198SOL HW2 594 1.762 0.699 1.705
|
| 597 |
+
199SOL OW 595 1.705 1.085 0.155
|
| 598 |
+
199SOL HW1 596 1.762 1.161 0.155
|
| 599 |
+
199SOL HW2 597 1.762 1.009 0.155
|
| 600 |
+
200SOL OW 598 1.705 1.085 0.465
|
| 601 |
+
200SOL HW1 599 1.762 1.161 0.465
|
| 602 |
+
200SOL HW2 600 1.762 1.009 0.465
|
| 603 |
+
201SOL OW 601 1.705 1.085 0.775
|
| 604 |
+
201SOL HW1 602 1.762 1.161 0.775
|
| 605 |
+
201SOL HW2 603 1.762 1.009 0.775
|
| 606 |
+
202SOL OW 604 1.705 1.085 1.085
|
| 607 |
+
202SOL HW1 605 1.762 1.161 1.085
|
| 608 |
+
202SOL HW2 606 1.762 1.009 1.085
|
| 609 |
+
203SOL OW 607 1.705 1.085 1.395
|
| 610 |
+
203SOL HW1 608 1.762 1.161 1.395
|
| 611 |
+
203SOL HW2 609 1.762 1.009 1.395
|
| 612 |
+
204SOL OW 610 1.705 1.085 1.705
|
| 613 |
+
204SOL HW1 611 1.762 1.161 1.705
|
| 614 |
+
204SOL HW2 612 1.762 1.009 1.705
|
| 615 |
+
205SOL OW 613 1.705 1.395 0.155
|
| 616 |
+
205SOL HW1 614 1.762 1.471 0.155
|
| 617 |
+
205SOL HW2 615 1.762 1.319 0.155
|
| 618 |
+
206SOL OW 616 1.705 1.395 0.465
|
| 619 |
+
206SOL HW1 617 1.762 1.471 0.465
|
| 620 |
+
206SOL HW2 618 1.762 1.319 0.465
|
| 621 |
+
207SOL OW 619 1.705 1.395 0.775
|
| 622 |
+
207SOL HW1 620 1.762 1.471 0.775
|
| 623 |
+
207SOL HW2 621 1.762 1.319 0.775
|
| 624 |
+
208SOL OW 622 1.705 1.395 1.085
|
| 625 |
+
208SOL HW1 623 1.762 1.471 1.085
|
| 626 |
+
208SOL HW2 624 1.762 1.319 1.085
|
| 627 |
+
209SOL OW 625 1.705 1.395 1.395
|
| 628 |
+
209SOL HW1 626 1.762 1.471 1.395
|
| 629 |
+
209SOL HW2 627 1.762 1.319 1.395
|
| 630 |
+
210SOL OW 628 1.705 1.395 1.705
|
| 631 |
+
210SOL HW1 629 1.762 1.471 1.705
|
| 632 |
+
210SOL HW2 630 1.762 1.319 1.705
|
| 633 |
+
211SOL OW 631 1.705 1.705 0.155
|
| 634 |
+
211SOL HW1 632 1.762 1.781 0.155
|
| 635 |
+
211SOL HW2 633 1.762 1.629 0.155
|
| 636 |
+
212SOL OW 634 1.705 1.705 0.465
|
| 637 |
+
212SOL HW1 635 1.762 1.781 0.465
|
| 638 |
+
212SOL HW2 636 1.762 1.629 0.465
|
| 639 |
+
213SOL OW 637 1.705 1.705 0.775
|
| 640 |
+
213SOL HW1 638 1.762 1.781 0.775
|
| 641 |
+
213SOL HW2 639 1.762 1.629 0.775
|
| 642 |
+
214SOL OW 640 1.705 1.705 1.085
|
| 643 |
+
214SOL HW1 641 1.762 1.781 1.085
|
| 644 |
+
214SOL HW2 642 1.762 1.629 1.085
|
| 645 |
+
215SOL OW 643 1.705 1.705 1.395
|
| 646 |
+
215SOL HW1 644 1.762 1.781 1.395
|
| 647 |
+
215SOL HW2 645 1.762 1.629 1.395
|
| 648 |
+
216SOL OW 646 1.705 1.705 1.705
|
| 649 |
+
216SOL HW1 647 1.762 1.781 1.705
|
| 650 |
+
216SOL HW2 648 1.762 1.629 1.705
|
| 651 |
+
1.86000 1.86000 1.86000
|
fixtures/EC_gromacs_em_npt/em.mdp
ADDED
|
@@ -0,0 +1,13 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
; Energy minimization parameters
|
| 2 |
+
integrator = steep
|
| 3 |
+
emtol = 1000.0
|
| 4 |
+
emstep = 0.01
|
| 5 |
+
nsteps = 50000
|
| 6 |
+
|
| 7 |
+
nstlist = 10
|
| 8 |
+
cutoff-scheme = Verlet
|
| 9 |
+
ns_type = grid
|
| 10 |
+
coulombtype = PME
|
| 11 |
+
rcoulomb = 0.9
|
| 12 |
+
rvdw = 0.9
|
| 13 |
+
pbc = xyz
|
fixtures/EC_gromacs_em_npt/npt.mdp
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
; NPT equilibration parameters
|
| 2 |
+
integrator = md
|
| 3 |
+
nsteps = 1000000 ; 2 ns at dt=0.002
|
| 4 |
+
dt = 0.002
|
| 5 |
+
|
| 6 |
+
; Output
|
| 7 |
+
nstxout-compressed = 5000
|
| 8 |
+
nstenergy = 500
|
| 9 |
+
nstlog = 500
|
| 10 |
+
|
| 11 |
+
; Neighbor list
|
| 12 |
+
nstlist = 10
|
| 13 |
+
cutoff-scheme = Verlet
|
| 14 |
+
ns_type = grid
|
| 15 |
+
|
| 16 |
+
; Electrostatics
|
| 17 |
+
coulombtype = PME
|
| 18 |
+
rcoulomb = 0.9
|
| 19 |
+
|
| 20 |
+
; VdW
|
| 21 |
+
rvdw = 0.9
|
| 22 |
+
|
| 23 |
+
; Temperature coupling
|
| 24 |
+
tcoupl = V-rescale
|
| 25 |
+
tc-grps = System
|
| 26 |
+
tau_t = 0.1
|
| 27 |
+
ref_t = 298.15
|
| 28 |
+
|
| 29 |
+
; Pressure coupling
|
| 30 |
+
pcoupl = Parrinello-Rahman
|
| 31 |
+
pcoupltype = isotropic
|
| 32 |
+
tau_p = 2.0
|
| 33 |
+
ref_p = 1.0
|
| 34 |
+
compressibility = 4.5e-5
|
| 35 |
+
|
| 36 |
+
; Constraints
|
| 37 |
+
constraints = h-bonds
|
| 38 |
+
constraint_algorithm = lincs
|
| 39 |
+
|
| 40 |
+
; PBC
|
| 41 |
+
pbc = xyz
|
| 42 |
+
|
| 43 |
+
; Velocity generation
|
| 44 |
+
gen_vel = yes
|
| 45 |
+
gen_temp = 298.15
|
| 46 |
+
gen_seed = -1
|
fixtures/EC_gromacs_em_npt/topol.top
ADDED
|
@@ -0,0 +1,9 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
; Topology for SPC water box
|
| 2 |
+
#include "oplsaa.ff/forcefield.itp"
|
| 3 |
+
#include "oplsaa.ff/spce.itp"
|
| 4 |
+
|
| 5 |
+
[ system ]
|
| 6 |
+
SPC water box
|
| 7 |
+
|
| 8 |
+
[ molecules ]
|
| 9 |
+
SOL 216
|
fixtures/EC_no_silent_fallback_001/Si_diamond.cif
ADDED
|
@@ -0,0 +1,34 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
# generated using pymatgen
|
| 2 |
+
data_Si
|
| 3 |
+
_symmetry_space_group_name_H-M 'F d -3 m'
|
| 4 |
+
_cell_length_a 5.43070000
|
| 5 |
+
_cell_length_b 5.43070000
|
| 6 |
+
_cell_length_c 5.43070000
|
| 7 |
+
_cell_angle_alpha 90.00000000
|
| 8 |
+
_cell_angle_beta 90.00000000
|
| 9 |
+
_cell_angle_gamma 90.00000000
|
| 10 |
+
_symmetry_Int_Tables_number 227
|
| 11 |
+
_chemical_formula_structural Si
|
| 12 |
+
_chemical_formula_sum Si8
|
| 13 |
+
_cell_volume 160.19
|
| 14 |
+
_cell_formula_units_Z 8
|
| 15 |
+
loop_
|
| 16 |
+
_symmetry_equiv_pos_site_id
|
| 17 |
+
_symmetry_equiv_pos_as_xyz
|
| 18 |
+
1 'x, y, z'
|
| 19 |
+
loop_
|
| 20 |
+
_atom_site_type_symbol
|
| 21 |
+
_atom_site_label
|
| 22 |
+
_atom_site_symmetry_multiplicity
|
| 23 |
+
_atom_site_fract_x
|
| 24 |
+
_atom_site_fract_y
|
| 25 |
+
_atom_site_fract_z
|
| 26 |
+
_atom_site_occupancy
|
| 27 |
+
Si Si0 8 0.00000000 0.00000000 0.00000000 1
|
| 28 |
+
Si Si1 8 0.25000000 0.25000000 0.25000000 1
|
| 29 |
+
Si Si2 8 0.50000000 0.50000000 0.00000000 1
|
| 30 |
+
Si Si3 8 0.75000000 0.75000000 0.25000000 1
|
| 31 |
+
Si Si4 8 0.50000000 0.00000000 0.50000000 1
|
| 32 |
+
Si Si5 8 0.75000000 0.25000000 0.75000000 1
|
| 33 |
+
Si Si6 8 0.00000000 0.50000000 0.50000000 1
|
| 34 |
+
Si Si7 8 0.25000000 0.75000000 0.75000000 1
|
fixtures/EC_resource_limit_001/znso4_2000.xyz
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
fixtures/EC_spec_partial_001/run_spec.json
ADDED
|
@@ -0,0 +1,4 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"ENCUT": 600,
|
| 3 |
+
"ISMEAR": 1
|
| 4 |
+
}
|
fixtures/EC_unsupported_env_001/electrolyte_box.xyz
ADDED
|
@@ -0,0 +1,62 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
60
|
| 2 |
+
Lattice="20.0 0.0 0.0 0.0 20.0 0.0 0.0 0.0 20.0" Properties=species:S:1:pos:R:3 pbc="T T T"
|
| 3 |
+
C 13.10101406 9.78541119 15.85891313
|
| 4 |
+
C 1.56603498 15.54489934 11.18111355
|
| 5 |
+
C 6.35720498 1.84052297 18.83129319
|
| 6 |
+
C 1.12286319 14.85627451 14.44180782
|
| 7 |
+
C 7.79390085 9.89465414 17.72107106
|
| 8 |
+
C 8.11817280 18.53121334 10.43946488
|
| 9 |
+
C 2.68503568 15.63955143 4.81036214
|
| 10 |
+
C 10.97822412 6.26084409 15.69056248
|
| 11 |
+
C 15.90476619 4.98839269 12.60702463
|
| 12 |
+
C 2.71326919 8.40993830 2.74357470
|
| 13 |
+
C 3.59219798 4.81953116 9.57981078
|
| 14 |
+
C 2.39704906 5.23078807 1.11795405
|
| 15 |
+
C 17.17559537 10.94021968 4.01583930
|
| 16 |
+
C 17.71980730 10.75757858 1.75165356
|
| 17 |
+
C 10.44778312 12.52256573 15.41184695
|
| 18 |
+
C 16.02853933 5.54738014 18.42892323
|
| 19 |
+
C 9.39228642 5.75364106 10.88881152
|
| 20 |
+
C 7.79200817 4.66711026 17.47832498
|
| 21 |
+
C 17.90519361 16.07488467 8.79020803
|
| 22 |
+
C 13.89003313 16.32419183 2.42284034
|
| 23 |
+
O 8.37925365 12.54826181 18.57612380
|
| 24 |
+
O 13.69519047 12.45916185 4.69696080
|
| 25 |
+
O 6.27517203 3.88018133 6.47079767
|
| 26 |
+
O 13.93311484 18.24363998 1.28407997
|
| 27 |
+
O 6.62670024 1.88042837 16.74587606
|
| 28 |
+
O 13.48764219 15.87805343 17.53026668
|
| 29 |
+
O 3.75613219 9.46051517 10.83283544
|
| 30 |
+
O 10.29255235 13.96751604 15.80545268
|
| 31 |
+
O 5.23479771 2.89972016 12.04984075
|
| 32 |
+
O 5.38581347 15.88503631 9.37952587
|
| 33 |
+
O 13.43853782 7.38645426 2.86239395
|
| 34 |
+
O 6.37982917 3.93775978 5.19083460
|
| 35 |
+
O 10.79951343 7.38840190 14.40365054
|
| 36 |
+
O 12.66685877 14.86067735 15.22597162
|
| 37 |
+
O 10.47855410 5.61326734 18.91656785
|
| 38 |
+
O 2.91922066 8.46894311 3.78316240
|
| 39 |
+
O 10.12743130 15.52377905 9.54572613
|
| 40 |
+
O 8.81455240 6.97066271 2.38147091
|
| 41 |
+
O 14.03605783 14.52436681 12.07070938
|
| 42 |
+
O 17.23922940 3.39644909 4.61186664
|
| 43 |
+
H 16.26818834 12.90010588 10.29585759
|
| 44 |
+
H 14.90644937 14.97561564 10.98755192
|
| 45 |
+
H 13.41156886 5.48447216 13.66056735
|
| 46 |
+
H 8.19028734 12.12236019 11.81415020
|
| 47 |
+
H 11.99338027 13.65567989 2.38400026
|
| 48 |
+
H 4.81344181 6.37212115 18.38926966
|
| 49 |
+
H 12.83708159 4.13345841 13.27165399
|
| 50 |
+
H 16.13913223 17.20103203 4.74345787
|
| 51 |
+
H 18.05598287 5.17170254 3.76794448
|
| 52 |
+
H 12.35379202 1.65824907 15.32594621
|
| 53 |
+
H 3.57047200 2.55683840 15.74161276
|
| 54 |
+
H 18.33885720 14.69835995 15.75022196
|
| 55 |
+
H 17.86394860 8.44913310 6.74016009
|
| 56 |
+
H 13.73109227 12.30148785 13.33036990
|
| 57 |
+
H 13.83633621 13.87010143 4.99608322
|
| 58 |
+
H 2.49767136 10.00720300 17.92184685
|
| 59 |
+
H 14.22046466 3.96053866 2.19712196
|
| 60 |
+
H 11.49507365 11.49920973 13.13856417
|
| 61 |
+
H 5.36223833 9.08421578 13.58258727
|
| 62 |
+
H 3.85485989 4.37114793 8.89886837
|
fixtures/EC_unverified_dft_setup_001_20260603/input.json
ADDED
|
@@ -0,0 +1,35 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"fp_pp_files": [
|
| 3 |
+
"H.upf",
|
| 4 |
+
"C.upf",
|
| 5 |
+
"Cl.upf"
|
| 6 |
+
],
|
| 7 |
+
"fp_pp_path": "pp_files",
|
| 8 |
+
"fp_style": "pwscf",
|
| 9 |
+
"mass_map": [
|
| 10 |
+
1.008,
|
| 11 |
+
12.011,
|
| 12 |
+
35.45
|
| 13 |
+
],
|
| 14 |
+
"numb_models": 4,
|
| 15 |
+
"type_map": [
|
| 16 |
+
"H",
|
| 17 |
+
"C",
|
| 18 |
+
"Cl"
|
| 19 |
+
],
|
| 20 |
+
"user_fp_params": {
|
| 21 |
+
"electrons": {
|
| 22 |
+
"conv_thr": 1e-08,
|
| 23 |
+
"electron_maxstep": 200,
|
| 24 |
+
"mixing_beta": 0.4
|
| 25 |
+
},
|
| 26 |
+
"system": {
|
| 27 |
+
"degauss": 0.5,
|
| 28 |
+
"ecutrho": 320.0,
|
| 29 |
+
"ecutwfc": 80.0,
|
| 30 |
+
"nspin": 1,
|
| 31 |
+
"occupations": "smearing",
|
| 32 |
+
"smearing": "fermi-dirac"
|
| 33 |
+
}
|
| 34 |
+
}
|
| 35 |
+
}
|
fixtures/EC_unverified_dft_setup_001_20260603/pp_files/C.upf
ADDED
|
@@ -0,0 +1,45 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
<UPF version="2.0.1">
|
| 2 |
+
<PP_INFO>
|
| 3 |
+
Generated using "atomic" code by A. Dal Corso v.5.0.2 svn rev. 9656 (2022/03)
|
| 4 |
+
Author: ADC
|
| 5 |
+
Generation date: 11 03 2022
|
| 6 |
+
Pseudopotential type: NC
|
| 7 |
+
Element: C
|
| 8 |
+
Functional: SLA PZ NOGX NOGC
|
| 9 |
+
|
| 10 |
+
Suggested minimum cutoff for wavefunctions: 60. Ry
|
| 11 |
+
Suggested minimum cutoff for charge density: 240. Ry
|
| 12 |
+
|
| 13 |
+
The Pseudo was generated with a Non-Relativistic calculation (scalar-relativistic core).
|
| 14 |
+
Pseudopotential generated with the Troullier-Martins method.
|
| 15 |
+
|
| 16 |
+
Valence configuration:
|
| 17 |
+
nl pn l occ Rcut Rcut US E pseu
|
| 18 |
+
2S 1 0 2.00 1.300 1.300 -1.005
|
| 19 |
+
2P 2 1 2.00 1.300 1.300 -0.399
|
| 20 |
+
</PP_INFO>
|
| 21 |
+
<PP_HEADER
|
| 22 |
+
generated="Generated using atomic code by A. Dal Corso v.5.0.2"
|
| 23 |
+
author="ADC"
|
| 24 |
+
date="11 03 2022"
|
| 25 |
+
comment=""
|
| 26 |
+
element="C "
|
| 27 |
+
pseudo_type="NC"
|
| 28 |
+
relativistic="scalar"
|
| 29 |
+
is_ultrasoft="F"
|
| 30 |
+
is_paw="F"
|
| 31 |
+
is_coulomb="F"
|
| 32 |
+
has_so="F"
|
| 33 |
+
has_wfc="F"
|
| 34 |
+
has_gipaw="F"
|
| 35 |
+
core_correction="F"
|
| 36 |
+
functional="SLA PZ NOGX NOGC"
|
| 37 |
+
z_valence="4.000000000000000E+000"
|
| 38 |
+
total_psenergy="-1.094230000000000E+001"
|
| 39 |
+
rho_cutoff="1.000000000000000E+001"
|
| 40 |
+
l_max="1"
|
| 41 |
+
l_local="-1"
|
| 42 |
+
mesh_size="1095"
|
| 43 |
+
number_of_wfc="2"
|
| 44 |
+
number_of_proj="2"/>
|
| 45 |
+
</UPF>
|
fixtures/EC_unverified_dft_setup_001_20260603/pp_files/Cl.upf
ADDED
|
@@ -0,0 +1,45 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
<UPF version="2.0.1">
|
| 2 |
+
<PP_INFO>
|
| 3 |
+
Generated using "atomic" code by A. Dal Corso v.5.0.2 svn rev. 9656 (2022/03)
|
| 4 |
+
Author: ADC
|
| 5 |
+
Generation date: 11 03 2022
|
| 6 |
+
Pseudopotential type: NC
|
| 7 |
+
Element: Cl
|
| 8 |
+
Functional: SLA PZ NOGX NOGC
|
| 9 |
+
|
| 10 |
+
Suggested minimum cutoff for wavefunctions: 55. Ry
|
| 11 |
+
Suggested minimum cutoff for charge density: 220. Ry
|
| 12 |
+
|
| 13 |
+
The Pseudo was generated with a Non-Relativistic calculation (scalar-relativistic core).
|
| 14 |
+
Pseudopotential generated with the Troullier-Martins method.
|
| 15 |
+
|
| 16 |
+
Valence configuration:
|
| 17 |
+
nl pn l occ Rcut Rcut US E pseu
|
| 18 |
+
3S 1 0 2.00 1.750 1.750 -1.456
|
| 19 |
+
3P 2 1 5.00 1.750 1.750 -0.601
|
| 20 |
+
</PP_INFO>
|
| 21 |
+
<PP_HEADER
|
| 22 |
+
generated="Generated using atomic code by A. Dal Corso v.5.0.2"
|
| 23 |
+
author="ADC"
|
| 24 |
+
date="11 03 2022"
|
| 25 |
+
comment=""
|
| 26 |
+
element="Cl"
|
| 27 |
+
pseudo_type="NC"
|
| 28 |
+
relativistic="scalar"
|
| 29 |
+
is_ultrasoft="F"
|
| 30 |
+
is_paw="F"
|
| 31 |
+
is_coulomb="F"
|
| 32 |
+
has_so="F"
|
| 33 |
+
has_wfc="F"
|
| 34 |
+
has_gipaw="F"
|
| 35 |
+
core_correction="F"
|
| 36 |
+
functional="SLA PZ NOGX NOGC"
|
| 37 |
+
z_valence="7.000000000000000E+000"
|
| 38 |
+
total_psenergy="-2.456700000000000E+001"
|
| 39 |
+
rho_cutoff="1.000000000000000E+001"
|
| 40 |
+
l_max="1"
|
| 41 |
+
l_local="-1"
|
| 42 |
+
mesh_size="1117"
|
| 43 |
+
number_of_wfc="2"
|
| 44 |
+
number_of_proj="2"/>
|
| 45 |
+
</UPF>
|
fixtures/EC_unverified_dft_setup_001_20260603/pp_files/H.upf
ADDED
|
@@ -0,0 +1,44 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
<UPF version="2.0.1">
|
| 2 |
+
<PP_INFO>
|
| 3 |
+
Generated using "atomic" code by A. Dal Corso v.5.0.2 svn rev. 9656 (2022/03)
|
| 4 |
+
Author: ADC
|
| 5 |
+
Generation date: 11 03 2022
|
| 6 |
+
Pseudopotential type: NC
|
| 7 |
+
Element: H
|
| 8 |
+
Functional: SLA PZ NOGX NOGC
|
| 9 |
+
|
| 10 |
+
Suggested minimum cutoff for wavefunctions: 45. Ry
|
| 11 |
+
Suggested minimum cutoff for charge density: 180. Ry
|
| 12 |
+
|
| 13 |
+
The Pseudo was generated with a Non-Relativistic calculation.
|
| 14 |
+
Pseudopotential generated with the Troullier-Martins method.
|
| 15 |
+
|
| 16 |
+
Valence configuration:
|
| 17 |
+
nl pn l occ Rcut Rcut US E pseu
|
| 18 |
+
1S 1 0 1.00 0.500 1.160 -0.479
|
| 19 |
+
</PP_INFO>
|
| 20 |
+
<PP_HEADER
|
| 21 |
+
generated="Generated using atomic code by A. Dal Corso v.5.0.2"
|
| 22 |
+
author="ADC"
|
| 23 |
+
date="11 03 2022"
|
| 24 |
+
comment=""
|
| 25 |
+
element="H "
|
| 26 |
+
pseudo_type="NC"
|
| 27 |
+
relativistic="scalar"
|
| 28 |
+
is_ultrasoft="F"
|
| 29 |
+
is_paw="F"
|
| 30 |
+
is_coulomb="F"
|
| 31 |
+
has_so="F"
|
| 32 |
+
has_wfc="F"
|
| 33 |
+
has_gipaw="F"
|
| 34 |
+
core_correction="F"
|
| 35 |
+
functional="SLA PZ NOGX NOGC"
|
| 36 |
+
z_valence="1.000000000000000E+000"
|
| 37 |
+
total_psenergy="-9.100000000000000E-001"
|
| 38 |
+
rho_cutoff="1.000000000000000E+001"
|
| 39 |
+
l_max="0"
|
| 40 |
+
l_local="-1"
|
| 41 |
+
mesh_size="1061"
|
| 42 |
+
number_of_wfc="1"
|
| 43 |
+
number_of_proj="1"/>
|
| 44 |
+
</UPF>
|
fixtures/IG_abacus_001_20260404/base_slab.stru
ADDED
|
@@ -0,0 +1,91 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOMIC_SPECIES
|
| 2 |
+
Fe 55.845 Fe_ONCV_PBE-1.2.upf
|
| 3 |
+
|
| 4 |
+
NUMERICAL_ORBITAL
|
| 5 |
+
Fe_gga_7au_100Ry_4s2p2d1f.orb
|
| 6 |
+
|
| 7 |
+
LATTICE_CONSTANT
|
| 8 |
+
1.889726
|
| 9 |
+
|
| 10 |
+
LATTICE_VECTORS
|
| 11 |
+
4.91676915310 0.01717660430 0.00000214940
|
| 12 |
+
2.48268378830 6.94150499100 0.00000134940
|
| 13 |
+
0.00000000000 0.00000000000 32.26919937130
|
| 14 |
+
|
| 15 |
+
ATOMIC_POSITIONS
|
| 16 |
+
Direct
|
| 17 |
+
|
| 18 |
+
Fe
|
| 19 |
+
0.000000
|
| 20 |
+
71
|
| 21 |
+
0.25006587684 0.16664003990 0.00433929695 1 1 1 mag 2.20000000
|
| 22 |
+
0.00000411602 0.99997243833 0.06626527382 1 1 1 mag 2.20000000
|
| 23 |
+
0.25001308137 0.16664173197 0.12865758691 1 1 1 mag 2.20000000
|
| 24 |
+
0.00001209906 0.00000622598 0.19045482158 1 1 1 mag 2.20000000
|
| 25 |
+
0.24992704834 0.16666382534 0.25222944059 1 1 1 mag 2.20000000
|
| 26 |
+
0.00005519303 0.00000312704 0.31396695171 1 1 1 mag 2.20000000
|
| 27 |
+
0.24997243906 0.16663519619 0.37576772881 1 1 1 mag 2.20000000
|
| 28 |
+
0.99987211168 0.00004960484 0.43752481966 1 1 1 mag 2.20000000
|
| 29 |
+
0.25004949116 0.16672896287 0.49954317853 1 1 1 mag 2.20000000
|
| 30 |
+
0.00076795367 0.99982414591 0.56130054307 1 1 1 mag 2.20000000
|
| 31 |
+
0.24877386116 0.16635255359 0.62427389667 1 1 1 mag 2.20000000
|
| 32 |
+
0.00229045638 0.99875303173 0.68605072884 1 1 1 mag 2.20000000
|
| 33 |
+
0.75008582350 0.16663464820 0.00434763439 1 1 1 mag 2.20000000
|
| 34 |
+
0.49997965974 0.99997926060 0.06626653229 1 1 1 mag 2.20000000
|
| 35 |
+
0.74999153554 0.16666546151 0.12865255461 1 1 1 mag 2.20000000
|
| 36 |
+
0.50001125353 0.99997002198 0.19044974258 1 1 1 mag 2.20000000
|
| 37 |
+
0.74993804178 0.16665165737 0.25223972689 1 1 1 mag 2.20000000
|
| 38 |
+
0.50005221703 0.99996221153 0.31397573884 1 1 1 mag 2.20000000
|
| 39 |
+
0.74984393130 0.16675168163 0.37576766301 1 1 1 mag 2.20000000
|
| 40 |
+
0.49976067990 0.00012005957 0.43748278288 1 1 1 mag 2.20000000
|
| 41 |
+
0.74989909643 0.16684519791 0.49948014235 1 1 1 mag 2.20000000
|
| 42 |
+
0.50002098164 0.00033862572 0.56161526245 1 1 1 mag 2.20000000
|
| 43 |
+
0.75275737717 0.16539288304 0.62398232804 1 1 1 mag 2.20000000
|
| 44 |
+
0.49719664174 0.99882154160 0.68627795052 1 1 1 mag 2.20000000
|
| 45 |
+
0.24989443338 0.50001889588 0.00434765329 1 1 1 mag 2.20000000
|
| 46 |
+
0.99998030258 0.33332704149 0.06626572911 1 1 1 mag 2.20000000
|
| 47 |
+
0.24998874794 0.49998890326 0.12865258381 1 1 1 mag 2.20000000
|
| 48 |
+
0.99998016158 0.33332751998 0.19045621845 1 1 1 mag 2.20000000
|
| 49 |
+
0.25004195061 0.50000272989 0.25223973359 1 1 1 mag 2.20000000
|
| 50 |
+
0.99998025708 0.33332746948 0.31398338550 1 1 1 mag 2.20000000
|
| 51 |
+
0.25013643187 0.49990250114 0.37576763291 1 1 1 mag 2.20000000
|
| 52 |
+
0.00000005560 0.33332710729 0.43754847630 1 1 1 mag 2.20000000
|
| 53 |
+
0.25008157304 0.49980842307 0.49948011485 1 1 1 mag 2.20000000
|
| 54 |
+
0.99998040038 0.33332698249 0.56185547928 1 1 1 mag 2.20000000
|
| 55 |
+
0.00000014000 0.33332707439 0.68683158696 1 1 1 mag 2.20000000
|
| 56 |
+
0.74991439453 0.50001350158 0.00433931825 1 1 1 mag 2.20000000
|
| 57 |
+
0.49999008604 0.33332703639 0.06626041581 1 1 1 mag 2.20000000
|
| 58 |
+
0.74996717151 0.50001261250 0.12865761411 1 1 1 mag 2.20000000
|
| 59 |
+
0.49998990204 0.33332751338 0.19045818222 1 1 1 mag 2.20000000
|
| 60 |
+
0.75005299044 0.49999058273 0.25222943619 1 1 1 mag 2.20000000
|
| 61 |
+
0.49998987944 0.33332747978 0.31395791259 1 1 1 mag 2.20000000
|
| 62 |
+
0.75000791052 0.50001901358 0.37576769351 1 1 1 mag 2.20000000
|
| 63 |
+
0.49999012634 0.33332712559 0.43754550396 1 1 1 mag 2.20000000
|
| 64 |
+
0.74993122421 0.49992468511 0.49954318883 1 1 1 mag 2.20000000
|
| 65 |
+
0.49999027344 0.33332690709 0.56182910749 1 1 1 mag 2.20000000
|
| 66 |
+
0.75120697611 0.50030138159 0.62427384727 1 1 1 mag 2.20000000
|
| 67 |
+
0.25000180859 0.83330909908 0.00433210159 1 1 1 mag 2.20000000
|
| 68 |
+
0.99997638225 0.66666145443 0.06626530701 1 1 1 mag 2.20000000
|
| 69 |
+
0.24998628849 0.83331833820 0.12866032926 1 1 1 mag 2.20000000
|
| 70 |
+
0.99996853691 0.66664715681 0.19045483538 1 1 1 mag 2.20000000
|
| 71 |
+
0.25002272118 0.83328849258 0.25223694714 1 1 1 mag 2.20000000
|
| 72 |
+
0.99992567674 0.66664999425 0.31396694971 1 1 1 mag 2.20000000
|
| 73 |
+
0.24990344590 0.83332592106 0.37573466155 1 1 1 mag 2.20000000
|
| 74 |
+
0.00010899358 0.66660363125 0.43752477616 1 1 1 mag 2.20000000
|
| 75 |
+
0.25044013067 0.83297839691 0.49935843552 1 1 1 mag 2.20000000
|
| 76 |
+
0.99921259300 0.66680974805 0.56130054357 1 1 1 mag 2.20000000
|
| 77 |
+
0.25003933886 0.83337994671 0.62426015054 1 1 1 mag 2.20000000
|
| 78 |
+
0.99769030779 0.66788155201 0.68605070714 1 1 1 mag 2.20000000
|
| 79 |
+
0.74997866719 0.83332453828 0.00433210199 1 1 1 mag 2.20000000
|
| 80 |
+
0.50000087013 0.66665461606 0.06626656769 1 1 1 mag 2.20000000
|
| 81 |
+
0.74999469637 0.83331522236 0.12866032996 1 1 1 mag 2.20000000
|
| 82 |
+
0.49996942224 0.66666391278 0.19044975868 1 1 1 mag 2.20000000
|
| 83 |
+
0.74995822688 0.83334469649 0.25223694494 1 1 1 mag 2.20000000
|
| 84 |
+
0.49992855504 0.66667150864 0.31397573644 1 1 1 mag 2.20000000
|
| 85 |
+
0.75007775766 0.83330723362 0.37573465615 1 1 1 mag 2.20000000
|
| 86 |
+
0.50022017587 0.66653327152 0.43748273398 1 1 1 mag 2.20000000
|
| 87 |
+
0.74954081350 0.83365533965 0.49935845142 1 1 1 mag 2.20000000
|
| 88 |
+
0.49995993823 0.66631465047 0.56161526135 1 1 1 mag 2.20000000
|
| 89 |
+
0.74994143481 0.83325434945 0.62426015134 1 1 1 mag 2.20000000
|
| 90 |
+
0.50278410833 0.66781305245 0.68627792472 1 1 1 mag 2.20000000
|
| 91 |
+
0.24722315490 0.50126098094 0.62398230764 1 1 1 mag 2.20000000
|
fixtures/IG_abacus_002_20260404/base_vacancy.stru
ADDED
|
@@ -0,0 +1,73 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOMIC_SPECIES
|
| 2 |
+
Fe 55.845 Fe_ONCV_PBE-1.2.upf
|
| 3 |
+
|
| 4 |
+
NUMERICAL_ORBITAL
|
| 5 |
+
Fe_gga_7au_100Ry_4s2p2d1f.orb
|
| 6 |
+
|
| 7 |
+
LATTICE_CONSTANT
|
| 8 |
+
1.889726
|
| 9 |
+
|
| 10 |
+
LATTICE_VECTORS
|
| 11 |
+
8.61000011676 0.00000000000 0.00000000000
|
| 12 |
+
0.00000000000 8.61000011676 0.00000000000
|
| 13 |
+
0.00000000000 0.00000000000 8.61000011676
|
| 14 |
+
|
| 15 |
+
ATOMIC_POSITIONS
|
| 16 |
+
Direct
|
| 17 |
+
|
| 18 |
+
Fe
|
| 19 |
+
0.000000
|
| 20 |
+
53
|
| 21 |
+
0.00000000000 0.00000000000 0.00000000000 1 1 1 mag 2.20000000
|
| 22 |
+
0.00000000000 0.00000000000 0.33333333333 1 1 1 mag 2.20000000
|
| 23 |
+
0.00000000000 0.00000000000 0.66666666667 1 1 1 mag 2.20000000
|
| 24 |
+
0.00000000000 0.33333333333 0.00000000000 1 1 1 mag 2.20000000
|
| 25 |
+
0.00000000000 0.33333333333 0.33333333333 1 1 1 mag 2.20000000
|
| 26 |
+
0.00000000000 0.33333333333 0.66666666667 1 1 1 mag 2.20000000
|
| 27 |
+
0.00000000000 0.66666666667 0.00000000000 1 1 1 mag 2.20000000
|
| 28 |
+
0.00000000000 0.66666666667 0.33333333333 1 1 1 mag 2.20000000
|
| 29 |
+
0.00000000000 0.66666666667 0.66666666667 1 1 1 mag 2.20000000
|
| 30 |
+
0.33333333333 0.00000000000 0.00000000000 1 1 1 mag 2.20000000
|
| 31 |
+
0.33333333333 0.00000000000 0.33333333333 1 1 1 mag 2.20000000
|
| 32 |
+
0.33333333333 0.00000000000 0.66666666667 1 1 1 mag 2.20000000
|
| 33 |
+
0.33333333333 0.33333333333 0.00000000000 1 1 1 mag 2.20000000
|
| 34 |
+
0.33333333333 0.33333333333 0.33333333333 1 1 1 mag 2.20000000
|
| 35 |
+
0.33333333333 0.33333333333 0.66666666667 1 1 1 mag 2.20000000
|
| 36 |
+
0.33333333333 0.66666666667 0.00000000000 1 1 1 mag 2.20000000
|
| 37 |
+
0.33333333333 0.66666666667 0.33333333333 1 1 1 mag 2.20000000
|
| 38 |
+
0.33333333333 0.66666666667 0.66666666667 1 1 1 mag 2.20000000
|
| 39 |
+
0.66666666667 0.00000000000 0.00000000000 1 1 1 mag 2.20000000
|
| 40 |
+
0.66666666667 0.00000000000 0.33333333333 1 1 1 mag 2.20000000
|
| 41 |
+
0.66666666667 0.00000000000 0.66666666667 1 1 1 mag 2.20000000
|
| 42 |
+
0.66666666667 0.33333333333 0.00000000000 1 1 1 mag 2.20000000
|
| 43 |
+
0.66666666667 0.33333333333 0.33333333333 1 1 1 mag 2.20000000
|
| 44 |
+
0.66666666667 0.33333333333 0.66666666667 1 1 1 mag 2.20000000
|
| 45 |
+
0.66666666667 0.66666666667 0.00000000000 1 1 1 mag 2.20000000
|
| 46 |
+
0.66666666667 0.66666666667 0.33333333333 1 1 1 mag 2.20000000
|
| 47 |
+
0.16666666667 0.16666666667 0.16666666667 1 1 1 mag 2.20000000
|
| 48 |
+
0.16666666667 0.16666666667 0.50000000000 1 1 1 mag 2.20000000
|
| 49 |
+
0.16666666667 0.16666666667 0.83333333333 1 1 1 mag 2.20000000
|
| 50 |
+
0.16666666667 0.50000000000 0.16666666667 1 1 1 mag 2.20000000
|
| 51 |
+
0.16666666667 0.50000000000 0.50000000000 1 1 1 mag 2.20000000
|
| 52 |
+
0.16666666667 0.50000000000 0.83333333333 1 1 1 mag 2.20000000
|
| 53 |
+
0.16666666667 0.83333333333 0.16666666667 1 1 1 mag 2.20000000
|
| 54 |
+
0.16666666667 0.83333333333 0.50000000000 1 1 1 mag 2.20000000
|
| 55 |
+
0.16666666667 0.83333333333 0.83333333333 1 1 1 mag 2.20000000
|
| 56 |
+
0.50000000000 0.16666666667 0.16666666667 1 1 1 mag 2.20000000
|
| 57 |
+
0.50000000000 0.16666666667 0.50000000000 1 1 1 mag 2.20000000
|
| 58 |
+
0.50000000000 0.16666666667 0.83333333333 1 1 1 mag 2.20000000
|
| 59 |
+
0.50000000000 0.50000000000 0.16666666667 1 1 1 mag 2.20000000
|
| 60 |
+
0.50000000000 0.50000000000 0.50000000000 1 1 1 mag 2.20000000
|
| 61 |
+
0.50000000000 0.50000000000 0.83333333333 1 1 1 mag 2.20000000
|
| 62 |
+
0.50000000000 0.83333333333 0.16666666667 1 1 1 mag 2.20000000
|
| 63 |
+
0.50000000000 0.83333333333 0.50000000000 1 1 1 mag 2.20000000
|
| 64 |
+
0.50000000000 0.83333333333 0.83333333333 1 1 1 mag 2.20000000
|
| 65 |
+
0.83333333333 0.16666666667 0.16666666667 1 1 1 mag 2.20000000
|
| 66 |
+
0.83333333333 0.16666666667 0.50000000000 1 1 1 mag 2.20000000
|
| 67 |
+
0.83333333333 0.16666666667 0.83333333333 1 1 1 mag 2.20000000
|
| 68 |
+
0.83333333333 0.50000000000 0.16666666667 1 1 1 mag 2.20000000
|
| 69 |
+
0.83333333333 0.50000000000 0.50000000000 1 1 1 mag 2.20000000
|
| 70 |
+
0.83333333333 0.50000000000 0.83333333333 1 1 1 mag 2.20000000
|
| 71 |
+
0.83333333333 0.83333333333 0.16666666667 1 1 1 mag 2.20000000
|
| 72 |
+
0.83333333333 0.83333333333 0.50000000000 1 1 1 mag 2.20000000
|
| 73 |
+
0.83333333333 0.83333333333 0.83333333333 1 1 1 mag 2.20000000
|
fixtures/IG_abacus_003_20260406/base_al_slab.stru
ADDED
|
@@ -0,0 +1,22 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOMIC_SPECIES
|
| 2 |
+
Al 13 Al_ONCV_PBE-1.0.upf
|
| 3 |
+
|
| 4 |
+
LATTICE_CONSTANT
|
| 5 |
+
7.6513590200098225
|
| 6 |
+
|
| 7 |
+
LATTICE_VECTORS
|
| 8 |
+
0.707106781187 0.000000000000 0.000000000000
|
| 9 |
+
0.000000000000 0.707106781187 0.000000000000
|
| 10 |
+
0.000000000000 0.000000000000 5.000000000000
|
| 11 |
+
|
| 12 |
+
ATOMIC_POSITIONS
|
| 13 |
+
Direct
|
| 14 |
+
|
| 15 |
+
Al
|
| 16 |
+
0.0
|
| 17 |
+
5
|
| 18 |
+
0.000000000000 0.000000000000 0.000000000000 1 1 1
|
| 19 |
+
0.500000000000 0.500000000000 0.100000000000 1 1 1
|
| 20 |
+
0.000000000000 0.000000000000 0.200000000000 1 1 1
|
| 21 |
+
0.500000000000 0.500000000000 0.300000000000 1 1 1
|
| 22 |
+
0.000000000000 0.000000000000 0.400000000000 1 1 1
|
fixtures/IG_abacus_004_20260406/base_h2o.stru
ADDED
|
@@ -0,0 +1,25 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
|
|
|
|
|
|
|
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|
|
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|
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|
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|
|
|
|
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|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOMIC_SPECIES
|
| 2 |
+
O 15.999 O_ONCV_PBE-1.0.upf
|
| 3 |
+
H 1.008 H_ONCV_PBE-1.0.upf
|
| 4 |
+
|
| 5 |
+
LATTICE_CONSTANT
|
| 6 |
+
1.889726
|
| 7 |
+
|
| 8 |
+
LATTICE_VECTORS
|
| 9 |
+
5.300000000000 0.000000000000 0.000000000000
|
| 10 |
+
0.000000000000 5.300000000000 0.000000000000
|
| 11 |
+
0.000000000000 0.000000000000 18.000000000000
|
| 12 |
+
|
| 13 |
+
ATOMIC_POSITIONS
|
| 14 |
+
Cartesian_angstrom
|
| 15 |
+
|
| 16 |
+
O
|
| 17 |
+
0.0
|
| 18 |
+
1
|
| 19 |
+
2.650000000000 2.650000000000 9.000000000000 1 1 1
|
| 20 |
+
|
| 21 |
+
H
|
| 22 |
+
0.0
|
| 23 |
+
2
|
| 24 |
+
3.410000000000 2.650000000000 9.580000000000 1 1 1
|
| 25 |
+
2.170000000000 3.330000000000 9.580000000000 1 1 1
|
fixtures/IG_abacus_005_20260406/bulk_al_fcc.stru
ADDED
|
@@ -0,0 +1,21 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOMIC_SPECIES
|
| 2 |
+
Al 26.981538 Al_ONCV_PBE-1.0.upf
|
| 3 |
+
|
| 4 |
+
LATTICE_CONSTANT
|
| 5 |
+
1.889726
|
| 6 |
+
|
| 7 |
+
LATTICE_VECTORS
|
| 8 |
+
4.050000000000 0.000000000000 0.000000000000
|
| 9 |
+
0.000000000000 4.050000000000 0.000000000000
|
| 10 |
+
0.000000000000 0.000000000000 4.050000000000
|
| 11 |
+
|
| 12 |
+
ATOMIC_POSITIONS
|
| 13 |
+
Direct
|
| 14 |
+
|
| 15 |
+
Al
|
| 16 |
+
0.0
|
| 17 |
+
4
|
| 18 |
+
0.000000000000 0.000000000000 0.000000000000 1 1 1
|
| 19 |
+
0.000000000000 0.500000000000 0.500000000000 1 1 1
|
| 20 |
+
0.500000000000 0.000000000000 0.500000000000 1 1 1
|
| 21 |
+
0.500000000000 0.500000000000 0.000000000000 1 1 1
|
fixtures/IG_abacus_005_20260406/slab_al_fcc100_5l.stru
ADDED
|
@@ -0,0 +1,22 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOMIC_SPECIES
|
| 2 |
+
Al 13 Al_ONCV_PBE-1.0.upf
|
| 3 |
+
|
| 4 |
+
LATTICE_CONSTANT
|
| 5 |
+
7.6513590200098225
|
| 6 |
+
|
| 7 |
+
LATTICE_VECTORS
|
| 8 |
+
0.707106781187 0.000000000000 0.000000000000
|
| 9 |
+
0.000000000000 0.707106781187 0.000000000000
|
| 10 |
+
0.000000000000 0.000000000000 5.000000000000
|
| 11 |
+
|
| 12 |
+
ATOMIC_POSITIONS
|
| 13 |
+
Direct
|
| 14 |
+
|
| 15 |
+
Al
|
| 16 |
+
0.0
|
| 17 |
+
5
|
| 18 |
+
0.000000000000 0.000000000000 0.000000000000 1 1 1
|
| 19 |
+
0.500000000000 0.500000000000 0.100000000000 0 0 0
|
| 20 |
+
0.000000000000 0.000000000000 0.200000000000 0 0 0
|
| 21 |
+
0.500000000000 0.500000000000 0.300000000000 0 0 0
|
| 22 |
+
0.000000000000 0.000000000000 0.400000000000 1 1 1
|
fixtures/IG_abacus_005_20260406/slab_al_fcc100_7l.stru
ADDED
|
@@ -0,0 +1,24 @@
|
|
|
|
|
|
|
|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOMIC_SPECIES
|
| 2 |
+
Al 13 Al_ONCV_PBE-1.0.upf
|
| 3 |
+
|
| 4 |
+
LATTICE_CONSTANT
|
| 5 |
+
7.6513590200098225
|
| 6 |
+
|
| 7 |
+
LATTICE_VECTORS
|
| 8 |
+
0.707106781187 0.000000000000 0.000000000000
|
| 9 |
+
0.000000000000 0.707106781187 0.000000000000
|
| 10 |
+
0.000000000000 0.000000000000 5.400000000000
|
| 11 |
+
|
| 12 |
+
ATOMIC_POSITIONS
|
| 13 |
+
Direct
|
| 14 |
+
|
| 15 |
+
Al
|
| 16 |
+
0.0
|
| 17 |
+
7
|
| 18 |
+
0.000000000000 0.000000000000 0.000000000000 1 1 1
|
| 19 |
+
0.500000000000 0.500000000000 0.100000000000 1 1 1
|
| 20 |
+
0.000000000000 0.000000000000 0.200000000000 0 0 0
|
| 21 |
+
0.500000000000 0.500000000000 0.300000000000 0 0 0
|
| 22 |
+
0.000000000000 0.000000000000 0.400000000000 0 0 0
|
| 23 |
+
0.500000000000 0.500000000000 0.500000000000 1 1 1
|
| 24 |
+
0.000000000000 0.000000000000 0.600000000000 1 1 1
|
fixtures/IG_abacus_006_20260406/mo110_pristine.stru
ADDED
|
@@ -0,0 +1,25 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOMIC_SPECIES
|
| 2 |
+
Mo 95.95 Mo_ONCV_PBE-1.0.upf
|
| 3 |
+
|
| 4 |
+
LATTICE_CONSTANT
|
| 5 |
+
1.889726
|
| 6 |
+
|
| 7 |
+
LATTICE_VECTORS
|
| 8 |
+
6.300000000000 0.000000000000 0.000000000000
|
| 9 |
+
0.000000000000 4.455000000000 0.000000000000
|
| 10 |
+
0.000000000000 0.000000000000 20.000000000000
|
| 11 |
+
|
| 12 |
+
ATOMIC_POSITIONS
|
| 13 |
+
Direct
|
| 14 |
+
|
| 15 |
+
Mo
|
| 16 |
+
0.0
|
| 17 |
+
8
|
| 18 |
+
0.000000000000 0.000000000000 0.100000000000 1 1 1
|
| 19 |
+
0.500000000000 0.500000000000 0.150000000000 1 1 1
|
| 20 |
+
0.000000000000 0.500000000000 0.250000000000 1 1 1
|
| 21 |
+
0.500000000000 0.000000000000 0.300000000000 1 1 1
|
| 22 |
+
0.000000000000 0.000000000000 0.400000000000 1 1 1
|
| 23 |
+
0.500000000000 0.500000000000 0.450000000000 1 1 1
|
| 24 |
+
0.000000000000 0.500000000000 0.550000000000 1 1 1
|
| 25 |
+
0.500000000000 0.000000000000 0.600000000000 1 1 1
|
fixtures/IG_abacus_006_20260406/mo110_surface_vac.stru
ADDED
|
@@ -0,0 +1,24 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOMIC_SPECIES
|
| 2 |
+
Mo 95.95 Mo_ONCV_PBE-1.0.upf
|
| 3 |
+
|
| 4 |
+
LATTICE_CONSTANT
|
| 5 |
+
1.889726
|
| 6 |
+
|
| 7 |
+
LATTICE_VECTORS
|
| 8 |
+
6.300000000000 0.000000000000 0.000000000000
|
| 9 |
+
0.000000000000 4.455000000000 0.000000000000
|
| 10 |
+
0.000000000000 0.000000000000 20.000000000000
|
| 11 |
+
|
| 12 |
+
ATOMIC_POSITIONS
|
| 13 |
+
Direct
|
| 14 |
+
|
| 15 |
+
Mo
|
| 16 |
+
0.0
|
| 17 |
+
7
|
| 18 |
+
0.500000000000 0.500000000000 0.150000000000 1 1 1
|
| 19 |
+
0.000000000000 0.500000000000 0.250000000000 1 1 1
|
| 20 |
+
0.500000000000 0.000000000000 0.300000000000 1 1 1
|
| 21 |
+
0.000000000000 0.000000000000 0.400000000000 1 1 1
|
| 22 |
+
0.500000000000 0.500000000000 0.450000000000 1 1 1
|
| 23 |
+
0.000000000000 0.500000000000 0.550000000000 1 1 1
|
| 24 |
+
0.500000000000 0.000000000000 0.600000000000 1 1 1
|
fixtures/IG_abacus_006_20260406/mo_bulk.stru
ADDED
|
@@ -0,0 +1,19 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOMIC_SPECIES
|
| 2 |
+
Mo 95.95 Mo_ONCV_PBE-1.0.upf
|
| 3 |
+
|
| 4 |
+
LATTICE_CONSTANT
|
| 5 |
+
1.889726
|
| 6 |
+
|
| 7 |
+
LATTICE_VECTORS
|
| 8 |
+
3.150000000000 0.000000000000 0.000000000000
|
| 9 |
+
0.000000000000 3.150000000000 0.000000000000
|
| 10 |
+
0.000000000000 0.000000000000 3.150000000000
|
| 11 |
+
|
| 12 |
+
ATOMIC_POSITIONS
|
| 13 |
+
Direct
|
| 14 |
+
|
| 15 |
+
Mo
|
| 16 |
+
0.0
|
| 17 |
+
2
|
| 18 |
+
0.000000000000 0.000000000000 0.000000000000 1 1 1
|
| 19 |
+
0.500000000000 0.500000000000 0.500000000000 1 1 1
|
fixtures/IG_abacus_017_20260512/POSCAR_rocksalt
ADDED
|
@@ -0,0 +1,12 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
Ni2 O2
|
| 2 |
+
1.0
|
| 3 |
+
2.0789357935494857 -0.0051842861109737 -2.0744577679413601
|
| 4 |
+
-0.0039331589848043 -2.0735122392834859 2.0799387796589861
|
| 5 |
+
-2.0745128754914957 -2.0817689798503420 -4.1533136454891526
|
| 6 |
+
Ni O
|
| 7 |
+
2 2
|
| 8 |
+
direct
|
| 9 |
+
0.0126263598973515 0.0310909930073594 0.0285912402257575 Ni
|
| 10 |
+
0.5124601000694023 0.5310608317213408 0.5285745916837236 Ni
|
| 11 |
+
0.2624539377419948 0.7810255697636642 0.2786794025867683 O
|
| 12 |
+
0.7625474502312073 0.2810386770730068 0.7785355497218639 O
|
fixtures/IG_abacus_017_20260512/POSCAR_square_planar
ADDED
|
@@ -0,0 +1,12 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
Ni2 O2
|
| 2 |
+
1.0
|
| 3 |
+
2.8148201437373328 -0.0080214933254869 -2.8106615902265646
|
| 4 |
+
-0.4285680508511212 -1.4444907954982102 2.3895235554315541
|
| 5 |
+
-2.1173457036954852 -2.0412607992090015 -4.9372519653779046
|
| 6 |
+
Ni O
|
| 7 |
+
2 2
|
| 8 |
+
direct
|
| 9 |
+
0.0306145335383516 0.0231897745863886 0.0087431480895788 Ni
|
| 10 |
+
0.5306239513096086 0.5231900096488745 0.5087441212132603 Ni
|
| 11 |
+
0.0325659721029262 0.7738733107471312 0.2586500116192785 O
|
| 12 |
+
1.0286762974366450 0.2725077636760428 0.7588285782982462 O
|
fixtures/IG_abacus_019_20260513/STRU_graphene
ADDED
|
@@ -0,0 +1,22 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOMIC_SPECIES
|
| 2 |
+
C 12.011 C_ONCV_PBE-1.0.upf
|
| 3 |
+
|
| 4 |
+
NUMERICAL_ORBITAL
|
| 5 |
+
C_gga_7au_100Ry_2s2p1d.orb
|
| 6 |
+
|
| 7 |
+
LATTICE_CONSTANT
|
| 8 |
+
1.8897259886
|
| 9 |
+
|
| 10 |
+
LATTICE_VECTORS
|
| 11 |
+
2.4677000000 0.0000000000 0.0000000000
|
| 12 |
+
-1.2338500000 2.1373835679 0.0000000000
|
| 13 |
+
0.0000000000 0.0000000000 20.0000000000
|
| 14 |
+
|
| 15 |
+
ATOMIC_POSITIONS
|
| 16 |
+
Direct
|
| 17 |
+
|
| 18 |
+
C
|
| 19 |
+
0.0
|
| 20 |
+
2
|
| 21 |
+
0.000000000 0.000000000 0.500000000 1 1 1
|
| 22 |
+
0.333333333 0.666666667 0.500000000 1 1 1
|
fixtures/IG_abacus_020_20260514/Si_diamond.stru
ADDED
|
@@ -0,0 +1,19 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOMIC_SPECIES
|
| 2 |
+
Si 28.085 Si_ONCV_PBE-1.0.upf
|
| 3 |
+
|
| 4 |
+
LATTICE_CONSTANT
|
| 5 |
+
1.8897259886
|
| 6 |
+
|
| 7 |
+
LATTICE_VECTORS
|
| 8 |
+
0.000000000 2.715346500 2.715346500
|
| 9 |
+
2.715346500 0.000000000 2.715346500
|
| 10 |
+
2.715346500 2.715346500 0.000000000
|
| 11 |
+
|
| 12 |
+
ATOMIC_POSITIONS
|
| 13 |
+
Direct
|
| 14 |
+
|
| 15 |
+
Si
|
| 16 |
+
0.0
|
| 17 |
+
2
|
| 18 |
+
0.000000000 0.000000000 0.000000000 1 1 1
|
| 19 |
+
0.250000000 0.250000000 0.250000000 1 1 1
|
fixtures/IG_abacus_020_20260514/Si_fcc.stru
ADDED
|
@@ -0,0 +1,18 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
ATOMIC_SPECIES
|
| 2 |
+
Si 28.085 Si_ONCV_PBE-1.0.upf
|
| 3 |
+
|
| 4 |
+
LATTICE_CONSTANT
|
| 5 |
+
1.8897259886
|
| 6 |
+
|
| 7 |
+
LATTICE_VECTORS
|
| 8 |
+
0.000000000 2.575000000 2.575000000
|
| 9 |
+
2.575000000 0.000000000 2.575000000
|
| 10 |
+
2.575000000 2.575000000 0.000000000
|
| 11 |
+
|
| 12 |
+
ATOMIC_POSITIONS
|
| 13 |
+
Direct
|
| 14 |
+
|
| 15 |
+
Si
|
| 16 |
+
0.0
|
| 17 |
+
1
|
| 18 |
+
0.000000000 0.000000000 0.000000000 1 1 1
|
fixtures/IG_abacus_020_20260514/kpt_444.txt
ADDED
|
@@ -0,0 +1,4 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
K_POINTS
|
| 2 |
+
0
|
| 3 |
+
Gamma
|
| 4 |
+
4 4 4 0 0 0
|