Discrepencies and error metrics -- ColabFit
Collection
Datasets from Liu, He & Mo, NPJ 2023 (https://doi.org/10.1038/s41524-023-01123-3) in ColabFit format
•
5 items
•
Updated
Dataset Viewer
property_id
string | property_hash
string | last_modified
timestamp[us] | dataset_id
string | multiplicity
int32 | software
string | method
string | energy
float64 | atomic_forces
list | cauchy_stress
list | cauchy_stress_volume_normalized
bool | electronic_band_gap
float64 | electronic_band_gap_type
string | formation_energy
float64 | adsorption_energy
float64 | atomization_energy
float64 | max_force_norm
float64 | mean_force_norm
float64 | energy_above_hull
float64 | configuration_id
string | configuration_hash
string | structure_hash
string | cell
list | positions
list | pbc
list | chemical_formula_hill
string | chemical_formula_reduced
string | chemical_formula_anonymous
string | elements
list | elements_ratios
list | atomic_numbers
list | nsites
int32 | nelements
int32 | nperiodic_dimensions
int32 | dimension_types
list | names
list | labels
list | property_metadata_path
string | configuration_metadata_path
string | hash
string | configuration_metadata
string | property_metadata
string |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
PO_1000750454749552517258227
|
10007504547495525172582275592153549205770949033661597982114196729440883127960113843573316848093951577019484345447492601286189116798578745949796069004256443
| 2025-04-16T21:22:14
|
DS_dhe9aqs9q1wf_0
| 1
|
VASP 5.4.4
|
DFT-PBE
| -338.671554
|
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] | null | null | null | null | null | null | null | 3.890536
| 1.790947
| null |
CO_9142358490262778245416846
|
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|
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] |
[
true,
true,
true
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Si65
|
Si
|
A
|
[
"Si"
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[
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[
"Interstitial-RE_Testing_Set__DFT_K1__97"
] | null |
data/MD/2794/MD_1267883600539355957832794.json
|
data/MD/1452/MD_1441116133498153906021452.json
| null |
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|
{"input": {"value": {"kpoints": {"value": "2x2x2"}, "encut": {"value": 520}}}, "hash": "12678836005393559578327948573445002546511994135465896275751099241573907940589357642251841809333692916637830051235168679060695627355230588897679382375744463", "id": "MD_1267883600539355957832794"}
|
PO_4950339829294269200488473
|
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| 2025-04-16T17:15:37
|
DS_dhe9aqs9q1wf_0
| 1
|
VASP 5.4.4
|
DFT-PBE
| null |
[
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DS_dhe9aqs9q1wf_0
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VASP 5.4.4
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DFT-PBE
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data/MD/8910/MD_9853815620216127715358910.json
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PO_1050159857971113105991975
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DS_dhe9aqs9q1wf_0
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VASP 5.4.4
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DFT-PBE
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data/MD/8235/MD_9440170961997286098318235.json
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DS_dhe9aqs9q1wf_0
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VASP 5.4.4
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DFT-PBE
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| 2025-04-16T21:13:40
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DS_dhe9aqs9q1wf_0
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VASP 5.4.4
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DFT-PBE
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[] |
data/MD/5762/MD_5760338139807708513145762.json
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data/MD/8966/MD_1024719155494512060548966.json
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PO_4535526992742079780507056
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| 2025-04-16T21:29:37
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DS_dhe9aqs9q1wf_0
| 1
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VASP 5.4.4
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DFT-PBE
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Si65
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Si
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A
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data/MD/0571/MD_4382028136033721287760571.json
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data/MD/4274/MD_6009557133075821979314274.json
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PO_1053528316736799327127829
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| 2025-04-16T22:04:30
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DS_dhe9aqs9q1wf_0
| 1
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VASP 5.4.4
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DFT-PBE
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DS_dhe9aqs9q1wf_0
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DS_dhe9aqs9q1wf_0
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Si
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[
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[] |
data/MD/2794/MD_1267883600539355957832794.json
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data/MD/1808/MD_4950015682063077522811808.json
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DS_dhe9aqs9q1wf_0
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DFT-PBE
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data/MD/4487/MD_3147938452485145114874487.json
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DS_dhe9aqs9q1wf_0
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VASP 5.4.4
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DFT-PBE
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data/MD/2758/MD_4579723487692079150662758.json
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data/MD/8145/MD_1129558729527387314688145.json
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{"input": [{"value": {"kpoints": {"value": "single gamma-point"}, "encut": {"value": 520}}}], "hash": "4579723487692079150662758961345587118982168314723692341430205577163418725037914381334151097401366361684048275393001149694922323507504851062484730650988306", "id": "MD_4579723487692079150662758"}
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PO_1022341344952065566747295
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| 2025-04-16T21:43:16
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DS_dhe9aqs9q1wf_0
| 1
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VASP 5.4.4
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DFT-PBE
| null |
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A
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data/MD/4005/MD_1134781387419449211194005.json
|
data/MD/3370/MD_1209102164125220758453370.json
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{"input": [{"value": {"kpoints": {"value": "single gamma-point"}, "encut": {"value": 520}}}], "hash": "11347813874194492111940052981576223183462855855723650608591810673459611390065556398679678617042175541278881372363094945088871119457175380332280981969371392", "id": "MD_1134781387419449211194005"}
|
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Cite this dataset
Liu, Y., He, X., and Mo, Y. discrepencies and error metrics NPJ 2023 interstitial re testing set. ColabFit, 2023. https://doi.org/10.60732/81a7ca9e
Cite this dataset
Liu, Y., He, X., and Mo, Y. discrepencies and error metrics NPJ 2023 interstitial re testing set. ColabFit, 2023. https://doi.org/10.60732/81a7ca9eThis dataset has been curated and formatted for the ColabFit Exchange
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Dataset Name
discrepencies and error metrics NPJ 2023 interstitial re testing set
Description
Structures from discrepencies_and_error_metrics_NPJ_2023 test set; these include an interstitial. The full discrepencies_and_error_metrics_NPJ_2023 dataset includes the original mlearn_Si_train dataset, modified with the purpose of developing models with better diffusivity scores by replacing ~54% of the data with structures containing migrating interstitials. The enhanced validation set contains 50 total structures, consisting of 20 structures randomly selected from the 120 replaced structures of the original training dataset, 11 snapshots with vacancy rare events (RE) from AIMD simulations, and 19 snapshots with interstitial RE from AIMD simulations. We also construct interstitial-RE and vacancy-RE testing sets, each consisting of 100 snapshots of atomic configurations with a single migrating vacancy or interstitial, respectively, from AIMD simulations at 1230 K.
Dataset authors
Yunsheng Liu, Xingfeng He, Yifei Mo
Publication
https://doi.org/10.1038/s41524-023-01123-3
Original data link
https://github.com/mogroupumd/Silicon_MLIP_datasets
License
CC-BY-4.0
Number of unique molecular configurations
100
Number of atoms
6500
Elements included
Si
Properties included
energy, atomic forces
Usage
ds.parquet: Aggregated dataset information.co/directory: Configuration rows each include a structure, calculated properties, and metadata.cs/directory : Configuration sets are subsets of configurations grouped by some common characteristic. Ifcs/does not exist, no configurations sets have been defined for this dataset.cs_co_map/directory : The mapping of configurations to configuration sets (if defined).
ColabFit Exchange documentation includes descriptions of content and example code for parsing parquet files:
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