amorphous carbon -- ColabFit
Collection
Datasets from Minimatani et al., JCP 2023 (https://doi.org/10.1063/5.0159349)
•
3 items
•
Updated
Datasets:
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_1000973035066785776212852
|
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| 2025-04-16T18:07:48
|
DS_20h8o5d0ltx1_0
| 1
|
VASP
|
DFT-LDA
| -1,647.217472
|
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[] | null | null | null | null | null | null | 30.14678
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[
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data/MD/5202/MD_1086845055867124744315202.json
|
data/MD/9672/MD_3096035736227726011599672.json
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{"density": 3.5, "process": "quench1", "hash": "3096035736227726011599672941939089728172253003571373060394495777339499077058068057125052463063819343542124388285350233978617507469183693301286077624447025", "id": "MD_3096035736227726011599672"}
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{"hash": "10868450558671247443152026947160338505683745266658651051718065983487878962987857602829315249215796444208488632888003673539585986066311769564391053988452926", "id": "MD_1086845055867124744315202"}
|
End of preview. Expand
in Data Studio
Cite this dataset
Minamitani, E., Obayashi, I., Shimizu, K., and Watanabe, S. aC JCP 2023 train. ColabFit, 2023. https://doi.org/10.60732/ee630a62
Cite this dataset
Minamitani, E., Obayashi, I., Shimizu, K., and Watanabe, S. aC JCP 2023 train. ColabFit, 2023. https://doi.org/10.60732/ee630a62This dataset has been curated and formatted for the ColabFit Exchange
This dataset is also available on the ColabFit Exchange:
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Dataset Name
aC JCP 2023 train
Description
Train split from the 216-atom amorphous portion of the aC_JCP_2023 dataset. The amorphous carbon dataset was generated using ab initio calculations with VASP software. We utilized the LDA exchange-correlation functional and the PAW potential for carbon. Melt-quench simulations were performed to create amorphous and liquid-state structures. A simple cubic lattice of 216 carbon atoms was chosen as the initial state. Simulations were conducted at densities of 1.5, 1.7, 2.0, 2.2, 2.4, 2.6, 2.8, 3.0, 3.2, 3.4, and 3.5 g/cm3 to produce a variety of structures. The NVT ensemble was employed for all melt-quench simulations, and the density was adjusted by modifying the size of the simulation cell. A time step of 1 fs was used for the simulations. For all densities, only the Γ points were sampled in the k-space. To increase structural diversity, six independent simulations were performed.In the melt-quench simulations, the temperature was raised from 300 K to 9000 K over 2 ps to melt carbon. Equilibrium molecular dynamics (MD) was conducted at 9000 K for 3 ps to create a liquid state, followed by a decrease in temperature to 5000 K over 2 ps, with the system equilibrating at that temperature for 2 ps. Finally, the temperature was lowered from 5000 K to 300 K over 2 ps to generate an amorphous structure.During the melt-quench simulation, 30 snapshots were taken from the equilibrium MD trajectory at 9000 K, 100 from the cooling process between 9000 and 5000 K, 25 from the equilibrium MD trajectory at 5000 K, and 100 from the cooling process between 5000 and 300 K. This yielded a total of 16,830 data points.Data for diamond structures containing 216 atoms at densities of 2.4, 2.6, 2.8, 3.0, 3.2, 3.4, and 3.5 g/cm3 were also prepared. Further data on the diamond structure were obtained from 80 snapshots taken from the 2 ps equilibrium MD trajectory at 300 K, resulting in 560 data points.To validate predictions for larger structures, we generated data for 512-atom systems using the same procedure as for the 216-atom systems. A single simulation was conducted for each density. The number of data points was 2,805 for amorphous and liquid states
Dataset authors
Emi Minamitani, Ippei Obayashi, Koji Shimizu, Satoshi Watanabe
Publication
https://doi.org/10.1063/5.0159349
Original data link
https://doi.org/10.5281/zenodo.7905585
License
CC-BY-4.0
Number of unique molecular configurations
13462
Number of atoms
2907792
Elements included
C
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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Size of downloaded dataset files:
80.9 MB
Size of the auto-converted Parquet files:
80.9 MB
Number of rows:
13,463