cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.60732/43a0cef7
title: Si-H-GAP_training

description: A set of training configurations of hydrogenated liquid and amorphous silicon from the datasets for Si-H-GAP. Includes virial sigmas used for configurations used in the corresponding publication (virial-sigma-paper) as well as an alternate configuration defined by doubled virial sigma prefactors (from 0.025 to 0.05).
DOI: 10.60732/09d00e4e
title: 3BPA_test_dih_beta120

description: Test configurations with fixed value for dihedral beta in alpha-gamma plane of 120 degreesfrom 3BPA dataset. Used to showcase the performance of linear atomic cluster expansion (ACE) force fields in a machine learning model to predict the potential energy surfaces of organic molecules.
DOI: 10.15468/dl.udd765
title: Occurrence Download

description: A dataset containing 56 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mauloutchia parvifolia Capuron"
 ]
}

 The dataset includes 56 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050762-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60732/4e8857ac
title: CGM-MLP_natcomm2023_Ti-C_deposition

description: Training simulations from CGM-MLP_natcomm2023 of carbon deposition on a Ti surface. This dataset was one of the datasets used in training during the process of producing an active learning dataset for the purposes of exploring substrate-catalyzed deposition on metal surfaces such as Cu(111), Cr(110), Ti(001), and oxygen-contaminated Cu(111) as a means of controllable synthesis of carbon nanomaterials. The combined dataset includes structures from the Carbon_GAP_20 dataset and additional configurations of carbon clusters on a Cu, Cr and Ti surfaces.
DOI: 10.60732/e359e8ed
title: BOTnet_ACAC_2022_train_300K_MD

description: 500 decorrelated geometries sampled from 300 K xTB MD run. Acetylacetone dataset generated from a long molecular dynamics simulation at 300 K using a Langevin thermostat at the semi-empirical GFN2-xTB level of theory. Configurations were sampled at an interval of 1 ps and the resulting set of configurations were recomputed with density functional theory using the PBE exchange-correlation functional with D3 dispersion correction and def2-SVP basis set and VeryTightSCF convergence settings using the ORCA electronic structure package.
DOI: 10.60732/37c26dae
title: JARVIS_C2DB

description: The JARVIS-C2DB dataset is part of the joint automated repository for various integrated simulations (JARVIS) database. This subset contains configurations from the Computational 2D Database (C2DB), which contains a variety of properties for 2-dimensional materials across more than 30 differentcrystal structures. JARVIS is a set of tools and datasets built to meet current materials design challenges.
DOI: 10.15468/dl.t9nkvk
title: Occurrence Download

description: A dataset containing 158 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lygodium versteegii Christ"
 ]
}

 The dataset includes 158 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050763-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60732/01b77268
title: DFT_polymorphs_PNAS_2022_PBE_TS_benzene_validation

description: Benzene validation PBE-TS dataset from "Semi-local and hybrid functional DFT data for thermalised snapshots of polymorphs of benzene, succinic acid, and glycine". DFT reference energies and forces were calculated using Quantum Espresso v6.3. The calculations were performed with the semi-local PBE xc functional, Tkatchenko-Scheffler dispersion correction, optimised norm-conserving Vanderbilt pseudopotentials, a Monkhorst-Pack k-point grid with a maximum spacing of 0.06 x 2π A^-1, and a plane-wave energy cut-off of 100 Ry for the wavefunction.
DOI: 10.60732/682fe04a
title: rMD17

description: A dataset of 10 molecules (aspirin, azobenzene, benzene, ethanol, malonaldehyde, naphthalene, paracetamol, salicylic, toluene, uracil) with 100,000 structures calculated for each at the PBE/def2-SVP level of theory using ORCA. Based on the MD17 dataset, but with refined measurements.
DOI: 10.60732/a3ca9725
title: sGDML_Benzene_ccsdt_NC2018_train

description: The train set of a train/test pair from the benzene dataset from sGDML. To create the coupled cluster datasets, the data used for training the models were created by running ab initio MD in the NVT ensemble using the Nosé-Hoover thermostat at 500 K during a 200 ps simulation with a resolution of 0.5 fs. Energies and forces were recalculated using all-electron coupled cluster with single , double and perturbative triple excitations (CCSD(T)). The Dunning correlation-consistent basis set cc-pVDZ was used for benzene. All calculations were performed with the Psi4 software suite.
DOI: 10.60732/ef6f5966
title: 23-Single-Element-DNPs_RSCDD_2023-Al

description: Configurations of Al from Andolina & Saidi, 2023. One of 23 minimalist, curated sets of DFT-calculated properties for individual elements for the purpose of providing input to machine learning of deep neural network potentials (DNPs). Each element set contains on average ~4000 structures with 27 atoms per structure. Configuration metadata includes Materials Project ID where available, as well as temperatures at which MD trajectories were calculated.These temperatures correspond to the melting temperature (MT) and 0.25*MT for elements with MT &lt; 2000K, and MT, 0.6*MT and 0.25*MT for elements with MT &gt; 2000K.
DOI: 10.15468/dl.3twa6z
title: Occurrence Download

description: A dataset containing 926 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Soldanella minima Hoppe"
 ]
}

 The dataset includes 926 records from 68 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050764-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60732/95c19122
title: CA-9_BB_validation

description: Binning-binning configurations from CA-9 dataset used during validation step for NNP_BB potential. CA-9 consists of configurations of carbon with curated subsets chosen to test the effects of intentionally choosing dissimilar configurations when training neural network potentials
DOI: 10.60732/33767c4f
title: 23-Single-Element-DNPs_RSCDD_2023-Ge

description: Configurations of Ge from Andolina & Saidi, 2023. One of 23 minimalist, curated sets of DFT-calculated properties for individual elements for the purpose of providing input to machine learning of deep neural network potentials (DNPs). Each element set contains on average ~4000 structures with 27 atoms per structure. Configuration metadata includes Materials Project ID where available, as well as temperatures at which MD trajectories were calculated.These temperatures correspond to the melting temperature (MT) and 0.25*MT for elements with MT &lt; 2000K, and MT, 0.6*MT and 0.25*MT for elements with MT &gt; 2000K.
DOI: 10.60732/8b765383
title: CA-9_training

description: Configurations from CA-9 dataset used for training NNP_CA-9 potential. CA-9 consists of configurations of carbon with curated subsets chosen to test the effects of intentionally choosing dissimilar configurations when training neural network potentials
DOI: 10.15468/dl.fvbqr9
title: Occurrence Download

description: A dataset containing 149 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Macrosolen formosus (Blume) Miq."
 ]
}

 The dataset includes 149 records from 11 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050765-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60732/7eb1fefb
title: Zeo-1_SD_2022

description: 130,000 configurations of zeolite from the Database of Zeolite Structures. Calculations performed using Amsterdam Modeling Suite software.
DOI: 10.60732/a82feb87
title: LiSiPS_SSE_PBE

description: Approximately 9,100 configurations of Li10SiP2S12, based on crystal structures from the Materials Project database, material ID mp-696129. One of two LiSiPS datasets from this source. The other uses the PBEsol functional, rather than the PBE functional.
DOI: 10.60732/b88c7676
title: JARVIS_MEGNet

description: The JARVIS-MEGNet dataset is part of the joint automated repository for various integrated simulations (JARVIS) database. This subset contains configurations with 3D materials properties from the 2018 version of Materials Project, as used in the training of the MEGNet ML model. JARVIS is a set of tools and datasets built to meet current materials design challenges.
DOI: 10.15468/dl.vs6euh
title: Occurrence Download

description: A dataset containing 2 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ligularia lingiana S.W.Liu"
 ]
}

 The dataset includes 2 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050766-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60732/e75f2602
title: TSFF_PLOS_2022

description: One configuration of an enzyme: training data for a quantum-guided molecular mechanics model.
DOI: 10.60732/e2e38c83
title: doped_CsPbI3_energetics_test

description: The test set from the doped CsPbI3 energetics dataset. This dataset was created to explore the effect of Cd and Pb substitutions on the structural stability of inorganic lead halide perovskite CsPbI3. CsPbI3 undergoes a direct to indirect band-gap phase transition at room temperature. The dataset contains configurations of CsPbI3 with low levels of Cd and Zn, which were used to train a GNN model to predict the energetics of structures with higher levels of substitutions.
DOI: 10.15468/dl.qrtvv9
title: Occurrence Download

description: A dataset containing 38 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mauloutchia sambiranensis (Capuron) Sauquet"
 ]
}

 The dataset includes 38 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050767-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60732/54bc0a93
title: Si-H-GAP_reference

description: A reference set of configurations of hydrogenated liquid and amorphous silicon from the datasets for Si-H-GAP. These configurations were used to evaluate training on a GAP model.
DOI: 10.60732/85e47ff3
title: Ti_NPJCM_2021

description: Approximately 7,400 configurations of titanium used for training a deep potential using the DeePMD-kit molecular dynamics package and DP-GEN training scheme.
DOI: 10.60732/f127f7e7
title: alpha_brass_nanoparticles

description: 53,841 structures of alpha-brass (less than 40% Zinc). Includes atomic forces and total energy. Calculated using VASP at the DFT level of theory.
DOI: 10.60732/7b135132
title: COLL_test

description: Test set from COLL. Consists of configurations taken from molecular collisions of different small organic molecules. Energies and forces for 140,000 random snapshots taken from these trajectories were recomputed with density functional theory (DFT). These calculations were performed with the revPBE functional and def2-TZVP basis, including D3 dispersion corrections
DOI: 10.15468/dl.gx2n2p
title: Occurrence Download

description: A dataset containing 54 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lygodium yunnanense Ching"
 ]
}

 The dataset includes 54 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050769-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60732/d0801836
title: reactive_hydrogen_ACS_2023

description: This dataset contains structures of Cu, including Cu(111), Cu(100), Cu(110), and Cu(211). Slab settings are as follows: 3 x 3, 6-layered slabs for Cu(111), (100), and (110) surfaces; 1 x 3, 6-layered slabs for Cu(211) surface. Includes some structures representing interation of H2 with one of the Cu surfaces and some structures of Cu sampled at different temperatures.
DOI: 10.60732/ae1c7e2f
title: JARVIS_Open_Catalyst_100K

description: The JARVIS_Open_Catalyst_100K dataset is part of the joint automated repository for various integrated simulations (JARVIS) DFT database. This subset contains configurations from the 100K training, rest validation and test dataset from the Open Catalyst Project (OCP). JARVIS is a set of tools and datasets built to meet current materials design challenges.
DOI: 10.60732/358cb5ee
title: DFT_polymorphs_PNAS_2022_PBE0_MBD_glycine_train

description: Glycine training PBE0-MBD dataset from "Semi-local and hybrid functional DFT data for thermalised snapshots of polymorphs of benzene, succinic acid, and glycine". DFT reference energies and forces were calculated using Quantum Espresso v6.3. The calculations were performed with the semi-local PBE xc functional, Tkatchenko-Scheffler dispersion correction, optimised norm-conserving Vanderbilt pseudopotentials, a Monkhorst-Pack k-point grid with a maximum spacing of 0.06 x 2π A^-1, and a plane-wave energy cut-off of 100 Ry for the wavefunction.
DOI: 10.60732/95b38454
title: solute_strengthening_of_prism_edge_locations_in_Mg_alloys

description: This dataset includes Mg and Mg-Zn alloy structures with solute atoms at the prism edge locations. The dataset was created to study the strengthening effect of solute atoms at the prism edge locations in Mg alloys.
DOI: 10.60732/692a415c
title: JARVIS_AGRA_COOH

description: The JARVIS_AGRA_COOH dataset is part of the joint automated repository for various integrated simulations (JARVIS) DFT database. This dataset contains data from the CO2 reduction reaction (CO2RR) dataset from Chen et al., as used in the automated graph representation algorithm (AGRA) training dataset: a collection of DFT training data for training a graph representation method to extract the local chemical environment of metallic surface adsorption sites. JARVIS is a set of tools and datasets built to meet current materials design challenges.
DOI: 10.60732/b6ece7fd
title: 23-Single-Element-DNPs_RSCDD_2023-Mo

description: Configurations of Mo from Andolina & Saidi, 2023. One of 23 minimalist, curated sets of DFT-calculated properties for individual elements for the purpose of providing input to machine learning of deep neural network potentials (DNPs). Each element set contains on average ~4000 structures with 27 atoms per structure. Configuration metadata includes Materials Project ID where available, as well as temperatures at which MD trajectories were calculated.These temperatures correspond to the melting temperature (MT) and 0.25*MT for elements with MT &lt; 2000K, and MT, 0.6*MT and 0.25*MT for elements with MT &gt; 2000K.
DOI: 10.60732/eeb61a0d
title: aC_JCP_2023

description: 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
DOI: 10.60732/d1e27447
title: ANI-Al_NC2021-test

description: Approximately 2800 configurations from a test dataset–one of a pair of train/test datasets of aluminum in crystal and melt phases, used for training and testing an ANI neural network model.
DOI: 10.15468/dl.jmt39y
title: Occurrence Download

description: A dataset containing 83 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Macrosolen geminatus (Merr.) Danser"
 ]
}

 The dataset includes 83 records from 19 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050770-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60732/4b13be86
title: Mg_edmonds_2022

description: 16748 configurations of magnesium with gathered energy, stress and forces at the DFT level of theory.
DOI: 10.60732/8d563e8a
title: DFT_polymorphs_PNAS_2022_PBE0_MBD_benzene_train

description: Benzene training PBE0-MBD dataset from "Semi-local and hybrid functional DFT data for thermalised snapshots of polymorphs of benzene, succinic acid, and glycine". DFT reference energies and forces were calculated using Quantum Espresso v6.3. The calculations were performed with the semi-local PBE xc functional, Tkatchenko-Scheffler dispersion correction, optimised norm-conserving Vanderbilt pseudopotentials, a Monkhorst-Pack k-point grid with a maximum spacing of 0.06 x 2π A^-1, and a plane-wave energy cut-off of 100 Ry for the wavefunction.
DOI: 10.60732/f95867ef
title: COLL_train

description: Training set from COLL. Consists of configurations taken from molecular collisions of different small organic molecules. Energies and forces for 140,000 random snapshots taken from these trajectories were recomputed with density functional theory (DFT). These calculations were performed with the revPBE functional and def2-TZVP basis, including D3 dispersion corrections
DOI: 10.60732/dc6b8a39
title: reduced-perovskite_and_oxidized-marokite_oxides

description: Dataset contains DFT calculations of oxygen-deficient perovskites from the Ca2Fe2O5-brownmillerite and Ca2Mn2O5 structures; and tunnel CaMn4O8, a derivative of the CaMn2O4-marokite with Ca vacancies. The dataset was produced to investigate the effects of oxygen introduction or Ca vacancy introduction in ternary transition metal oxides, as a means to assess potential new Ca-ion battery materials.
DOI: 10.60732/cd8c58b7
title: Paramagnetic_lanthanide_compounds

description: This dataset is composed of fully-deuterated Gd(III) analogue d-[GdL] in a variety of solvent materials, including MeOH, D2O and d6-DMSO.
DOI: 10.60732/bddeac8f
title: HME21_test

description: The test set from HME21. The high-temperature multi-element 2021 (HME21) dataset comprises approximately 25,000 configurations, including 37 elements, used in the training of a universal NNP called PreFerential Potential (PFP). The dataset specifically contains disordered and unstable structures, and structures that include irregular substitutions, as well as varied temperature and density.
DOI: 10.60732/0a15fe72
title: glass-ceramic_lithium_thiophosphate_electrolytes_

description: This database contains computationally generated atomic structures of glass-ceramics lithium thiophosphates (gc-LPS) with the general composition (Li2S)x(P2S5)1-x. Total energies and interatomic forces from density-functional theory (DFT) calculations are included. The DFT calculations used projector-augmented-wave (PAW) pseudopotentials and the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional as implemented in the Vienna Ab Initio Simulation Package (VASP) and a kinetic energy cutoff of 520 eV. The first Brillouin zone was sampled using VASP's fully automatic k-point scheme with a length parameter Rk = 25Å. The gc-LPS structures were generated using a combination of different sampling methods. Initial amorphous structure models were generated with ab initio molecular dynamics (AIMD) simulations of supercells at 1200 K using a Nose-Hoover thermostat with a time step of 1 fs. To obtain near-ground-state structures as reference for the machine-learning potential, 150 evenly spaced snapshots were extracted from the AIMD trajectories that were reoptimized with DFT geometry optimizations at zero Kelvin. Additional structures were generated by scaling the lattice parameters of the crystalline LPS structures (see below) by ±15% and perturbing atomic positions in AIMD simulations as described above.The resulting database was used to train a specialized ANN potential for the sampling of structures along the Li2S-P2S5 composition line with a genetic-algorithm (GA) as implemented in the atomistic evolution (ævo) package, following a previously reported protocol. Starting from supercells of the ideal crystal structures, either Li and S atoms were removed with a ratio of 2:1, or P and S atoms were removed with a ratio of 2:5, and low-energy configurations were determined with GA sampling. A population size of 32 trials and a mutation rate of 10% were employed. The ANN potential was iteratively refined by including additional sampled structures in the training. For each composition, at least 10 lowest energy structure models identified with the ANN-GA approach were selected and fully relaxed with DFT.Also included in the present database are the XSF files of the previously reported crystalline phases LiPS3, Li2PS3, Li4P2S7, Li7P3S11, α-Li3PS4, β-Li3PS4, γ-Li3PS4, and Li48P16S61. The crystal structures were obtained from the Inorganic Crystal Structure Database (ICSD). the Materials Project (MP) database, the Open Quantum Materials Database (OQMD), and the AFLOW database. The configuration names indicate the journal reference and the database.
DOI: 10.60732/c4731f07
title: solvated_protein_fragments_JCTC_2019

description: The solvated protein fragments dataset was generated as a partner benchmark dataset, along with SN2, for measuring the performance of machine learning models, in particular PhysNet, at describing chemical reactions, long-range interactions, and condensed phase systems. The dataset contains structures for all possible "amons" (hydrogen-saturated covalently bonded fragments) of up to eight heavy atoms (C, N, O, S) that can be derived from chemical graphs of proteins containing the 20 natural amino acids connected via peptide bonds or disulfide bridges. For amino acids that can occur in different charge states due to (de)protonation (i.e., carboxylic acids that can be negatively charged or amines that can be positively charged), all possible structures with up to a total charge of +-2e are included. In total, the dataset provides reference energies, forces, and dipole moments for 2,731,180 structures calculated at the revPBE-D3(BJ)/def2-TZVP level of theory using ORCA 4.0.1.