SOURCES_AND_PROCESSING.md

Neo Dataset Sources and Processing Declaration

Scope of this declaration

Neo is a derived, mixed-granularity atomistic training corpus. It aggregates published periodic materials, molecular response, finite-field water, Born effective charge, and magnetic spin data into one mask-aware HDF5 schema. Neo does not claim authorship of upstream first-principles calculations.

The conversion pipeline does not infer or fabricate missing physical labels. It copies documented upstream quantities, performs the unit conversions listed below, assigns provenance and group identifiers, and explicitly masks labels that are absent or physically incompatible with a shared loss.

The machine-readable companion to this statement is provenance/source_registry.json. File integrity records are in checksums.sha256, manifest.json, and the validation reports under reports/.

Upstream source register

Neo source IDs	Upstream record	Upstream terms	Redistribution status
OMat24/*	OMat24 (Open Materials 2024), official FAIR Chemistry data page; manuscript DOI 10.48550/arXiv.2410.12771; ColabFit subdataset records	CC BY 4.0	Cleared with attribution and modification notice
MPtrj-v2022.9-large, MPtrj-v2022.9-magnetic, MPtrj-static-recovered	MPtrj, DOI 10.6084/m9.figshare.23713842.v2	MIT	Cleared with attribution
JARVIS-DFT-3D-v2025.09, JARVIS-DFT-DFPT-v2025.09	JARVIS-DFT 3D, DOI 10.6084/m9.figshare.6815699.v11	CC BY 4.0	Cleared with attribution
QM7-X	QM7-X, DOI 10.5281/zenodo.4288677; article DOI 10.1038/s41597-021-00812-2	CC BY 4.0	Cleared with attribution
DES15K, TorsionNet500, SPICE_dipeptides	SO3LR data release, DOI 10.5281/zenodo.14779793	CC BY 4.0	Cleared with attribution
SCFNN/zero-field, SCFNN/finite-field	SCFNN training data, DOI 10.5281/zenodo.5521328	CC BY 4.0	Cleared with attribution
DeepSPIN-NiO	yangtengleo/DeepSPIN commit 526ade353906f21cf4d8cb32db3d53ce83e1ed53	GPL-3.0	Redistributable subject to GPL-3.0 notices and source access
BEC/H2O, BEC/MAPbI3, BEC/dimer	MLFF_and_BEC archive associated with Schmiedmayer and Kresse, article DOI 10.1063/5.0217243	Article: CC BY 4.0; archive: no standalone license found	Archive-level rights review remains open

The article license for the last row is evidence about the publication, not by itself a conclusive license for a separately supplied data archive. The three BEC/* source IDs are therefore not treated as cleared. Every current portable tier includes some of these rows.

OMat24 chain of custody

The OMat24 portions of SE, Plus, and Max originate from the eleven OMat24 training subdatasets mirrored by ColabFit and documented by FAIR Chemistry. Their source cards identify Luis Barroso-Luque, Muhammed Shuaibi, Xiang Fu, Brandon M. Wood, Misko Dzamba, Meng Gao, Ammar Rizvi, C. Lawrence Zitnick, and Zachary W. Ulissi as dataset authors, link the OMat24 manuscript at https://doi.org/10.48550/arXiv.2410.12771, and declare CC BY 4.0. Neo removes duplicate configuration_id records, assigns deterministic leakage-safe splits, selects rows for each Composite tier, and repackages retained Arrow records inside HDF5. It does not alter the retained float64 geometry, energy, force, or stress values. selection/source_row_index, source paths, and checksums retain the audit trail. These are modified and repackaged derivatives, not official Meta, FAIR Chemistry, or ColabFit releases.

Meta Platforms, Inc., FAIR Chemistry, ColabFit, and the named OMat24 authors have not endorsed Neo. Their names and marks are used only for provenance and attribution. Users must comply with CC BY 4.0, cite the authoritative OMat24 record, preserve attribution and the license link, and identify Neo's selection, deduplication, split assignment, and repackaging changes.

Chain of custody and integrity

The following identifiers anchor the data used by the conversion. Local paths are deliberately omitted from public metadata.

Artifact	Bytes	Integrity identifier
Official MPtrj JSON	12,188,168,685	MD5 50ead5f27f9a4f6beb7564c4188f1e9f; SHA-256 05a675acd4f17a1dadd8a4ea6ea79fe58d3ffb28ca20277383b8f990d4787cf6
Official JARVIS 3D ZIP	48,447,610	MD5 c3179161ef0d029cf1fa70da463aac6e; SHA-256 f9e0a3309f0000d5de1ec9e49c93963109ea45e63f451103f8f6595d2eabf7f5
Official QM7-X 8000.xz	89,426,884	MD5 c893ae88b8f5c32541c3f024fc1daa45; SHA-256 9868f7781bf7f0a53c24d982b5dc31aa11d059d220d1894d1beaba9671526d73
Decompressed QM7-X HDF5	826,408,960	SHA-256 04c4ed110eae21f719bc361e4a550d9b628232063df844e75d559a69e070679a
SO3LR DES15K HDF5	106,850,728	SHA-256 a0cc8b509ae3d10d3612b47ae973a4a28b6b661424b36c816b0371ac15c9f794
SO3LR TorsionNet500 HDF5	108,233,896	SHA-256 2b4cfead21ee9f3b7fdc92e9d85697098c1aca267ec6170e50d0f29177648016
SO3LR SPICE dipeptides HDF5	399,683,424	SHA-256 f779afd3fb466c011cd21a22bb7f21c1c861ffd6caee9db57439feaf65577e35
Official SCFNN train_test_data.tar.gz	178,468,151	MD5 5361bc9ceb59fdd42250ee2ff1f06a8d
DeepSPIN source	Git commit	526ade353906f21cf4d8cb32db3d53ce83e1ed53
MLFF_and_BEC.tar.gz supplied source	81,959,223	SHA-256 957cb5dd80918a0ccc62bbb4a5a2f32ad5b433933df3c370de79e18691b9c98a
Combined static.extxyz.gz	local aggregate	SHA-256 40569a015be62218e34cba63623317819e1ec777a082a3fc3678a1c2ab797484
Combined response.extxyz.gz	local aggregate	SHA-256 06d6245c892558d69d50562e909ba766e798d29449fac3e8dd911196737161db

The combined extXYZ archives are intermediate aggregation artifacts and are not the preferred public provenance record where an official source is available. Their fixed half-open frame ranges are:

Archive range	Contents	Canonical treatment
static[0:200000]	MPtrj structures	IDs and MP2020-corrected energies recovered against the source data; a balanced 40,000-material shard was retained
static[200000:201590]	SCFNN zero-field water	Recovered into neo_l2_scfnn_field.h5
response[0:101993]	Legacy molecular response prefix	Replaced for canonical construction by the official QM7-X and SO3LR HDF5 sources
response[101993:105179]	SCFNN finite-field water	Recovered and geometry-grouped with zero-field variants
response[105179:105729]	H2O, MAPbI3, and dimer BEC records	Recovered into neo_l2_bec.h5; rights review remains open

Source-specific transformations

MPtrj

• Structures, cells, forces, VASP stress, and atom-wise magmom values are read from the official archive.
• Total energy is corrected_total_energy, which applies Materials Project MP2020 compatibility to GGA/GGA+U calculations.
• A site with abs(magmom) >= 0.05 mu_B receives a z-directed unit spin with the sign of magmom; its vector magnetic moment retains the signed magnitude. Smaller values become zero-valued nonmagnetic sites inside a structure whose spin mask is active. Missing structure-level magmom arrays are masked, not replaced by zeros.
• The large core keeps all required legacy sample IDs and at most four frames per material family. All frames sharing an mp_id share one split.
• The standard corpus uses one selected magnetic frame per material and a separately recovered static subset, then removes poorer duplicates by material group.
• Source stress is the VASP compressive-positive tensor in kBar. Neo symmetrizes it and multiplies by -0.0006241509074460763 to store tensile-positive Cauchy stress in eV/angstrom^3. No volume division is applied because the source value is already intensive.
• The complete archive was streamed once to match canonical sample IDs. Stress was recovered for 40,000 static records, 24,000 magnetic records, and 505,736 Large-core records; 72,929 Large-core stress records also carry spin labels. MPtrj does not provide the paired reference spin state required for a differential magnetoelastic target.

QM7-X

• Geometry and the published ePBE0, eMBD, ePBE0+MBD, force, Hirshfeld, dipole, polarizability, and dispersion fields are read directly from the official HDF5 shard.
• energy = ePBE0+MBD, energy_base = ePBE0, and energy_dispersion = eMBD in the source-specific canonical shard.
• forces, forces_base, and forces_dispersion map to totFOR, pbe0FOR, and vdwFOR.
• Atomic dipoles are multiplied by 0.529177210903 to convert e*bohr to e*angstrom.
• Molecular and atomic polarizabilities are multiplied by 0.529177210903^3 to convert bohr^3 to angstrom^3.
• Atomic C6 values are multiplied by 27.211386245988 * 0.529177210903^6 to convert Hartree*bohr^6 to eV*angstrom^6.
• All conformers of a QM7-X molecule share a group and split.
• QM7-X absolute energies are masked from the default shared periodic MPtrj energy loss. Response labels remain active.

SO3LR molecular families

• DES15K, TorsionNet500, and SPICE dipeptide records come from the official SO3LR data release and its PBE0+MBD/tight calculations.
• Atomic dipoles use the same e*bohr to e*angstrom conversion as QM7-X.
• Total charge is the nearest integer to the sum of published Hirshfeld charges. The original atomic charges are retained.
• Parent identities are derived from the documented family naming convention, so related conformers and geometries remain in one split.
• Their absolute energies are retained in independent shards but masked from the default mixed shared-energy loss.

JARVIS-DFT

• The L1 shard converts published OptB88vdW energy per atom to total energy.
• The DFPT shard reads each published per-ion born_charges 3x3 tensor from vasprun.xml without projecting it onto the acoustic sum rule.
• The same raw archives provide a VASP stress tensor and the electronic PIEZOELECTRIC TENSOR for field block. Neo stores stress with the same tensile-positive conversion used for MPtrj and expands VASP columns XX YY ZZ XY YZ ZX into a full tensor with no engineering-shear rescaling.
• Of the selected 120 archives, 112 pass the BEC sanity gate and jointly carry stress, BEC, and electronic clamped-ion piezoelectric labels. They form the explicit L2 electromechanical bridge in every Tiny-Large tier.
• Records are rejected if max(abs(BEC)) > 50 e or the maximum component of the acoustic-sum residual exceeds 0.5 e. Rejections are recorded in the build metadata.
• Structure-total magnetization and dimensionless dielectric constants are not relabeled as atom-wise moments or molecular polarizabilities.

SCFNN

• The official dataset contains periodic 64-water boxes at zero and finite electric field. The Neo conversion retains supplied energy, forces, field, and dipole values in its independent shard and sets the known neutral total charge to zero.
• A SHA-256 hash of atomic numbers, positions, cell, and PBC rounded to 1e-7 groups field variants of the same geometry. Grouped variants cannot cross train, validation, or test boundaries.
• The default mixed corpus keeps field, dipole, and total-charge supervision; its SCFNN absolute energy and force reference is not mixed into MPtrj.

DeepSPIN NiO

• The 48-site raw representation contains 32 real atoms plus 16 pseudo-atoms. The periodic minimum-image displacement from each Ni atom to its pseudo-atom is divided by the documented virtual length (0.4 angstrom) to recover the unit spin direction.
• Magnetic moments use the documented magnitude 1.2737 mu_B.
• Effective spin field is 0.4 * pseudo_atom_force, in eV/spin.
• The author's five 20-frame blocks are preserved: blocks 0-3 are train and block 4 is validation.
• DeltaSpin energy and real-atom forces remain in the independent shard but are masked from the default mixed energy/force loss.

Schmiedmayer-Kresse BEC archive

• The supplied archive contains 100 liquid-water, 300 MAPbI3, and 150 water dimer DFPT structures. This matches the systems and calculations described in DOI 10.1063/5.0217243; the tar owner is bernhard, and the included VASP settings match the article methodology.
• Neo extracts atomic numbers, positions, cell, forces, energy, and the published per-atom 3x3 Born effective charge tensors. The mixed corpus keeps only BEC, zero field, and known neutral total charge for these records.
• The raw OUTCAR files include VASP/POTCAR notices and must never be uploaded.
• Identification, scientific attribution, and current public hosting do not resolve the absent archive license. Written confirmation or removal of these records is still needed for a fully cleared redistribution record.

Aggregation, masking, and energy domains

config/neo_mixed_source_policy.json and config/neo_large_source_policy.json define source order, retained labels, deduplication keys, and per-group limits. The conversion writes every supported label dataset densely, but masks/<label>[i] is the sole authority for whether structure i owns that target.

The default shared energy/force domain is MPtrj with MP2020-compatible energy. QM7-X, SO3LR, SCFNN, JARVIS OptB88vdW, local BEC, and DeepSPIN energies have different electronic-structure references. They are either kept in independent source shards or masked in mixed tiers. No offset fitting is used to pretend that these absolute references are interchangeable.

J_effective, Di, Di_effective, and DMI_effective are absent from the released tiers. Their masks are all false. Zero-valued placeholders outside a mask are not physical labels.

Group-safe splits

Most groups use a stable SHA-256 bucket: 80 percent train, 10 percent validation, and 10 percent test. The grouping unit is the physical parent, not the individual row: MPtrj material, QM7-X molecule, SO3LR parent, SCFNN geometry, or DeepSPIN author block. Consequently, related trajectories, conformers, and field variants cannot leak across splits.

The portable-tier builder also guarantees that every element appearing in an evaluation split appears in train. This is a coverage rule, not evidence of predictive accuracy.

Portable tier sampling

Tiny and small are deterministic nested subsets of standard:

tiny subset small subset standard

Sampling seed 20260720 uses source weights proportional to sqrt(N), then stratifies over source, fixed split, active-label family, chemical complexity, atom-count class, and element. Tiny uses a non-rare maximum of two structures per group; small uses four. Sources containing at most 128 structures are preserved in full. Missing labels and their masks are copied unchanged.

The exact configuration and audit are in config/neo_dataset_tiers.json and reports/neo_tier_hierarchy_audit.json.

Validation performed

• Canonical schema and pointer consistency.
• Finite geometry and finite values under every active label mask.
• Unique sample IDs and no group crossing split boundaries.
• No response family crossing split boundaries.
• Charge-sum residual, active-spin unit norm, and BEC acoustic-sum diagnostics.
• Fully 3D periodic nonsingular cells for stress, finite symmetric stress, and explicit source method/sign/unit metadata.
• Symmetry of the two strain axes in piezoelectric and magnetoelastic tensors.
• Mechanism-stratified counts for total stress, stress+BEC+piezoelectric, stress+spins, and paired magnetoelastic response.
• Exact nesting of tiny in small and small in standard.
• Source and active-label coverage in every portable tier.
• Train coverage of all elements appearing in validation or test.
• Full-physics forward/backward smoke tests on CPU and Apple MPS.

The current paired magnetoelastic count is zero. This is a scientific negative result, not missing bookkeeping: total magnetic stress cannot be converted into stress(S) - stress(S_ref) without a same-geometry, same-method reference calculation. The released presets therefore keep w_magnetoelastic = 0.

These checks establish structural validity, provenance traceability, numerical sanity, and leakage controls. They do not establish production accuracy. That requires a converged model and held-out, domain-specific evaluation.

OMat24 Plus curriculum

Plus combines a deterministic material-family quarter of all 11 locally verified OMat24 corpora with the complete Neo Large corpus. A material is selected when the first byte of SHA-256("neo-plus-v1|" + material_id) is below 64. Exact duplicate configuration_id values are removed before the final selector is written; all configurations from one material share a split determined by the neo-split-v1 namespace.

The portable SE HDF5 embeds every Standard geometry, label, mask, and provenance field and selects an exact stratified 1/180 of the Max OMat24 selector. Plus and Max embed every Large geometry, label, mask, and provenance field. All three convert selected rows from the 635 OMat24 source shards into ragged packed HDF5 arrays, retaining source names, original row indices, byte checksums, and float64 numerical values without quantization. Unselected rows are not embedded. The runtime reads contiguous packed batch spans, so each portable artifact has no dependency on the original OMat24 directory. A final portable SE, Plus, or Max artifact must declare both sources/neo_large.embedded = true and sources/omat24.embedded = true; a file containing only paths to either source is an intermediate manifest and must not be published as a portable tier.

The training curriculum keeps incompatible absolute-energy references apart. Base fits OMat24 PBE+U atomic references from OMat24 only. Response uses Large records carrying L2/L3 response or spin labels. Mixed Joint balances the embedded Large response corpus against rotating OMat24 foundation windows; Large absolute energy is masked in that stage while compatible force and response labels remain active.

OMat24 Max curriculum

Max scans every configuration row in the same 11 verified OMat24 corpora. Rows are deduplicated globally by exact upstream configuration_id, while material-family IDs continue to define leakage-safe train, validation, and test assignments. The current build scanned 100,824,534 source rows, removed 154,252 repeated IDs, and retained 100,670,282 unique OMat24 configurations. It then adds the complete 613,267-structure Large corpus, for 101,283,549 training records in total. Max uses the same Base, Response, and Joint energy reference policy as Plus.

Reproducibility boundary

All executable conversion, sampling, validation, and release-staging logic is in Datasets_Preparation.py. Runtime HDF5/Parquet readers remain in E3_miu_GNN.py. The public Hugging Face staging package omits raw archives, selection-candidate dumps, local paths, checkpoints, and VASP outputs. The original raw archives must be obtained from their authoritative sources under their respective terms.