Molecular and basis-set data sources
The repository-root DATA_SOURCES.md is the authoritative record. Its contents
are included below so the source notes are available in the published manual
as well.
Molecular and basis-set data sources
This file records the provenance of molecular geometries and basis-set data currently checked into RustiQ. Coordinates in the XYZ files are in ångströms. For geometries without an external citation, no external provenance is recorded in the repository; do not cite them as experimental or independently optimized reference data.
Molecular geometries
| Molecule | Repository files | Provenance and reuse notes |
|---|---|---|
| Hydrogen, H₂ | samples/h2/molecule.xyz; crates/rustiq-core/tests/data/samples/h2/molecule.xyz | Project sample/test geometry, with atoms 0.74 Å apart. No external geometry source is recorded. The core fixture duplicates the sample. |
| Water, H₂O | samples/h2o/h2o.xyz; crates/rustiq-core/tests/data/samples/h2o/h2o.xyz | Project sample/test geometry. No external geometry source is recorded. The core fixture duplicates the sample. |
| Hydroxyl radical, OH | samples/oh/oh.xyz; crates/rustiq-core/tests/data/samples/oh/oh.xyz | Project sample/test geometry, with an O–H distance of 0.970 Å. No external geometry source is recorded. The core fixture duplicates the sample. |
| Lithium hydride, LiH | samples/lih/lih.xyz | Project-authored, fixed test geometry: Li at the origin and H at z = 1.60 Å. Chosen as a rounded equilibrium-like distance, consistent with the 1.5957 Å spectroscopic distance discussed in Gottlieb and Weishäupl, Comput. Theor. Chem. 1007, 82–89 (2013), author manuscript. It is not an experimental coordinate file or an optimization result. Neutral singlet; reused by the 6-31G RHF reference. |
| Carbon monoxide, CO | samples/co/co.xyz | Project-authored, fixed test geometry: C at the origin and O at z = 1.13 Å. A deliberately rounded equilibrium-like test distance; not an experimental coordinate file or an optimization result. Neutral singlet; the STO-3G RHF and RHF-MP2 references use this identical file. |
| Ethanol | samples/ethanol/ethanol.xyz | The file describes this as an approximate gas-phase geometry. No external source or calculation provenance is recorded; treat it as an illustrative project geometry, not as a sourced equilibrium structure. |
| Benzene | samples/benzene/benzene.xyz | 3D conformer identified by the file as PubChem CID 241 and retrieved through PubChem PUG REST. PubChem record; PUG REST documentation. PubChem’s policy states that PubChem-generated information and participant-provided information are made available without cost and restriction, while warning that some contributed information may be copyrighted. The record labels this as a PubChem 3D conformer. |
| Cholesterol | samples/cholesterol/cholesterol.xyz | 3D conformer identified by the file as PubChem CID 5997. PubChem record. PubChem’s policy states that PubChem-generated information and participant-provided information are made available without cost and restriction, while warning that some contributed information may be copyrighted. The record labels this as a PubChem 3D conformer. |
| Anthracene | samples/anthracene/anthracene.xyz | PubChem 3D conformer for CID 8418, obtained as an SDF record through the PubChem PUG REST 3D SDF endpoint; PubChem compound record. The XYZ stores the 24 atom coordinates from that conformer in ångströms. PubChem policy says PubChem-generated and participant-provided information is made available without cost and restriction, but warns that some contributed information may be copyrighted; verify provenance-specific notices when present. |
PubChem’s data submission policy also places responsibility on users to respect restrictions that apply to third-party contributed content. The PubChem attribution here describes the geometry provenance recorded by the files; it is not a blanket clearance for every item associated with a PubChem record.
Geometry reuse review for the HF/MP2 extension
Reviewed on 2026-10-21. The new XYZ files are constructed by the project; no third-party coordinate file, database table, spectrum, image, or article text is redistributed. LiH uses a rounded test distance with literature attribution; CO uses a project-selected rounded test distance. Existing water and OH geometries are reused byte-for-byte, with their original unsourced status preserved above. A new reference calculation does not establish external provenance for an old geometry.
The U.S. Copyright Office distinguishes facts from protected expression. This is not a blanket license for database compilations or a determination of rights in every jurisdiction. In particular, the NIST SRD policy reserves compilation copyright under the Standard Reference Data Act, and the NIST Chemistry WebBook is SRD 69. Its government origin must not be treated as automatic public-domain status. The WebBook was consulted to check physical plausibility; its coordinate exports and tables are not imported. The test geometries above intentionally use project-selected rounded distances instead of copied database records. No NIST license is claimed or granted by this repository.
Locally stored basis sets
These are the basis-set datasets present in the repository’s versioned reference store. No other basis-set dataset is listed here. The reference store README identifies them as unmodified files downloaded from the Basis Set Exchange (BSE) using RustiQ. Their embedded revision metadata is reproduced below.
| Basis set | Local source file | Embedded BSE revision metadata | Foundational reference |
|---|---|---|---|
| STO-3G | tests/data/reference/RustiQ/basis_sets/sto-3g.json | Data from Gaussian09, revision date 2018-06-19, version 1 | Hehre, Stewart, and Pople, “Self-consistent molecular-orbital methods. I. Use of Gaussian expansions of Slater-type atomic orbitals,” J. Chem. Phys. 51, 2657 (1969), DOI 10.1063/1.1672392. |
| 6-31G | tests/data/reference/RustiQ/basis_sets/6-31g.json | Data from Gaussian 09/GAMESS, revision date 2018-06-19, version 1 | Hehre, Ditchfield, and Pople, “Self-Consistent Molecular Orbital Methods. XII. Further Extensions of Gaussian-Type Basis Sets for Use in Molecular Orbital Studies of Organic Molecules,” J. Chem. Phys. 56, 2257 (1972), DOI 10.1063/1.1677527. |
| cc-pVDZ | tests/data/reference/RustiQ/basis_sets/cc-pvdz.json | Data from ccRepo/Grant Hill, revision date 2018-10-03, version 1 | Dunning, “Gaussian basis sets for use in correlated molecular calculations. I. The atoms boron through neon and hydrogen,” J. Chem. Phys. 90, 1007 (1989), DOI 10.1063/1.456153. |
The BSE recommends citing its database papers when publishing work that uses the exchange: Pritchard et al., “A New Basis Set Exchange: An Open, Up-to-date Resource for the Molecular Sciences Community” (2019), and, for the earlier database, Schuchardt et al., “Basis Set Exchange: A Community Database for Computational Sciences” (2007). The BSE documentation identifies the software code as BSD-3-Clause; that statement alone does not establish a license for all contributed basis data. The local JSON records do not state a separate data license. Retain their attribution and review the applicable source terms before republishing these datasets beyond the repository.
The HF/MP2 extension reuses the existing 6-31G lithium (elements["3"])
and STO-3G carbon (elements["6"]) records. No BSE data was added,
modified, or downloaded for this extension. The reference environment copies
the existing versioned files into an isolated store. PySCF independently
normalizes their raw coefficients for the new cases. The upstream
BSE software license
was checked on 2026-10-21; its BSD redistribution conditions concern software
and do not resolve separate contributed-data rights. The attribution and
existing data-license limitation above continue to apply.
The repository also contains byte-identical copies of STO-3G at
tests/data/sto-3g.json and crates/rustiq-core/tests/data/sto-3g.json. Their
SHA-256 is db3478afbe34866ed9ee8720e1bf8513d4de16dea22e568e7c1e838fd1231e40.
They are project fixtures, distinct from the BSE snapshot above (SHA-256
6e9edeb7ae5ee1c4155dbc84b8bad9b74f07077f8136c7531f86d7f0d358b638); they
have no separate provenance metadata and are not described as a BSE download.
The project uses NIST’s Computational Chemistry Comparison and Benchmark Database (CCCBDB, SRD 101) as a possible reference resource only when its terms permit. It is not the provenance of any geometry listed above, and no CCCBDB geometry is bundled here. NIST identifies CCCBDB as SRD 101; consult the NIST license and terms before any reuse.