| # C2DB 2D-property data file |
|
|
| ## Usage |
|
|
| ```bash |
| bash download.sh # runs the scraper; writes data.csv and schema.json |
| ``` |
|
|
| The scrape walks the live C2DB browse UI at <https://c2db.fysik.dtu.dk/> |
| (the 2DHub redirect target) page by page. The run takes ~8–12 minutes end |
| to end; progress prints to stdout. Re-running the script is idempotent |
| (it overwrites ``data.csv``). |
|
|
| ``data.csv`` is gitignored per the repo-wide rule |
| (``benchmarks/**/data/data.*`` in ``.gitignore``) — you always rebuild it |
| locally from this script. Only this ``README.md`` and the optional |
| ``schema.json`` are kept in git. |
|
|
| ## Source and license |
|
|
| - Upstream landing: <https://2dhub.org/c2db/c2db.html> |
| - Browse UI (what we scrape): <https://c2db.fysik.dtu.dk/> |
| - DTU Figshare record: <https://doi.org/10.11583/DTU.14616660.v1> |
| - License: CC-BY-4.0 (declared on the Figshare record). |
| - Primary citation: Haastrup et al., *2D Mater.* **5**, 042002 (2018), |
| <https://doi.org/10.1088/2053-1583/aacfc1>; update Gjerding et al., |
| *2D Mater.* **8**, 044002 (2021), |
| <https://doi.org/10.1088/2053-1583/ac1059>. |
|
|
| When redistributing or publishing work that uses this ``data.csv``, cite |
| the Haastrup and Gjerding papers (both are vendored offline in |
| ``../reference/``). |
|
|
| ## Filter applied |
|
|
| The C2DB browse UI ships a server-side default filter |
| ``ehull in [0.0, 0.2] eV/atom`` and rejects wider ranges with HTTP 500 |
| (tried: ``to_ehull`` = 0.5, 1.0, 2.0, 5.0, 10.0 — all 500). The scraper |
| therefore collects the 9706 visible rows out of the 17001 total C2DB |
| entries. This is the same "energetically accessible" subset the official |
| web UI shows to anyone clicking "Browse data"; the remaining ~7000 |
| entries are above 0.2 eV/atom above the convex hull and likely not |
| synthesizable. |
|
|
| If you need the full 17k entries, you have to contact the C2DB authors |
| ("The full dataset is provided upon request", per 2dhub.org). This entry |
| deliberately does not try to back-door that process. |
|
|
| ## Column order in ``data.csv`` |
|
|
| Column 0 is the primary output (``hform``, heat of formation eV/atom). |
| Columns 1..N are inputs, in this order: |
|
|
| 1. ``hform`` — **output** — Heat of formation [eV/atom] (PBE) |
| 2. ``uid`` — C2DB unique material identifier (string) |
| 3. ``formula`` — chemical formula (string) |
| 4. ``layergroup`` — 2D layer group symbol (string) |
| 5. ``is_magnetic`` — Magnetic Yes/No |
| 6. ``dyn_stab`` — Dynamically stable Yes/No/Unknown |
|
|
| Then every other scalar column the C2DB web UI exposes, in alphabetical |
| order. Depending on the live schema at build time, this includes: |
|
|
| | key | description | unit | |
| |------------------------|--------------------------------------------------|----------------| |
| | ``A`` | Single-ion anisotropy (out-of-plane) | meV | |
| | ``E_B`` | Exciton binding energy (BSE) | eV | |
| | ``J`` | Nearest-neighbour exchange coupling | meV | |
| | ``N_nn`` | Number of nearest neighbours | (int) | |
| | ``Px`` / ``Py`` / ``Pz`` | Spontaneous polarization components | pC/m | |
| | ``P_spontaneous_norm`` | Spontaneous polarization norm | pC/m | |
| | ``alphax`` / ``alphay`` / ``alphaz`` | Static polarizability (ph + el) | Ã… | |
| | ``alphax_el`` / ``alphay_el`` / ``alphaz_el`` | Interband polarizability | Ã… | |
| | ``alphax_lat`` / ``alphay_lat`` / ``alphaz_lat`` | Phonon polarizability | Ã… | |
| | ``area`` | 2D unit-cell area | Ų | |
| | ``bravais_type`` | 2D Bravais type (e.g. Hexagonal (hp)) | (text) | |
| | ``cbm`` / ``cbm_evac`` / ``cbm_u`` / ``cbm_hse`` / ``cbm_gw`` | CBM vs vacuum (PBE/PBE+U/HSE/GW) | eV | |
| | ``cod_id`` | Parent bulk structure in COD | (int) | |
| | ``dE_zx`` / ``dE_zy`` | Magnetic anisotropy energy | meV/unit cell | |
| | ``dipz`` | Out-of-plane dipole moment | e·Å/unit cell | |
| | ``efermi`` / ``efermi_u`` / ``efermi_hse`` / ``efermi_gw`` | Fermi level vs vacuum | eV | |
| | ``ehull`` | Energy above convex hull | eV/atom | |
| | ``emass_cbm`` / ``emass_vbm`` | DOS effective masses (PBE) | m_e | |
| | ``energy`` | PBE total energy | eV | |
| | ``evac`` / ``evacdiff`` | Vacuum level and vacuum-level shift | eV | |
| | ``gap`` / ``gap_u`` / ``gap_hse`` / ``gap_gw`` | Indirect band gaps | eV | |
| | ``gap_dir`` / ``gap_dir_u`` / ``gap_dir_hse`` / ``gap_dir_gw`` | Direct gaps | eV | |
| | ``halfmetal_gap`` / ``halfmetal_gap_hse`` / ``halfmetal_gap_dir`` / ``halfmetal_gap_dir_hse`` | Minority-spin gaps | eV | |
| | ``has_inversion_symmetry`` | Inversion symmetry flag | (bool) | |
| | ``icsd_id`` | Parent bulk structure in ICSD | (int) | |
| | ``is_ferroelectric`` | Ferroelectric flag | (bool) | |
| | ``is_magnetic_u`` | Magnetic flag (PBE+U) | (bool) | |
| | ``label`` | Origin label (e.g. Original18, ICSD-derived) | (text) | |
| | ``lam`` | Anisotropic exchange (out-of-plane) | meV | |
| | ``lgnum`` | Layer group number | (int) | |
| | ``magmom`` | Total magnetic moment | μ_B | |
| | ``natoms`` | Number of atoms per unit cell | (int) | |
| | ``nspecies`` | Number of distinct chemical species | (int) | |
| | ``number`` | Bulk space group number (AA-stacked) | (int) | |
| | ``plasmafrequency_x`` / ``plasmafrequency_y`` | Drude plasma frequency | eV·Å^0.5 | |
| | ``spin`` | Max S_z at magnetic sites | (dim-less) | |
| | ``thickness`` | 2D layer thickness (out-of-plane extent) | Ã… | |
| | ``vbm`` / ``vbm_evac`` / ``vbm_u`` / ``vbm_hse`` / ``vbm_gw`` | VBM vs vacuum (PBE/PBE+U/HSE/GW) | eV | |
| | ``workfunction`` | Work function (averaged for polar slabs) | eV | |
|
|
| Text-only / internal columns are intentionally skipped by the download |
| script: ``doi`` (free-text citation), ``publication`` (free-text), |
| ``folder`` (internal DTU path), ``olduid`` (legacy id), ``stoichiometry`` |
| (redundant text), ``reduced`` (redundant text), ``international`` / |
| ``pointgroup`` (text symbols). The exact runtime column set is saved to |
| ``schema.json`` by ``download.sh`` for auditing. |
|
|
| ## Missing values |
|
|
| A cell is empty ("") whenever that property is undefined for a given |
| material or simply wasn't computed in the run the web UI serves: |
|
|
| - ``gap_gw`` / ``gap_dir_gw`` / ``vbm_gw`` / ``cbm_gw`` / ``efermi_gw`` |
| / ``E_B`` — computed only for the ~300-material GW/BSE subset. |
| - ``workfunction`` / ``efermi`` — often blank for metals, where |
| vacuum-alignment is ambiguous in the presence of dipoles. |
| - ``emass_cbm`` / ``emass_vbm`` — undefined for metals / half-metals. |
| - ``J`` / ``lam`` / ``A`` / ``dE_zx`` / ``dE_zy`` / ``magmom`` — blank for |
| non-magnetic materials. |
| - ``Px`` / ``Py`` / ``Pz`` / ``P_spontaneous_norm`` — blank for |
| non-ferroelectric materials. |
| - ``cod_id`` / ``icsd_id`` — blank for materials derived from generative |
| models rather than from ICSD/COD parents. |
| - Many properties (especially optical / phonon) may be blank for newer, |
| partially-computed entries (the 2022-09 generative-model additions |
| and the 2024-05 restructuring). |
|
|
| Pandas users: ``pd.read_csv('data.csv', na_values=[''], keep_default_na=True)`` |
| is the recommended reader. |
|
|
| ## Known build-time quirks |
|
|
| - The ``sid`` session id in the scraper URL is server-side state; it gets |
| reallocated on every ``GET /`` hit. The script creates exactly one sid |
| and sticks with it. |
| - Toggle requests are sent with the ``HX-Request: true`` header to match |
| the htmx client the UI was built around. Server-side toggling is purely |
| per-session, so concurrent scrapers would interfere with each other on |
| shared sids — do not parallelize this script. |
| - A 0.35 s sleep between page GETs keeps the rate well below what the |
| CAMD web server serves to an interactive user; this is intentional. |
|
|
