Extend parsing functionality#148
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Add 14 Specs covering band eigenvalues, magnetism, run-status flags, and HOMO/LUMO levels: - `eigenvalues` and `occupations_kpoint` as numpy arrays of shape `(n_kpoints, n_spin, n_bands)`, derived from `band_structure.ks_energies`. - Run-shape scalars from XML: `number_of_electrons`, `number_of_atoms`, `number_of_species`, `lsda`, `alat` (Å), `ibrav`. - Magnetism (μB/cell): `total_magnetization`, `absolute_magnetization`. - Run-status flags: `scf_converged` (from `convergence_info.scf_conv`) and `job_done` (presence of `<closed>`), each defaulting to `False` when the corresponding XML element is missing. - `highest_occupied_level` / `lowest_unoccupied_level` (eV) parsed from the pw.x stdout. `PwStdoutParser.parse` matches both the single-value `highest occupied level (ev): X` line and the paired `highest occupied, lowest unoccupied levels (ev): X Y` line.
The `bands.x` post-processor reorders the raw `pw.x` band eigenvalues into a plottable band-structure path and (optionally) labels each `(k, band)` with its symmetry representation. The qe-tools side had no parser for the `filband` family — users had to hand-roll text parsing and reshape arithmetic to lift an `(n_kpoints, n_bands)` array out of the gnuplot-flavoured output. Add a dedicated `BandsOutput` class plus three parsers: - `BandsDatParser` reads the `&plot nbnd=..., nks=... /` header and reshapes the body into `k_points` `(n_kpoints, 3)` and `eigenvalues` `(n_kpoints, n_bands)` arrays (eV). - `BandsRapParser` decodes the `*.dat.rap` symmetry-rep file when bands.x was run with `lsym=.true.`, exposing per-`(k, band)` representation indices and a `(n_kpoints,)` boolean flag for high-symmetry points. - `BandsStdoutParser` lifts the `high-symmetry point: kx ky kz x coordinate X` lines out of the bands.x stdout, so plot tick labels can be placed at the correct cumulative path-length.
`projwfc.x` writes projected-DOS data into one file per `(atom, wavefunction)` pair following the `<filpdos>.pdos_atm#N(El)_wfc#M(L)[_j#J]` naming scheme, plus a `<filpdos>.pdos_tot` summary. Decoding the filename, parsing the column-variable header, and reshaping the per-magnetic-quantum-number columns into a usable array is fiddly enough that callers were inevitably reinventing it. Add a dedicated `ProjwfcOutput` class plus two file parsers: - `PdosAtmWfcParser` reads a single `pdos_atm#N(El)_wfc#M(L)[_j#J]` file. It handles the spin-unpolarised, spin-polarised LSDA, and spin-orbit cases by counting `ldos`-prefixed columns and reshaping the trailing `pdos`-columns into `(n_energies, [spin,] 2*l + 1)`. - `PdosTotParser` reads `<filpdos>.pdos_tot` into the matching `dos_total` / `pdos_total` arrays. `ProjwfcOutput.from_dir` discovers every PDOS file in a directory via `collect_pdos_files`, sorts the resulting records numerically by `(atom, wfc, j)` so systems with more than nine atoms don't get scrambled by lexical order, and skips the consumed paths when sniffing for the projwfc.x stdout. The output exposes: - `pdos`: a flat list of records keyed by `(atom, element, wfc, l, l_label[, j])` with the parsed `energies`, `ldos`, and per-magnetic-quantum-number `pdos_m` arrays. Filtering by element or `l` is a one-line list comprehension on the caller side. - `pdos_total`: dict with `energies`, `dos_total`, `pdos_total`.
Codecov Report❌ Patch coverage is Additional details and impacted files@@ Coverage Diff @@
## main #148 +/- ##
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- Coverage 89.77% 88.08% -1.70%
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Files 11 23 +12
Lines 489 1032 +543
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+ Hits 439 909 +470
- Misses 50 123 +73 ☔ View full report in Codecov by Sentry. 🚀 New features to boost your workflow:
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