docs: remove redundant page-title H1s
Remove the leading H1 (and the blank line after it) from the 16 pages
where it only repeats the GitHub Wiki filename-derived page title,
including decorative emoji. Pages whose H1 adds information (Home,
VASP, band structure, high-throughput, USPEX, XtalOpt, SQS, Reading &
Editing, PyMatGen, Tutorial-Y/YY, Hebrew pages) are unchanged.
No other content, code blocks, links or anchors changed.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01DHgs1a4r3pZ6JVJ5dXQvoR
docs: document BMD Compute automatic DFT+U v1 in Advanced Options
- Advanced Options: rewrite the DFT+U section to describe the adopted
BMD Compute automatic DFT+U behaviour (bmd_compute c241a64): the
Materials Project/pymatgen oxide/fluoride rule and U values (Dudarev,
J = 0), the conservative BMD d0 screen with fallback to the MP rule
when no oxidation-state guess exists, representative examples, NiO
worked example, stage placement per Desired Output (PBE stages only,
never HSE06), independence from spin/SOC/dispersion, Custom workflow
control, and why BMD energies are not strictly MP-compatible. Cite
Anisimov 1991, Dudarev 1998, Wang 2006, Jain 2011 and MP docs.
- Intro, INCARs, VASP and Workflows: stop describing DFT+U as purely
optional; point to the automatic behaviour.
SOC section, reference INCARs and POTCAR path unchanged.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01DHgs1a4r3pZ6JVJ5dXQvoR
docs: apply review corrections (Pulay formula, NCORE/NPAR, provenance)
- Workflows: remove the explicit Pulay-stress formula; keep the
qualitative finite-basis and repeated-relaxation explanation.
- VASP: explain that NCORE and NPAR parameterize the band parallel
decomposition differently; prefer NCORE and do not set both.
- INCARs: provenance states generation from BMD Compute on
26 September 2026; exact Compute/dependency versions not retained.
Reference INCARs, Band NCORE omission and POTCAR path unchanged.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01DHgs1a4r3pZ6JVJ5dXQvoR
docs: record Si as the reference structure for BMD Compute INCARs
Compute commit and pymatgen/atomate2 versions remain unspecified.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01DHgs1a4r3pZ6JVJ5dXQvoR
docs: use complete BMD Compute workflow INCARs as references
- INCARs: replace the isolated references with the complete, correctly
numbered stage INCARs of the four standard workflows (Static Energy;
Relaxed Structure; Density of States; Band Structure), reproduced
exactly. Add HSE06 Static Energy. Comparisons now: PBE GO vs PBE
Static; PBE vs HSE06 Static; HSE06 Static vs DOS vs Band (TIME
operative only with ALGO = Damped). Reference structure marked
"to be confirmed".
- Workflows: rename Geometry Optimisation to Relaxed Structure (two
identical PBE stages, Stage 2 from Stage 1 structure); separate
"BMD workflow facts" from general physics; Pulay stress presented as
one reason for repeated relaxation, not BMD's stated rationale;
remove "HSE06@PBE"; file hand-offs and KPOINTS left unspecified.
- Advanced Options: drop Si-specific wording for the base references.
Supplied INCAR settings, SOC status and POTCAR path unchanged.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01DHgs1a4r3pZ6JVJ5dXQvoR
docs: organise BMD Compute Workflows around the four desired outputs
- Workflows: rebuild around the supplied workflows (Static Energy;
Geometry Optimisation x2; PBE relax -> HSE06 static -> HSE06 DOS;
PBE relax -> HSE06 static -> HSE06 band structure). For each: the
scientific result, why prerequisite stages are needed, and the
conceptual hand-off. Substantive Pulay-stress / repeated variable-
cell relaxation discussion without claiming it as the sole rationale;
HSE06@PBE caveat; DOS (BZ integral, uniform mesh) vs E_n(k) (path,
zero-weight approach). File-level hand-offs marked unspecified.
- INCARs: comparisons renamed "vs" (not sequences); remove the stale
list of other stages; point sequence questions to Workflows.
Reference INCAR blocks, SOC status and POTCAR path unchanged.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01DHgs1a4r3pZ6JVJ5dXQvoR
docs: add BMD Compute Workflows page and four-page structure
- VASP: expand into DFT fundamentals (Kohn-Sham SCF, exchange-
correlation and hybrids, plane-wave truncation and PAW, Brillouin-
zone sampling, occupations/smearing, forces and relaxation); FCC-Si
teaching example unchanged.
- BMD-Compute-Workflows (new): why calculations are staged, what can
pass between stages, relax->static rationale incl. Pulay stress,
repeated relaxation, PBE non-SCF vs HSE06 zero-weight approach;
BMD Compute-specific sequences and hand-offs marked "to be provided".
- BMD-Compute-INCARs: keep stage-level explanations only; move Pulay
and sequence reasoning to Workflows. Reference INCAR blocks unchanged.
- Advanced Options, Home: navigation for the four-page sequence.
POTCAR path and SOC status unchanged.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01DHgs1a4r3pZ6JVJ5dXQvoR
docs: tighten BMD Compute INCARs commentary
- Fix "four kinds" -> "five kinds" of settings.
- Soften Pulay-stress text; drop unsourced Si ENMAX value.
- Reword PBE/HSE06 band-gap claim.
- State that TIME is retained but not operative with ALGO = Normal.
- Explain LORBIT/NEDOS in the static stage without conflating it with
the dedicated DOS stage.
- Add provenance placeholders (Compute commit, pymatgen, atomate2).
Reference INCAR blocks unchanged.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01DHgs1a4r3pZ6JVJ5dXQvoR
docs: add BMD Compute INCAR teaching pages and fix Agent CLI
- VASP: rework into a fundamentals page (inputs, SCF/ionic loops,
ENCUT, k-points, smearing, EDIFF/EDIFFG, relaxation, restarts,
parallelisation); FCC-Si example kept and labelled as teaching.
- BMD-Compute-INCARs (new): the four supplied BMD Compute Si reference
INCARs reproduced exactly, with settings grouped by role and
Relax->Static, PBE->HSE06 and HSE06 DOS->Band comparisons.
- BMD-Compute-Advanced-Options (new): concept pages for spin, DFT+U,
dispersion, Gamma-only and ions-only; reference deltas pending;
SOC marked under validation.
- BMD-Agent: correct bmd-agent / JOB_ID / PATH semantics, document
--verbose, keep expert subcommands secondary; adopt agreed authority
wording.
- Manual HSE band-structure and USPEX pages: keep as teaching/manual
workflows and link to the reference page; Home links new pages.
POTCAR path unchanged pending verification.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01DHgs1a4r3pZ6JVJ5dXQvoR