docs: reorganise Home around a BMD-first learning pathway
- Home: replace the historical Tutorial 1-20 list with sections:
Start here (Using BMD Compute, Workflows, INCARs, Advanced Options;
BMD Agent and VASP fundamentals as optional background); Next steps
(Tutorials 1-11 kept numbered with English/Hebrew links, grouped as
Linux / Remote computing and POWER / Python and pymatgen, plus
running and extending calculations yourself); Research methods and
specialist tools by topic (SQS; USPEX incl. Hebrew page, XtalOpt;
high-throughput, Materials Project); Research practice. States that
sections are suggestions, not prerequisites.
- Former Tutorials 12-20: replace obsolete "Tutorial N" navigation
lines with page-name or return-to-Home links (including the stale
USPEX "Tutorial 8" and High-throughput "tutorial 9/14" references).
No page renames, URL changes or scientific content changes.
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: 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: 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
docs: separate teaching examples from BMD Compute policy
- VASP: label FCC-Si INCAR as a teaching example, not BMD Compute
production policy; fix Unicode minus in EDIFF; drop EDIFFG line
that has no effect with NSW = 0.
- HSE06 band structure: mark the workflow and INCAR settings as an
educational/manual example; BMD Compute takes precedence.
- USPEX: relabel "BMD's Recommended INCAR Files" as workflow examples.
- BMD Agent: make bmd-agent, bmd-agent JOB_ID and bmd-agent PATH the
primary interface, with expert subcommands under Advanced usage;
BMD Compute owns calculation methodology, BMDex supplies curated
supporting evidence and tools.
POTCAR path intentionally unchanged pending verification on POWER.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01DHgs1a4r3pZ6JVJ5dXQvoR
docs: canonicalize BMDwiki wiki links
Updated Tutorial 08 (markdown)