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: 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 Crystal Structure Prediction Using USPEX (markdown)
Updated Tutorial 14 (markdown)