Skip to content

feature/SOF-8065 Feature: tutorial for graphene on SiO2, doping and gap at the Dirac point - #414

Open
VsevolodX wants to merge 10 commits into
mainfrom
feature/SOF-8065
Open

VsevolodX wants to merge 10 commits into
mainfrom
feature/SOF-8065

Conversation

@VsevolodX

@VsevolodX VsevolodX commented Oct 7, 2026 •

Copy link
Copy Markdown
Member

Adds the simulation tutorial for graphene on O-terminated α-quartz SiO₂(0001) — p-type doping and the
gap at the Dirac point — and updates the structure tutorial it builds on.

SOF-8065. Notebook side: mat3ra/api-examples#383.

  • New page interface-2d-3d-graphene-silicon-dioxide-simulation.md, the ten sections of the
    graphene substitution simulation page. §4 quotes the notebook's parameter cells verbatim. §6 puts
    our values beside the paper's (p-type; E_D − E_F +1.171 eV against +1.28; gap at K 0.062 eV against
    0.130, unrelaxed), with a crop of Kang Fig. 3(a) and our band structure on the same path and energy
    window. The relaxed regime did not converge in the 4 h limit; the band structure after 5 relaxation
    steps (+1.179 eV, 0.071 eV) is given beside it.
  • Structure page: thickness 5 conventional cells (15 Si planes; the manuscript has 14 bilayers),
    about 20 Å of vacuum above graphene, graphene shifted to the manuscript's metastable registry, the
    cell in the 120° setting and centered along z — each quoted from the notebook. A side view of the
    built interface replaces the screenshots that showed thickness 7.
  • Nav lines in mkdocs.yml and mkdocs-guide.yml; the "(Coming Soon)" entries in overview.md and
    index-guide.md link to the page. @Kang2008 already existed. Three images (LFS).

mkdocs build exits 0 on both sites. The JupyterLite embed resolves after api-examples merges and
JupyterLite is rebuilt.

🤖 Generated with Claude Code

VsevolodX and others added 7 commits October 6, 2026 17:42
…d index links

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
…simulation cells at current HEAD

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
…ustomization trimmed to what the notebook does, naming, re-quoted cells

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
…-M-K-Gamma

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
…mples c06e072e

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
…stance value, neutral wording, caption axis

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
@netlify

netlify Bot commented Oct 7, 2026 •

Copy link
Copy Markdown

✅ Deploy Preview for mat3ra-documentation ready!

Name Link
🔨 Latest commit 830d0d4
🔍 Latest deploy log https://app.netlify.com/projects/mat3ra-documentation/deploys/6ac70b573c52dc000826c266
😎 Deploy Preview https://deploy-preview-414--mat3ra-documentation.netlify.app
📱 Preview on mobile
Toggle QR Code...

QR Code

Use your smartphone camera to open QR code link.
🤖 Make changes Run an agent on this branch

To edit notification comments on pull requests, go to your Netlify project configuration.

VsevolodX and others added 3 commits October 7, 2026 18:55
…xation in the same job, paper values side by side

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
…table geometry, observed relaxation result, wording

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
…ult run

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

1 participant