Repository navigation
Docs: formation energy beside the band structure in the graphene defect tutorial - #407
Merged
Merged
Conversation
…SE pages Rewrites the simulation tutorial in place, keeping its ten-section list, file name and URL. The run-profile subsection goes, replaced by the RELAX switch; the pseudopotential line is corrected from norm-conserving ONCV to GBRV ultrasoft, which is the only LDA set the platform publishes for C and N and the one deviation from the manuscript's method. Expected results now compares the formation energy with Table I's 2.51 eV at 15 %, names the 0.89 uB moment as a manual pw_scf.out check, and keeps the band-structure comparison figure. The measured values wait on the live run and are marked TODO(live run). The structure page's save section covers both materials the notebook now saves, and the nav label in mkdocs.yml and mkdocs-guide.yml names both properties. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
✅ Deploy Preview for mat3ra-documentation ready!
To edit notification comments on pull requests, go to your Netlify project configuration. |
timurbazhirov
approved these changes
Oct 7, 2026
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Rewrites the graphene substitutional-defect simulation tutorial so it covers the formation
energy alongside the band structure it already documented, and corrects two things that were
wrong on the page.
SOF-8063. Notebook side: mat3ra/api-examples#372.
The page keeps its ten sections, their order and its URL — it is the page every other Specific
Example page is diffed against, so only the content changes. It is the same length it was.
RUN_PROFILEdebug/productiontoggle; the section now documents the
RELAXswitch and quotes the real parameter cell verbatim.there is no norm-conserving LDA set published for C or N, only GBRV ultrasoft. The page now says
so and names it as the one deviation from the manuscript's method.
E_f against Fujimoto & Saito Table I's 2.51 eV at 15 % tolerance, with both offsets named — solid
N₂ standing in for the free molecule, GBRV ultrasoft for Troullier–Martins — and the total
magnetic moment against 0.89 μB as a manual read of the job's
pw_scf.out, which the notebookdeliberately does not parse. The band-structure comparison figure stays.
N-doped Graphenenow fails the load, because the structure notebook savesgraphene 4x4andgraphene 4x4 N3V pyridinic (C28N3).mkdocs.ymlandmkdocs-guide.ymlbecomes "(Formation Energy and Band Structure)". The filename does not move.mkdocs buildis clean on both sites, with no warning naming either page.🤖 Generated with Claude Code