SOF-8014: tutorial for twisted MoS2 bilayer band structure - #396
Open
VsevolodX wants to merge 6 commits into
Open
SOF-8014: tutorial for twisted MoS2 bilayer band structure#396VsevolodX wants to merge 6 commits into
VsevolodX wants to merge 6 commits into
Conversation
Reproduces the electronic-structure result of Liu et al., Nat. Commun. 5, 4966 (2014): the indirect gap of a MoS2 bilayer is set by the interlayer distance, while the K-valley direct gap barely moves. Covers the prerequisite structure notebook, the structures computed, where the settings differ from the manuscript's and why, and the results. Registered in both mkdocs.yml and mkdocs-guide.yml, as the sibling simulation tutorial is. 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. |
The out-of-plane cell is now 20 A as in the manuscript, so it is no longer a divergence. The cutoff row is: 140 Ry is a norm-conserving wavefunction cutoff and is not comparable with an ultrasoft one, which converges lower and needs a higher charge-density cutoff instead. Drop the walkthrough of the Mo-Mo to sulfur-plane conversion; the notebook prints the resulting separation and cell height for checking. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
The band-structure page did not read as the second half of the MoS2 manuscript reproduction: - nav titled it "Twisted Bilayer MoS2 Band Structure" instead of the structure page's title plus "(Band Structure)", the form already used for the graphene pair - in mkdocs-guide.yml it sat seven rows above its own structure page, directly under the graphene pair - overview.md still advertised its Properties entry as "Coming Soon" Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Follows the _SIMULATION rename in api-examples. Two references in the page - the GitHub source path and the jupyterlite_embed notebook_name. The page slug is unchanged, so no published URL moves. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
The cost-lever paragraph still named INTERFACE_VACUUM, which no longer exists - the structure notebook takes TOTAL_CELL_HEIGHT and derives the builder's vacuum from it. It also framed the cell as more generous than the manuscript's, which stopped being true when it moved to 20 A. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Sections 3 and 4 documented create_twisted_interface_with_commnesurate_ lattices.ipynb, while section 5 embeds specific_examples/interface_bilayer_twisted_commensurate_lattices_ molybdenum_disulfide.ipynb. None of the variables the page told the reader to set - TARGET_TWIST_ANGLE, INTERFACE_DISTANCE, INTERFACE_VACUUM, MAX_SUPERCELL_MATRIX_INT, USE_CONVENTIONAL_CELL, STACKING_DIRECTION - exist in the embedded notebook, so the prerequisite step of the band structure tutorial could not be followed as written. Rewritten against the embedded notebook: the INTERFACE_PARAMETERS list replaces the one-angle-at-a-time walkthrough, TOTAL_CELL_HEIGHT replaces INTERFACE_VACUUM, and the six angle snippets become uncommented entries. Two things the old text got wrong about the physics, now called out: d_mo_mo is the Mo-Mo separation Table S1 tabulates, not a gap - passing 6.5 A through as a gap separates the layers ~3 A too far; and the interlayer distance belongs to the stacking registry, 6.1-6.2 A for AA1/AB1 and AA2/AB2 against 6.8 A for AA3/AB3. Atom counts, Mo-Mo separations, cell heights and the two registry classifications in the new text were built and measured, not inferred. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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
1 participant
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.
SOF-8014 — tutorial: band structure of twisted MoS2 bilayers
Companion to mat3ra/api-examples#358, which adds the notebooks this page describes.
Reproduces the electronic-structure result of Liu et al., Evolution of interlayer coupling in
twisted molybdenum disulfide bilayers, Nat. Commun. 5, 4966 (2014) —
10.1038/ncomms5966: the indirect gap of a MoS2 bilayer is set
by the interlayer distance, while the K-valley direct gap barely moves.
Contents
reports
than relaxed here
Where it differs from the manuscript
The manuscript used LDA with norm-conserving pseudopotentials. The platform carries none for Mo or S
under LDA, so the tutorial uses the ultrasoft GBRV set at the same functional — keeping LDA matters,
since it is what binds this bilayer. Absolute gaps land ~0.2 eV low as a result; differences between
structures computed with identical settings are much less affected, and the page says so.
Verified
and 1.297 eV at 6.5 Å, a +0.199 eV shift against the manuscript's +0.20 eV, with the
K-valley gap moving 0.012 eV
jupyterlite_embedtarget and the@Liu2014citation resolvemkdocs.ymlandmkdocs-guide.yml, matching the sibling simulation tutorial;both parse
Not rendered locally — mkdocs is not installed in this worktree, so the build is unverified beyond
the checks above.
🤖 Generated with Claude Code