From 4542c14775a5cfc86a91ce5e55248249fe3c47d0 Mon Sep 17 00:00:00 2001 From: VsevolodX Date: Sun, 23 Aug 2026 18:38:19 -0700 Subject: [PATCH 1/3] =?UTF-8?q?update:=20index=20=C2=A71.2=20by=20publicat?= =?UTF-8?q?ion,=20one=20row=20each?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Rename "Reproducing Published Structures" to "Reproducing Publications" and give each publication one row carrying both the structure it builds and the properties calculated from it, instead of a second row per simulation. 24 rows, 22 publications. The per-publication model already existed in tutorials/materials/specific/overview.md (**Structure** / **Properties** / **DOI**, with "Coming Soon" where no simulation page exists yet); this brings the flat table into line with it rather than inventing a second convention. Property names follow §2.1's existing vocabulary in this same file — "Band gap", "Density of states" — not overview.md's prose, and the index states the headline properties rather than restating the tutorial's full list. Also wires up the footnotes. index-guide.md defined [^1]-[^22] — one DOI per publication — and nothing referenced any of them: the built page had 22 fn: list items and 0 fnref: markers, so the citations rendered as an unlabelled list with no way to tell which row each belonged to. Every Reference cell now carries its [^N]. Row order is unchanged from the old table, which is the order the footnotes were numbered in, so the definitions are untouched. The legacy site keeps its own name for this section ("Reproducing Specific Manuscripts", in both mkdocs.yml and tutorials/overview.md). Those two are a hand-maintained duplicate of the same 22 links and they agree with each other; renaming one without the other puts two names on one rendered page. Converging all four surfaces — better still, generating the duplicate list — is its own change, filed in plan/log/findings.md. Anchor changes: #12-reproducing-published-structures -> #12-reproducing-publications. Nothing in the repo links to the old one. A fragment is never sent to the server, so no redirect can act on it; external inbound links to the old anchor will land on the page. --- lang/en/docs/index-guide.md | 58 ++++++++++++++++++------------------- mkdocs-guide.yml | 2 +- 2 files changed, 29 insertions(+), 31 deletions(-) diff --git a/lang/en/docs/index-guide.md b/lang/en/docs/index-guide.md index be5222ea..0d04221e 100644 --- a/lang/en/docs/index-guide.md +++ b/lang/en/docs/index-guide.md @@ -27,36 +27,34 @@ Designing and constructing [material structures]({{ reference_url }}/materials/o | Interface (JupyterLite) | Construct a minimal-strain interface via the ZSL algorithm | [Link](tutorials/materials/jupyterlite-zsl.md) | | VESTA via Remote Desktop| Visualize structures in VESTA through a remote desktop session | [Link](tutorials/materials/vesta-remote-desktop.md) | -### 1.2. Reproducing Published Structures - -Step-by-step recipes reproducing structures from the literature. The [full overview](tutorials/materials/specific/overview.md) page contains figures and additional context for each entry. - -| Structure Type | Material | Reference | Link | -|:--------------------------|:--------------------|:-------------------------|:-----| -| Substitutional defect | Graphene | Fujimoto et al. (2011) | [Link](tutorials/materials/specific/defect-point-substitution-graphene.md) | -| Substitutional defect (band structure) | Graphene | Fujimoto et al. (2011) | [Link](tutorials/materials/specific/defect-point-substitution-graphene-simulation.md) | -| Vacancy-substitution pair | GaN | Miceli et al. (2016) | [Link](tutorials/materials/specific/defect-point-pair-gallium-nitride.md) | -| Vacancy defect | h-BN | Bertoldo et al. (2022) | [Link](tutorials/materials/specific/defect-point-vacancy-boron-nitride.md) | -| Interstitial defect | SnO | Togo et al. (2006) | [Link](tutorials/materials/specific/defect-point-interstitial-tin-oxide.md) | -| Island surface defect | TiN | Sangiovanni et al. (2018)| [Link](tutorials/materials/specific/defect-surface-island-titanium-nitride.md) | -| Step surface defect | Pt(111) | Šljivančanin et al. (2002)| [Link](tutorials/materials/specific/defect-surface-step-platinum.md) | -| Adatom surface defects | Graphene | Chan et al. (2008) | [Link](tutorials/materials/specific/defect-surface-adatom-graphene.md) | -| Twisted bilayer | h-BN nanoribbons | Xian et al. (2019) | [Link](tutorials/materials/specific/interface-bilayer-twisted-nanoribbons-boron-nitride.md) | -| Twisted bilayer | MoS2 | Liu et al. (2014) | [Link](tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md) | -| Twisted bilayer (band structure) | MoS2 | Liu et al. (2014) | [Link](tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide-simulation.md) | -| 2D–2D interface | Graphene / h-BN | Jung et al. (2015) | [Link](tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md) | -| 3D–3D interface | Cu / SiO2 | Shan et al. (2011) | [Link](tutorials/materials/specific/interface-3d-3d-copper-silicon-dioxide.md) | -| 2D–3D interface | Graphene / SiO2 | Kang et al. (2008) | [Link](tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md) | -| Interface optimization | Graphene / Ni(111) | Dahal et al. (2014) | [Link](tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel.md) | -| Adatom island | Pt on MoS2 | Saidi et al. (2015) | [Link](tutorials/materials/specific/defect-point-adatom-island-molybdenum-disulfide-platinum.md) | -| H-passivated nanowire | Si | Aradi et al. (2007) | [Link](tutorials/materials/specific/passivation-edge-nanowire-silicon.md) | -| H-passivated surface | Si(100) | Hansen et al. (1998) | [Link](tutorials/materials/specific/passivation-surface-silicon.md) | -| Nanoclusters | Au | Larsen et al. (2011) | [Link](tutorials/materials/specific/nanocluster-gold.md) | -| Slab | SrTiO3 | Eglitis et al. (2008) | [Link](tutorials/materials/specific/slab-strontium-titanate.md) | -| High-k metal gate stack | Si/SiO2/HfO2/TiN | Muller et al. (1999) | [Link](tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md) | -| Ripple perturbation | Graphene | Thompson-Flagg et al. (2009) | [Link](tutorials/materials/specific/perturbation-ripples-graphene.md) | -| Grain boundary (3D) | Cu (FCC) | Frolov et al. (2013) | [Link](tutorials/materials/specific/defect-planar-grain-boundary-3d-fcc-metals-copper.md) | -| Grain boundary (2D) | h-BN | Li et al. (2015) | [Link](tutorials/materials/specific/defect-planar-grain-boundary-2d-boron-nitride.md) | +### 1.2. Reproducing Publications + +Step-by-step recipes reproducing published work, one row per publication: the structure each recipe builds, and the properties calculated from that structure. A Properties cell reading Coming Soon means no simulation tutorial exists yet. The [full overview](tutorials/materials/specific/overview.md) page contains figures and additional context for each entry. + +| Reference | Structure Type | Material | Structure | Properties | +|:----------------------------------|:--------------------------|:-------------------|:----------|:-----------| +| Fujimoto et al. (2011)[^1] | Substitutional defect | Graphene | [Create](tutorials/materials/specific/defect-point-substitution-graphene.md) | [Band structure](tutorials/materials/specific/defect-point-substitution-graphene-simulation.md) | +| Miceli et al. (2016)[^2] | Vacancy-substitution pair | GaN | [Create](tutorials/materials/specific/defect-point-pair-gallium-nitride.md) | Defect formation energies (Coming Soon) | +| Bertoldo et al. (2022)[^3] | Vacancy defect | h-BN | [Create](tutorials/materials/specific/defect-point-vacancy-boron-nitride.md) | Formation energies (Coming Soon) | +| Togo et al. (2006)[^4] | Interstitial defect | SnO | [Create](tutorials/materials/specific/defect-point-interstitial-tin-oxide.md) | Formation energies, band structure (Coming Soon) | +| Sangiovanni et al. (2018)[^5] | Island surface defect | TiN | [Create](tutorials/materials/specific/defect-surface-island-titanium-nitride.md) | Island formation energy (Coming Soon) | +| Šljivančanin et al. (2002)[^6] | Step surface defect | Pt(111) | [Create](tutorials/materials/specific/defect-surface-step-platinum.md) | Energy of dissociation (Coming Soon) | +| Chan et al. (2008)[^7] | Adatom surface defects | Graphene | [Create](tutorials/materials/specific/defect-surface-adatom-graphene.md) | Adsorption energy, density of states, diffusion barriers (Coming Soon) | +| Xian et al. (2019)[^8] | Twisted bilayer | h-BN nanoribbons | [Create](tutorials/materials/specific/interface-bilayer-twisted-nanoribbons-boron-nitride.md) | Band structure, total energies versus twist angle (Coming Soon) | +| Liu et al. (2014)[^9] | Twisted bilayer | MoS2 | [Create](tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md) | [Band structure](tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide-simulation.md) | +| Jung et al. (2015)[^10] | 2D–2D interface | Graphene / h-BN | [Create](tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md) | Band structure, total energies (Coming Soon) | +| Shan et al. (2011)[^11] | 3D–3D interface | Cu / SiO2 | [Create](tutorials/materials/specific/interface-3d-3d-copper-silicon-dioxide.md) | Band structure (Coming Soon) | +| Kang et al. (2008)[^12] | 2D–3D interface | Graphene / SiO2 | [Create](tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md) | Band structure (Coming Soon) | +| Dahal et al. (2014)[^13] | Interface optimization | Graphene / Ni(111) | [Create](tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel.md) | Total energies versus lateral shift, band structure (Coming Soon) | +| Saidi et al. (2015)[^14] | Adatom island | Pt on MoS2 | [Create](tutorials/materials/specific/defect-point-adatom-island-molybdenum-disulfide-platinum.md) | Binding energy per Pt atom, density of states (Coming Soon) | +| Aradi et al. (2007)[^15] | H-passivated nanowire | Si | [Create](tutorials/materials/specific/passivation-edge-nanowire-silicon.md) | Band gap, density of states, formation energy (Coming Soon) | +| Hansen et al. (1998)[^16] | H-passivated surface | Si(100) | [Create](tutorials/materials/specific/passivation-surface-silicon.md) | Diffusion, reaction and desorption barriers (Coming Soon) | +| Larsen et al. (2011)[^17] | Nanoclusters | Au | [Create](tutorials/materials/specific/nanocluster-gold.md) | Total energy per atom, density of states (Coming Soon) | +| Eglitis et al. (2008)[^18] | Slab | SrTiO3 | [Create](tutorials/materials/specific/slab-strontium-titanate.md) | Surface energy (Coming Soon) | +| Muller et al. (1999)[^19] | High-k metal gate stack | Si/SiO2/HfO2/TiN | [Create](tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md) | Band structure, valence band offset (Coming Soon) | +| Thompson-Flagg et al. (2009)[^20] | Ripple perturbation | Graphene | [Create](tutorials/materials/specific/perturbation-ripples-graphene.md) | Coming Soon | +| Frolov et al. (2013)[^21] | Grain boundary (3D) | Cu (FCC) | [Create](tutorials/materials/specific/defect-planar-grain-boundary-3d-fcc-metals-copper.md) | Defect energy per atom (Coming Soon) | +| Li et al. (2015)[^22] | Grain boundary (2D) | h-BN | [Create](tutorials/materials/specific/defect-planar-grain-boundary-2d-boron-nitride.md) | Band gap, local density of states (Coming Soon) | [^1]: Fujimoto et al., Phys. Rev. B 84, 245446 (2011). [DOI](https://doi.org/10.1103/PhysRevB.84.245446){:target='_blank'} [^2]: Miceli et al., Phys. Rev. B 93, 165207 (2016). [DOI](https://doi.org/10.1103/PhysRevB.93.165207){:target='_blank'} diff --git a/mkdocs-guide.yml b/mkdocs-guide.yml index ea40f040..31c6c13c 100644 --- a/mkdocs-guide.yml +++ b/mkdocs-guide.yml @@ -190,7 +190,7 @@ nav: - Interface, quick setup (3D Editor): tutorials/materials/slabs-interface.md - Interface, minimal strain (JupyterLite): tutorials/materials/jupyterlite-zsl.md - VESTA via Remote Desktop: tutorials/materials/vesta-remote-desktop.md - - 1.2. Reproducing Published Structures: + - 1.2. Reproducing Publications: - Overview: tutorials/materials/specific/overview.md - Substitutional Defects in Graphene: tutorials/materials/specific/defect-point-substitution-graphene.md - Substitutional Defects in Graphene (Band Structure): tutorials/materials/specific/defect-point-substitution-graphene-simulation.md From 403d53b3b62f6257639b120616654d29e8433cd6 Mon Sep 17 00:00:00 2001 From: VsevolodX Date: Mon, 24 Aug 2026 14:24:57 -0700 Subject: [PATCH 2/3] chore: [Link] not [Create] in the Structure column MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Matches the 45 other [Link] cells in this file — §1.1 and §2.1 both use a constant label per link column rather than a per-row verb. --- lang/en/docs/index-guide.md | 44 ++++++++++++++++++------------------- 1 file changed, 22 insertions(+), 22 deletions(-) diff --git a/lang/en/docs/index-guide.md b/lang/en/docs/index-guide.md index 0d04221e..4d58f556 100644 --- a/lang/en/docs/index-guide.md +++ b/lang/en/docs/index-guide.md @@ -33,28 +33,28 @@ Step-by-step recipes reproducing published work, one row per publication: the st | Reference | Structure Type | Material | Structure | Properties | |:----------------------------------|:--------------------------|:-------------------|:----------|:-----------| -| Fujimoto et al. (2011)[^1] | Substitutional defect | Graphene | [Create](tutorials/materials/specific/defect-point-substitution-graphene.md) | [Band structure](tutorials/materials/specific/defect-point-substitution-graphene-simulation.md) | -| Miceli et al. (2016)[^2] | Vacancy-substitution pair | GaN | [Create](tutorials/materials/specific/defect-point-pair-gallium-nitride.md) | Defect formation energies (Coming Soon) | -| Bertoldo et al. (2022)[^3] | Vacancy defect | h-BN | [Create](tutorials/materials/specific/defect-point-vacancy-boron-nitride.md) | Formation energies (Coming Soon) | -| Togo et al. (2006)[^4] | Interstitial defect | SnO | [Create](tutorials/materials/specific/defect-point-interstitial-tin-oxide.md) | Formation energies, band structure (Coming Soon) | -| Sangiovanni et al. (2018)[^5] | Island surface defect | TiN | [Create](tutorials/materials/specific/defect-surface-island-titanium-nitride.md) | Island formation energy (Coming Soon) | -| Šljivančanin et al. (2002)[^6] | Step surface defect | Pt(111) | [Create](tutorials/materials/specific/defect-surface-step-platinum.md) | Energy of dissociation (Coming Soon) | -| Chan et al. (2008)[^7] | Adatom surface defects | Graphene | [Create](tutorials/materials/specific/defect-surface-adatom-graphene.md) | Adsorption energy, density of states, diffusion barriers (Coming Soon) | -| Xian et al. (2019)[^8] | Twisted bilayer | h-BN nanoribbons | [Create](tutorials/materials/specific/interface-bilayer-twisted-nanoribbons-boron-nitride.md) | Band structure, total energies versus twist angle (Coming Soon) | -| Liu et al. (2014)[^9] | Twisted bilayer | MoS2 | [Create](tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md) | [Band structure](tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide-simulation.md) | -| Jung et al. (2015)[^10] | 2D–2D interface | Graphene / h-BN | [Create](tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md) | Band structure, total energies (Coming Soon) | -| Shan et al. (2011)[^11] | 3D–3D interface | Cu / SiO2 | [Create](tutorials/materials/specific/interface-3d-3d-copper-silicon-dioxide.md) | Band structure (Coming Soon) | -| Kang et al. (2008)[^12] | 2D–3D interface | Graphene / SiO2 | [Create](tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md) | Band structure (Coming Soon) | -| Dahal et al. (2014)[^13] | Interface optimization | Graphene / Ni(111) | [Create](tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel.md) | Total energies versus lateral shift, band structure (Coming Soon) | -| Saidi et al. (2015)[^14] | Adatom island | Pt on MoS2 | [Create](tutorials/materials/specific/defect-point-adatom-island-molybdenum-disulfide-platinum.md) | Binding energy per Pt atom, density of states (Coming Soon) | -| Aradi et al. (2007)[^15] | H-passivated nanowire | Si | [Create](tutorials/materials/specific/passivation-edge-nanowire-silicon.md) | Band gap, density of states, formation energy (Coming Soon) | -| Hansen et al. (1998)[^16] | H-passivated surface | Si(100) | [Create](tutorials/materials/specific/passivation-surface-silicon.md) | Diffusion, reaction and desorption barriers (Coming Soon) | -| Larsen et al. (2011)[^17] | Nanoclusters | Au | [Create](tutorials/materials/specific/nanocluster-gold.md) | Total energy per atom, density of states (Coming Soon) | -| Eglitis et al. (2008)[^18] | Slab | SrTiO3 | [Create](tutorials/materials/specific/slab-strontium-titanate.md) | Surface energy (Coming Soon) | -| Muller et al. (1999)[^19] | High-k metal gate stack | Si/SiO2/HfO2/TiN | [Create](tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md) | Band structure, valence band offset (Coming Soon) | -| Thompson-Flagg et al. (2009)[^20] | Ripple perturbation | Graphene | [Create](tutorials/materials/specific/perturbation-ripples-graphene.md) | Coming Soon | -| Frolov et al. (2013)[^21] | Grain boundary (3D) | Cu (FCC) | [Create](tutorials/materials/specific/defect-planar-grain-boundary-3d-fcc-metals-copper.md) | Defect energy per atom (Coming Soon) | -| Li et al. (2015)[^22] | Grain boundary (2D) | h-BN | [Create](tutorials/materials/specific/defect-planar-grain-boundary-2d-boron-nitride.md) | Band gap, local density of states (Coming Soon) | +| Fujimoto et al. (2011)[^1] | Substitutional defect | Graphene | [Link](tutorials/materials/specific/defect-point-substitution-graphene.md) | [Band structure](tutorials/materials/specific/defect-point-substitution-graphene-simulation.md) | +| Miceli et al. (2016)[^2] | Vacancy-substitution pair | GaN | [Link](tutorials/materials/specific/defect-point-pair-gallium-nitride.md) | Defect formation energies (Coming Soon) | +| Bertoldo et al. (2022)[^3] | Vacancy defect | h-BN | [Link](tutorials/materials/specific/defect-point-vacancy-boron-nitride.md) | Formation energies (Coming Soon) | +| Togo et al. (2006)[^4] | Interstitial defect | SnO | [Link](tutorials/materials/specific/defect-point-interstitial-tin-oxide.md) | Formation energies, band structure (Coming Soon) | +| Sangiovanni et al. (2018)[^5] | Island surface defect | TiN | [Link](tutorials/materials/specific/defect-surface-island-titanium-nitride.md) | Island formation energy (Coming Soon) | +| Šljivančanin et al. (2002)[^6] | Step surface defect | Pt(111) | [Link](tutorials/materials/specific/defect-surface-step-platinum.md) | Energy of dissociation (Coming Soon) | +| Chan et al. (2008)[^7] | Adatom surface defects | Graphene | [Link](tutorials/materials/specific/defect-surface-adatom-graphene.md) | Adsorption energy, density of states, diffusion barriers (Coming Soon) | +| Xian et al. (2019)[^8] | Twisted bilayer | h-BN nanoribbons | [Link](tutorials/materials/specific/interface-bilayer-twisted-nanoribbons-boron-nitride.md) | Band structure, total energies versus twist angle (Coming Soon) | +| Liu et al. (2014)[^9] | Twisted bilayer | MoS2 | [Link](tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md) | [Band structure](tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide-simulation.md) | +| Jung et al. (2015)[^10] | 2D–2D interface | Graphene / h-BN | [Link](tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md) | Band structure, total energies (Coming Soon) | +| Shan et al. (2011)[^11] | 3D–3D interface | Cu / SiO2 | [Link](tutorials/materials/specific/interface-3d-3d-copper-silicon-dioxide.md) | Band structure (Coming Soon) | +| Kang et al. (2008)[^12] | 2D–3D interface | Graphene / SiO2 | [Link](tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md) | Band structure (Coming Soon) | +| Dahal et al. (2014)[^13] | Interface optimization | Graphene / Ni(111) | [Link](tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel.md) | Total energies versus lateral shift, band structure (Coming Soon) | +| Saidi et al. (2015)[^14] | Adatom island | Pt on MoS2 | [Link](tutorials/materials/specific/defect-point-adatom-island-molybdenum-disulfide-platinum.md) | Binding energy per Pt atom, density of states (Coming Soon) | +| Aradi et al. (2007)[^15] | H-passivated nanowire | Si | [Link](tutorials/materials/specific/passivation-edge-nanowire-silicon.md) | Band gap, density of states, formation energy (Coming Soon) | +| Hansen et al. (1998)[^16] | H-passivated surface | Si(100) | [Link](tutorials/materials/specific/passivation-surface-silicon.md) | Diffusion, reaction and desorption barriers (Coming Soon) | +| Larsen et al. (2011)[^17] | Nanoclusters | Au | [Link](tutorials/materials/specific/nanocluster-gold.md) | Total energy per atom, density of states (Coming Soon) | +| Eglitis et al. (2008)[^18] | Slab | SrTiO3 | [Link](tutorials/materials/specific/slab-strontium-titanate.md) | Surface energy (Coming Soon) | +| Muller et al. (1999)[^19] | High-k metal gate stack | Si/SiO2/HfO2/TiN | [Link](tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md) | Band structure, valence band offset (Coming Soon) | +| Thompson-Flagg et al. (2009)[^20] | Ripple perturbation | Graphene | [Link](tutorials/materials/specific/perturbation-ripples-graphene.md) | Coming Soon | +| Frolov et al. (2013)[^21] | Grain boundary (3D) | Cu (FCC) | [Link](tutorials/materials/specific/defect-planar-grain-boundary-3d-fcc-metals-copper.md) | Defect energy per atom (Coming Soon) | +| Li et al. (2015)[^22] | Grain boundary (2D) | h-BN | [Link](tutorials/materials/specific/defect-planar-grain-boundary-2d-boron-nitride.md) | Band gap, local density of states (Coming Soon) | [^1]: Fujimoto et al., Phys. Rev. B 84, 245446 (2011). [DOI](https://doi.org/10.1103/PhysRevB.84.245446){:target='_blank'} [^2]: Miceli et al., Phys. Rev. B 93, 165207 (2016). [DOI](https://doi.org/10.1103/PhysRevB.93.165207){:target='_blank'} From e4144a18e58faa5cd6b2948d7756f41846b12e4d Mon Sep 17 00:00:00 2001 From: VsevolodX Date: Tue, 25 Aug 2026 20:58:11 -0700 Subject: [PATCH 3/3] update: fold the Structure column into Material The Material name is now the link to the structure tutorial, so the cell says what the structure is instead of saying "Link". Five columns become four, which also takes the widest table in this file back down to the width of its neighbours. --- lang/en/docs/index-guide.md | 48 ++++++++++++++++++------------------- 1 file changed, 24 insertions(+), 24 deletions(-) diff --git a/lang/en/docs/index-guide.md b/lang/en/docs/index-guide.md index 4d58f556..0a59279f 100644 --- a/lang/en/docs/index-guide.md +++ b/lang/en/docs/index-guide.md @@ -31,30 +31,30 @@ Designing and constructing [material structures]({{ reference_url }}/materials/o Step-by-step recipes reproducing published work, one row per publication: the structure each recipe builds, and the properties calculated from that structure. A Properties cell reading Coming Soon means no simulation tutorial exists yet. The [full overview](tutorials/materials/specific/overview.md) page contains figures and additional context for each entry. -| Reference | Structure Type | Material | Structure | Properties | -|:----------------------------------|:--------------------------|:-------------------|:----------|:-----------| -| Fujimoto et al. (2011)[^1] | Substitutional defect | Graphene | [Link](tutorials/materials/specific/defect-point-substitution-graphene.md) | [Band structure](tutorials/materials/specific/defect-point-substitution-graphene-simulation.md) | -| Miceli et al. (2016)[^2] | Vacancy-substitution pair | GaN | [Link](tutorials/materials/specific/defect-point-pair-gallium-nitride.md) | Defect formation energies (Coming Soon) | -| Bertoldo et al. (2022)[^3] | Vacancy defect | h-BN | [Link](tutorials/materials/specific/defect-point-vacancy-boron-nitride.md) | Formation energies (Coming Soon) | -| Togo et al. (2006)[^4] | Interstitial defect | SnO | [Link](tutorials/materials/specific/defect-point-interstitial-tin-oxide.md) | Formation energies, band structure (Coming Soon) | -| Sangiovanni et al. (2018)[^5] | Island surface defect | TiN | [Link](tutorials/materials/specific/defect-surface-island-titanium-nitride.md) | Island formation energy (Coming Soon) | -| Šljivančanin et al. (2002)[^6] | Step surface defect | Pt(111) | [Link](tutorials/materials/specific/defect-surface-step-platinum.md) | Energy of dissociation (Coming Soon) | -| Chan et al. (2008)[^7] | Adatom surface defects | Graphene | [Link](tutorials/materials/specific/defect-surface-adatom-graphene.md) | Adsorption energy, density of states, diffusion barriers (Coming Soon) | -| Xian et al. (2019)[^8] | Twisted bilayer | h-BN nanoribbons | [Link](tutorials/materials/specific/interface-bilayer-twisted-nanoribbons-boron-nitride.md) | Band structure, total energies versus twist angle (Coming Soon) | -| Liu et al. (2014)[^9] | Twisted bilayer | MoS2 | [Link](tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md) | [Band structure](tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide-simulation.md) | -| Jung et al. (2015)[^10] | 2D–2D interface | Graphene / h-BN | [Link](tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md) | Band structure, total energies (Coming Soon) | -| Shan et al. (2011)[^11] | 3D–3D interface | Cu / SiO2 | [Link](tutorials/materials/specific/interface-3d-3d-copper-silicon-dioxide.md) | Band structure (Coming Soon) | -| Kang et al. (2008)[^12] | 2D–3D interface | Graphene / SiO2 | [Link](tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md) | Band structure (Coming Soon) | -| Dahal et al. (2014)[^13] | Interface optimization | Graphene / Ni(111) | [Link](tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel.md) | Total energies versus lateral shift, band structure (Coming Soon) | -| Saidi et al. (2015)[^14] | Adatom island | Pt on MoS2 | [Link](tutorials/materials/specific/defect-point-adatom-island-molybdenum-disulfide-platinum.md) | Binding energy per Pt atom, density of states (Coming Soon) | -| Aradi et al. (2007)[^15] | H-passivated nanowire | Si | [Link](tutorials/materials/specific/passivation-edge-nanowire-silicon.md) | Band gap, density of states, formation energy (Coming Soon) | -| Hansen et al. (1998)[^16] | H-passivated surface | Si(100) | [Link](tutorials/materials/specific/passivation-surface-silicon.md) | Diffusion, reaction and desorption barriers (Coming Soon) | -| Larsen et al. (2011)[^17] | Nanoclusters | Au | [Link](tutorials/materials/specific/nanocluster-gold.md) | Total energy per atom, density of states (Coming Soon) | -| Eglitis et al. (2008)[^18] | Slab | SrTiO3 | [Link](tutorials/materials/specific/slab-strontium-titanate.md) | Surface energy (Coming Soon) | -| Muller et al. (1999)[^19] | High-k metal gate stack | Si/SiO2/HfO2/TiN | [Link](tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md) | Band structure, valence band offset (Coming Soon) | -| Thompson-Flagg et al. (2009)[^20] | Ripple perturbation | Graphene | [Link](tutorials/materials/specific/perturbation-ripples-graphene.md) | Coming Soon | -| Frolov et al. (2013)[^21] | Grain boundary (3D) | Cu (FCC) | [Link](tutorials/materials/specific/defect-planar-grain-boundary-3d-fcc-metals-copper.md) | Defect energy per atom (Coming Soon) | -| Li et al. (2015)[^22] | Grain boundary (2D) | h-BN | [Link](tutorials/materials/specific/defect-planar-grain-boundary-2d-boron-nitride.md) | Band gap, local density of states (Coming Soon) | +| Reference | Structure Type | Material | Properties | +|:----------------------------------|:--------------------------|:---------|:-----------| +| Fujimoto et al. (2011)[^1] | Substitutional defect | [Graphene](tutorials/materials/specific/defect-point-substitution-graphene.md) | [Band structure](tutorials/materials/specific/defect-point-substitution-graphene-simulation.md) | +| Miceli et al. (2016)[^2] | Vacancy-substitution pair | [GaN](tutorials/materials/specific/defect-point-pair-gallium-nitride.md) | Defect formation energies (Coming Soon) | +| Bertoldo et al. (2022)[^3] | Vacancy defect | [h-BN](tutorials/materials/specific/defect-point-vacancy-boron-nitride.md) | Formation energies (Coming Soon) | +| Togo et al. (2006)[^4] | Interstitial defect | [SnO](tutorials/materials/specific/defect-point-interstitial-tin-oxide.md) | Formation energies, band structure (Coming Soon) | +| Sangiovanni et al. (2018)[^5] | Island surface defect | [TiN](tutorials/materials/specific/defect-surface-island-titanium-nitride.md) | Island formation energy (Coming Soon) | +| Šljivančanin et al. (2002)[^6] | Step surface defect | [Pt(111)](tutorials/materials/specific/defect-surface-step-platinum.md) | Energy of dissociation (Coming Soon) | +| Chan et al. (2008)[^7] | Adatom surface defects | [Graphene](tutorials/materials/specific/defect-surface-adatom-graphene.md) | Adsorption energy, density of states, diffusion barriers (Coming Soon) | +| Xian et al. (2019)[^8] | Twisted bilayer | [h-BN nanoribbons](tutorials/materials/specific/interface-bilayer-twisted-nanoribbons-boron-nitride.md) | Band structure, total energies versus twist angle (Coming Soon) | +| Liu et al. (2014)[^9] | Twisted bilayer | [MoS2](tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide.md) | [Band structure](tutorials/materials/specific/interface-bilayer-twisted-commensurate-lattices-molybdenum-disulfide-simulation.md) | +| Jung et al. (2015)[^10] | 2D–2D interface | [Graphene / h-BN](tutorials/materials/specific/interface-2d-2d-graphene-boron-nitride.md) | Band structure, total energies (Coming Soon) | +| Shan et al. (2011)[^11] | 3D–3D interface | [Cu / SiO2](tutorials/materials/specific/interface-3d-3d-copper-silicon-dioxide.md) | Band structure (Coming Soon) | +| Kang et al. (2008)[^12] | 2D–3D interface | [Graphene / SiO2](tutorials/materials/specific/interface-2d-3d-graphene-silicon-dioxide.md) | Band structure (Coming Soon) | +| Dahal et al. (2014)[^13] | Interface optimization | [Graphene / Ni(111)](tutorials/materials/specific/optimization-interface-film-xy-position-graphene-nickel.md) | Total energies versus lateral shift, band structure (Coming Soon) | +| Saidi et al. (2015)[^14] | Adatom island | [Pt on MoS2](tutorials/materials/specific/defect-point-adatom-island-molybdenum-disulfide-platinum.md) | Binding energy per Pt atom, density of states (Coming Soon) | +| Aradi et al. (2007)[^15] | H-passivated nanowire | [Si](tutorials/materials/specific/passivation-edge-nanowire-silicon.md) | Band gap, density of states, formation energy (Coming Soon) | +| Hansen et al. (1998)[^16] | H-passivated surface | [Si(100)](tutorials/materials/specific/passivation-surface-silicon.md) | Diffusion, reaction and desorption barriers (Coming Soon) | +| Larsen et al. (2011)[^17] | Nanoclusters | [Au](tutorials/materials/specific/nanocluster-gold.md) | Total energy per atom, density of states (Coming Soon) | +| Eglitis et al. (2008)[^18] | Slab | [SrTiO3](tutorials/materials/specific/slab-strontium-titanate.md) | Surface energy (Coming Soon) | +| Muller et al. (1999)[^19] | High-k metal gate stack | [Si/SiO2/HfO2/TiN](tutorials/materials/specific/heterostructure-silicon-silicon-dioxide-hafnium-dioxide-titanium-nitride.md) | Band structure, valence band offset (Coming Soon) | +| Thompson-Flagg et al. (2009)[^20] | Ripple perturbation | [Graphene](tutorials/materials/specific/perturbation-ripples-graphene.md) | Coming Soon | +| Frolov et al. (2013)[^21] | Grain boundary (3D) | [Cu (FCC)](tutorials/materials/specific/defect-planar-grain-boundary-3d-fcc-metals-copper.md) | Defect energy per atom (Coming Soon) | +| Li et al. (2015)[^22] | Grain boundary (2D) | [h-BN](tutorials/materials/specific/defect-planar-grain-boundary-2d-boron-nitride.md) | Band gap, local density of states (Coming Soon) | [^1]: Fujimoto et al., Phys. Rev. B 84, 245446 (2011). [DOI](https://doi.org/10.1103/PhysRevB.84.245446){:target='_blank'} [^2]: Miceli et al., Phys. Rev. B 93, 165207 (2016). [DOI](https://doi.org/10.1103/PhysRevB.93.165207){:target='_blank'}