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VsevolodX merged 3 commits into from
Aug 26, 2026
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feature/SOF-8014-1 Update: index §1.2 by publication, one row each #399

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4542c14
update: index §1.2 by publication, one row each
VsevolodX Aug 24, 2026
403d53b
chore: [Link] not [Create] in the Structure column
VsevolodX Aug 24, 2026
e4144a1
update: fold the Structure column into Material
VsevolodX Aug 26, 2026
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58 changes: 28 additions & 30 deletions lang/en/docs/index-guide.md
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Expand Up @@ -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 | 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'}
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2 changes: 1 addition & 1 deletion mkdocs-guide.yml
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Expand Up @@ -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
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