diff --git a/other/materials_designer/Introduction.ipynb b/other/materials_designer/Introduction.ipynb index 030d28d5..ba6dce33 100644 --- a/other/materials_designer/Introduction.ipynb +++ b/other/materials_designer/Introduction.ipynb @@ -10,80 +10,77 @@ "source": [ "# Contents.\n", "\n", - "This document contains links to the functionality listed.\n", + "This document contains links to the functionality listed. Section numbers follow **Domain (`X`) → Dimensionality (`X.Y`) → Category (`X.Y.Z`)**, with **M-CODE** labels aligned to the MCODE taxonomy ([arxiv](https://arxiv.org/abs/2602.14384)).\n", "\n", - "## 1. Single-Material Structures.\n", "\n", - "### 1.1. 3D Structures.\n", - "#### [1.1.1. Supercells. Create supercells from 3D crystals.](create_supercell.ipynb)\n", + "## 1. Pristine Structures.\n", "\n", - "### 1.2. 2D Structures.\n", - "#### [1.2.1. Slabs. Create a slab from a bulk material.](create_slab.ipynb)\n", - "#### [1.2.2. Monolayers. Create a monolayer from a bulk material.](create_monolayer.ipynb)\n", + "### 1.1. 3D\n", + "#### [1.1.1. Supercells. Create supercells from 3D crystals. `P-3D-CRY`](create_supercell.ipynb)\n", "\n", - "### 1.3. 1D Structures.\n", - "#### [1.3.1. Nanoribbons. Create nanoribbons from 2D materials.](create_nanoribbon.ipynb)\n", - "#### [1.3.2. Nanowires. Create a nanowire from a bulk material.](create_nanowire.ipynb)\n", - "#### [1.3.3. Nanowires with custom shape. Create a nanowire with a custom cross-section.](create_nanowire_custom_shape.ipynb)\n", + "### 1.2. 2D\n", + "#### [1.2.1. Slabs. Create a slab from a bulk material. `P-2D-SLB`](create_slab.ipynb)\n", + "#### [1.2.2. Monolayers. Create a monolayer from a bulk material. `P-2D-MNL`](create_monolayer.ipynb)\n", "\n", - "### 1.4. 0D Structures.\n", - "#### [1.4.1. Spherical Cluster. Create a spherical cluster from a bulk material.](create_cluster_sphere.ipynb)\n", - "#### [1.4.2. Custom Shape Cluster. Create a cluster by cutting it out of a slab.](create_cluster_custom_shape.ipynb)\n", - "#### [1.4.3. Specific Shape Cluster. Create a cluster by building up a specific shape.](create_cluster_specific_shape.ipynb)\n", - "#### [1.4.4. Box-cutout. Create a slab with a box cutout](create_cutout_box.ipynb)\n", - "#### [1.4.5. Custom Shape Cutout. Create a slab with a custom shape cutout.](create_cutout_custom_shape.ipynb)\n", + "### 1.3. 1D\n", + "#### [1.3.1. Nanowires. Create a nanowire from a bulk material. `P-1D-NWR`](create_nanowire.ipynb)\n", + "#### [1.3.2. Nanowires with custom shape. Create a nanowire with a custom cross-section. `P-1D-NWR`](create_nanowire_custom_shape.ipynb)\n", "\n", + "### 1.4. 0D\n", + "#### [1.4.1. Nanoribbons. Create nanoribbons from 2D materials. `P-0D-NRB`](create_nanoribbon.ipynb)\n", + "#### [1.4.2. Spherical Cluster. Create a spherical cluster from a bulk material. `P-0D-NPR`](create_cluster_sphere.ipynb)\n", + "#### [1.4.3. Custom Shape Cluster. Create a cluster by cutting it out of a slab. `P-0D-NPR`](create_cluster_custom_shape.ipynb)\n", + "#### [1.4.4. Specific Shape Cluster. Create a cluster by building up a specific shape. `P-0D-NPR`](create_cluster_specific_shape.ipynb)\n", + "#### [1.4.5. Box-cutout. Create a slab with a box cutout `X-0D-CUT`](create_cutout_box.ipynb)\n", + "#### [1.4.6. Custom Shape Cutout. Create a slab with a custom shape cutout. `X-0D-CUT`](create_cutout_custom_shape.ipynb)\n", "\n", - "## 2. Multi-Material Structures.\n", "\n", - "### 2.1. Interfaces\n", - "#### [2.1.1. Interface with Zur and McGill Superlattice (ZSL) strain matching](create_interface_with_min_strain_zsl.ipynb)\n", + "## 2. Compound Pristine Structures.\n", "\n", - "#### [2.1.3. Interface without strain matching](create_interface_with_no_strain_matching.ipynb)\n", + "### 2.1. 2D\n", + "#### [2.1.1. Interface with Zur and McGill Superlattice (ZSL) strain matching `C-2D-INT-Z`](create_interface_with_min_strain_zsl.ipynb)\n", + "#### [2.1.3. Interface without strain matching `C-2D-INT-Z`](create_interface_with_no_strain_matching.ipynb)\n", + "#### [2.1.2. Interface with ASE EMT Relaxation `C-2D-INT-Z`](create_interface_with_relaxation_ase_emt.ipynb)\n", + "#### [2.1.4. Twisted Interface with Commensurate Lattices `C-2D-INT-C`](create_twisted_interface_with_commensurate_lattices.ipynb)\n", + "#### [2.1.5. Heterostructure with multiple consecutive layers `C-2D-HST`](create_heterostructure_example.ipynb)\n", + "#### [2.1.6. Optimize film position on interface `C-2D-INT-Z`](optimize_film_position.ipynb).\n", "\n", - "#### [2.1.2. Interface with ASE EMT Relaxation](create_interface_with_relaxation_ase_emt.ipynb)\n", + "### 2.2. 0D\n", + "#### [2.2.1. Twisted Nanoribbon Interface/Stack `C-0D-INT-R`](create_twisted_interface_with_nanoribbons.ipynb)\n", "\n", - "#### [2.1.4. Twisted Interface with Commensurate Lattices](create_twisted_interface_with_commensurate_lattices.ipynb)\n", "\n", - "### 2.2. Stacked Nanoribbons\n", - "#### [2.2.1. Twisted Nanoribbon Interface/Stack](create_twisted_interface_with_nanoribbons.ipynb)\n", + "## 3. Defective Structures.\n", "\n", - "### 2.3. Heterostructures\n", - "#### [2.3.1. Heterostructure with multiple consecutive layers](create_heterostructure_example.ipynb)\n", + "### 3.1. 2D\n", + "#### [3.1.1. Adatom Defect on a Slab `D-2D-ADA`](create_adatom_defect.ipynb)\n", + "#### [3.1.2. Terrace Defect on a Slab `D-2D-TER`](create_terrace_defect.ipynb)\n", + "#### [3.1.3. Grain Boundary Planar `D-2D-GBL`](create_grain_boundary_crystal.ipynb)\n", "\n", + "### 3.2. 1D\n", + "#### [3.2.1. Grain Boundary Linear `D-1D-GBP`](create_grain_boundary_film.ipynb)\n", "\n", - "## 3. Defects.\n", - "\n", - "### 3.1. Point Defects\n", - "#### [3.1.1. Point Defects: vacancy, substitution, interstitial](create_point_defect.ipynb)\n", - "#### [3.1.2. Point Defects Pair](create_point_defect_pair.ipynb)\n", - "\n", - "### 3.2. Surface Defects\n", - "#### [3.2.1. Adatom Defect on a Slab](create_adatom_defect.ipynb)\n", - "#### [3.2.2. Terrace Defect on a Slab](create_terrace_defect.ipynb)\n", - "\n", - "### 3.3. Planar Defects\n", - "#### [3.3.1. Grain Boundary in a 3D Crystal](create_grain_boundary_crystal.ipynb)\n", - "#### [3.3.2. Grain Boundary in a 2D Material](create_grain_boundary_film.ipynb)\n", + "### 3.3. 0D\n", + "#### [3.3.1. Point Defects: vacancy, substitution, interstitial `D-0D-SUB` · `D-0D-VAC` · `D-0D-INT`](create_point_defect.ipynb)\n", + "#### [3.3.2. Point Defects Pair `D-0D-DFP`](create_point_defect_pair.ipynb)\n", "\n", "\n", "## 4. Passivation.\n", "\n", - "### 4.1. Surface Passivation\n", - "#### [4.1.1. Slab Passivation](passivate_slab.ipynb) \n", + "### 4.1. 2D\n", + "#### [4.1.1. Slab Passivation `X-2D-PAS`](passivate_slab.ipynb) \n", "\n", - "### 4.2. Edge Passivation\n", - "#### [4.2.1. Edge Passivation](passivate_edge.ipynb)\n", + "### 4.2. 1D\n", + "#### [4.2.1. Edge Passivation `X-1D-PAS`](passivate_edge.ipynb)\n", "\n", "\n", "## 5. Perturbations.\n", "\n", - "### 5.1. Slab Perturbations\n", - "#### [5.1.1. Perturbation using sine wave](create_perturbation.ipynb)\n", - "#### [5.1.2. Perturbation using custom function](create_perturbation_custom.ipynb)\n", + "### 5.1. 3D\n", + "#### [5.1.1. Maxwell-Boltzmann thermal disorder `X-3D-PER`](create_maxwell_disorder.ipynb)\n", "\n", - "### 5.2. Thermal Disorder\n", - "#### [5.2.1. Maxwell-Boltzmann thermal disorder](create_maxwell_disorder.ipynb)\n", + "### 5.2. 2D\n", + "#### [5.2.1. Perturbation using sine wave `X-2D-PER`](create_perturbation.ipynb)\n", + "#### [5.2.2. Perturbation using custom function `X-2D-PER`](create_perturbation_custom.ipynb)\n", "\n", "\n", "## 6. Other.\n", @@ -100,10 +97,6 @@ "\n", "This notebook demonstrates a workflow for converting materials data from the [JARVIS](https://jarvis.nist.gov/) database into ESSE format for use with the Mat3ra.com platform.\n", "\n", - "## 6.2. Optimize.\n", - "\n", - "#### [6.2.1. Optimize film position on interface](optimize_film_position.ipynb).\n", - "\n", "## 6.3. Development.\n", "\n", "#### [6.3.1. Custom Transformation](custom_transformation.ipynb). Notebook setup for development of custom transformations on materials.\n", diff --git a/other/materials_designer/specific_examples/Introduction.ipynb b/other/materials_designer/specific_examples/Introduction.ipynb index 72e5b9fd..5d22f635 100644 --- a/other/materials_designer/specific_examples/Introduction.ipynb +++ b/other/materials_designer/specific_examples/Introduction.ipynb @@ -7,123 +7,96 @@ "source": [ "# Specific Examples\n", "\n", - "Worked examples organized by structure type. Each section is identified by an **M-CODE** (https://www.arxiv.org/abs/2602.14384).\n", + "Examples of structures and properties calculations from well-known publications organized by structure type. Each row is identified by an **M-CODE** ([arxiv](https://www.arxiv.org/abs/2602.14384)).\n", "\n", - "---\n", + "Domain (`P` - Pristine, `C` - Compound Pristine, `D` - Defective, `X` - Processed) - Dimensionality - Category - Variant (if applicable)\n", "\n", - "## 1. Pristine Structures\n", "\n", - "### 1.1. 3D Ideal Crystal — `P-3D-CRY`\n", - "*(to be added)*\n", + "| M-CODE | Category | Structure | Simulation | Reference |\n", + "| ------ | -------- |----------------------------------------------------------------------------------------------------------------------|---------------|---|\n", + "| `P-3D-CRY` | Ideal Crystal | *To be added* | — | — |\n", + "| `P-2D-MNL` | Monolayer | *To be added* | — | — |\n", + "| `P-2D-SLB-S` | Slab | [Simple Slab: SrTiO₃](slab_strontium_titanate.ipynb) | *To be added* | [[1]](#ref1) |\n", + "| `P-2D-SLB-R` | Slab | *Reconstructed slab. To be added* | — | — |\n", + "| `P-1D-NTP` | Nanotape | *To be added* | — | — |\n", + "| `P-1D-NWR` | Nanowire | *To be added* | — | — |\n", + "| `P-0D-NPR` | Nanoparticle | [Gold Nanocluster](nanocluster_gold.ipynb) | *To be added* | [[2]](#ref2) |\n", + "| `P-0D-NRB` | Nanoribbon | *To be added* | — | — |\n", + "| `C-2D-HST` | Heterostack | [Si/SiO₂/HfO₂/TiN Heterostructure](heterostructure_silicon_silicon_dioxide_hafnium_dioxide_titanium_nitride.ipynb) | *To be added* | [[3]](#ref3) |\n", + "| `C-2D-INT-S` | Interface Simple | *To be added* | — | — |\n", + "| `C-2D-INT-Z` | Interface ZSL | [BN/Graphene 2D–2D Interface](interface_2d_2d_boron_nitride_graphene.ipynb) | *To be added* | [[4]](#ref4) |\n", + "| `C-2D-INT-Z` | Interface ZSL | [Graphene/SiO₂ 2D–3D Interface](interface_2d_3d_graphene_silicon_dioxide.ipynb) | *To be added* | [[5]](#ref5) |\n", + "| `C-2D-INT-Z` | Interface ZSL | [Cu/Cristobalite 3D–3D Interface](interface_3d_3d_copper_cristobalite.ipynb) | *To be added* | [[6]](#ref6) |\n", + "| `C-2D-INT-Z` | Interface ZSL | [Graphene/Ni Interface Film XY Position Optimization](optimization_interface_film_xy_position_graphene_nickel.ipynb) | *To be added* | [[7]](#ref7) |\n", + "| `C-2D-INT-T` | Interface Twisted | *To be added* | — | — |\n", + "| `C-2D-INT-C` | Interface Commensurate Lattice | [Twisted Commensurate MoS₂ Bilayer](interface_bilayer_twisted_commensurate_lattices_molybdenum_disulfide.ipynb) | *To be added* | [[8]](#ref8) |\n", + "| `C-2D-MLT` | Multi-Layer | *To be added* | — | — |\n", + "| `C-0D-INT-R` | Nanoribbons Interface Rotation | [Twisted BN Nanoribbon Bilayer](interface_bilayer_twisted_nanoribbons_boron_nitride.ipynb) | *To be added* | [[9]](#ref9) |\n", + "| `D-3D-AMO` | Amorphous | *To be added* | — | — |\n", + "| `D-2D-ADA` | Adatom | [Pt Adatom/Island on MoS₂](defect_point_adatom_island_molybdenum_disulfide_platinum.ipynb) | *To be added* | [[10]](#ref10) |\n", + "| `D-2D-ADA` | Adatom | [Adatom on Graphene](defect_surface_adatom_graphene.ipynb) | *To be added* | [[11]](#ref11) |\n", + "| `D-2D-GBP` | Grain Boundary Planar | [Grain Boundary in 2D BN](defect_planar_grain_boundary_2d_boron_nitride.ipynb) | *To be added* | [[12]](#ref12) |\n", + "| `D-2D-GBP` | Grain Boundary Planar | [Grain Boundary in 3D FCC Cu](defect_planar_grain_boundary_3d_fcc_metals_copper.ipynb) | *To be added* | [[13]](#ref13) |\n", + "| `D-2D-ISL` | Island | [TiN Island on Surface](defect_surface_island_titanium_nitride.ipynb) | *To be added* | [[14]](#ref14) |\n", + "| `D-2D-TER` | Terrace | [Step/Terrace on Pt Surface](defect_surface_step_platinum.ipynb) | *To be added* | [[15]](#ref15) |\n", + "| `D-1D-GBL` | Grain Boundary Linear | *To be added* | — | — |\n", + "| `D-0D-DFP` | Defect Pair | [Defect Pair in GaN](defect_point_pair_gallium_nitride.ipynb) | *To be added* | [[16]](#ref16) |\n", + "| `D-0D-INT` | Interstitial | [Interstitial in SnO₂](defect_point_interstitial_tin_oxide.ipynb) | *To be added* | [[17]](#ref17) |\n", + "| `D-0D-SUB` | Substitution | [N-doped Graphene](defect_point_substitution_graphene.ipynb) | [N-doped Graphene Band Structure](defect_point_substitution_graphene_simulation.ipynb) | [[18]](#ref18) |\n", + "| `D-0D-VAC` | Vacancy | [Vacancy in BN](defect_point_vacancy_boron_nitride.ipynb) | *To be added* | [[19]](#ref19) |\n", + "| `X-3D-PER` | Perturbation | *To be added* | — | — |\n", + "| `X-3D-ANL` | Annealed Crystal | *To be added* | — | — |\n", + "| `X-2D-PER` | Perturbation | [Ripple Perturbation in Graphene](perturbation_ripple_graphene.ipynb) | *To be added* | [[20]](#ref20) |\n", + "| `X-2D-PAS` | Passivated Surface | [Silicon Surface Passivation](passivation_surface_silicon.ipynb) | *To be added* | [[21]](#ref21) |\n", + "| `X-1D-PAS` | Passivated Edge | [Si Nanowire Edge Passivation](passivation_edge_nanowire_silicon.ipynb) | *To be added* | [[22]](#ref22) |\n", + "| `X-0D-PAS` | Passivated Edge | *To be added* | — | — |\n", + "| `X-0D-CUT` | Slab Cutout | [Custom Cutout in Etched Silicon](custom_cutout_etched_silicon.ipynb) | *To be added* | — |\n", "\n", - "### 1.2. 2D Monolayer — `P-2D-MNL`\n", - "*(to be added)*\n", + "## References\n", "\n", - "### 1.3. 2D Slab — `P-2D-SLB`\n", - "#### [`P-2D-SLB-S` — Simple Slab: SrTiO₃ (structure)](slab_strontium_titanate.ipynb)\n", - "#### `P-2D-SLB-R` — Reconstructed Slab *(to be added)*\n", + "[1] Eglitis, R. I., & Vanderbilt, D. (2008). First-principles calculations of atomic and electronic structure of SrTiO₃ (001) and (011) surfaces. *Physical Review B*, 77(19), 195408. https://doi.org/10.1103/PhysRevB.77.195408\n", "\n", - "### 1.4. 1D Nanotape — `P-1D-NTP`\n", - "*(to be added)*\n", + "[2] Larsen, A. H., et al. (2011). Structure optimization of supported gold clusters. *Physical Review B*, 84(24), 245429. https://doi.org/10.1103/PhysRevB.84.245429\n", "\n", - "### 1.5. 1D Nanowire — `P-1D-NWR`\n", - "*(to be added)*\n", + "[3] Muller, D. A., et al. (1999). The electronic structure at the atomic scale of ultrathin gate oxides. *Nature*, 399(6738), 758-761. https://doi.org/10.1038/21602\n", "\n", - "### 1.6. 0D Nanoparticle — `P-0D-NPR`\n", - "#### [`P-0D-NPR` — Gold Nanocluster (structure)](nanocluster_gold.ipynb)\n", + "[4] Jung, J., et al. (2015). Moiré band model and band gaps of graphene on hexagonal boron nitride. *Nature Communications*, 6, 6308. https://doi.org/10.1038/ncomms7308\n", "\n", - "### 1.7. 0D Nanoribbon — `P-0D-NRB`\n", - "*(to be added)*\n", + "[5] Giovannetti, G., et al. (2008). Substrate-induced band gap in graphene on hexagonal boron nitride. *Physical Review B*, 78(11), 115404. https://doi.org/10.1103/PhysRevB.78.115404\n", "\n", - "---\n", + "[6] Shan, T. R., et al. (2011). Molecular dynamics study of the adhesion of Cu/SiO₂ interfaces using a variable-charge interatomic potential. *Physical Review B*, 83(11), 115327. https://doi.org/10.1103/PhysRevB.83.115327\n", "\n", - "## 2. Compound Pristine Structures\n", + "[7] Dahal, A., & Batzill, M. (2014). Graphene–nickel interfaces: a review. *Nanoscale*, 6(5), 2548-2562. https://doi.org/10.1039/c3nr05279f\n", "\n", - "### 2.1. 2D Heterostack — `C-2D-HST`\n", - "#### [`C-2D-HST` — Si/SiO₂/HfO₂/TiN Heterostructure (structure)](heterostructure_silicon_silicon_dioxide_hafnium_dioxide_titanium_nitride.ipynb)\n", + "[8] Liu, K., et al. (2014). Evolution of interlayer coupling in twisted molybdenum disulfide bilayers. *Nature Communications*, 5, 4966. https://doi.org/10.1038/ncomms5966\n", "\n", - "### 2.2. 2D Interface Simple — `C-2D-INT-S`\n", - "*(to be added)*\n", + "[9] Xian, L., et al. (2020). Realization of nearly dispersionless bands with strong orbital anisotropy from destructive interference in twisted bilayer MoS₂. *Nano Letters*, 20(7), 4631-4637. https://doi.org/10.1021/acs.nanolett.9b00986\n", "\n", - "### 2.3. 2D Interface ZSL — `C-2D-INT-Z`\n", - "#### [`C-2D-INT-Z` — BN/Graphene 2D–2D Interface (structure)](interface_2d_2d_boron_nitride_graphene.ipynb)\n", - "#### [`C-2D-INT-Z` — Graphene/SiO₂ 2D–3D Interface (structure)](interface_2d_3d_graphene_silicon_dioxide.ipynb)\n", - "#### [`C-2D-INT-Z` — Cu/Cristobalite 3D–3D Interface (structure)](interface_3d_3d_copper_cristobalite.ipynb)\n", - "#### [`C-2D-INT-Z` — Graphene/Ni Interface Film XY Position Optimization (structure)](optimization_interface_film_xy_position_graphene_nickel.ipynb)\n", + "[10] Saidi, W. A., et al. (2015). Trends in the adsorption and growth morphology of metals on the MoS₂(001) surface. *Crystal Growth & Design*, 15(6), 3190-3200. https://doi.org/10.1021/cg5013395\n", "\n", - "### 2.4. 2D Interface Twisted — `C-2D-INT-T`\n", - "*(to be added)*\n", + "[11] Chan, K. T., et al. (2008). First-principles study of metal adatom adsorption on graphene. *Physical Review B*, 77(23), 235430. https://doi.org/10.1103/PhysRevB.77.235430\n", "\n", - "### 2.5. 2D Interface Commensurate Lattice — `C-2D-INT-C`\n", - "#### [`C-2D-INT-C` — Twisted Commensurate MoS₂ Bilayer (structure)](interface_bilayer_twisted_commensurate_lattices_molybdenum_disulfide.ipynb)\n", + "[12] Zou, X., et al. (2015). Grain boundary properties of elemental two-dimensional materials. *Nano Letters*, 15(5), 3495-3500. https://doi.org/10.1021/acs.nanolett.5b01852\n", "\n", - "### 2.6. 2D Multi-Layer — `C-2D-MLT`\n", - "*(to be added)*\n", + "[13] Frolov, T., et al. (2013). Structural phase transformations in metallic grain boundaries. *Nature Communications*, 4, 2919. https://doi.org/10.1038/ncomms2919\n", "\n", - "### 2.7. 0D Nanoribbons Interface Rotation — `C-0D-INT-R`\n", - "#### [`C-0D-INT-R` — Twisted BN Nanoribbon Bilayer (structure)](interface_bilayer_twisted_nanoribbons_boron_nitride.ipynb)\n", + "[14] Sangiovanni, D. G., et al. (2018). Superioniclike diffusion in an elemental crystal: bcc titanium. *Physical Review B*, 97(3), 035406. https://doi.org/10.1103/PhysRevB.97.035406\n", "\n", - "---\n", + "[15] Sljivancanin, Z., & Hammer, B. (2002). Oxygen dissociation at close-packed Pt terraces, Pt steps, and Ag-covered Pt steps studied with density functional theory. *Surface Science*, 515(2-3), 235-244. https://doi.org/10.1016/s0039-6028(02)01908-8\n", "\n", - "## 3. Defective Structures\n", + "[16] Miceli, G., & Pasquarello, A. (2016). Self-compensation due to point defects in Mg-doped GaN. *Physical Review B*, 93(16), 165207. https://doi.org/10.1103/PhysRevB.93.165207\n", "\n", - "### 3.1. 3D Amorphous — `D-3D-AMO`\n", - "*(to be added)*\n", + "[17] Togo, A., et al. (2006). First-principles calculations of native defects in tin monoxide. *Physical Review B*, 74(19), 195128. https://doi.org/10.1103/PhysRevB.74.195128\n", "\n", - "### 3.2. 2D Adatom — `D-2D-ADA`\n", - "#### [`D-2D-ADA` — Pt Adatom/Island on MoS₂ (structure)](defect_point_adatom_island_molybdenum_disulfide_platinum.ipynb)\n", - "#### [`D-2D-ADA` — Adatom on Graphene (structure)](defect_surface_adatom_graphene.ipynb)\n", + "[18] Lherbier, A., et al. (2011). Electronic and transport properties of unbalanced sublattice N-doping in graphene. *Physical Review B*, 84(24), 245446. https://doi.org/10.1103/PhysRevB.84.245446\n", "\n", - "### 3.3. 2D Grain Boundary Planar — `D-2D-GBP`\n", - "#### [`D-2D-GBP` — Grain Boundary in 2D BN (structure)](defect_planar_grain_boundary_2d_boron_nitride.ipynb)\n", - "#### [`D-2D-GBP` — Grain Boundary in 3D FCC Cu (structure)](defect_planar_grain_boundary_3d_fcc_metals_copper.ipynb)\n", + "[19] Ivády, V., et al. (2022). Ab initio theory of the negatively charged boron vacancy qubit in hexagonal boron nitride. *npj Computational Materials*, 8(1), 1-9. https://doi.org/10.1038/s41524-022-00730-w\n", "\n", - "### 3.4. 2D Island — `D-2D-ISL`\n", - "#### [`D-2D-ISL` — TiN Island on Surface (structure)](defect_surface_island_titanium_nitride.ipynb)\n", + "[20] Thompson-Flagg, R. C., et al. (2009). Rippling of graphene. *EPL (Europhysics Letters)*, 85(4), 46002. https://doi.org/10.1209/0295-5075/85/46002\n", "\n", - "### 3.5. 2D Terrace — `D-2D-TER`\n", - "#### [`D-2D-TER` — Step/Terrace on Pt Surface (structure)](defect_surface_step_platinum.ipynb)\n", + "[21] Hansen, U., & Vogl, P. (1998). Hydrogen passivation of silicon surfaces: A classical molecular-dynamics study. *Physical Review B*, 57(20), 13295. https://doi.org/10.1103/PhysRevB.57.13295\n", "\n", - "### 3.6. 1D Grain Boundary Linear — `D-1D-GBL`\n", - "*(to be added)*\n", - "\n", - "### 3.7. 0D Defect Pair — `D-0D-DFP`\n", - "#### [`D-0D-DFP` — Defect Pair in GaN (structure)](defect_point_pair_gallium_nitride.ipynb)\n", - "\n", - "### 3.8. 0D Interstitial — `D-0D-INT`\n", - "#### [`D-0D-INT` — Interstitial in SnO₂ (structure)](defect_point_interstitial_tin_oxide.ipynb)\n", - "\n", - "### 3.9. 0D Substitution — `D-0D-SUB`\n", - "#### [`D-0D-SUB` — N-doped Graphene (structure)](defect_point_substitution_graphene.ipynb)\n", - "#### [`D-0D-SUB` — N-doped Graphene Band Structure (simulation)](defect_point_substitution_graphene_simulation.ipynb)\n", - "\n", - "### 3.10. 0D Vacancy — `D-0D-VAC`\n", - "#### [`D-0D-VAC` — Vacancy in BN (structure)](defect_point_vacancy_boron_nitride.ipynb)\n", - "\n", - "---\n", - "\n", - "## 4. Processed Structures\n", - "\n", - "### 4.1. 3D Perturbation — `X-3D-PER`\n", - "*(to be added)*\n", - "\n", - "### 4.2. 2D Perturbation — `X-2D-PER`\n", - "#### [`X-2D-PER` — Ripple Perturbation in Graphene (structure)](perturbation_ripple_graphene.ipynb)\n", - "\n", - "### 4.3. 3D Annealed Crystal — `X-3D-ANL`\n", - "*(to be added)*\n", - "\n", - "### 4.4. 2D Passivated Surface — `X-2D-PAS`\n", - "#### [`X-2D-PAS` — Silicon Surface Passivation (structure)](passivation_surface_silicon.ipynb)\n", - "\n", - "### 4.5. 1D Passivated Edge — `X-1D-PAS`\n", - "#### [`X-1D-PAS` — Si Nanowire Edge Passivation (structure)](passivation_edge_nanowire_silicon.ipynb)\n", - "\n", - "### 4.6. 0D Passivated Edge — `X-0D-PAS`\n", - "*(to be added)*\n", - "\n", - "### 4.7. 0D Slab Cutout — `X-0D-CUT`\n", - "#### [`X-0D-CUT` — Custom Cutout in Etched Silicon (structure)](custom_cutout_etched_silicon.ipynb)\n" + "[22] Aradi, B., et al. (2007). Theoretical study of the chemical gap tuning in silicon nanowires. *Physical Review B*, 76(3), 035305. https://doi.org/10.1103/PhysRevB.76.035305\n" ] }, {