diff --git a/other/materials_designer/specific_examples/Introduction.ipynb b/other/materials_designer/specific_examples/Introduction.ipynb index 1e8d0022..5376a9b5 100644 --- a/other/materials_designer/specific_examples/Introduction.ipynb +++ b/other/materials_designer/specific_examples/Introduction.ipynb @@ -12,45 +12,44 @@ "Domain (`P` - Pristine, `C` - Compound Pristine, `D` - Defective, `X` - Processed) - Dimensionality - Category - Variant (if applicable)\n", "\n", "\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", + "| 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-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", + "| `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 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 | [Grain Boundary in 2D BN](defect_planar_grain_boundary_2d_boron_nitride.ipynb) | *To be added* | [[12]](#ref12) |\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", "## References\n", "\n", diff --git a/other/materials_designer/specific_examples/defect_planar_grain_boundary_2d_boron_nitride.ipynb b/other/materials_designer/specific_examples/defect_planar_grain_boundary_2d_boron_nitride.ipynb index b895ff09..4fb6085f 100644 --- a/other/materials_designer/specific_examples/defect_planar_grain_boundary_2d_boron_nitride.ipynb +++ b/other/materials_designer/specific_examples/defect_planar_grain_boundary_2d_boron_nitride.ipynb @@ -44,7 +44,7 @@ "# Grain boundary parameters\n", "TARGET_TWIST_ANGLE = 9.0 # in degrees\n", "BOUNDARY_GAP = 0.0 # Gap between two orientations in X direction, in Angstroms\n", - "OVERLAP_TOLERANCE = 0.8 # Tolerance to remove overlapping atoms, in Angstroms\n", + "OVERLAP_TOLERANCE = 1.2 # Tolerance to remove overlapping atoms, in Angstroms\n", "\n", "# Search algorithm parameters\n", "MAX_REPETITION = None # Maximum supercell matrix element value\n",