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Specific Materials Examples

This document provides a comprehensive catalog of materials science tutorials organized by the MCODE (Materials Categorization by Ontology, Dimensionality and Evolution) system. Each entry includes:

  • Structure Notebook: Creates the atomic structure from published manuscripts
  • Properties Notebook: Calculates and reproduces key properties from the manuscript
  • DOI Reference: Link to the original scientific publication

1. Pristine Structures

1.1. 2D Structures

1.1.1. Slab

1.1.1.1. SrTiO3 Slab P-2D-SLB-S

Structure: Create SrTiO3 Slab Structure
Properties: Calculate surface energy (Coming Soon)
DOI: 10.1103/PhysRevB.77.195408 12

Strontium Titanate Slabs

1.2. 0D Structures

1.2.1. Nanoparticle

1.2.1.1. Gold Nanoclusters P-0D-NPR

Structure: Create Gold Nanocluster Structure
Properties: Calculate total energy per atom and density of states (Coming Soon)
DOI: 10.1103/PhysRevB.84.245429 3

Gold Nanoparticles

2. Compound Pristine Structures

2.1. 2D Structures

2.1.1. Interface

2.1.1.1. Graphene/h-BN Interface C-2D-INT-Z

Structure: Create Graphene/h-BN Interface
Properties: Calculate band structure and total energies (Coming Soon)
DOI: 10.1038/ncomms7308 4

Graphene on Hexagonal Boron Nitride

2.1.1.2. Graphene/SiO2 Interface C-2D-INT-Z

Structure: Create Graphene/SiO2 Interface
Properties: Calculate band structure (Coming Soon)
DOI: 10.1103/PhysRevB.78.115404

Graphene on Silicon Dioxide

2.1.1.3. Copper/SiO2 Interface C-2D-INT-Z

Structure: Create Copper/Cristobalite Interface
Properties: Calculate band structure (Coming Soon)
DOI: 10.1103/PhysRevB.83.115327 5

Copper on Cristobalite

2.1.1.4. Graphene/Ni(111) Interface Optimization C-2D-INT-Z

Structure: Create Graphene/Ni(111) Interface
Properties: Calculate total energies versus lateral shift and band structure (Coming Soon)
DOI: 10.1039/c3nr05279f 678

Gr/Ni Interface

2.1.2. Heterostack

2.1.2.1. High-k Metal Gate Stack (Si/SiO2/HfO2/TiN) C-2D-HST

Structure: Create High-k Metal Gate Stack
Properties: Calculate band structure and valence band offset (Coming Soon)
Reference: QuantumATK Tutorial 910

High-k Metal Gate Stack

2.1.3. Interface - Twisted

2.1.3.1. Twisted Bilayer h-BN Nanoribbons C-2D-INT-T

Structure: Create Twisted h-BN Nanoribbons
Properties: Calculate band structure and total energies versus twist angle (Coming Soon)
DOI: 10.1021/acs.nanolett.9b00986 11

Twisted Bilayer Boron Nitride

2.1.4. Interface - Commensurate

2.1.4.1. Twisted Bilayer MoS2 Commensurate Lattices C-2D-INT-C

Structure: Create Twisted MoS2 Commensurate Lattices
Properties: Calculate band gaps and band structure (Coming Soon)
DOI: 10.1038/ncomms5966 1213

Twisted Bilayer Molybdenum Disulfide

3. Defective Structures

3.1. 2D Structures

3.1.1. Island

3.1.1.1. Island Surface Defect Formation in TiN D-2D-ISL

Structure: Create Island Defect on TiN Surface
Properties: Calculate island formation energy (Coming Soon)
DOI: 10.1103/PhysRevB.97.035406 14

Surface Defect

3.1.1.2. Pt Adatoms Island on MoS2 D-2D-ISL

Structure: Create Pt Island on MoS2
Properties: Calculate binding energy per Pt atom and density of states (Coming Soon)
DOI: 10.1021/cg5013395 1516171819

Pt Island on MoS2

3.1.2. Terrace

3.1.2.1. Step Surface Defect on Pt(111) D-2D-TER

Structure: Create Step Defect on Pt(111)
Properties: Calculate energy of dissociation (Coming Soon)
DOI: 10.1016/s0039-6028(02)01908-8 20

Step Surface Defect on Pt

3.1.3. Adatom

3.1.3.1. Adatom Surface Defects on Graphene D-2D-ADA

Structure: Create Adatom Defects on Graphene
Properties: Calculate adsorption energy, density of states, work function, dipole moment, and diffusion barriers (Coming Soon)
DOI: 10.1103/PhysRevB.77.235430

Adatom on Graphene Surface

3.1.4. Grain Boundary Planar

3.1.4.1. Grain Boundary in h-BN D-2D-GBP

Structure: Create Grain Boundary in h-BN
Properties: Calculate band gaps and LDOS (Coming Soon)
DOI: 10.1021/acs.nanolett.5b01852

h-BN Grain Boundary

3.2. 1D Structures

3.2.1. Grain Boundary Linear

3.2.1.1. Grain Boundary in FCC Metals (Copper) D-1D-GBL

Structure: Create Grain Boundary in Copper
Properties: Calculate defect energy per atom (Coming Soon)
DOI: 10.1038/ncomms2919 21

Copper Grain Boundary

3.3. 0D Structures

3.3.1. Substitution

3.3.1.1. Substitutional Point Defects in Graphene D-0D-SUB

Structure: Create Substitutional Defects in Graphene
Properties: Calculate formation energies and band structure (Coming Soon)
DOI: 10.1103/PhysRevB.84.245446

Point Defect, Substitution, 0

3.3.2. Defect Pair

3.3.2.1. Vacancy-Substitution Pair Defects in GaN D-0D-DFP

Structure: Create Vacancy-Substitution Pair in GaN
Properties: Calculate defect formation energies (Coming Soon)
DOI: 10.1103/PhysRevB.93.165207 22

Point Pair Defects: Mg Substitution and Vacancy in GaN

3.3.3. Vacancy

3.3.3.1. Vacancy Point Defect in h-BN D-0D-VAC

Structure: Create Vacancy Defect in h-BN
Properties: Calculate formation energies (Coming Soon)
DOI: 10.1038/s41524-022-00730-w

Vacancy in h-BN

3.3.4. Interstitial

3.3.4.1. Interstitial Point Defect in SnO D-0D-INT

Structure: Create Interstitial Defect in SnO
Properties: Calculate formation energies and band structure (Coming Soon)
DOI: 10.1103/PhysRevB.74.195128 232425

SnO O-interstitial

4. Processed Structures

4.1. 3D Structures

4.1.1. Perturbation

4.1.1.1. Ripple Perturbation of Graphene Sheet X-3D-PER

Structure: Create Rippled Graphene Structure

DOI: 10.1209/0295-5075/85/46002 262728

Rippled Graphene

4.2. 2D Structures

4.2.1. Passivated Surface

4.2.1.1. H-Passivated Silicon (100) Surface X-2D-PAS

Structure: Create H-Passivated Si(100) Surface
Properties: Calculate H and D diffusion barriers, reaction and desorption barriers (Coming Soon)
DOI: 10.1103/PhysRevB.57.13295 293031

Si(100) H-Passivated Surface

4.3. 1D Structures

4.3.1. Passivated Edge

4.3.1.1. H-Passivated Silicon Nanowire X-1D-PAS

Structure: Create H-Passivated Si Nanowire
Properties: Calculate band gap, density of states, and formation energy (Coming Soon)
DOI: 10.1103/PhysRevB.76.035305 32

Passivated Silicon nanowire

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