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 Energies of SrTiO3(011) and (001) Terminations
DOI: 10.1103/PhysRevB.77.195408 ¹²

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

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 Stacking Energy and Band Gap of Graphene on h-BN
DOI: 10.1038/ncomms7308 ⁴

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

Structure: Create Graphene/SiO2 Interface
Properties: Calculate Doping and Gap at the Dirac Point of Graphene on SiO2
DOI: 10.1103/PhysRevB.78.115404

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

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

2.1.1.5. Si/Ge (001) Interface C-2D-INT-S

Structure: Create Si/Ge (001) Interface
Properties: Calculate Si/Ge (001) Valence Band Offset
DOI: 10.1103/PhysRevB.34.5621 ⁹

2.1.1.6. GaAs/AlAs (110) Interface C-2D-INT-S

Structure: Create GaAs/AlAs (110) Interface
Properties: Calculate GaAs/AlAs (110) Valence Band Offset
DOI: 10.1103/PhysRevB.90.155405 ¹⁰

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 ¹¹¹²

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 ¹³

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 Structure of Twisted MoS2 Bilayers
DOI: 10.1038/ncomms5966 ¹⁴¹⁵

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 ¹⁶

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 on MoS2
DOI: 10.1021/cg5013395 ^1718192021

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 ²²

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

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

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 ²³

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 Band Structure of N-doped Graphene
DOI: 10.1103/PhysRevB.84.245446

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 Formation Energy of the Mg_Ga-V_N Pair in GaN
DOI: 10.1103/PhysRevB.93.165207 ²⁴

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 Energy of a Boron Vacancy in h-BN
DOI: 10.1038/s41524-022-00730-w

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 Energy and Density of States of the V_Sn-O_i Pair in SnO
DOI: 10.1103/PhysRevB.74.195128 ²⁵²⁶²⁷

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 ²⁸²⁹³⁰

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 ³¹³²³³

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 ³⁴

References

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