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PeriodicBoundaryCondition
Atomic Scale Materials Modeling
Introduction to Atomic-Scale Materials Modeling
Key Takeaways
1. What is Atomic-Scale Materials Modeling?
Definition
Key Characteristics
2. The Foundation: Atoms, Interactions, and Energy
Atoms as Building Blocks
How Atoms Interact
Total Energy: The Central Concept
The Potential Energy Surface
Finding Equilibrium: Energy Minimization
The Many-Body Challenge
3. Two Fundamental Approaches
3.1 Force Fields
3.2 Density Functional Theory (DFT)
4. The Materials Modeling Hierarchy
Scale Bridging in Materials Science
Understanding the Hierarchy
Where Atomic-Scale Modeling Fits
5. When to Use Atomic-Scale Modeling
Primary Use Cases
Force Fields & Molecular Dynamics
1. From Quantum Complexity to Classical Approximation
What Do We Gain?
What Do We Lose?
The Fundamental Trade-off
2. Classical Force Fields: Mathematical Description
What is a Force Field?
2.1 Bonded Force Fields
2.2 Metallic Force Fields
2.3 Covalent/Semiconductor Force Fields
2.4 Ionic Force Fields
Force Field Parameters
3. Introduction to Molecular Dynamics (MD)
What is Molecular Dynamics?
The MD Algorithm: Step by Step
Understanding MD Output: The Trajectory
4. Material Properties from MD Simulations
What Can We Calculate?
5. Simple Application Example: Thermal Expansion of Aluminum
The Problem
The Simulation Approach
Expected Results
Extending the Example
Electronic Structure: Density Functional Theory
1. Introduction: What is Electronic Structure?
From Force Fields to Electrons
Why Electrons Matter
Electronic Structure: The Electron Distribution
From Classical to Quantum
Why Calculate Electronic Structure?
2. The Quantum Mechanical Many-Body Problem
The Schrödinger Equation
Key Approximations
DFT: The Practical Solution
3. What Can DFT Calculate?
4. DFT Workflow and Best Practices
Typical DFT Calculation Workflow
5. DFT vs. Force Fields: Making the Choice
Comparison Table
6. Brief Introduction to SemiEmpirical Methods
Machine learned Force Fields
1. The Speed-Accuracy Trade-off
The Fundamental Challenge
The Machine Learning Solution
The Key Insight
Why MLFFs Maintain Accuracy
2. How MLFFs Achieve DFT Accuracy at High Speed
The Core Concept
The Learning Process
3. When to Use MLFFs vs. DFT or Classical Force Fields
The MLFF Sweet Spot
Cost-Benefit Analysis for training a specific MLFF
4. Universal Machine Learned Force Fields
A New Paradigm: Pre-trained Models
What Are Universal MLFFs?
Advantages of Universal MLFFs
Limitations and Caveats
Fine-Tuning Universal Models
When to Use Universal vs. Custom MLFFs
The Future of Universal MLFFs
5. Summary: Breaking the Speed-Accuracy Trade-off
The MLFF Promise
Comparison of Computational Methods
Getting started with QuantumATK
Installation Guide
Access to SolvNet
Access to a License Server
Linux only: Download and use Synopsys Installer
Downloading, Installing and Configuring QuantumATK
Downloading QuantumATK
Installing QuantumATK
Configuring the QuantumATK License
System Requirements
Using QuantumATK from the command line
Troubleshooting
Slow Startup on Windows
libGL.so: Cannot Open Shared Object File
libGLU.so.1: Cannot Open Shared Object File
Could Not Find or Load the Qt Platform Plugin “xcb”
ATKError: Exceeded Maximum Number of Self-Consistent Iterations
Failure to Initialize
ImportError: No Module Named
Pulay Mixing Inversion Failed. Using Only Last Step
Why are so many
k
-points needed in the transport direction in a device calculation?
ATKError: St9bad_alloc
Runtime Terminates an Application
Killed by Signal 9
Not Enough Space to Allocate vblock
Can’t Allocate Memory for Array
ATKError: Bad Allocation
ATKError: Inverse(DZMatrix const&) : Could Not LU Factorize!
Cannot Run QuantumATK P-2019.03
Network or Nodelocked Licenses
License for QuantumATK Parallel Run
Basic License Troubleshooting
Advanced License Troubleshooting
Maintenance, Updates and Support
License and QuantumATK Upgrading
Updating the License File
License Server Cannot Be Started
SSH License Server Access
Restricting Access to a License Server
Introductory Tutorials
Geometry Optimization
Prerequisites
Importing Structures from the NanoLab Database
Setting up Geometry Optimization Workflow
References
Band Structure, Projected Density of States and Effective Mass Calculations
Prerequisites
Setting up Band Structure Calculation Workflow
Analyzing Band Structure Results
Restarting to Obtain Projected Density of States
Analyzing Projected Density of State Results
Calculation of Effective Masses
References
Optical Property Calculations
Prerequisites
Setting up an Optical Property Calculation Workflow
Analyzing Results
Outlook
References
Molecular Dynamics Simulations for Generating Amorphous Structures
Prerequisites
Setting-Up Molecular Dynamics Simulations
Analyzing Molecular Dynamics Simulations
References
NEGF Simulations of Electron Transport in Devices
Prerequisites
Building Si p-n Junction Device
Setting up Electron Transport Simulations for the Si p-n Junction at 0 V Bias
Analyzing Results at 0 V Bias
Setting up Electron Transport Simulations for the Si p-n Junction at Finite Bias
Analyzing Results at Finite Bias
Summary and Outlook
References
Feature List
Referencing QuantumATK
NanoLab Guides
Overview of NanoLab
Typical workflow
Create atomistic structure
Set up calculation
Run a job
Analyze results
What’s next
Projects in NanoLab
Organize your data in the Nanolab data view
The Nanolab Data View
1. The File Browser
2. The Search Field
The advanced SQL search
The Query Builder
3. The Data Table
The Quantum ID (qid)
Unpack
Analyzers and Preferences
4. The Data Preview
The Keywords
5. The Data Filters
6. The Data Sources
Data Inspectors
Builder Manual
Introduction
Layout and basic operations
Importing, adding, and exporting structures
Adding an already existing structure
Creating a new structure
Saving and exporting structures
Sending the structure to other QuantumATK tools
Mouse and key operations
Controlling the 3D view
Selection
Deleting atoms
Undo
Using the Move Tool
Selection control
Translation
Advanced Move
Overview of built-in Builder plugins
Builder Toolbar plugins
Builder Panelbar plugins
Custom builder plugins
Supported file formats for import and export
Third-party plugins
Managing plugins using the AddOn Manager
Workflows Manual
Introduction to the Workflow Builder
What is the Workflow Builder?
The Workflow Builder overview
What is a workflow block and how to edit it
Creating a simple workflow
Re-running a workflow
Workflow with multiple branches
Workflow with multiple configurations
Block of blocks
Common operations in the Workflow Builder
Using Tables in the Workflow Builder
How to collect data in a table
How to collect data in a table using an Iteration block
How to extract data from a table using a TableIteration block
Introduction to Array Jobs
How to build an array script in the Workflow Builder
How to submit an array script
Jobs manual
Job Manager for local execution of QuantumATK scripts
Execute QuantumATK simulations via the Job Manager
Serial execution
Threading
MPI parallelization
Adding Computers
Job Manager for remote execution of QuantumATK scripts
A single remote machine
Custom job settings
Debugging
Adding several remote machines
Plots
Plot Gallery
Bars
Contour
Density
Density For Weighted Lines
Filled Area
Line And Annotations
Line With Fit
Linegroup
Multiple Axes
Rolling Average
Scatter And Bars
Transformed Line
Working with Plots in NanoLab
Manage 3D View and Select Atoms
Rotations
Reset View
Zoom
Drag
Camera and View Planes
Selections
Importing and exporting files
Import/Export files in QuantumATK
Stash Items
Add from Database
Add from Files
Add from Plugins
Save and Export Structures
Export XYZ, CIF, CAR, VASP Files in QuantumATK
Built-in export filters
Exporting from scripts
Import XYZ, CIF, CAR, VASP Files in QuantumATK
Drag and Drop
Importing structures in a script
Molecular builder
Ethanol molecule
Caffeine molecule
Going further
Export the Stash Configuration file
Using the Crystal Builder
Introduction
Crystal structure of black phosphorus
Phosphorene and its bandstructure
Bandstructure
References
The Builder Console
Special variables
The active configuration
The selected atoms
The active camera
The Builder Stash
Console Snippets
The console in Builder plugin development
Questions
AddOns
Creating AddOns
Disabling or Uninstalling AddOns
Getting Addons
Installing AddOn
Install AddOns as limited access users
Installing AddOns on the local system
Failing AddOn Installation
AddOns Location
Updating AddOns
What Is an AddOn
Check Installed AddOns
Tutorials
New or Updated
Training and Fine-Tuning of MACE Models
Prerequisites
Overview of MACE Training in QuantumATK
Training a MACE Model from Scratch
Naive Fine-tuning of Foundation MACE Models
Multihead Replay Fine-tuning of Foundation MACE Models
Validation of Trained Models Using the MLFFAnalyzer
Using Custom MACE Models with Calculators in the Workflow Builder
Key Parameters for MACE Training
Best Practices for MACE Training and Important Distinctions
Summary
References
Moment Tensor Potential (MTP) Training for Crystal and Amorphous Structures
Prerequisites
Overview of the MTP Training Workflow
Crystal Training Data
Amorphous Active Learning
Final MTP Fitting
Submitting the MTP Training Calculation
Analyzing MTP Training Results
MTP Validation for Crystals
MTP Validation for Amorphous
Summary and Outlook
References
2D Database and potentials
Importing a Structure from the 2D Materials Database
Creating and Setting a Calculator from a 2D Potential Set
Phonon Bandstructure calculation
References
MRAM workflow in QuantumATK: Study of STT-MRAM free layer stability
Video
Introduction
Workflow for calculating the free layer stability in a STT-MRAM MTJ structure
Vampire
References
Generating A Magnetoresistive RAM (MRAM) Stack using the MRAM-Builder
Introduction
Workflow to generate the MgO-FeCo-MgO MRAM structure
Generating A High-k Metal Gate Stack Using the HKMG-Builder
Introduction
Workflow
How to select the right calculator
The Calculator types
The DFT Calculators (LCAO and Plane Wave)
The Semi Empirical Calculator
The Force Field Calculator
Using Thermochemistry Analyzer to Compare Chemical Reactions
Background
Getting started
Understanding the Thermochemistry Analyzer GUI
Example: Temperature Window for Thermal Atomic Layer Etching of HfO
2
and ZrO
2
General Uses
Electronic Properties of Phase Change Material Ge
2
Sb
2
Te
5
Geometry
Bandgap Calculation
Lattice Parameters
Cohesive Energies
Neutral Vacancy Formation Energies
Total DOS With and Without Ge Vacancy
STM simulations of tunneling anisotropic magneto resistance (TAMR)
Introduction
Setting up the 2LFe/W(110) structure
Local Density of States calculations
Analyzing the results
Co adatom on 2LFe/W(110)
COSMICS project
References
Bulk Magnetic Anisotropy Energy
Introduction
Theory
MAE of FePt
TotalEnergy calculations
Convergence of results
COSMICS project
Magnetic Anisotropy Energy of Fe-MgO-Fe MTJ structure
Introduction
Fe-MgO-Fe MTJ structure
MagneticAnisotropyEnergy calculation
What causes the PMA?
COSMICS project
Heisenberg exchange coupling of iron and cobalt
Introduction
Theory
Setting up calculations
Analyzing the results
COSMICS project
References
Building an model of an epoxy thermoset material
Theory
Building the thermoset model
Analyzing the Thermoset Reaction
Conclusions
Analyzing the thermo-mechanical properties of a polymer material
Glass Transition Temperature
Young’s Modulus and Poisson Ratio
Conclusions
Generating A Moment Tensor Potential for HfO
2
Using Active Learning
Background
Getting Started
Workflow
Step 1: Prepare Initial Reference Configurations
Step 2: Compute Reference Data and Setup Active Learning
Step 3: Find an MTP with Lowest Error
Validation MD Simulation
References
FAQ Section
Simulating Si Deposition using Silane
Background
Getting started
Step 1: Reference Calculations
Step 2: Adsorption and Dissociation of SiH
4
Step 3: Formation and Desorption of H
2
Conclusions
References
Electronic structure of NiO with DFT+U
Prerequisites
Introduction
The electronic structure of NiO calculated with DFT
DFT+U calculation for the NiO crystal
DFT +
Ab initio
U calculation for the NiO crystal
References
Semiconductors
Phonon-limited mobility in graphene using the Boltzmann transport equation
Geometry and electronic structure of graphene
Phonons in Graphene
Mobility of graphene
Convergence of q- and k-point sampling
Theory section
References
Effective mass of electrons in silicon
Introduction
Background
Set up the calculation
Analyze the results
Going further
References
Spin-orbit splitting of semiconductor band structures
Relavistic effects in Kohn-Sham DFT
Silicon band splitting with ATK-DFT
SO+MGGA band gap
GaAs band structure with ATK-SE and SO coupling
References
Silicon p-n junction
Silicon bulk: Slater-Koster vs DFT-MGGA
Silicon device
Analyzing the results
References
Optical Properties of Silicon
Introduction
Electronic structure and optical properties of silicon
References
NiSi
2
–Si interface
Create the NiSi
2
/Si device
Set-up the calculation for the undoped device
Dope the device
Analysis of the results
Finite-bias calculations
References
Bi
2
Se
3
topological insulator
Build the Bi
2
Se
3
crystal
Bi
2
Se
3
bulk band structure
Bi2Se3 surface: Spin-orbit band structure
DOS analysis: Dirac cone finger print
Penetration depth of surface states
Fermi surface and spin directions
Topological Invariants
References
Effective band structure of random alloy InGaAs
Methodology
Band structures of InAs
In
0.53
Ga
0.47
As random alloy
Finite broadening
Final comments
References
Complex band structure of Si(100)
Background
Si crystal cleaved in (100) direction
Complex band structure calculation
Analysing the results
3D visualizations
References
InAs p-i-n junction
Setting up the device geometry
Running the calculations
Defining the work function of the metal gate
Performing a gate scan
References
Inelastic current in a silicon p-n junction
Creating the silicon p-n junction
Transmission calculation without electron-phonon interactions
Transmission calculation with electron-phonon interactions
Speeding up the calculations
References
Elastic scattering, mean free path, mobility: Impurity scattering in a silicon nanowire
Introduction
Defected silicon nanowires
Elastic scattering mean free path
Fermi levels in doped nanowires
Doping dependent mobility
Summary and discussion
Appendix: Building the nanowires
References
Virtual Crystal Approximation for InGaAs random alloy simulations
Introduction
Setting up the VCA calculations for In
x
Ga
1
-
x
As
Analyzing the results for VCA with In
x
Ga
1
-
x
As
Calculating effective masses
Summary and discussion
References
DFT-1/2 and DFT-PPS density functional methods for electronic structure calculations
DFT-1/2 methods
DFT-PPS method
References
Electrical characteristics of devices using the IVCharacteristics study object
Prerequisites
Calculation and analysis of the
\(\mathrm{I_{ds}-V_{gs}}\)
curve for the FET on-state
Extending the range of the
\(\mathrm{I_{ds}-V_{gs}}\)
curve to the FET off-state
Analysis of the
\(\mathrm{I_{ds}-V_{gs}}\)
curve in the subthreshold region
Calculating the drain-induced barrier lowering
References
Formation energies and transition levels of charged defects
Procedure for calculating the formation energy
Setting up the calculation
Analyzing the results
Discussion and summary
Appendix
References
Introduction
Methods
HSE
Nomenclature
Pseudopotential Projector-Shift
Silicon
Summary
Convergence
Timing
Results
Appendix
References
Germanium
Summary
Convergence
Timing
Results
Appendix
Si
0
.
5
Ge
0
.
5
Summary
Convergence
Timing
Results
Appendix
References
Batteries & Energy Storage
Li-air battery interface
Li
2
O
2
bulk and surface structures
Li
2
CO
3
bulk and surface structures
The Li
2
O
2
/Li
2
CO
3
interface
References
Li-ion diffusion in LiFePO
4
for battery applications
Import LiFePO
4
bulk structure
Optimize LiFePO
4
lattice parameters
Create the Li
\(_{1-x}\)
FePO
4
structures
Optimize initial and final configurations
Create initial NEB trajectories
Optimize Li diffusion path
Calculate the reaction rates using harmonic transition state theory
References
Open-circuit voltage profile of a Li-S battery: ReaxFF molecular dynamics
Amorphous Li
0
.
4
S compound
Simulated annealing
Open-circuit voltage
Full open-circuit voltage profile
Radial distribution functions
References
Photocurrent in a silicon p-n junction
Device ground state
Photocurrent
References
Complex Interfaces
Building an interface between Ag(100) and Au(111)
Import silver and gold crystals
Building the Ag(100) and Au(111) crystals
Building the interface
Building the device configuration
Advanced device relaxation - manual workflow
Introduction
Preparations
Electrode relaxation
Central region relaxation
1DMIN optimization of the interface using 2-probe calculations
Relaxation of devices using the OptimizeDeviceConfiguration study object
Introduction
Unrelaxed Ag(100)|Ag(111) device
Set up and run the device geometry optimization
Relaxed device structures
Appendix
Atomic-scale capacitance
Build the parallel plate capacitor
Calculations
Analysis
Bias-dependent capacitance
Dielectric spacer material
Graphene–Nickel interface
Creating the structure
More configurations
Building a Si-Si
3
N
4
Interface
Preparations: Two crystals
Building the interface
Final adjustment
Doubling down: Buried layer model
Interface as a device model
NiSi
2
–Si interface
Create the NiSi
2
/Si device
Set-up the calculation for the undoped device
Dope the device
Analysis of the results
Finite-bias calculations
References
Determination of low strain interfaces via geometric matching
Method description
Input and output description
Example 1: Lattice match between two bulk systems
Example 2: Lattice match between a bulk system with a predefined surface
References
Generating A High-k Metal Gate Stack Using the HKMG-Builder
Introduction
Workflow
Generating A Magnetoresistive RAM (MRAM) Stack using the MRAM-Builder
Introduction
Workflow to generate the MgO-FeCo-MgO MRAM structure
Modeling Schottky barrier heights: The Ag–Si interface
Creating the device
Zero-bias calculations
Projected local density of states
Finite-bias calculations
Summary
References
Appendix - Note on the variation of the current
Resistivity calculations using the MD-Landauer method
1. Theory and numerical procedure
2. Calculation setup
3. Data analysis
References
Electron transport calculations with electron-phonon coupling included via the special thermal displacement method - STD-Landauer
Building the device
Calculations
Analysis and discussion
References
1D Nanostructures
Transport in graphene nanoribbons
Introduction
Band structure of 2D graphene
Band structure of an armchair ribbon
Transport properties of a zigzag nanoribbon
Transmission spectrum of a spin-polarized atomic chain
Building the 1D carbon chain
Spin-parallel transmission spectrum
Spin anti-parallel transmission spectrum
Introduction to noncollinear spin
From collinear to noncollinear spin
Getting started
Spin rotation of 120°
Analysis
Spin-orbit interactions
Carbon Nanotube Junctions
Setting up the geometry
Capping a carbon nanotube
Build an extended (5,5) carbon nanotube
Cut the fullerene in half
Capping the tube
Finalizing the geometry
Simple carbon nanotube device
Build and geometry optimize a short CNT
CNT device configuration
Thermoelectric effects in a CNT with isotope doping
CNT device with tags for
14
C doping
Phonon transmission
Electron transmission
Thermoelectric transport properties
References
Graphene nanoribbon device: Electric properties
Electron transmission spectrum
Effect of the Gate Potential
I–V characteristics
When is the linear response approximation valid?
Further analysis with ATK-SE
Temperature dependent conductance
Comparison to results for a longer device
References
Silicon nanowire field-effect transistor
Introduction
Band structure of a Si(100) nanowire
Setting up and running the calculations
Si(100) nanowire FET device
Zero gate voltage calculation
Exploring Graphene
Build a graphene sheet
Build a CNT
Transmission spectrum of a GNR
Twisted nanoribbon
Möbius nanoribbon
Buckling a graphene sheet
Elastic scattering, mean free path, mobility: Impurity scattering in a silicon nanowire
Introduction
Defected silicon nanowires
Elastic scattering mean free path
Fermi levels in doped nanowires
Doping dependent mobility
Summary and discussion
Appendix: Building the nanowires
References
2D Materials
Meta-GGA and 2D confined InAs
TB09 meta-GGA
Bulk InAs band structure with TB09 meta-GGA
Setting up and passivating an InAs slab
Band structure with default hydrogen atoms
Analyzing the results
Passivation using pseudo-hydrogen
Results
Passivation using compensation charges
Results
Non-parabolicity in confined structures
Nanowire band structure
References
Opening a band gap in silicene and bilayer graphene with an electric field
Bilayer graphene
Silicene
References
More reading
Commensurate supercells for rotated graphene layers
Additional rotated structures
References
Spin-dependent Bloch states in graphene nanoribbons
Band structure of a zigzag nanoribbon
Bloch states
Introducing spin
Electron density and Mulliken populations
References
Exploring Graphene
Build a graphene sheet
Build a CNT
Transmission spectrum of a GNR
Twisted nanoribbon
Möbius nanoribbon
Buckling a graphene sheet
2D Database and potentials
Importing a Structure from the 2D Materials Database
Creating and Setting a Calculator from a 2D Potential Set
Phonon Bandstructure calculation
References
Phonons & Thermal Transport
Calculating and using Dynamical Matrix
Prerequisites
Create the Workflow
LCAOCalculator Settings
Lattice optimization Settings
Dynamical matrix Settings
Running the calculation
Analyzing the results
Speeding up the calculation with ForceFields
Vibrational modes and Vibration Visualizer
MoS
2
monolayer
Nanophononic metamaterials
Phonons, Bandstructure and Thermoelectrics
Introduction
Phonon Bandstructure of a Graphene Nanoribbon
Analyzing the Results
Algorithmic Details of the Phonon Calculator
Calculating Electrical and Heat Transport for a Graphene Nanoribbon
Phonon-limited mobility in graphene using the Boltzmann transport equation
Geometry and electronic structure of graphene
Phonons in Graphene
Mobility of graphene
Convergence of q- and k-point sampling
Theory section
References
Thermoelectric effects in a CNT with isotope doping
CNT device with tags for
14
C doping
Phonon transmission
Electron transmission
Thermoelectric transport properties
References
Inelastic Electron Spectroscopy of an H
2
molecule placed between 1D Au chains
Introduction
Device setup
Calculation of IETS
Analysis
References
Using Thermochemistry Analyzer to Compare Chemical Reactions
Background
Getting started
Understanding the Thermochemistry Analyzer GUI
Example: Temperature Window for Thermal Atomic Layer Etching of HfO
2
and ZrO
2
General Uses
Interfacial thermal conductance
Introduction
Reverse non-equilibrium molecular dynamics (RNEMD)
Non-equilibrium Green’s function method
References
Molecular Dynamics
How to Setup Basic Molecular Dynamics Simulations
Pre-requisites
NVE Simulations
NVT Simulations
NPT Simulations
Conclusion
Simulating Thin Film Growth via Vapor Deposition
Introduction
Simulation Strategies
Preparing the System
Setting up the Deposition Simulation
Running the Simulation
General Remarks
Simulating Si Deposition using Silane
Background
Getting started
Step 1: Reference Calculations
Step 2: Adsorption and Dissociation of SiH
4
Step 3: Formation and Desorption of H
2
Conclusions
References
Simulating Ion Bombardment on Graphene Sheets
Setting up the Graphene Sheet:
Adding a Bombardment Atom
Setting up the Simulation
Modifying the Script
References
Uniaxial and Biaxial Stress in Silicon
Introduction
Uniaxial Stress
Biaxial Stress
Adding, Combining, and Modifying Classical Potentials
Introduction
Adding a New Classical Potential from Scratch
A Potential for Amorphous Oxides
Combining a Tersoff and a Lennard-Jones Potential
Intra- and Inter-Layer Cohesion in MoS
2
Generating Amorphous Structures
Introduction
Amorphous Structure Generation with Classical MD Simulations
Refining Amorphous Structures
Creating Crystal/Amorphous Interfaces
Further Examples
Young’s modulus of a CNT with a defect
CNT bulk configuration
Configuring the MD simulation
Adding Python hooks
Computing Young’s modulus
Visualize and analyse the results
References
Interfacial thermal conductance
Introduction
Reverse non-equilibrium molecular dynamics (RNEMD)
Non-equilibrium Green’s function method
References
Diffusion in Liquids from Molecular Dynamics Simulations
Theory
Computational Procedure
Analysis
Simulating a creep experiment of polycrystalline copper
Installing the polycrystal builder plugin
Building the polycrystalline cell
Analyzing the grain structure
Setting up the creep simulation
Running the simulation
Analyzing the results
Outlook
References
Metadynamics Simulation of Cu Vacancy Diffusion on Cu(111) - Using PLUMED
Introduction
Theoretical Background
Metadynamics Simulation of Cu Vacancy on Cu(111)
References
Open-circuit voltage profile of a Li-S battery: ReaxFF molecular dynamics
Amorphous Li
0
.
4
S compound
Simulated annealing
Open-circuit voltage
Full open-circuit voltage profile
Radial distribution functions
References
Viscosity in liquids from molecular dynamics simulations
Theory
Computational procedure
Analyzing the results
Extending the results
Building an model of an epoxy thermoset material
Theory
Building the thermoset model
Analyzing the Thermoset Reaction
Conclusions
Analyzing the thermo-mechanical properties of a polymer material
Glass Transition Temperature
Young’s Modulus and Poisson Ratio
Conclusions
Moment Tensor Potential (MTP) Training for Crystal and Amorphous Structures
Prerequisites
Overview of the MTP Training Workflow
Crystal Training Data
Amorphous Active Learning
Final MTP Fitting
Submitting the MTP Training Calculation
Analyzing MTP Training Results
MTP Validation for Crystals
MTP Validation for Amorphous
Summary and Outlook
References
Generating A Moment Tensor Potential for HfO
2
Using Active Learning
Background
Getting Started
Workflow
Step 1: Prepare Initial Reference Configurations
Step 2: Compute Reference Data and Setup Active Learning
Step 3: Find an MTP with Lowest Error
Validation MD Simulation
References
FAQ Section
Training and Fine-Tuning of MACE Models
Prerequisites
Overview of MACE Training in QuantumATK
Training a MACE Model from Scratch
Naive Fine-tuning of Foundation MACE Models
Multihead Replay Fine-tuning of Foundation MACE Models
Validation of Trained Models Using the MLFFAnalyzer
Using Custom MACE Models with Calculators in the Workflow Builder
Key Parameters for MACE Training
Best Practices for MACE Training and Important Distinctions
Summary
References
Molecular Electronics
Building molecule–surface systems: Benzene on Au(111)
Summary of workflow
Detailed instructions
References
Building a molecular junction
Benzene to DTB: Building the molecule
Cleaving gold into two surfaces
Combining the molecule and the surfaces
Converting the central region to a device configuration
References
Molecular Device
Zero-bias calculation
Analysis of the zero-bias results
I-V characteristics
References
Inelastic Electron Spectroscopy of an H
2
molecule placed between 1D Au chains
Introduction
Device setup
Calculation of IETS
Analysis
References
Spintronics
Spin Transfer Torque
Introduction
Getting Started
Calculate the STT
Angle Dependence
References
Transmission spectrum of a spin-polarized atomic chain
Building the 1D carbon chain
Spin-parallel transmission spectrum
Spin anti-parallel transmission spectrum
Introduction to noncollinear spin
From collinear to noncollinear spin
Getting started
Spin rotation of 120°
Analysis
Spin-orbit interactions
Spin transport in magnetic tunnel junctions
Introduction
Getting started
Parallel spin
Anti-parallel spin
Tunneling magnetoresistance
Adaptive k-point grid
Spin-transfer torque
Relaxing the device central region
References
Relativistic effects in bulk gold
GGA band structure
Spin-orbit GGA band structure
References
Spin-orbit splitting of semiconductor band structures
Relavistic effects in Kohn-Sham DFT
Silicon band splitting with ATK-DFT
SO+MGGA band gap
GaAs band structure with ATK-SE and SO coupling
References
Bi
2
Se
3
topological insulator
Build the Bi
2
Se
3
crystal
Bi
2
Se
3
bulk band structure
Bi2Se3 surface: Spin-orbit band structure
DOS analysis: Dirac cone finger print
Penetration depth of surface states
Fermi surface and spin directions
Topological Invariants
References
Noncollinear calculations for metallic nanowires
Building the device
Setting up the collinear calculation and analyzing the results
Setting up the noncollinear calculation
Analyzing the results
Including spin-orbit coupling in noncollinear calculations
References
Electronic structure of NiO with DFT+U
Prerequisites
Introduction
The electronic structure of NiO calculated with DFT
DFT+U calculation for the NiO crystal
DFT +
Ab initio
U calculation for the NiO crystal
References
Bulk Magnetic Anisotropy Energy
Introduction
Theory
MAE of FePt
TotalEnergy calculations
Convergence of results
COSMICS project
Magnetic Anisotropy Energy of Fe-MgO-Fe MTJ structure
Introduction
Fe-MgO-Fe MTJ structure
MagneticAnisotropyEnergy calculation
What causes the PMA?
COSMICS project
STM simulations of tunneling anisotropic magneto resistance (TAMR)
Introduction
Setting up the 2LFe/W(110) structure
Local Density of States calculations
Analyzing the results
Co adatom on 2LFe/W(110)
COSMICS project
References
Heisenberg exchange coupling of iron and cobalt
Introduction
Theory
Setting up calculations
Analyzing the results
COSMICS project
References
Generating A Magnetoresistive RAM (MRAM) Stack using the MRAM-Builder
Introduction
Workflow to generate the MgO-FeCo-MgO MRAM structure
MRAM workflow in QuantumATK: Study of STT-MRAM free layer stability
Video
Introduction
Workflow for calculating the free layer stability in a STT-MRAM MTJ structure
Vampire
References
Materials, Surfaces and Chemistry
Polymer Builder
Procedure of the Polymer Builder
Green’s function surface calculations
Atomistic models of a surface
NEGF calculation with a single electrode
Work function of Ag(100)
Convergence wrt. metal layers
Polarization
Introduction
Modern theory of polarization
Spontaneous polarization of ferroelectric BaTiO
3
References
Vibrational modes and Vibration Visualizer
MoS
2
monolayer
Nanophononic metamaterials
Visualize the LUMO state of a water molecule
Building the molecule
Calculating the LUMO state
How to calculate reaction barriers using the Nudged Elastic Band (NEB) method
Create the initial and final states for the NEB
Set up and run the NEB calculations
Analyze the results
Summary
References
Ammonia inversion reaction barrier using DFTB and NEB
Setting up the NEB object
Performing the NEB simulation
Analyzing the NEB simulation
A recipe for faster calculations
Reconstruction of the Si (100) surface - a geometry optimization study with QuantumATK
Introduction
Building the geometry
Setting up the calculation
Results
Summary
Computing the work function of a metal surface using ghost atoms
Why use ghost atoms?
Setting up the geometry
Defining the parameters of the calculation
Calculation and analysis
Comments
Tuning the work function of silver by deposition of ultrathin oxide layers
Ag(100) and MgO(100) surfaces
Ag/MgO interface
DFT calculations
Analyzing the results
1D Projector plugin
References
Calculating Reaction Rates using Harmonic Transition State Theory
Introduction
Modeling Pt Adatom Diffusion on Pt(100)
Calculating the Rate for Multiple Elementary Reaction Steps
References
Simulating Si Deposition using Silane
Background
Getting started
Step 1: Reference Calculations
Step 2: Adsorption and Dissociation of SiH
4
Step 3: Formation and Desorption of H
2
Conclusions
References
Calculation of Formation Energies
Formation energy calculations (or cohesive energy)
Cohesive energy of a bulk system
Defect formation energy calculations
References
Uniaxial and Biaxial Stress in Silicon
Introduction
Uniaxial Stress
Biaxial Stress
Elastic constants
Methodology
Calculating elastic constants using classical potentials
Calculate elastic constants using DFT
Young’s modulus of a CNT with a defect
CNT bulk configuration
Configuring the MD simulation
Adding Python hooks
Computing Young’s modulus
Visualize and analyse the results
References
Relativistic effects in bulk gold
GGA band structure
Spin-orbit GGA band structure
References
Geometry optimization: CO/Pd(100)
Bulk palladium
Build the Pd(100) surface and relax it
Relax the CO/Pd(100) system
Relax the CO molecule
Adsorption energy
Modeling Vacancy Diffusion in Si
0.5
Ge
0.5
with AKMC
Obtaining an Initial Structure
Running the AKMC Simulation
Conclusion
Computing the piezoelectric tensor for AlN
Introduction
Computing the piezoelectric tensor
Alternative way of calculating the piezoelectric coefficient
\({e}_{33}\)
Computing the Born effective charge
References
Formation energies of charged defects - manual workflow
Procedure for calculating the formation energy
Neutral As vacancy in GaAs
Charged As vacancies in GaAs
Appendix
References
Boron diffusion in bulk silicon
Creating the B-doped Si crystal
Running the AKMC simulation
Adaptive Kinetic Monte Carlo Simulation of Pt Island Ripening
Introduction
Creating the initial configuration
Setting up the AKMC Simulation
Running the Simulation
Analyzing the AKMC Simulation
Conclusion
References
Adaptive Kinetic Monte Carlo Simulation of Pt on Pt(100)
Introduction
The AKMC method
Creating the initial configuration
Creating the AKMC script
Analyzing the results
Conclusion
References
Crystal Structure Prediction Scripter: Phases of TiO
2
Setting up the calculation
Running the calculations and analyzing results
References
Electronic structure of NiO with DFT+U
Prerequisites
Introduction
The electronic structure of NiO calculated with DFT
DFT+U calculation for the NiO crystal
DFT +
Ab initio
U calculation for the NiO crystal
References
DFT-D and basis-set superposition error
The DFT-D dispersion corrections
D2 correction
D3 correction
BSSE and the counterpoise correction
Set-up the graphene bilayer system
Geometry optimization without counterpoise correction
Including the counterpoise correction
Including the D2 dispersion correction
Including the D3 dispersion correction
Summary of the results
References
Formation energies and transition levels of charged defects
Procedure for calculating the formation energy
Setting up the calculation
Analyzing the results
Discussion and summary
Appendix
References
Using Thermochemistry Analyzer to Compare Chemical Reactions
Background
Getting started
Understanding the Thermochemistry Analyzer GUI
Example: Temperature Window for Thermal Atomic Layer Etching of HfO
2
and ZrO
2
General Uses
Electronic Properties of Phase Change Material Ge
2
Sb
2
Te
5
Geometry
Bandgap Calculation
Lattice Parameters
Cohesive Energies
Neutral Vacancy Formation Energies
Total DOS With and Without Ge Vacancy
Miscellaneous
The DFTB model in ATK-SE
Installing DFTB parameters
Testing the installation
Spin polarized calculations with DFTB
Accessing QuantumATK internal variables
Internal matrices accessible in QuantumATK
Multi-terminal conduction
Transmission projection
AC conductance
References
Slater-Koster tight-binding models in ATK-SE
Introduction
Onsite matrix element
Offsite matrix elements
Defining the full Slater-Koster table
Silicon band structure
Adding hydrogen
Band gaps of passivated silicon nanowires
References
Linear response current – how to compute it, and why it is often not a good idea
Make Movies from QuantumATK Trajectory Files
Creating Animated GIF
Rotation Animator
Movie from Trajectory Files
Converting lattices: Rhombohedral to hexagonal and back
Conversion between hP and hR representations
Converting hP supercell to hR primitive cell
Crystal classifications
References
Reusing electrodes in device calculations
Separate scripts for electrodes and device
Initialize from a converged state
Introduction
Examples
Restarting a stopped calculation
Saving the checkpoint file
Restarting the calculation from the checkpoint file
Compute quantities from converged simulations
POV-Ray images from QuantumATK
Elementary functionalities through an example
Examining the .pov file
Exporting pictures with POV-Ray
Generating A High-k Metal Gate Stack Using the HKMG-Builder
Introduction
Workflow
Generating A Magnetoresistive RAM (MRAM) Stack using the MRAM-Builder
Introduction
Workflow to generate the MgO-FeCo-MgO MRAM structure
How to select the right calculator
The Calculator types
The DFT Calculators (LCAO and Plane Wave)
The Semi Empirical Calculator
The Force Field Calculator
Transport calculations with QuantumATK
Introduction
Geometry for transport calculations
Getting started
Convergence of electrode parameters
Zero-bias analysis
Finite-bias calculations
Summary
Calculate the band structure of a crystal
Start QuantumATK and create a new project
Import the Silicon structure from the Database and send it to the Scripter
Set up the calculation and analyse the band structure
Phonons, Bandstructure and Thermoelectrics
Introduction
Phonon Bandstructure of a Graphene Nanoribbon
Analyzing the Results
Algorithmic Details of the Phonon Calculator
Calculating Electrical and Heat Transport for a Graphene Nanoribbon
Introducing the QuantumATK plane-wave DFT calculator
Introduction
How to calculate reaction barriers using the Nudged Elastic Band (NEB) method
Create the initial and final states for the NEB
Set up and run the NEB calculations
Analyze the results
Summary
References
Carbon Nanotube Junctions
Setting up the geometry
Capping a carbon nanotube
Build an extended (5,5) carbon nanotube
Cut the fullerene in half
Capping the tube
Finalizing the geometry
Simple carbon nanotube device
Build and geometry optimize a short CNT
CNT device configuration
Building a Si-Si
3
N
4
Interface
Preparations: Two crystals
Building the interface
Final adjustment
Doubling down: Buried layer model
Interface as a device model
Build a graphene nanoribbon transistor
Small nanoribbon transistor
A longer nanoribbon transistor
Commensurate supercells for rotated graphene layers
Additional rotated structures
References
Nanosheet with a hole
MoS
2
Nanotubes
Graphene–Nickel interface
Creating the structure
More configurations
Stone–Wales Defects in Nanotubes
Creating the defect and wrapping the tube
Optimizing the structure
Transmission spectrum
References
Building a molecular junction
Benzene to DTB: Building the molecule
Cleaving gold into two surfaces
Combining the molecule and the surfaces
Converting the central region to a device configuration
References
Application Examples
Applying Depth (Z-coordinate)-Dependent Heat Pulse in Molecular Dynamics Simulations
System Overview
Simulation Workflow
Step 1: Structure Setup and Initial Equilibration
Step 2: Heat Pulse Application
Step 3: Production Run with Temperature Control
Analysis and Observations
Temperature Profiles
Energy Flow
Customization Options
Adjusting Heat Parameters
Temperature Control
Output Files
Using the NanoLab Workflow
Running the Script
Performance Considerations
Summary
Battery Open Circuit Voltage (OCV) Prediction for Lithium-Ion Cathode Materials
Theoretical Background: What is OCV?
Open Circuit Voltage (OCV) Fundamentals
Thermodynamic Basis
Computational Approach: The Difference Method
Why Computational OCV Prediction is Valuable
System Overview
Simulation Workflow
Inputs and Configuration
Overview of Computational Steps
Step 1: Structure Preparation
Step 2: Configurational Sampling
Step 3: Energy Calculation and Ground State Identification
Step 4: Li Metal Reference Energy
Step 5: Voltage Calculation
Step 6: Results Visualization
Analysis and Observations
OCV Curves for Different NMC Compositions
OCV Curve for LiFePO₄
Computational Performance
Running the Scripts
Output Files
Advanced Extensions
Entropy Corrections for Finite Temperature
Structural Analysis
Summary
References
Atomic Layer Etching: Cl
2
Adsorption and Ar Ion Bombardment on Si(100)
System Overview
Simulation Workflow
Step 0: Choice of Calculator
Step 1: Surface Preparation and Equilibration
Step 2: Chlorine Adsorption Phase
Step 3: Argon Ion Bombardment Phase
Step 4: Post-Processing Analysis
Analysis and Observations
Chlorine Saturation Behavior
Etching Yield and Material Removal
Customization Options
Process Parameter Optimization
Cycle Timing Optimization
Output Files
Using the NanoLab Workflow
Running the Script
Performance Considerations
Summary
Automated Precursor Molecule Generation for Vapor Deposition
System Overview
Simulation Workflow
Step 0: Ligand Library Preparation
Step 1: Define Central Atom and Coordination
Step 2: Combinatorial Precursor Generation
Step 3: Calculator Selection
Step 4: Molecular Geometry Optimization
Step 5: Subsequent Analysis Suggestion for Selection
Customization Options
Distance Control
Ligand Types
Central Atom Options
Coordination Numbers
Running the Script
Performance Considerations
Best Practices
Summary
Surface Phase Diagram Construction
Scientific Background
Surface Phase Diagrams in Catalysis
Theoretical Framework
Example System: RuO
2
in H
2
O/O
2
Environment
Surface Configurations
Workflow Overview
STEP 1: Generate Surface Configurations
STEP 2: Calculate Thermochemistry Properties
STEP 3: Upload Thermochemistry to Database
STEP 4: Define System Parameters
STEP 5: Configure Script Parameters
STEP 6: Run the Phase Diagram Script
Temperature-Pressure Phase Diagrams
Alternative Representation
Advanced Usage
Multiple Temperature Comparison
Running the Script
Output Files
Further Reading
Summary
ALD Precursor Bond Dissociation Energies
Application Goal and Workflow
Objective
Automated Workflow Steps
Scientific Background
Bond Dissociation Energy in ALD
Computational Approach
Automatic Identification of Unique Ligands
Critical Automation Step
Example: Al(CH₃)₂Cl (Dimethylaluminum Chloride)
How the Automation Works
Automated Output
Summary
SMI-Cluster Adsorption Energy Calculations
Application Goal and Workflow
Objective
Automated Workflow Steps
Scientific Background
Adsorption Energy for SMI-Cluster Interactions
Computational Approach
Automatic Identification of Unique Ligands
Critical Automation Step
Ligand Identification Process
Workflow Modes
Semi-Automated Workflow
Fully Automated Workflow
Complex Formation with Adsorption Tool
Workflow
Output
Summary
Manual
General
Introduction
New in QuantumATK Y-2026.03
Installing and running the software
How to read this manual
Atomic-Scale Calculators
DFT: LCAO
Introduction
Background information
DFT: Plane Wave
Introduction
Background information
Semi Empirical
Introduction
Background information
Parameters
Force Field
Introduction
TremoloX
TremoloX potential classes
Neural network based force field parameter sets
How to choose the right pretrained neural network based force field
TremoloX potential parameter sets
Pretrained moment tensor potential (MTP) parameter sets
NEGF: Device Calculators
Introduction
Device configuration
Non-equilibrium electron distribution
Effective potential
Total energy and forces
Transmission coefficient
Electrical current
References
Python in QuantumATK
ATK-Python
Python packages in QuantumATK
Using NumPy with QuantumATK
Cloning of QuantumATK Python objects
Plotting using pylab
Physical quantities and units
Usage Examples
Units available in
QuantumATK
Read and Write Support
HDF5 (Default File Format)
Metatext
Spin
Usage Example
Note about Spin.All
Note on Spin in low level interface functions
Command Line Usage with QATK Shell Environments
Introduction
Use QuantumATK effectively from CLI: Shell Environments
Customize the environment: Python venvs
QuantumATK Reference Manual
Geometry
Lattices
Calculators
Common Parameters
DFT Calculators
Machine Learning DFT
MBPT Calculators
Semi-Empirical Calculator
Counterpoise Correction
Low level entities
Analysis
Common Analysis
Bulk Analysis
Device Analysis
DFT + U
Study
Dynamics and Optimization
Optimization
Molecular Dynamics
Soft Matter Dynamics
Surface Process Simulation
Training Data Generation
Machine-Learned Force Field Training
Machine-Learned Property Prediction
Monte Carlo
Hyperdynamics
Constraints
MD Analysis
Image Interpolation Algorithms (NEB)
Defects
Characterization
Migration
COSMO-RS
Material Descriptions
Properties
Stored Data
Polymers
Builders And Equilibration
Potentials
Analysis
Input and Output
Periodic Table
Utilities
Plot
NanoLab Plot Reference Manual
Plot
Full QuantumATK package
QuantumATK
Technical Notes
Poisson solvers
The Hartree potential
Boundary conditions
Boundary Conditions in NEGF
Dielectric and metallic regions
Poisson solvers
References
Occupation Methods
Background
Comparison of smearing methods
References
Pseudopotentials and basis sets available in QuantumATK
Pseudopotentials
LCAO basis sets
Accuracy tests for elemental solids
Accuracy tests for mixed solids
Notes for each pseudopotential type
References
Doping methods available in QuantumATK
General background
Explicit charge
Atomic compensation charges
Optical response functions
Linear response coefficients
Hybrid Functionals
Background
ACE Implementation
Usage Examples
References
NEGF Convergence Guide
Introduction
Zero-bias NEGF calculations
Finite-bias NEGF calculations
SCF iteration control parameters
Contact support
Spin-Polarized NEGF Convergence Guide
Systems investigated
Calculating the self-energy matrix
Zero and finite-bias convergence: mixing parameters
Zero and finite-bias convergence: electrode-length and k-point sampling
Electrode validator
Contact support
Noncollinear spins and spin transfer torque in devices
Parallelization of QuantumATK calculations
Unit-of-work
Parallelization levels in QuantumATK
Bulk calculations
NEGF calculations
Examples of multi-level parallelisms in QuantumATK
References
GPU acceleration of proprietary feature calculations
Enabling GPU acceleration
LCAOCalculator and SemiEmpiricalCalculator
DeviceLCAOCalculator and DeviceSemiEmpiricalCalculator
Poisson solvers
GWCalculator
Force Field
Machine-learned Force Field Training
Parallelization
Performance tips for DFT and Semi-Empirical
Examples
Performance troubleshooting guide
Running out of memory?
Want to make it run faster?
Study objects
Restart example
Finding Transition States
Nudged Elastic Band
Minimum Mode Following Techniques
Best Practices and Recommendations
References
Molecular Dynamics
Introduction
Methodology
NVE Simulations
NVT Simulations
NPT Simulations
Non-Equilibrium Simulations
MD Simulations with Constraints
Device Configurations
Molecules
Charged Point Defects
Defining defects
Pristine Reference Configuration
Chemical Potentials in Compound Materials
Charged Point Defect Calculation
Analyzing charged point defect calculations
Defect migration
Diffusivity of defects
Analyzing Diffusion Results
\(G_0W_0\)
calculator in QuantumATK
Imaginary time and frequency grid
Coulomb integrals and Polarizability using Auxiliary Basis Sets and PARI
Greens functions in imaginary time
Polarizability in imaginary time
Transform from imaginary time to imaginary frequency
Dielectric tensor and screened Coulomb potential
Exchange and correlation Self-energy calculation
Solving the quasi-particle equation to get the band energies
Schematic view of the algorithm
\(\Gamma\)
point correction for k-point convergence
Parallelization of the algorithm
Usage Examples
References
External machine-learned force fields in QuantumATK
Setting up the virtual environment
SevenNet
Orb models
DeePMD-kit
MatterSim
CHGnet
FAIRChem UMA
Other Models
Atomic data
Element data
Built-in semiempirical parameter sets in QuantumATK
Slater–Koster basis sets
Extended Hückel basis sets
Sentaurus Materials Workbench Reference Manual
Introduction
Material specifications
Single defect specification and convergence studies
Multilayer Builder
GrainBoundaryScattering
Full SMW package
SMW
Publications
Referencing
List of Publications
QuantumATK
PeriodicBoundaryCondition
¶
Included in QATK.Core
class
PeriodicBoundaryCondition
¶
A periodic boundary condition.
