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Tutorials
New or Recently Updated Tutorials
New for QuantumATK Q-2019.12
Polymer Builder
New for QuantumATK P-2019.03
Using the Sentaurus Materials Workbench for studying point defects
Viscosity in liquids from molecular dynamics simulations
New for QuantumATK O-2018.06
Dynamical Matrix study object: Phonons in bulk silicon
Formation energies and transition levels of charged defects
Relaxation of devices using the OptimizeDeviceConfiguration study object
Electrical characteristics of devices using the IVCharacteristics study object
Photocurrent in a silicon p-n junction
New for QuantumATK 2017.0
DFT-1/2 and DFT-PPS density functional methods for electronic structure calculations
Introducing the QuantumATK plane-wave DFT calculator
Metadynamics Simulation of Cu Vacancy Diffusion on Cu(111) - Using PLUMED
Determination of low strain interfaces via geometric matching
Open-circuit voltage profile of a Li-S battery: ReaxFF molecular dynamics
Updated for QuantumATK 2017.0
Inelastic current in a silicon p-n junction
Slater-Koster tight-binding models in ATK-SE
Elastic scattering, mean free path, mobility: Impurity scattering in a silicon nanowire
Phonon-limited mobility in graphene using the Boltzmann transport equation
Getting started
Introduction to QuantumATK
Getting Familiar with QuantumATK
Band Structure of a SiC Crystal
Transport in a graphene nanoribbon with a distortion
Building a Graphene Nanoribbon Device
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
Manage 3D View and Select Atoms
Rotations
Reset View
Zoom
Drag
Camera and View Planes
Selections
Import/Export files in QuantumATK
Stash Items
Add from Database
Add from Files
Add from Plugins
Save and Export Structures
Builder Manual
Introduction
Importing, adding, and exporting structures
Mouse and key operations
Using the Move Tool
Overview of built-in plugins
Managing plugins using the AddOn Manager
Introducing the QuantumATK plane-wave DFT calculator
Introduction
Tips and tricks
SSH keys
Create a pair of public and private SSH keys
Add the public key to authorized SSH keys on the remote cluster
Test the password-less SSH connection
How to create AddOns for QuantumATK
Basic Structure of a AddOn Module
Example 1: A Plugin to Read XYZ Files
Example 2: Plugin to export configurations
Example 3: Plugin to read electron densities
How to install AddOns
Test the NPZFilters AddOn
Make Movies from QuantumATK Trajectory Files
Creating Animated GIF
Rotation Animator
Movie from Trajectory Files
Pymatgen in QuantumATK
Installation
Testing
Updating
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
QuantumATK tasks and workflows
Job Manager for local execution of QuantumATK scripts
Execute QuantumATK simualtions via the Job Manager
Serial execution
Threading
MPI parallelization
Machine Manager
Job Manager for remote execution of QuantumATK scripts
A single remote machine
Custom job settings
Debugging
Adding several remote machines
How to create AddOns for QuantumATK
Basic Structure of a AddOn Module
Example 1: A Plugin to Read XYZ Files
Example 2: Plugin to export configurations
Example 3: Plugin to read electron densities
How to install AddOns
Test the NPZFilters AddOn
Make CIF File Defining Crystal Structure
Description and Need
Example
Import XYZ, CIF, CAR, VASP Files in QuantumATK
Drag and Drop
Importing structures in a script
Export XYZ, CIF, CAR, VASP Files in QuantumATK
Built-in export filters
Exporting from scripts
Manage 3D View and Select Atoms
Rotations
Reset View
Zoom
Drag
Camera and View Planes
Selections
POV-Ray images from QuantumATK
Elementary functionalities through an example
Examining the .pov file
Exporting pictures with POV-Ray
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
Molecular builder
Ethanol molecule
Caffeine molecule
Going further
Export the Stash Configuration file
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
Using the Crystal Builder
Introduction
Crystal structure of black phosphorus
Phosphorene and its bandstructure
References
ATK explained
Why are so many
k
-points needed in the transport direction in a device calculation?
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
Introducing the QuantumATK plane-wave DFT calculator
Introduction
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 bandstructure of Si(100)
Background
Si(100) surface
Complex bandstructure calculation
Analysing the results
3D and 2D 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
Coupling QuantumATK with Synopsys tools
Preparations
Installing the addon
New project
Silicon crystal
DFT model setup
Running the calculation
Visualizing the band structure
Exporting the band structure to SAI format
Batch processing and command line usage
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
Introduction
Calculation and preliminary analysis of the
\(V_{DG}\)
curve
Extending the range of the
\(V_{DG}\)
curve
Analysis of the
\(V_{DG}\)
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
Using the Sentaurus Materials Workbench for studying point defects
Background
Getting started
Setting up the calculation
Run the calculation
Analyzing the results
Including vibrational contributions
Conclusions
References
Batteries and 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
Infographics
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
Tubes, ribbons and other 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
Graphene and other 2D materials
Transmission spectrum of perfect sheets of graphene and MoS
2
Introduction
Unit cell for transmission
Graphene
MoS
2
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
Phonons and thermal transport
Dynamical Matrix study object: Phonons in bulk silicon
Introduction
Phonons
ATK-ForceField
References
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
Molecular dynamics
Molecular Dynamics: Basics
Introduction
Methodology
NVE Simulations
NVT Simulations
NPT Simulations
MD Simulations with Constraints
Device Configurations
Simulating Thin Film Growth via Vapor Deposition
Introduction
Simulation Strategies
Preparing the System
Setting up the Deposition Simulation
Running the Simulation
General Remarks
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
Spintronics
Spin Transfer Torque
Introduction
Getting Started
Calculate the STT
Angle Dependence
Finite-Bias Calculations
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
Introduction
The electronic structure of NiO calculated with DFT
DFT+U calculation for the NiO crystal
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
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
Pt diffusion on Pt surfaces using NEB calculations
Introduction
Creating the Pt ad-atom on Pt(100) structure
Creating the final configuration for the exchange diffusion process
Creating the final configuration for the direct jump process
Constructing the NEB paths
Setting up and running the NEB calculations
Analyzing the results
Conclusions
Bibliography
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
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
Introduction
The electronic structure of NiO calculated with DFT
DFT+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 the Sentaurus Materials Workbench for studying point defects
Background
Getting started
Setting up the calculation
Run the calculation
Analyzing the results
Including vibrational contributions
Conclusions
References
Sentaurus Materials Workbench
Using the Sentaurus Materials Workbench for studying point defects
Background
Getting started
Setting up the calculation
Run the calculation
Analyzing the results
Including vibrational contributions
Conclusions
References
QuantumATK as GUI for Quantum ESPRESSO
QuantumATK as GUI for Quantum ESPRESSO
Setting up a configuration using QuantumATK
Exporting a Quantum ESPRESSO input file
Adapting the input file
Running the ground state calculation
Analyzing results
More Quantum ESPRESSO calculations
Silicon bandstructure and DOS using QuantumATK and Quantum ESPRESSO
Bandstructure
Density of states
QuantumATK as GUI for VASP
The VASP Scripter AddOn
Create the structure in QuantumATK
Export the structure to the VASP scripter
Setup tab
Accuracy tab
Electrons tab
Ions tab
Properties tab
Configuaration tab
Bandstructure tab
Custom Options tab
Generate VASP files
Set up and analyze VASP calculations with QuantumATK
Setting up the configuration using QuantumATK
Use the VASP Scripter to set up the calculation
Analyzing the results
Using QuantumATK to work with Nudged Elastic Band calculations in VASP
Introduction
Creating the initial and final configurations
Setting up the VASP input for optimizing the bulk Pt
Creating and optimizing the end-points
Constructing the NEB path
Setting up the NEB calculation
Analyzing the results
References
QuantumATK as GUI for LAMMPS
LAMMPS trajectories into QuantumATK
Preparing a LAMMPS script
Running LAMMPS
Importing to QuantumATK
Postprocessing LAMMPS trajectories
References
Complete list
Introduction to QuantumATK
Getting Familiar with QuantumATK
Band Structure of a SiC Crystal
Transport in a graphene nanoribbon with a distortion
Building a Graphene Nanoribbon Device
Transport calculations with QuantumATK
Introduction
Geometry for transport calculations
Getting started
Convergence of electrode parameters
Zero-bias analysis
Finite-bias calculations
Summary
Transport in graphene nanoribbons
Introduction
Band structure of 2D graphene
Band structure of an armchair ribbon
Transport properties of a zigzag nanoribbon
Building molecule–surface systems: Benzene on Au(111)
Summary of workflow
Detailed instructions
References
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
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
Transmission spectrum of perfect sheets of graphene and MoS
2
Introduction
Unit cell for transmission
Graphene
MoS
2
Silicon p-n junction
Silicon bulk: Slater-Koster vs DFT-MGGA
Silicon device
Analyzing the results
References
Carbon Nanotube Junctions
Setting up the geometry
Advanced device relaxation - manual workflow
Introduction
Preparations
Electrode relaxation
Central region relaxation
1DMIN optimization of the interface using 2-probe calculations
Infographics
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
Capping a carbon nanotube
Build an extended (5,5) carbon nanotube
Cut the fullerene in half
Capping the tube
Finalizing the geometry
Graphene–Nickel interface
Creating the structure
More configurations
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
Thermoelectric effects in a CNT with isotope doping
CNT device with tags for
14
C doping
Phonon transmission
Electron transmission
Thermoelectric transport properties
References
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
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
Atomic-scale capacitance
Build the parallel plate capacitor
Calculations
Analysis
Bias-dependent capacitance
Dielectric spacer material
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
Spin-dependent Bloch states in graphene nanoribbons
Band structure of a zigzag nanoribbon
Bloch states
Introducing spin
Electron density and Mulliken populations
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
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
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 Electron Spectroscopy of an H
2
molecule placed between 1D Au chains
Introduction
Device setup
Calculation of IETS
Analysis
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
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
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
Photocurrent in a silicon p-n junction
Device ground state
Photocurrent
References
Electrical characteristics of devices using the IVCharacteristics study object
Introduction
Calculation and preliminary analysis of the
\(V_{DG}\)
curve
Extending the range of the
\(V_{DG}\)
curve
Analysis of the
\(V_{DG}\)
curve in the subthreshold region
Calculating the drain-induced barrier lowering
References
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
Effective mass of electrons in silicon
Introduction
Background
Set up the calculation
Analyze the results
Going further
References
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
Dynamical Matrix study object: Phonons in bulk silicon
Introduction
Phonons
ATK-ForceField
References
Optical Properties of Silicon
Introduction
Electronic structure and optical properties of silicon
References
Polarization
Introduction
Modern theory of polarization
Spontaneous polarization of ferroelectric BaTiO
3
References
Uniaxial and Biaxial Stress in Silicon
Introduction
Uniaxial Stress
Biaxial Stress
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
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 bandstructure of Si(100)
Background
Si(100) surface
Complex bandstructure calculation
Analysing the results
3D and 2D visualizations
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
Coupling QuantumATK with Synopsys tools
Preparations
Installing the addon
New project
Silicon crystal
DFT model setup
Running the calculation
Visualizing the band structure
Exporting the band structure to SAI format
Batch processing and command line usage
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
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 the Sentaurus Materials Workbench for studying point defects
Background
Getting started
Setting up the calculation
Run the calculation
Analyzing the results
Including vibrational contributions
Conclusions
References
Molecular Dynamics: Basics
Introduction
Methodology
NVE Simulations
NVT Simulations
NPT Simulations
MD Simulations with Constraints
Device Configurations
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
Simulating Thin Film Growth via Vapor Deposition
Introduction
Simulation Strategies
Preparing the System
Setting up the Deposition Simulation
Running the Simulation
General Remarks
Simulating Ion Bombardment on Graphene Sheets
Setting up the Graphene Sheet:
Adding a Bombardment Atom
Setting up the Simulation
Modifying the Script
References
Vibrational modes and Vibration Visualizer
MoS
2
monolayer
Nanophononic metamaterials
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
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
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
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
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
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
Pt diffusion on Pt surfaces using NEB calculations
Introduction
Creating the Pt ad-atom on Pt(100) structure
Creating the final configuration for the exchange diffusion process
Creating the final configuration for the direct jump process
Constructing the NEB paths
Setting up and running the NEB calculations
Analyzing the results
Conclusions
Bibliography
Calculation of Formation Energies
Formation energy calculations (or cohesive energy)
Cohesive energy of a bulk system
Defect formation energy calculations
References
Reconstruction of the Si (100) surface - a geometry optimization study with QuantumATK
Introduction
Building the geometry
Setting up the calculation
Results
Summary
Visualize the LUMO state of a water molecule
Building the molecule
Calculating the LUMO state
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
Generating Amorphous Structures
Introduction
Amorphous Structure Generation with Classical MD Simulations
Refining Amorphous Structures
Creating Crystal/Amorphous Interfaces
Further Examples
Opening a band gap in silicene and bilayer graphene with an electric field
Bilayer graphene
Silicene
References
More reading
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
Elastic constants
Methodology
Calculating elastic constants using classical potentials
Calculate elastic constants using DFT
Relativistic effects in bulk gold
GGA band structure
Spin-orbit GGA band structure
References
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
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
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
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 the Sentaurus Materials Workbench for studying point defects
Background
Getting started
Setting up the calculation
Run the calculation
Analyzing the results
Including vibrational contributions
Conclusions
References
Why are so many
k
-points needed in the transport direction in a device calculation?
Make Movies from QuantumATK Trajectory Files
Creating Animated GIF
Rotation Animator
Movie from Trajectory Files
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
Pymatgen in QuantumATK
Installation
Testing
Updating
The DFTB model in ATK-SE
Installing DFTB parameters
Testing the installation
Spin polarized calculations with DFTB
Reusing electrodes in device calculations
Separate scripts for electrodes and device
Initialize from a converged state
Introduction
Examples
Compute quantities from converged simulations
Restarting a stopped calculation
Saving the checkpoint file
Restarting the calculation from the checkpoint file
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
Electronic structure of NiO with DFT+U
Introduction
The electronic structure of NiO calculated with DFT
DFT+U calculation for the NiO crystal
References
Linear response current – how to compute it, and why it is often not a good idea
Introducing the QuantumATK plane-wave DFT calculator
Introduction
Builder Manual
Introduction
Importing, adding, and exporting structures
Mouse and key operations
Using the Move Tool
Overview of built-in plugins
Managing plugins using the AddOn Manager
Using the Crystal Builder
Introduction
Crystal structure of black phosphorus
Phosphorene and its bandstructure
References
Job Manager for local execution of QuantumATK scripts
Execute QuantumATK simualtions via the Job Manager
Serial execution
Threading
MPI parallelization
Machine Manager
Job Manager for remote execution of QuantumATK scripts
A single remote machine
Custom job settings
Debugging
Adding several remote machines
SSH keys
Create a pair of public and private SSH keys
Add the public key to authorized SSH keys on the remote cluster
Test the password-less SSH connection
Make CIF File Defining Crystal Structure
Description and Need
Example
How to create AddOns for QuantumATK
Basic Structure of a AddOn Module
Example 1: A Plugin to Read XYZ Files
Example 2: Plugin to export configurations
Example 3: Plugin to read electron densities
How to install AddOns
Test the NPZFilters AddOn
Import/Export files in QuantumATK
Stash Items
Add from Database
Add from Files
Add from Plugins
Save and Export Structures
Import XYZ, CIF, CAR, VASP Files in QuantumATK
Drag and Drop
Importing structures in a script
Export XYZ, CIF, CAR, VASP Files in QuantumATK
Built-in export filters
Exporting from scripts
Manage 3D View and Select Atoms
Rotations
Reset View
Zoom
Drag
Camera and View Planes
Selections
POV-Ray images from QuantumATK
Elementary functionalities through an example
Examining the .pov file
Exporting pictures with POV-Ray
Converting lattices: Rhombohedral to hexagonal and back
Conversion between hP and hR representations
Converting hP supercell to hR primitive cell
Crystal classifications
References
Simple carbon nanotube device
Build and geometry optimize a short CNT
CNT device configuration
Build a graphene nanoribbon transistor
Small nanoribbon transistor
A longer nanoribbon transistor
Commensurate supercells for rotated graphene layers
Additional rotated structures
References
Molecular builder
Ethanol molecule
Caffeine molecule
Going further
Export the Stash Configuration file
MoS
2
Nanotubes
Nanosheet with a hole
Stone–Wales Defects in Nanotubes
Creating the defect and wrapping the tube
Optimizing the structure
Transmission spectrum
References
Exploring Graphene
Build a graphene sheet
Build a CNT
Transmission spectrum of a GNR
Twisted nanoribbon
Möbius nanoribbon
Buckling a graphene sheet
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
The VASP Scripter AddOn
Create the structure in QuantumATK
Export the structure to the VASP scripter
Setup tab
Accuracy tab
Electrons tab
Ions tab
Properties tab
Configuaration tab
Bandstructure tab
Custom Options tab
Generate VASP files
Using QuantumATK to work with Nudged Elastic Band calculations in VASP
Introduction
Creating the initial and final configurations
Setting up the VASP input for optimizing the bulk Pt
Creating and optimizing the end-points
Constructing the NEB path
Setting up the NEB calculation
Analyzing the results
References
Set up and analyze VASP calculations with QuantumATK
Setting up the configuration using QuantumATK
Use the VASP Scripter to set up the calculation
Analyzing the results
QuantumATK as GUI for Quantum ESPRESSO
Setting up a configuration using QuantumATK
Exporting a Quantum ESPRESSO input file
Adapting the input file
Running the ground state calculation
Analyzing results
More Quantum ESPRESSO calculations
Silicon bandstructure and DOS using QuantumATK and Quantum ESPRESSO
Bandstructure
Density of states
LAMMPS trajectories into QuantumATK
Preparing a LAMMPS script
Running LAMMPS
Importing to QuantumATK
Postprocessing LAMMPS trajectories
References
Webinars
Simulation of Polymers with QuantumATK
Simulation of Optical Properties with QuantumATK
DFT Simulations with QuantumATK
New QuantumATK Release P-2019.03
Relaxation of Electronic Devices and Interfaces
Solar-Cell Devices Including Temperature Effects
New Framework for IV Curve Simulations
New QuantumATK Release O-2018.06
Simulating the Phonon-Limited Electron Mobility of Materials
Simulating Interfaces with QuantumATK
Electron-Phonon Scattering Effects in Large Scale Atomistic Device Simulations
New QuantumATK Release 2017
Introduction to Molecular Dynamics Simulations with QuantumATK-ForceField
Atomistic Simulation of Thermal Transport Across Interfaces
Manual
General
Introduction
New in QuantumATK Q-2019.12
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
TremoloX potential parameter sets
ASAP potential parameter sets
NEGF: Device Calculators
Introduction
Device configuration
Non-equilibrium electron distribution
Effective potential
Total energy and forces
Transmission coefficient
Electrical current
References
Technical Notes
The Hartree Potential
Occupation Methods
Pseudopotentials and basis sets available in QuantumATK
Doping methods available in QuantumATK
Optical response functions
Hybrid Functionals
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)
NetCDF
Metatext
Spin
Usage Example
Note about Spin.All
Note on Spin in low level interface functions
Python basics
Indentation
Comments
Importing modules
Lists
Tuples
Dictionaries
For-loops
Objects
Functions and arguments
QuantumATK Reference Manual
Geometry
Lattices
Calculators
Common Parameters
DFT Calculators
Semi-Empirical Calculator
Counterpoise Correction
Low level entities
Analysis
Common Analysis
Bulk Analysis
Device Analysis
Study
Dynamics and Optimization
Optimization
Molecular Dynamics
Monte Carlo
Constraints
MD Analysis
Image Interpolation Algorithms (NEB)
Polymers
Builders And Equilibration
Potentials
Analysis
Input and Output
Periodic Table
Utilities
Full QuantumATK package
Classes
Functions
Sentaurus Materials Workbench Reference Manual
Introduction
Material specifications
Bandstructure calibration
Single defect specification and convergence studies
Band diagram extraction
Defect characterization and migration
Empirical potential calculation
Defect characterization
Defect migration
Diffusion in amorphous materials
Using defect characterization and migration values in Sentaurus Process
Multilayer Builder
GrainBoundaryScattering
Full SMW package
Classes
Functions
Sentaurus Materials Workbench Technical Descriptions
Operating with defect lists
Introduction
Defect lists usage
Defect list types
Directory names
Usage example
Chemical Potentials in Compound Materials
Heat of Formation
Specific Element-Rich Condition
Grand Thermodynamic Potential (GTP)
Summarized chemical potentials in the TiN example
Diffusivity calculation in amorphous materials
Procedure
Example: Carbon diffusivity in amorphous silicon
Atomic data
Element data
Built-in parameter sets in ATK-SE
Slater–Koster basis sets
Extended Hückel basis sets
Case Studies
Modeling metal–semiconductor contacts: The Ag–Si interface
Creating the device
Initial guesses for the interface structure
Electrode relaxation
Central region relaxation
Device relaxation
Fitting the TB09-MGGA c-parameter
Silicon doping and depletion layer length
Projected local density of states
Finite-bias calculations
Ideality factor
Schottky barrier
Spectral current
Summing up the results
Note on the variation of the current
References
Resistivity calculations using the MD-Landauer method
1. Theory and numerical procedure
2. Calculation setup
2.1. Construction of the DeviceConfiguration
2.2. Setup of the script
2.3. Edit the python script
3. Data analysis
3.1. Transmission functions, conductance, and resistance
3.2. Resistivity
References
Electron transport calculations with electron-phonon coupling included via the special thermal displacement method - STD-Landauer
Building the device
Finding the lattice constant of silicon
Building the pristine device
Applying the special thermal displacement to the atomic positions
Calculations
Calculations at 0 K and zero bias
Calculations at 300 K and zero bias
Calculations at finite bias
Lowest Order Expansion (LOE) Calculations
Computational timings
Analysis and discussion
The STD method compared to the LOE method
References
Semiconductor Whitepapers
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
Posters
Guides
Installation guide
Introduction
Access to SolvNet
Access to a license server
Downloading, installing and configuring QuantumATK
Downloading QuantumATK
Installing QuantumATK
Configuring the QuantumATK license
Determining the host ID of your machine
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
Using Templates in QuantumATK
Quick access to Templates
Manage Templates
Import/Export Templates
Editing, Saving and Merging Plots
Video guide
Plot tools
Annotate plots
The Plot Editor
Save and load the plot in the PlotViewer
Merge plots
Drop next to, above or below an existing plot
Drop on the existing plot
Redo analysis
Scientific Publications
Referencing
List of Publications
Technical Notes
The Interface Builder in QuantumATK
Select Surface Cells
Shift Surfaces
NEGF Convergence Guide
Introduction
Troubleshooting steps
Zero-bias NEGF calculations
1. Increase the length of the device central region
2. Increase the length of the electrodes
3. Check that the boundary conditions are correct
4. Increase the number of k-points
5. Use the EquivalentBulk method for the initial density
6. Increase the electron temperature
7. Improve the accuracy of the contour integral
8. Try a different Poisson solver
9. Increase the density mesh cut-off energy
Finite-bias NEGF calculations
1. Always restart from a converged calculation
SCF iteration control parameters
1. Maximum steps
2. Pulay mixing
3. Tolerance
Contact support
Spin-Polarized NEGF Convergence Guide
Systems investigated
Computational parameters for the reference Fe|MgO structure
Computational parameters for the Fe|MgO|Fe device
Calculating the self-energy matrix
1. Method overview
2. Practical methods
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
MPI parallelization
Threading
ATK-DFT
Bulk calculations
Processes per
k
-point
Exercise I: Non-default number of processes per
k
-point
Speed-up and peak memory reduction
NEGF calculations
Automatic distribution of contour points
Processes per contour point
Speedup in a device calculation
Examples of multi-level parallelisms in QuantumATK
Nudged elastic band calculations
I-V curve calculations
Adaptive Kinetic Monte Carlo simulations
Crystal Structure Prediction
References
Performance troubleshooting guide
Running out of memory?
Want to make it run faster?
Study objects
Restart example
FAQ
Software Usage
Slow Startup of QuantumATK NanoLab
Log file Time Stamps in Windows Under Cygwin
Bonds Between Some Atoms are Missing
Difference Between Pseudopotentials and Basis Sets in QuantumATK
Importing Atomic Coordinates from Other Software in NanoLab
Running QuantumATK Using SLURM and MPICH (3.1.1+)
Running QuantumATK Under Cray MPI (aprun)
Technical
System Requirements for Running QuantumATK Q-2019.12
System Requirements for Running QuantumATK P-2019.06
System Requirements for Running QuantumATK P-2019.03
System Requirements for Running QuantumATK P-2019.06
System Requirements for Running ATK/VNL 2017
Running QuantumATK on a Virtual Machine
How Many Atoms Can Be Computed with QuantumATK
QuantumATK Parallelization
Extremely Dark Atoms for VNL-2016 on Windows 7
How Come the ATK-VNL Package is Larger than a Typical DFT Code
Error Messages
UnicodeDecodeError: ASCII Codec Can’t Decode
atkpython.exe Stopped Working
License Error: (Internal: 147 Feature: ATKDFT)
License Error: Access Denied
Error Installing VC++ Runtime
ATKError: Inverse(DZMatrix const&) : Could Not LU Factorize!
ATKError: Bad Allocation
There Is No Licenses Served by the License Server
locale.Error: Unsupported Locale Setting
ERROR: ‘dict’ object has no attribute ‘len’
Can’t Allocate Memory for Array
Not Enough Space to Allocate vblock
Killed by Signal 9
Pulay Mixing Inversion Failed. Using Only Last Step
Runtime Terminates an Application
Import error:.../_path.so: undefined symbol: _ZNSs4_Rep20_S_empty_rep_storageE
ImportError: No Module Named
White Builder or Viewer Background
Failure to Initialize
WARNING: Feature Not Licensed to Work on a Virtual Machine and is Ignored
libGL Warning: 3D Driver Claims to Not Support 0x5b
(Err:20) Feature Not Allowed to Run on a Virtual Machine
(Err:19) Feature Not Allowed to Run on Terminal Server Clients
(Err: 10) Hostid Does Not Match License
(Err: 6) Unable to Read File
glibc Detected ... Corrupted Double-Linked List
(Err: 15) Unable to Connect to License Server
(Err: 35) Feature Does Not Support Network Licensing
ATKError: St9bad_alloc
ATKError: Exceeded Maximum Number of Self-Consistent Iterations
ImportError: Gtk* Backend Requires pygtk to Be Installed
locale::facet::_S_create_c_locale Name Not Valid
The Computed TB09 meta-GGA Exchange-Correlation Potential Diverged ...
Could Not Find or Load the Qt Platform Plugin “xcb”
(Err: 51) Unable to Use Network License as a Local License
Back Engine Exception : Unable to Start License System
Licensing
Cannot Run QuantumATK P-2019.03
Basic License Troubleshooting
Advanced License Troubleshooting
Maintenance, Updates and Support
Floating or Nodelocked Licenses
NLLicenseError: Unable to Start the License System (Error Code 61)
License and QuantumATK Upgrading
Updating the License File
License Server Cannot Be Started
HostID Does Not Match License (Error Code 10)
SSH License Server Access
License for QuantumATK Parallel Run
Restricting Access to a License Server
Installation Issues
QuantumATK Slow Start on Windows
libjpeg.so.62: Cannot Open Shared Object File: No Such File or Directory
“Side-by-Side” Configuration Error
QuantumATK Segmentation Fault (Linux)
Command Not Found (Linux)
Cannot Start QuantumATK From the Desktop Icon
libpng12.so.0: Cannot Open Shared Object File
libGL.so: Cannot Open Shared Object File
Cannot Restore Segment Prot After Reloc: Permission Denied
“Send To” Button Stops Working on Ubuntu
QuantumATK Problems on Ubuntu
GLIBC_2.4 Not Found
Firewall Issues
No Module Named ipy_user_conf
Segmentation Fault QuantumATK Closes Down When Clicking an Icon
libGLU.so.1: Cannot Open Shared Object File
libgomp.so.1: Cannot Open Shared Object File: No Such File or Directory
ImportError: DLL Load Failed: The Specified Procedure Could Not Be Found
Could Not Find or Load the Qt Platform Plugin “xcb”
Interactive Mode Prints Black on Black in Windows 8 and 10 (QuantumATK 2015)
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LinearInterpolation
LinearInterpolation
¶
class
LinearInterpolation
¶
Use linear interpolation for generating images.
constraints
(
)
¶
Returns:
The constrained atoms.
Return type:
list of type int