Referencing QuantumATK

If you are preparing an article using QuantumATK, please read the instructions below on how to cite the software properly. You can download a bibtex file with all the relevant references here. All publications where QuantumATK software has been used should include:

  1. ✍  A reference to the version of the software used: QuantumATK version X-XXXX.XX, Synopsys QuantumATK (https://www.synopsys.com/quantumatk). For example:
    • QuantumATK W-2024.09
    • QuantumATK V-2023.12
    • QuantumATK V-2023.09
  2. ✍  The most important methodology papers listed below.

Citing QuantumATK Reference Paper

📙 We request users of QuantumATK to cite this paper in any publications reporting on results obtained with the software.

QuantumATK: An Integrated Platform of Electronic and Atomic-Scale Modelling Tools
Authors: Søren Smidstrup, Kurt Stokbro, Anders Blom, Troels Markussen, Jess Wellendorff, Julian Schneider, Tue Gunst, Brecht Verstichel, Petr A Khomyakov, Ulrik G Vej-Hansen, Mads Brandbyge and others
J. Phys: Condens. Matter (APS), Vol. 32, pp. 015901 (2020)
Abstract   |   BibTeX   |   DOI
Abstract: QuantumATK is an integrated set of atomic-scale modelling tools developed since 2003 by professional software engineers in collaboration with academic researchers. While different aspects and individual modules of the platform have been previously presented, the purpose of this paper is to give a general overview of the platform. The QuantumATK simulation engines enable electronic-structure calculations using density functional theory or tight-binding model Hamiltonians, and also offers bonded or reactive empirical force fields in many different parametrizations. Density functional theory is implemented using either a plane-wave basis or expansion of electronic states in a linear combination of atomic orbitals. The platform includes a long list of advanced modules, including Green's-function methods for electron transport simulations and surface calculations, first-principles electron-phonon and electron-photon couplings, simulation of atomic-scale heat transport, ion dynamics, spintronics, optical properties of materials, static polarization, and more. Seamless integration of the different simulation engines into a common platform allows for easy combination of different simulation methods into complex workflows. Besides giving a general overview and presenting a number of implementation details not previously published, we also present four different application examples. These are calculations of the phonon-limited mobility of Cu, Ag and Au, electron transport in a gated 2D device, multi-model simulation of lithium ion drift through a battery cathode in an external electric field, and electronic-structure calculations of the composition-dependent band gap of SiGe alloys.

BibTeX:
  • @article{ smidstrup2020,
  •   title = QuantumATK: An Integrated Platform of Electronic and Atomic-Scale Modelling Tools,
  •   author = Søren Smidstrup, Kurt Stokbro, Anders Blom, Troels Markussen, Jess Wellendorff, Julian Schneider, Tue Gunst, Brecht Verstichel, Petr A Khomyakov, Ulrik G Vej-Hansen, Mads Brandbyge and others,
  •   journal = J. Phys: Condens. Matter (APS),
  •   volume = 32,
  •   pages = 015901,
  •   doi = 10.1088/1361-648X/ab4007,
  •   url = https://iopscience.iop.org/article/10.1088/1361-648X/ab4007,
  •   year = 2020
  • }

Citing QuantumATK DFT (Density Functional Theory)

📙 SG15 Pseudo-Potentials:

First-Principles Green's-Function Method for Surface Calculations: A Pseudopotential Localized Basis Set Approach
Authors: Søren Smidstrup, Daniele Stradi, Jess Wellendorff, Petr A. Khomyakov, Ulrik G. Vej-Hansen, Maeng-Eun Lee, Tushar Ghosh, Elvar Jónsson, Hannes Jónsson, and Kurt Stokbro
Physical Review B (Elsevier), Vol. 96, pp. 195309 (2017)
Abstract   |   BibTeX   |   DOI
Abstract: We present an efficient implementation of a surface Green's-function method for atomistic modeling of surfaces within the framework of density functional theory using a pseudopotential localized basis set approach. In this method, the system is described as a truly semi-infinite solid with a surface region coupled to an electron reservoir, thereby overcoming several fundamental drawbacks of the traditional slab approach. The versatility of the method is demonstrated with several applications to surface physics and chemistry problems that are inherently difficult to address properly with the slab method, including metal work function calculations, band alignment in thin-film semiconductor heterostructures, surface states in metals and topological insulators, and surfaces in external electrical fields. Results obtained with the surface Green's-function method are compared to experimental measurements and slab calculations to demonstrate the accuracy of the approach.

BibTeX:
  • @article{ smidstrupa2017,
  •   title = First-Principles Green's-Function Method for Surface Calculations: A Pseudopotential Localized Basis Set Approach,
  •   author = Søren Smidstrup, Daniele Stradi, Jess Wellendorff, Petr A. Khomyakov, Ulrik G. Vej-Hansen, Maeng-Eun Lee, Tushar Ghosh, Elvar Jónsson, Hannes Jónsson, and Kurt Stokbro,
  •   journal = Physical Review B (Elsevier),
  •   volume = 96,
  •   pages = 195309,
  •   doi = 10.1103/PhysRevB.96.195309,
  •   url = https://journals.aps.org/prb/abstract/10.1103/PhysRevB.96.195309,
  •   year = 2017
  • }

📙 PseudoDojo Pseudo-Potentials:

The PseudoDojo: Training and Grading a 85 Element Optimized Norm-Conserving Pseudopotential Table
Authors: Van Setten, MJ and Giantomassi, Matteo and Bousquet, Eric and Verstraete, Matthieu J and Hamann, Don R and Gonze, Xavier and Rignanese, G-M
Computer Physics Communications (Elsevier), Vol. 226, pp. 39 (2018)
Abstract   |   BibTeX   |   DOI
Abstract: First-principles calculations in crystalline structures are often performed with a planewave basis set. To make the number of basis functions tractable two approximations are usually introduced: core electrons are frozen and the diverging Coulomb potential near the nucleus is replaced by a smoother expression. The norm-conserving pseudopotential was the first successful method to apply these approximations in a fully ab initio way. Later on, more efficient and more exact approaches were developed based on the ultrasoft and the projector augmented wave formalisms. These formalisms are however more complex and developing new features in these frameworks is usually more difficult than in the norm-conserving framework. Most of the existing tables of norm-conserving pseudopotentials, generated long ago, do not include the latest developments, are not systematically tested or are not designed primarily for high precision. In this paper, we present our PseudoDojo framework for developing and testing full tables of pseudopotentials, and demonstrate it with a new table generated with the ONCVPSP approach. The PseudoDojo is an open source project, building on the AbiPy package, for developing and systematically testing pseudopotentials. At present it contains 7 different batteries of tests executed with ABINIT, which are performed as a function of the energy cutoff. The results of these tests are then used to provide hints for the energy cutoff for actual production calculations. Our final set contains 141 pseudopotentials split into a standard and a stringent accuracy table. In total around 70,000 calculations were performed to test the pseudopotentials. The process of developing the final table led to new insights into the effects of both the core-valence partitioning and the non-linear core corrections on the stability, convergence, and transferability of norm-conserving pseudopotentials. The PseudoDojo hence provides a set of pseudopotentials and general purpose tools for further testing and development, focusing on highly accurate calculations and their use in the development of ab initio packages. The pseudopotential files are available on the PseudoDojo web-interface pseudo-dojo.org under the name NC (ONCVPSP) v0.4 in the psp8, UPF2, and PSML 1.1 formats. The webinterface also provides the inputs, which are compatible with the 3.3.1 and higher versions of ONCVPSP. All tests have been performed with ABINIT 8.4.

BibTeX:

Citing QuantumATK SemiEmpirical

Semiempirical model for nanoscale device simulations
Authors: Stokbro, Kurt and Petersen, Dan Erik and Smidstrup, Søren and Blom, Anders and Ipsen, Mads and Kaasbjerg, Kristen
Physical Review B (APS), Vol. 82, pp. 075420 (2010)
Abstract   |   BibTeX   |   DOI
Abstract: ${ABSTRACT}

BibTeX:

📙 Built-in parameter sets in QuantumATK SemiEmpirical: References can be found here.

Citing Non-Equilibrium Green's Function (NEGF) Method

Density-Functional Method for Non-Equilibrium Electron Transport
Authors: Brandbyge, Mads and Mozos, Jose-Luis and Ordejon, Pablo and Taylor, Jeremy and Stokbro, Kurt
Physical Review B (APS), Vol. 65, pp. 165401 (2002)
Abstract   |   BibTeX   |   DOI
Abstract: ${ABSTRACT}

BibTeX:

📙 2-Probe Setup:

General Atomistic Approach for Modeling Metal-Semiconductor Interfaces Using Density Functional Theory and Non-Equilibrium Green's Function
Authors: Daniele Stradi, Umberto Martinez, Anders Blom, Mads Brandbyge, and Kurt Stokbro
Physical Review B (APS), Vol. 93, pp. 155302 (2016)
Abstract   |   BibTeX   |   DOI
Abstract: Metal-semiconductor contacts are a pillar of modern semiconductor technology. Historically, their microscopic understanding has been hampered by the inability of traditional analytical and numerical methods to fully capture the complex physics governing their operating principles. Here we introduce an atomistic approach based on density functional theory and nonequilibrium Green's function, which includes all the relevant ingredients required to model realistic metal-semiconductor interfaces and allows for a direct comparison between theory and experiments via I-Vbias curve simulations. We apply this method to characterize an Ag-Si interface relevant for photovoltaic applications and study the rectifying-to-Ohmic transition as a function of the semiconductor doping. We also demonstrate that the standard activation energy method for the analysis of I-Vbias data might be inaccurate for nonideal interfaces as it neglects electron tunneling, and that finite-size atomistic models have problems in describing these interfaces in the presence of doping due to a poor representation of space-charge effects. Conversely, the present method deals effectively with both issues, thus representing a valid alternative to conventional procedures for the accurate characterization of metal-semiconductor interfaces.

BibTeX:
  • @article{ stradi2016general,
  •   title = General Atomistic Approach for Modeling Metal-Semiconductor Interfaces Using Density Functional Theory and Non-Equilibrium Green's Function,
  •   author = Daniele Stradi, Umberto Martinez, Anders Blom, Mads Brandbyge, and Kurt Stokbro,
  •   journal = Physical Review B (APS),
  •   volume = 93,
  •   pages = 155302,
  •   doi = 10.1103/PhysRevB.93.155302,
  •   url = https://journals.aps.org/prb/abstract/10.1103/PhysRevB.93.155302,
  •   year = 2016
  • }

📙 1-Probe Setup (for Surface Calculations):

First-Principles Green's-Function Method for Surface Calculations: A Pseudopotential Localized Basis Set Approach
Authors: Søren Smidstrup, Daniele Stradi, Jess Wellendorff, Petr A. Khomyakov, Ulrik G. Vej-Hansen, Maeng-Eun Lee, Tushar Ghosh, Elvar Jónsson, Hannes Jónsson, and Kurt Stokbro
Physical Review B (Elsevier), Vol. 96, pp. 195309 (2017)
Abstract   |   BibTeX   |   DOI
Abstract: We present an efficient implementation of a surface Green's-function method for atomistic modeling of surfaces within the framework of density functional theory using a pseudopotential localized basis set approach. In this method, the system is described as a truly semi-infinite solid with a surface region coupled to an electron reservoir, thereby overcoming several fundamental drawbacks of the traditional slab approach. The versatility of the method is demonstrated with several applications to surface physics and chemistry problems that are inherently difficult to address properly with the slab method, including metal work function calculations, band alignment in thin-film semiconductor heterostructures, surface states in metals and topological insulators, and surfaces in external electrical fields. Results obtained with the surface Green's-function method are compared to experimental measurements and slab calculations to demonstrate the accuracy of the approach.

BibTeX:
  • @article{ smidstrupb2017,
  •   title = First-Principles Green's-Function Method for Surface Calculations: A Pseudopotential Localized Basis Set Approach,
  •   author = Søren Smidstrup, Daniele Stradi, Jess Wellendorff, Petr A. Khomyakov, Ulrik G. Vej-Hansen, Maeng-Eun Lee, Tushar Ghosh, Elvar Jónsson, Hannes Jónsson, and Kurt Stokbro,
  •   journal = Physical Review B (Elsevier),
  •   volume = 96,
  •   pages = 195309,
  •   doi = 10.1103/PhysRevB.96.195309,
  •   url = https://journals.aps.org/prb/abstract/10.1103/PhysRevB.96.195309,
  •   year = 2017
  • }

📙 Special Thermal Displacement (STD)-Landauer Method for Including Electron-Phonon Scattering Effects:

First-Principles Electron Transport with Phonon Coupling: Large Scale at Low Cost
Authors: Tue Gunst, Troels Markussen, Mattias L. N. Palsgaard, Kurt Stokbro, and Mads Brandbyge
Physical Review B (APS), Vol. 96, pp. 161404 (2017)
Abstract   |   BibTeX   |   DOI
Abstract: Phonon-assisted tunneling plays a crucial role for electronic device performance and even more so with future size down-scaling. We show how one can include this effect in large-scale first-principles calculations using a single special thermal displacement (STD) of the atomic coordinates at almost the same cost as elastic transport calculations, by extending the recent method of Zacharias et al. [Phys. Rev. B 94, 075125 (2016)] to the important case of Landauer conductance. We apply the method to ultrascaled silicon devices and demonstrate the importance of phonon-assisted band-to-band and source-to-drain tunneling. In a diode the phonons lead to a rectification ratio suppression in good agreement with experiments, while in an ultrathin body transistor the phonons increase off currents by four orders of magnitude, and the subthreshold swing by a factor of 4, in agreement with perturbation theory.

BibTeX:

📙 Photo-Current Module:

Efficient First-Principles Calculation of Phonon-Assisted Photocurrent in Large-Scale Solar-Cell Devices
Authors: Tue Gunst, Troels Markussen, Mattias L. N. Palsgaard, Kurt Stokbro, and Mads Brandbyge
Physical Review Applied (APS), Vol. 10, pp. 014026 (2018)
Abstract   |   BibTeX   |   DOI
Abstract: Phonon-assisted tunneling plays a crucial role for electronic device performance and even more so with future size down-scaling. We show how one can include this effect in large-scale first-principles calculations using a single special thermal displacement (STD) of the atomic coordinates at almost the same cost as elastic transport calculations, by extending the recent method of Zacharias et al. ( Phys. Rev. B 94, 075125 (2016) ) to the important case of Landauer conductance. We apply the method to ultrascaled silicon devices and demonstrate the importance of phonon-assisted band-to-band and source-to-drain tunneling. In a diode the phonons lead to a rectification ratio suppression in good agreement with experiments, while in an ultrathin body transistor the phonons increase off currents by four orders of magnitude, and the subthreshold swing by a factor of 4, in agreement with perturbation theory.

BibTeX:
  • @article{ palsgaard2018efficient,
  •   title = Efficient First-Principles Calculation of Phonon-Assisted Photocurrent in Large-Scale Solar-Cell Devices,
  •   author = Tue Gunst, Troels Markussen, Mattias L. N. Palsgaard, Kurt Stokbro, and Mads Brandbyge,
  •   journal = Physical Review Applied (APS),
  •   volume = 10,
  •   pages = 014026,
  •   doi = 10.1103/PhysRevB.96.161404,
  •   url = https://journals.aps.org/prb/abstract/10.1103/PhysRevB.96.161404,
  •   year = 2018
  • }

📙 Spintronics Simulations:

Proximity Band Structure and Spin Textures on Both Sides of Topological-Insulator Ferromagnetic-Metal Interface and Their Charge Transport Probes
Authors: Marmolejo-Tejada, Juan Manuel and Dolui, Kapildeb and Lazic, Predrag and Chang, Po-Hao and Smidstrup, Søren and Stradi, Daniele and Stokbro, Kurt and Nikolic, Branislav K
Nano Letters (ACS Publications), Vol. 17, pp. 5626-5633 (2018)
Abstract   |   BibTeX   |   DOI
Abstract: The control of recently observed spintronic effects in topological-insulator-ferromagnetic-metal (TI-FM) heterostructures is thwarted by the lack of understanding of band structure and spin textures around their interfaces. Here we combine density functional theory with Green’s function techniques to obtain the spectral function at any plane passing through atoms of Bi2Se3 and Co or Cu layers comprising the interface. Instead of naively assumed Dirac cone gapped by the proximity exchange field spectral function, we find that the Rashba ferromagnetic model describes the spectral function on the surface of Bi2Se3 in contact with Co near the Fermi level EF0, where circular and snowflake-like constant energy contours coexist around which spin locks to momentum. The remnant of the Dirac cone is hybridized with evanescent wave functions from metallic layers and pushed, due to charge transfer from Co or Cu layers, a few tenths of an electron-volt below EF0 for both Bi2Se3-Co and Bi2Se3-Cu interfaces while hosting distorted helical spin texture wounding around a single circle. These features explain recent observation of sensitivity of spin-to-charge conversion signal at TI-Cu interface to tuning of EF0. Crucially for spin–orbit torque in TI/FM heterostructures, few monolayers of Co adjacent to Bi2Se3 host spectral functions very different from the bulk metal, as well as in-plane spin textures (despite Co magnetization being out-of-plane) due to proximity spin–orbit coupling in Co induced by Bi2Se3. We predict that out-of-plane tunneling anisotropic magnetoresistance in Cu-Bi2Se3-Co vertical heterostructure can serve as a sensitive probe of the type of spin texture residing at EF0.

BibTeX:
  • @article{ palsgaard2018proximity,
  •   title = Proximity Band Structure and Spin Textures on Both Sides of Topological-Insulator Ferromagnetic-Metal Interface and Their Charge Transport Probes,
  •   author = Marmolejo-Tejada, Juan Manuel and Dolui, Kapildeb and Lazic, Predrag and Chang, Po-Hao and Smidstrup, Søren and Stradi, Daniele and Stokbro, Kurt and Nikolic, Branislav K,
  •   journal = Nano Letters (ACS Publications),
  •   volume = 17,
  •   pages = 5626-5633,
  •   doi = 10.1021/acs.nanolett.7b02511,
  •   url = https://pubs.acs.org/doi/pdf/10.1021/acs.nanolett.7b02511,
  •   year = 2018
  • }

Citing QuantumATK ForceField

ATK-ForceField: A New Generation Molecular Dynamics Software Package
Authors: Schneider, Julian and Hamaekers, Jan and Chill, Samuel T and Smidstrup, Søren and Bulin, Johannes and Thesen, Ralph and Blom, Anders and Stokbro, Kurt
Modelling and Simulation in Materials Science and Engineering (IOP Publishing), Vol. 25, pp. 085007 (2017)
Abstract   |   BibTeX   |   DOI
Abstract: ATK-ForceField is a software package for atomistic simulations using classical interatomic potentials. It is implemented as a part of the Atomistix ToolKit (ATK), which is a Python programming environment that makes it easy to create and analyze both standard and highly customized simulations. This paper will focus on the atomic interaction potentials, molecular dynamics, and geometry optimization features of the software, however, many more advanced modeling features are available. The implementation details of these algorithms and their computational performance will be shown. We present three illustrative examples of the types of calculations that are possible with ATK-ForceField: modeling thermal transport properties in a silicon germanium crystal, vapor deposition of selenium molecules on a selenium surface, and a simulation of creep in a copper polycrystal.

BibTeX:
  • @article{ schneidera2017atk,
  •   title = ATK-ForceField: A New Generation Molecular Dynamics Software Package,
  •   author = Schneider, Julian and Hamaekers, Jan and Chill, Samuel T and Smidstrup, Søren and Bulin, Johannes and Thesen, Ralph and Blom, Anders and Stokbro, Kurt,
  •   journal = Modelling and Simulation in Materials Science and Engineering (IOP Publishing),
  •   volume = 25,
  •   pages = 085007,
  •   doi = 10.1088/1361-651X/aa8ff0,
  •   url = https://iopscience.iop.org/article/10.1088/1361-651X/aa8ff0,
  •   year = 2017
  • }

📙 Built-in potential parameter sets: References can be found here.

Citing NanoLab & NanoLab Links

ATK-ForceField: A New Generation Molecular Dynamics Software Package
Authors: Schneider, Julian and Hamaekers, Jan and Chill, Samuel T and Smidstrup, Søren and Bulin, Johannes and Thesen, Ralph and Blom, Anders and Stokbro, Kurt
Modelling and Simulation in Materials Science and Engineering (IOP Publishing), Vol. 25, pp. 085007 (2017)
Abstract   |   BibTeX   |   DOI
Abstract: ATK-ForceField is a software package for atomistic simulations using classical interatomic potentials. It is implemented as a part of the Atomistix ToolKit (ATK), which is a Python programming environment that makes it easy to create and analyze both standard and highly customized simulations. This paper will focus on the atomic interaction potentials, molecular dynamics, and geometry optimization features of the software, however, many more advanced modeling features are available. The implementation details of these algorithms and their computational performance will be shown. We present three illustrative examples of the types of calculations that are possible with ATK-ForceField: modeling thermal transport properties in a silicon germanium crystal, vapor deposition of selenium molecules on a selenium surface, and a simulation of creep in a copper polycrystal.

BibTeX:
  • @article{ schneidera2017atk,
  •   title = ATK-ForceField: A New Generation Molecular Dynamics Software Package,
  •   author = Schneider, Julian and Hamaekers, Jan and Chill, Samuel T and Smidstrup, Søren and Bulin, Johannes and Thesen, Ralph and Blom, Anders and Stokbro, Kurt,
  •   journal = Modelling and Simulation in Materials Science and Engineering (IOP Publishing),
  •   volume = 25,
  •   pages = 085007,
  •   doi = 10.1088/1361-651X/aa8ff0,
  •   url = https://iopscience.iop.org/article/10.1088/1361-651X/aa8ff0,
  •   year = 2017
  • }

📙 Interface builder in NanoLab:

Method for Determining Optimal Supercell Representation of Interfaces
Authors: Stradi, Daniele and Jelver, Line and Smidstrup, Søren and Stokbro, Kurt
Journal of Physics: Condensed Matter (IOP Publishing), Vol. 29, pp. 185901 (2017)
Abstract   |   BibTeX   |   DOI
Abstract: The geometry and structure of an interface ultimately determines the behavior of devices at the nanoscale. We present a generic method to determine the possible lattice matches between two arbitrary surfaces and to calculate the strain of the corresponding matched interface. We apply this method to explore two relevant classes of interfaces for which accurate structural measurements of the interface are available: (i) the interface between pentacene crystals and the (111) surface of gold, and (ii) the interface between the semiconductor indium-arsenide and aluminum. For both systems, we demonstrate that the presented method predicts interface geometries in good agreement with those measured experimentally, which present nontrivial matching characteristics and would be difficult to guess without relying on automated structure-searching methods.

BibTeX:

📙 Nudged Elastic Band (NEB) Simulation Set-Up Using Image-Dependent-Pair-Potential (IDPP):

Improved Initial Guess for Minimum Energy Path Calculations
Authors: Smidstrup, Søren and Pedersen, Andreas and Stokbro, Kurt and Jonsson, Hannes
The Journal of Chemical Physics (AIP), Vol. 140, pp. 214106 (2014)
Abstract   |   BibTeX   |   DOI
Abstract: A method is presented for generating a good initial guess of a transition path between given initial and final states of a system without evaluation of the energy. An objective function surface is constructed using an interpolation of pairwise distances at each discretization point along the path and the nudged elastic band method then used to find an optimal path on this image dependent pair potential (IDPP) surface. This provides an initial path for the more computationally intensive calculations of a minimum energy path on an energy surface obtained, for example, by ab initio or density functional theory. The optimal path on the IDPP surface is significantly closer to a minimum energy path than a linear interpolation of the Cartesian coordinates and, therefore, reduces the number of iterations needed to reach convergence and averts divergence in the electronic structure calculations when atoms are brought too close to each other in the initial path. The method is illustrated with three examples: (1) rotation of a methyl group in an ethane molecule, (2) an exchange of atoms in an island on a crystal surface, and (3) an exchange of two Si-atoms in amorphous silicon. In all three cases, the computational effort in finding the minimum energy path with DFT was reduced by a factor ranging from 50% to an order of magnitude by using an IDPP path as the initial path. The time required for parallel computations was reduced even more because of load imbalance when linear interpolation of Cartesian coordinates was used.

BibTeX: