# General¶

## Introduction¶

QuantumATK packages a powerful set of tools for calculating properties of nano-scale systems. These atomic-scale calculators are based on density functional theory, semi-empirical tight binding, and classical potentials. The non-equilibrium Green’s function method is a unique feature of QuantumATK; it allows simulations on nano-scale devices and interfaces, including support for non-zero bias between the electrode leads and device components such as electrostatic gates and dielectrics. More information may be found at the QuantumATK website.

ATK is controlled using ATK-Python, which is an extension to the well-established Python scripting language. Setting up and executing QuantumATK calculations is therefore done in an ATK-Python script or directly from the command line in an interactive Python shell.

The main purpose of this manual is to document all QuantumATK functionality. The QuantumATK Reference Manual therefore gives a detailed summary of all input and output parameters, as well as notes on relevant theory and usage examples.

We also provide a thorough exposition of the theoretical background for the atomic-scale simulators implemented in QuantumATK (see Atomic-Scale Calculators), and a detailed introduction to Python scripting and using ATK-Python to control QuantumATK (see Python in QuantumATK).

For tutorials on how to use QuantumATK we refer to the Tutorials website.

## New in QuantumATK Q-2019.12¶

The Q-2019.12 release of QuantumATK introduces a range of new features and performance improvements. The list below provides an introduction and, in most cases, direct links to the documentation for some of the most significant new features.

Calculators

• Plane-Wave Calculator is now ready for production calculations

• PAW method for the Plane-Wave Calculator

Two datasets of PAW potentials, see Pseudopotentials, are now implemented for the PlaneWaveCalculator (not for the LCAOCalculator). They can be used with unpolarized and polarized spins, and support LDA, GGA and hybrid GGA, such as HSE.

• ForceField: Improved MPI for force-field calculations

General improvements in algorithm for domain decomposition, MPI communicators and others. Python overhead is now reduced by 50%, which is significant at many threads.

NEGF: Device calculators

• Transverse electrode repetitions

For electrodes that are pure repetitions in the lateral directions perpendicular to the transport direction, QuantumATK can automatically detect this and reduce the electrode’s lateral dimensions to that of its minimal lateral unit cell. This makes the calculation of the corresponding self-energies of the electrodes much cheaper computationally. In the Builder and Viewer, this is indicated by dashed lines in the electrode, similar to the dashed lines indicating the electrode extension in the central region.

• Performance improvements

Parallelization over left/right self energies is now implemented in QuantumATK, allowing for memory reduction of up to 30% and computational time reduction of up to 50%.

General Analysis

• Improvements for electron mobility and electron-phonon coupling calculations

• k.p method for band structure calculations

This method allows computing the Bandstructure much faster for the PlaneWaveCalculator, especially for the HSE Hybrid Functionals band structure calculations.

• Density of States: Extra functionality

QuantumATK now allows for normalization of the density of states by the number of atoms, as well as for calculation of the carrier concentration of the specified contribution. See DensityOfStates.

• Local Density of States

New analysis object. Calculate the density of states corresponding to a specific range of electronic energies, bands, and k-points. Useful for simulating STM images within the Tersoff-Hamann approximation. See LocalDensityOfStates.

• Partial electron density

Calculate the electron density corresponding to a specific range of electronic energies, bands, and k-points. May be used for simulating STM images. See PartialElectronDensity.

• Bulk Transmission Spectrum now uses Green’s function

This feature enables calculation of TransmissionSpectrum and related conductance for bulk materials without and with spin-orbit coupling included, and also improves accuracy over the previous method.

• Custom mesh cutoff for Grid analysis objects

This feature allows obtaining better resolution in various analyses represented on a grid, e.g. potentials and densities, without having to re-run the SCF calculation.

• Projections in EffectiveBandstructure

Projection on atoms, orbitals, shells and so on is now possible in EffectiveBandstructure, similarly to FatBandstructure.

Spintronics

• Gilbert damping

QuantumATK now allows for computing the GilbertDamping tensor. This method is based on a simple physical picture: spin-orbit interaction induced non-equilibrium state of a magnetic system that relaxes to equilibrium via the electron-phonon coupling.

• Orbital moment

Calculate orbital magnetic moments in a bulk, see OrbitalMoment.

Optical and Electro-optical properties of materials

Dynamics and Optimization

• Improved logging for Molecular Dynamics

QuantumATK now has improved logging from MD simulations, which now show reservoir vs. instantaneous temperature (NVT) and pressure (NPT) in the log. These quantities can now also easily be shown in movie tool.

• MDMeasurement

In MD simulations, it is now possible to measure any quantity at a user-defined interval. QuantumATK comes with a pre-defined list of f.ex. the various stress, strain and pressure components, but users can define their own quantities. See MDMeasurement.

• SpecificHeatCapacity

It is now possible to calculate the specific heat capacity in the quasi-harmonic regime, directly from a MD simulation with relatively few atoms. See SpecificHeatCapacity.

• Custom fitness criteria for crystal structure prediction

The crystal structure prediction function now accepts a user-defined fitness function which can include any combination of material properties, for example both the enthalpy and a target band gap. See CrystalStructurePrediction.

• Geometry optimization improved

OptimizeGeometry can now automatically restart the geometry optimization from a previous run, has a new option for geometry optimization at constant volume, and by default removes any drift force from numerical noise, to keep the center of mass fixed in the system. See OptimizeGeometry().

Polymer Science and Engineering

## Installing and running the software¶

The QuantumATK binary installer is available for registered users at the SolvNet software portal. Access to a valid QuantumATK license is also needed. Detailed instructions are given in the Installation Guide. Note that an evaluation license may be requested using the Synopsys Eval Portal.

When QuantumATK has been installed on your machine you can run it from the command line using the atkpython executable, which should be in your PATH, and a properly prepared QuantumATK Python script (written in ATK-Python):

$atkpython script.py  You can download and use script.py to test this – the script defines a water molecule and relaxes the atomic coordinates using the BFGS algorithm to minimize the forces. Parallel execution ATK supports multi-level parallelism, using the Message Passing Interface (MPI) available on most supercomputing clusters for distributed memory parallelism, and OpenMP for shared memory parallelism. ## How to read this manual¶ This manual is typeset using in-line references to QuantumATK Python objects and functions, and contains several script examples. The following style conventions are used: • All QuantumATK objects and functions appear as links, e.g. MoleculeConfiguration. The link will take you to the relevant section of the QuantumATK Reference Manual, where a detailed description of the object “MoleculeConfiguration” is provided. • References to particular chapters and sections are also links. For example, the links For-loops and Tuples direct you to specific sections in the chapter Python in QuantumATK. • Boldface letters are used to highlight specific words, e.g. atkpython, while in-line names of Python variables, functions, parameters, and methods are in general typeset using a monospace serif, e.g. list_of_atoms for a Python variable and cartesianCoordinates() for a method of the MoleculeConfiguration object. • In-line names of files and directories are also typeset using a monospace serif, e.g. file.txt and $HOME/QuantumATK/.

• Python structures are visually enclosed in a box and typeset using a monospaced serif:

# This is a comment

for i in range(3):
print(i)


Scripts can often be downloaded by following a link, e.g. example_code.py.

• Instructions for using the command line are indicated by the $ prefix: $ atkpython script.py


while instructions for using an interactive Python session is indicated by the >>> prefix:

>>> myList = [1, 2, 3, 4, 5]
>>> print(myList)
[1, 2, 3, 4, 5]
>>> print(len(myList))
5