Simulation software for nanoscience

Download Atomistix ToolKit and Virtual NanoLab as one complete package and get started today.

ATK 13.8 released

Oct 23 2013

ATK 13.8 released with many new features, among others Phonon calculations, IV-curves, Noncollinear spin, Bandstructure Analyzer, New 3D Viewer, and more...

Enjoy all the new features!

  • Phonon calculations

  • IV-Curves

  • Noncollinear spin

  • Band structure analyzer

  • New 3D Viewer

    ...and a lot more!

Watch video demonstrations of the
new features (click player to enlarge).

{youtube}MytB68ZisBw|200|150{/youtube}

Download ATK 13.8 here

License

This release requires license version 13.8 or higher.

NOTE: An updated version ATK 13.8.1 has been released with a few new features and bug fixes.

New in ATK 13.8

ATK 13.8 introduces a long line of new features.

New interface - introducing Projects and the LabFloor

  • Group your files into projects
  • Easier and more transparent access to objects in NetCDF files
  • Complete overview of all files and data within a project on the LabFloor
  • Combine data sets from different files for analysis
  • The Builder "stash" is now persistent across sessions - and separate for different projects
  • But - if you like the old interface, you can also make ATK 13.8 look like 12.8 and still benefit from all the new features.
    This is also handy for quickly navigating around your directory structure to locate a file.

projects

labfloor

 Enhanced analysis

  • Transmission Analyzer - investigate specific transmission spectra in more detail. Calculate transmission eigenvalues and eigenstates interactively. Click to watch video demonstration.
  • Enhanced band structure analyzer - e.g. measure band gaps. Click to watch video demonstration.
  • I-V curve
  • Plotting tool for 3D grids projected to 1D
  • Defined by plugins - expect more, and write your own!

I-V Curve

transmission_analyzer    bandstructure

iv-curve

Phonon calculations

  • Compute the phonon band structure and density of states for bulk materials, nanowires, nanotubes, graphene, etc. ยท
  • Study thermal transport - compute the phonon transmission spectrum and calculate the Seebeck and other thermal coefficients
  • Parallelized with near-linear scaling up to 3N nodes (N=the number of atoms)
  • Video demonstration on phonon calculations.
phonon_transmission
phonon_bandstucture    phonon_dos  

Noncollinear spin

  • Available for both electronic structure and transport calculations
  • Specially developed novel methods for improved convergence, using a collinear initial state
polarization_visualizer
   

Crystal Builder

  • Build crystals from scratch, using Wyckoff positions
  • Strukturbericht templates
  • Symmetry recognition (spglib) - plugin the Builder
crystalbuilder2   crystalbuilder

New 3D Viewer

  • Improved performance for trajectory movies and large structures
  • Control atom color, radius etc individually
  • Set background color, control lighting in detail
  • Set atom properties by properties, like radius by Mulliken population or color by effective potential or forces (requires plugins)
  • Better support for old graphics drivers - performance may suffer, but at least VNL starts up properly.
  • Easy export of images from the Builder and Viewer in various bitmap formats.
  • There is also an update to the POVRay plugin for generating ray-traced images
  nanotorus

Doped systems

  • Doping can also be introduced in the central region (earlier it was only possible to do for the electrodes) via so-called compensation charges. This allows for simulations of a wide variety of semiconductor devices, like p-n junctions, p-i-n doped Si nanowires, etc, without the need to introduce explicit dopant atoms.
  • Doping charge can now be set in Scripter; the compensation.
  • Improved convergence of doped device systems.
InAs_pin_ldos

Molecular dynamics

  • Large set of Tersoff potentials from Tremolo-X
  • Pre/post step hooks for customized on-the-fly analysis or time-dependent modifications of the structure (to make a stress/strain curve, for instance)
  • NVT, NPT, NVTBerendsen, NPTBerendsen, Velocity Verlet

{youtube}qqGkiY3B76s|200|150{/youtube}

Plane wave method: ABINIT

  • Shipped with ATK 13.8 - both for Linux and Windows, with support for MPI parallelization
  • Fully integrated with the ATK Python scripting language for total energy, NEB, geometry optimization and band structure calculations
  • Other customized ABINIT tasks can be scripted too
abinit

Method improvements

  • ATK-SemiEmpirical
    • All models now available in fully nonself-consistent and selfconsistent form
    • Performance enhancements
  • New shell-wise Hubbard +U model
  • Counterpoise correction to compensate for the basis set superposition error (BSSE). Use this when optimizing molecules on surfaces etc to get high accuracy.
  • Grimme's DFT-D2 semi-empirical model for van der Waals interactions, both forces and stress; parameters for most elements up to Xe
  • Multigrid method
    • Added support for non-orthogonal cells
    • Performance improvements
 

Smaller changes, improvements and additions

  • The keyword grid_mesh_cutoff for NumericalAccuracyParameters has been renamed to density_mesh_cutoff which is more correct conceptually. The old keyword is still accepted for backwards compatibility.
  • It is now possible to save arbitrary numpy arrays in NC files. This is very handy when you have computed some results - possibly in a time-consuming post-processing step - and want to store them for later plotting etc.
  • Several small improvements to the Interface Builder, like a small inaccuracy in the positions of plot points in the surface cell picker, shift in Z kept consistent when adding layers, and the default suggestion for the surface cell is now really the smallest cell.
  • Device from Bulk - algorithmic improvements and new presentation of electrode Z-length choices.
  • A few performance improvements related to MD simulations and other cases where a copy is needed of a configuration.
  • Unit cells and coordinates are now slightly rounded to avoid 0 being represented as 1e-17 in generated scripts.
  • No question anymore for permission to overwrite existing NC files - ATK doesn't actually overwrite existing NC files, it just appends to them (normally, at least - unless you use an object ID already present in the file).
  • Memory Usage button in the Script Generator to provide an estimate of the required memory for a calculation. Can also be inserted in a script, since the estimate can take some time. See the dedicated tutorial for more details.
  • Transmission spectrum is now always identically zero for energies where there are no propagating states. This means you can trust that a small but non-zero value is not just numerical noise but actually indicates finite but small transmission.
  • Clearer which stash items you are about to delete.
  • Possibility to make the stash panel in the Builder larger.
  • The scipy package is now part of ATK.
  • Clearer error messages in cases where licenses (trial or usual ones) have expired.

Bug fixes (compared to 12.8.2)

No serious bugs in the calculation engine are known in ATK 12.8.2. The following are however real issues that were fixed:

  • Trajectories where the cell changes were not read correctly (nlread).
  • The method "lastImage()" for trajectories now works as intended.
  • MoS2 and MoSe2 structures corrected in the Database (cf. Phys. Chem. Chem. Phys. 4, 4078 (2002)).
  • Sealed a memory leak (self-energies) in device calculations.
  • Forces for non-selfconsistent Slater-Koster models corrected.
  • EMTCalculator ignored repeated images and therefore did not work correctly for bulk configurations.
  • No matter which k-point sampling you set in C, the Script Generator always generated the script with 100 points, which is always a safe choice, so it's not a serious problem, but anyway fixed now.
  • The maximum number of steps set for an optimization will now apply also to a stress optimization. Earlier the loop over stress would run forever if the criterion was not met.

In addition, the following minor cosmetic bugs were however fixed, mostly related to VNL.

  • Better handling of zero (or very small) or very large values of the lattice parameters (could force the Builder to crash). Also improved error messages for illegal lattice parameters.
  • Tags are now kept when systems are dragged and dropped onto each other in the Builder.
  • The "Fit cell" plugin has been improved for some difficult cases.
  • Passivate tool could cause VNL to segfault for some structures - fixed.
  • Z-matrix tool now handles the selection order of atoms correctly when switching stash items.
  • Spatial regions inside electrodes are now displayed correctly in the Builder and Viewer (and not shifted inside the central region as before).
  • Better handling of rare cases where atoms are deleted in the electrodes causing the device to become invalid.
  • Contour integral parameters now cloned correctly when upgrading a calculator.
  • Ctrl and Shift not always observed when clicking the 3D view when the Builder is not active.
  • Cube file export no longer prints the trailing line which could trip up some other programs that import Cube files.
  • Improvements to the license configuration tool, to correct for mistakenly set server port.
  • Effective Mass Analyzer prints unit for Cartesian k-points - was confusing that they appeared in 1/Bohr when most other output in ATK is in Angstrom.
  • The NEB preoptimization also uses the max_steps keyword set for the NEB calculation itself.
  • Eigenstates, small bug related to using default quantum numbers.
  • Again possible to add an extra image between other ones in a NEB path - worked in 12.2 but not in 12.8.
  • Ti-beta actually generated a structure with a Tl (thallium) atom - typo...
  • Nanowire plugin doesn't crash anymore when using a small radius
  • ... plus a few really small and esoteric issues

Known bugs and issues

See the ATK 13.8.1 release letter.

FOLLOW US: