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Topics - Umberto Martinez

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QuantumWise will host a free webinar on the release of ATK-VNL 2017.

The webinar is targeted to every VNL and ATK user who wants to learn more about the new features implemented in version 2017 of QuantumWise's atomic-scale modeling platform.
In particular, we will cover:
- New Builder features, measurement tool, database connectivity to Materials Project, NEB with varying cell size, ...
- New methods for accurate calculations of semiconductor and insulator band gaps
- New analysis features: Fermi surfaces, fat band structures and projected density of states, ...
- Updates to the Job Manager
- and much more.
The webinar will be held on August, 17th, 8-9 PM CEST, and on August 18th, 9-10 AM CEST.
The duration is about 40 minutes plus a Q&A session.
For more information about the ATK and VNL 2017 release, see the official release letter.

Register for the free webinar at this link.

QuantumWise is happy to announce that we will host a free webinar on atomistic simulations of thermal transport across materials interfaces using the Virtual NanoLab (VNL) and ATK-Classical software.

In a short lecture (30 minutes), you will learn the basic concepts of thermal transport. We will particularly focus on non-equilibrium molecular dynamics (NEMD) and phonon transmission based on non-equilibrium Green's functions (NEGF), which will be used in the following hands-on session (1 hour). Here, you will be guided through practical examples on how to simulate the thermal conductance across a grain boundary in silicon. Afterwards, there will be time for questions and discussion. The entire webinar will take two hours.

This is the second webinar in our series of webinars on molecular dynamics simulations. The slides of our first webinar can be found here.

More information on thermal transport simulations with ATK-Classical can be found in our recent paper, uploaded at this link: arXiv:1701.02495

The webinar will be held on February, 14th, 9-11 AM (CET), and on February 15th, 8-10 PM (CET).


After registering, you will receive a confirmation email containing information about joining the webinar

QuantumWise is happy to announce that we will host a webinar to give you an introduction to Molecular Dynamics (MD) simulations using the Virtual NanoLab (VNL) and ATK-Classical software.

In a short introductory lecture (30 minutes) you will learn about the basic underlying physics, different simulation techniques, and what you can do with MD simulations. In the following hands-on-session (one hour), you will be guided to set up and run your own MD simulations. Afterwards, there will be time for questions and discussions. The entire webinar will take two hours.

This webinar is primarily targeted at researchers and students who have some basic knowledge in atomistic modeling, but have not worked with MD before. For the hands-on part it would be beneficial if you already had VNL-ATK installed on your computer.

More information on ATK-Classical can be found in our recent paper, uploaded at this link: arXiv:1701.02495

The webinar will be held on January, 24th, 9-11 AM (CET), and on January 25th, 8-10 PM (CET).


After registering, you will receive a confirmation email containing information about joining the webinar

Learn how to use VNL and ATK to predict the stable crystal structures of bulk materials using atomic-scale modeling and a genetic algorithm!
Check out the new video tutorial available on youtube at this link:

Feel free to share your comments and feedback!

When installing VNL/ATK 2016.3 on Windows 10 the SmartScreen alert may show up and tell you that the VNL/ATK installer is not safe.

The installer is of course safe and signed with a secure certificate, we are working to fix for this warning and provide a fix as soon as possible.
In the meantime, please just click "More info" and run the installer anyhow.

News and Announcements / Bugfix update VNL-ATK 2016.3
« on: November 16, 2016, 10:58 »
A bugfix update to VNL-ATK 2016 has been released (version 2016.3).

Download it from

Please note that for this release, we are introducing a new end-user license agreement (EULA).
2016.3 updates
Important bugs or improvements, possibly affecting results or output, or hindering usage of the software
  • IETS analyzer: the total d2I/dV2 signal should be divided by the total dI/dV signal (not by the inelastic dI/dV signal, as it was)
  • Fix for VNL crash when showing density plots of device configuration
  • Avoid deadlocks in checkpoint files when running in parallel
  • Added terms to be able to correctly calculate forces with the Ozaki contour integration method
  • Save the transmission spectrum while running IVCurve
  • Fix for the doping plugin, to ensure it always writes tags and doping to electrodes

For the full list of updates please check the official 2016.3 bugfix release letter.

News and Announcements / VNL and ATK 2016 released
« on: July 21, 2016, 21:18 »
The new VNL and ATK 2016 is now released!

This version features, among many other things, better parallel performance, improved DFT accuracy, a new MD framework, as well as a very exciting new NEGF algorithm for surface calculation - and it's available also for Mac OS X.

See the full release letter.

Download the new VNL-ATK 2016.0 packages

  • New basis sets and pseudopotentials (SG15) which improve the accuracy of ATK-DFT substantially (GGA only)
  • Faster electron-phonon coupling calculations - up to 10x improvement in the general code, plus a new approximate spectral method that is even faster
  • Support for noncollinear spin and spin-orbit in the electron-phonon coupling module
  • More quantities can be obtained from a mobility calculation: Seebeck coefficient, thermal conductivity, and the Hall-coefficient and Hall-conductivity tensors
  • Multi-core parallelization per k-point turned on by default - scale bulk calculations to 100s of cores without using any extra options in the input file
  • Enhancements to the Script Generator, making it a lot easier to use also for more advanced features
  • Improved MD/NEB/AKMC framework - multilevel parallel, and entirely new, highly flexible back-engine code
  • State-of-the-art Martyna–Tobias–Klein barostat for MD
  • Lots of new plotting methods in VNL
  • SurfaceConfiguration, a.k.a. one-probe: a new unique approach to simulating real surfaces without resorting to the slab approximation, using NEGF with physically correct boundary conditions
  • PEXSI solver, for large-scale DFT calculations (10,000+ atoms)
  • New k-point grids: Γ-centered odd meshes, and regular grids to span the Brillouin zone edge-to-edge (or cut out a small region) for transmission spectra
  • New Hubbard-U method, with shifts applied to the pseudopotential projectors for each angular momentum channel (similar approach as used in plane-wave codes)
  • Ozaki equilibrium contour; highly stable calculation of the equilibrium density matrix in device calculations. Particularly useful if the electronic eigenvalue spectrum is very deep
  • Verbosity framework, to control the level of output from an ATK calculation in detail
  • Mac OS X version

News and Announcements / ATK and VNL hands-on workshop
« on: June 10, 2016, 11:56 »
QuantumWise would like to invite all ATK and VNL users to a hands-on workshop on atomic scale modeling of nanomaterials.
The workshop will take place at QuantumWise’s headquarters in Copenhagen on August 19, 2016. The day will end with a guided visit to Niels Bohr's office.

Read more and sign up today at this link!
Deadline for signing up is July 15th at 16.00 CET.

News and Announcements / Bugfix update VNL-ATK 2015.1 available
« on: December 2, 2015, 10:37 »
The 2015.1 update for Virtual NanoLab and Atomistix ToolKit is now available for download. This release fixes a few smaller and larger bugs.

Download VNL-ATK 2015.1 here

Fixed bugs and updates
  • Small truncations in the real-space density in GGA and MGGA could lead to bad convergence - should be much better now.
  • Nanowire and Wulff constructor plugins: fixed bug about unit of radius.
  • Bands below Fermi level can now be set to zero for effective mass in the Script Generator.
  • Spectral current plot in IV-Plot was not updated when changing the temperature.
  • Export dialog from builder would start up in the previous project, not the current.
  • The editor now saves in the project directory by default.
  • Grimme-D3 does not use the 3-center term by default - it incurs an extremely large performance penalty but typically only a small improvement of the results.
  • Generated script for SpinTransferTorque analysis improved.
  • GridSampling now has a minimal gridSize (4,4,4); smaller dimensions will lead to segmentation faults in FFT.
  • Using the Move Tool would reset the graphics properties of selected atoms.
  • Catch and show error messages from failed relaxations using the Quick Optimizer in a dialog.
  • Phonon Vibrational Visualizer: overlay mode fixed + don't reset the camera when the mode is changed.
  • SpinTransferTorque, fix for keyword "spin" + improved error message.
  • DynamicalMatrix - nlprint and nlsave/nlread implemented.
  • Sign error for Fermi shift in InelasticTransmissionSpectrum, elasticCurrent fixed.
  • Added license_file command-line argument for installer.
  • VNL now behaves better when you change to/from maximized window
  • The width of the file browser can now be made narrower than the longest filename
  • Give a color warning in "bulk to device"
  • ... and a few more minor, mostly technical issues

For more details on new features in VNL-ATK 2015, see the original release letter.

Known outstanding issues

A few remaining bugs could not be fixed in time for this release.

  • It is not possible to "nlprint" a ProjectedLocalDensityOfStates made from a DeviceDensityOfStates object. This also affects the "Text representation" plugin on the LabFloor. For a work-around, see
  • Issues with plotting transmission eigenstates for spin-polarized calculations.
  • Using interactive mode on Windows 8 or 10, all text is printed with the background color, making it impossible to read anything. A work-around is available:
  • VNL fails to run on LUbuntu - a work-around is available, contact us if help is required.
  • Be careful when using Undo/Redo for a NEB path, if you are editing the images; some issues have been observed.
  • Running MD in parallel on Windows doesn't work due to a bug in the ASE library. Anyway, you should not run MD with classical potentials in MPI parallel anyway (use threading though!) and for DFT-MD you probably want to use a Linux cluster!

News and Announcements / Parallel runs in ATK 2014
« on: December 3, 2014, 09:39 »
Dear users, just a reminder in case you run parallel calculations with ATK 2014.

As specified in the release letter:
you now need to set OMP_NUM_THREADS=1 if you place several MPI processes on the same node, else parallel performance degrades substantially.

Gallery / 1512 atoms on a plane...
« on: May 30, 2014, 09:04 »
Playing with VNL on the plane on our way back to Denmark from E-MRS.

With ATK-SE Extended-Huckel we calculated (and plotted) the charge density and an eigenstate (not shown here) of 1512 carbon atoms!
in 5m58s, just before landing :)

While waiting for spin-orbit interaction....
here a second tutorial about noncollinear calculations: Noncollinear calculations for metallic nanowires

Start from the Introduction to noncollinear calculations tutorial and move to a more complex system with this new tutorial.

New tutorial online, check it out!
Pt diffusion on Pt surfaces: NEB calculations

In this tutorial you will learn how to perform Nudged Elastic Band (NEB) calculations to investigate diffusion or reaction barriers.
As an example, you will calculate the diffusion barrier of a single Pt adatom on flat and stepped Pt surfaces.

General rule: always check the ATK Reference Manual to have more details about all the parameters used in the tutorial.
In this case the NudgedElasticBand class and the OptimizeNudgedElasticBand function.

Gallery / Pillared Graphene
« on: March 19, 2014, 22:48 »
take a CNT and a graphene sheet and mix them together in the Builder!

for a reference see for example G. Dimitrakakis et al. Nano Lett., Vol. 8, No. 10, 2008

In different flavours!

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