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Topics - Anders Blom

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16
The VASP POSCAR format is a bit "odd" compared to most other structure formats in that it doesn't contain a required specification of the chemical elements - only the coordinates. The elements are implicitly read from the pseudopotentials in the POTCAR file when the VASP calculation is run.

If you have a VASP POSCAR file that you would like to import into VNL, but for whatever reason you do not have a corresponding POTCAR file, then you can create a dummy POTCAR file with just the lines that ATK looks for to determine the element.

So let's say you have a structure of NaCl, which in POSCAR format would look like

Code
NaCl
 1.0
   0.00000000  2.82028000  2.82028000
   2.82028000  0.00000000  2.82028000
   2.82028000  2.82028000  0.00000000
1 1
Direct
   0.00000000  0.00000000  0.00000000 # Na
   0.50000000  0.50000000  0.50000000 # Cl

(This is the slightly edited file produced by the VASP Scripter in VNL).

Then you can make a file called POTCAR in the same directory, with the contents

Code
TITEL x x Na
TITEL x x Cl

The order of the elements must of course match the order of the species in the POSCAR file.

Note: In a real POTCAR file, the lines are actually "TITEL = PAW Au"; you can of course also use this format, the only important things is the keyword TITEL and then ATK looks for the 4rd element of items separated by spaces to be the element symbol.

17
News and Announcements / ATK 12.8.1 bug fix release
« on: February 7, 2013, 10:40 »
A bug fix release ATK 12.8.1 was released today. The bugs are not extremely serious, the only major one is about large NetCDF files.

For details, see the release letter.

18
News and Announcements / ATK 12.8 released
« on: November 30, 2012, 16:23 »
After a long series of preview version, the final release of ATK 12.8 is now available for download, with a long line of new features and updates!


19
News and Announcements / ATK 12.8 being finalized
« on: November 22, 2012, 11:19 »
If you have followed the progress of the release of ATK 12.8 via the website (primarily http://quantumwise.com/publications/news-archive/188) you will have seen that we are slowly but steadily approaching the final release. There have been some issues with the license systems that had to be fixed, but things are now looking very good and we are confident a final release can be made very soon.

Meanwhile there is a so-called release candidate, version number 12.8.r1, available for download from the address above. It has all the features of 12.8 and no serious known bugs at all, plus also no expiry date, so it can safely be used until the final release appears, which we hope will be in 1-2 weeks, tops.

20
News and Announcements / ATK 12.8.b1 released
« on: September 25, 2012, 22:01 »
There is now a preview (beta) version of ATK 12.8 available for download. This release contains a couple of new features, like non-collinear spin and updates to NEB, and a few bug fixes. For details, see http://quantumwise.com/publications/news-archive/188

21
Plugin Development / Fun with graphene
« on: August 29, 2012, 10:39 »
I have made a collection of 3 useful, fun, cool and hilarious plugins that can be applied to graphene (and in fact any other 2D material) to twist, bend, ripple the structure to create buckled structures, half-wrapped tubes, twisted nanoribbons, etc.

To install, please download the attached zip file, then go to Help>AddOn Manager in VNL and click "Local install" to install the file. You should restart VNL to make the plugin active (unless you haven't yet started the Builder in the current VNL session).

Attached are also some examples of systems you can build with this addon!

22
Plugin Development / New board for plugins
« on: June 14, 2012, 12:08 »
Today we have added one more board to the Forum, called Plugins. As the name indicates it's intended for discussions and sharing of plugins.

At this point you may ask Plugins - what's that?. Well, you may not have noticed them, but actually all the functionality in the new Builder, starting with VNL 12.2, are plugins. There are also plugins for the Custom Scripter, a tool that is still a little bit hidden, but which we have great plans for in the future. And, in upcoming versions of VNL there will be plugins for the Job Manager and various forms of analysis.

Plugins enable a completely new way to add functionality to VNL. For instance, it's no longer necessary to release a whole new version of VNL to fix a bug in a plugin - we just make a new version of the plugin, which you then can download and install in VNL by using the AddOn Manager, which you can find in the Help menu. We can also deliver previews of (or fully developed) new functionality before the next release, by making a new plugin available. You can for instance already now open the AddOn Manager and find plugins to set up VASP calculations or import/export QuantumEspresso geometries - features that are not present in the released 12.2 versions.

A note on names: the packages you download via the AddOn Manager are "addons". An addon can contain several plugins. For instance, the QuantumEspresso addon contains 2 plugins: one for export and one for import. They are separate plugins, because they are based on different API classes, but are bundled into one addon for distribution.

But the really cool thing is that users can write plugins themselves to implement new functionality - or we at QuantumWise can deliver customized functionality to an individual customer to solve a specific problem. Users can also share plugins with each other, just like you would do with extensions and addons for Thunderbird/Firefox, or for that matter apps for iPhone and Android!

This Forum board is the first step in this direction, and we encourage anyone who develop their own plugins to use it to share them with the ATK community. This board should also be used for discussions about plugin development, and in upcoming posts we will provide a bit more detailed information about how to develop and share plugins, so stay tuned!

23
Normally when you plot the k-point resolved transmission, it becomes a square plot of T vs kA and kB (the actual point K=kA*b1+kB*b2 where b1,2 are the reciprocal lattice vectors), because that is how we sample the Brillouin zone.

In the hexagonal case, it is more illustrative to see the plot in the actual Brillouin zone, i.e. as a function of kx,ky in the hexagon. To make that plot is rather challenging because as it turns out, the Monkhorst-Pack regular grid in kA,kB space actually samples points in the 2nd Brillouin zone, which you then have to map back into the first zone. And, there are some tricks needed in matplotlib to get a hexagonal axis plot. But in the end, you can get the attached picture!

The labels K and M have been added afterwards in an image editing program.

The inspiration for this came from PRB 80, 035408 (2009).

24
Ok - ready?

  • Start VNL and open the "AddOn Manager". Sort by name, and scroll down until you find the "TubeWrapper". Install it.
  • Open the Builder, and click "Coordinate Tools" to make sure you have the "Tube Wrapper" installed. If not - it's a bug in the beta-version, and I can suggest another (a bit more complicated) way to install the plugin.
  • Now, click "Add">"Add from Database" and locate molybdenite. Add it.
  • Use the mouse selection to delete the 3 atoms to the right in the cell. This leaves a single layer of MoS2, in the hexagonal cell.
  • Use the "Supercell" (Bulk Tools) plugin with A'=2A+B to get an orthorhombic cell.
  • Open the "Repeat" (Bulk Tools) plugin. You now have two choices: repeat in A or B - this will give either zigzag (B) or armchair (A) tubes. Repeat some decent number, like 20.
  • If you repeated in A, open the "Swap Axes" (Bulk Tools) plugin and click "A<>B" then "X<>Y".
  • In "Swap Axes", click "A<>C" then "X<>Z" (both for A and B repeat).
  • Open "Lattice Parameters" (Bulk Tools) and select "Cartesian" coordinates. Then change the first cell vector A so that the size of the cell in X is at least as large as in Y.
  • Open "Center" (Coordinate Tools) and center the system, only in A.
  • Open the new plugin, "Tube Wrapper" (Coordinate Tools) and wrap the tube! You can use 360 directly to get a tube, or perhaps 180 :)
  • Finally, adjust the cell size (it's a bit big) and then center the system in A and B.

Now you can perform calculations on MoS2 nanotubes. Note that the article uses DFTB, this model is also available in ATK, and you can as academic request the Mo/S parameters from http://www.dftb.org for free, and run ATK with those. How to install DFTB parameters is described in a tutorial.

Have fun!

PS: The recipe above looks complicated perhaps, but compare it to trying to make it yourself ;) Besides, all operations have a point: we need to go from hexagonal to ortho, we need to repeat, and to extend the unit cell to fit the tube. The only non-obvious thing is perhaps the Swap Axes operations. These are there because the Tube Wrapper assumes a certain orientation of the system. The alternative would have been to allow selection of axes in the plugin, but that also comes with some logical complications.

PS2: As you can guess, you can of course also use the same method to make carbon nanotubes. There is of course existing functionality in VNL for that, but you could use this plugin to make "open" or partially wrapped nanotubes!

25
As of ATK 11.8, we have started working on a rather general way to set up calculations in other codes than ATK from our graphical user interface Virtual NanoLab (VNL). We already have prototypes for VASP and a few other codes.

For users who until now have used VNL to set up GPAW calculations, there are few changes in version 11.8. Since we unfortunately have not had time to update the tutorial to reflect these changes, let me outline the changes below.

The most immediate change is that we have included a brand new GPAW Scripter in 11.8. However, it is no longer located in the Script Generator, as it was before. To find the new GPAW interface, go to the Tools menu in VNL (the main window) and choose Custom Scripter. In there, go to the menu Scripters and choose GPAW Scripter. Hopefully it's easy to work with; to get an atomic configuration into it, just drop the configuration from the Builder or Database etc onto the Scripter window (you can drop it anywhere).

This is still an early version of the GPAW scripter, thus there are some limitations. But at least you can build structures, using the other tools in VNL (and, most notably, in 12.2 coming out soon, there will be a completely new and radically improved Builder!), and get a basic GPAW input script with very little effort. Then you can edit the script manually if there are some calculations you want to do which our Scripter does not support yet.

The second part of the change will be that we will no longer ship a precompiled GPAW with the ATK package; this will take effect from version 12.2. This means a somewhat more involved procedure for the user, who needs to download and compile GPAW (unless you are able to use one of their precompiled versions), but one should note that the GPAW shipped with ATK 11.8 and earlier is
a) an older version (0.6.5147, while the latest official GPAW is already 0.9), and
b) only capable of running in serial - if you know a bit about GPAW, you will realize that the whole point of the code is to run in parallel (or else performance suffers a lot).

For now, you can still in principle use our 0.6 version, but I wouldn't recommend it, esp. since I know there were a few bugs back in 2009, which should have been fixed by now in 0.8.

Our plan is to extend the support for GPAW quite a lot in the near future. Thus we value any feedback users can provide on the current Scripter, so we know how to improve it - and VNL in general.

For more information about GPAW, and to download the latest version, please go to https://wiki.fysik.dtu.dk/gpaw/.

26
Short version:
1. Check the FAQ first!
2. Search the Forum - your problem is very likely reported before...
3. Include all files and error messages in the post.



We have collected many of the most common error messages that you may encounter when running ATK and VNL in the FAQ. There is a short description of the cause of the error, and a hint what to try in order to resolve it. Searching the Forum for the error message often provides a longer discussion, not least about potential solutions.

There are several different error messages that in reality mean that the calculation is too large for the amount of memory available. We have collected some general tips and information about memory usage in a tutorial.

Also, if you do post a question about an error message etc, make sure to include the FULL and EXACT error message in the post, and any input or output files used or generated during the run that triggered the problem. If your files contain sensitive information, you may mask them (e.g. by removing all the elements) or send them to us privately, upon request. We treat all user file with the strictest confidentiality.

27
A rather annoying "feature" of running calculations on a remote host, such as a cluster, is that if you are not careful, the calculation will be interrupted if you lose the network connection.

The way I used to get around this was to submit my jobs under "nohup", like

Code
nohup atkpython myscript.py > myscript.log &

Note the ampersand "&" at the end, so that the processes goes into the background.

Now, there are certain disadvantages with nohup, which I will not go into. One very notable feature is also that if you launch "mpiexec" under nohup, you must redirect stdin too:

Code
nohup mpiexec atkpython myscript.py > myscript.log < /dev/null &

otherwise your log file will fill up with warning messages real fast.

Fortunately, there is an alternative to nohup, called screen. There is a very nice tutorial for it here:
http://www.rackaid.com/resources/linux-screen-tutorial-and-how-to/

To summarize briefly how to run ATK on a detached screen (we assume screen is installed on the remote host; if not, please confer with the sysadm of that system):

1. Log into the remote host where you want to run, e.g. using ssh
2. Use the command "screen" to start a new screen (there is some information screen that pops up, it can be avoided with "screen -q")
3. Start ATK as you would normally, for instance

Code
atkpython myscript.py

(we use an example without a log file, it works fine with one as well, of course)

4. Hit Ctrl-A-D to detach the screen
5. You will be returned to the login session on the node, from which you can now safely log off ("exit") and the calculation will continue to run in the background.

Some time later, you want to check if the calculation finished.

1. ssh back into the remote host
2. Type "screen -r" to resume the screen (if you have several screens running, you will be prompted to provide the pid, like "screen -r 1234")
3. You are now back in the session where you started ATK, and you can operate as usual. If the calculation didn't finish, just detach the screen with Ctrl-A-D again. If it finished and you want to exit permanently, type "exit"

There are more options, like switching between different screens (Ctrl-A-N), etc. For details, see the tutorial mentioned above.

28
We have learned that sometimes the error

Code
locale.Error: unsupported locale setting

appears when starting VNL 2008.10 on machines running Linux distributions configured for e.g. Korean or Chinese locale (language settings).

To resolve this, insert the line

Code
export LC_ALL=C

in your .bashrc file in your home directory. Restart the shell for the change to take effect.

29
News and Announcements / FFT bug in ATK 2010.02
« on: May 5, 2010, 10:58 »
A bug in the FFT routines for two-probe (device) calculation has been found in ATK 2010.02.4185. We recommend all users to switch to the multi-grid method until the problem is resolved.

We wish to point out that ATK 2010.02 is an alpha version, and contains known bugs (besides the one mentioned above). A new major, stable release is expected by summer 2010, which will replace the 2008.10 and 2010.xx packages.

30
As a follow-up to my VASP importer, I would like to share with the community a VASP exporter.

Update: Scroll down to the last post in this thread to download the latest version of the script.
It's really simple to use: drop the attached file on the "Custom" builder icon in VNL2010.02, then drop your geometry (must be a bulk configuration) on the drop zone, and the resulting POSCAR data will be written in the Log panel.

The first line (the comment line) contains the element ordering; use this to create your POTCAR file (which for obvious reasons VNL cannot generate).

Thus, now you can build a very complex system, using the nice GUI tools in VNL, and then export the geometry to run it with VASP! (Of course, we'd prefer that you would run the system with ATK, but we understand why VASP is useful too ;) )

As always, feedback is very welcome! Would you like an option to write Cartesian coordinates (right now it writes only "direct")? Other features?

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