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Messages - Petr Khomyakov

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General Questions / Re: Building grain boundaries
« on: Today at 21:54 »
Please read the post above.

Which script? And what is actually your problem?

Please provide more details of your simulations, scripts and related log files.

Please could you describe this issue in a step-by-step manner, as well as information about your QATK version and operating system, attach the configuration, and send all that to Does this issue appear with one particular configuration or you experienced that for other systems/configurations as well?

Questions and Answers / Re: Li+
« on: Yesterday at 08:56 »
There is no special Li+ pseudopotenial, at least not in QuantumATK. My guess that you should use regular Li atoms described with a conventional pseudopotential. I guess Li atoms may become ionic (Li+) after inserting them into some specific environment/material by donating an electron or its fraction to other species in the system, which is system-dependent indeed.

Questions and Answers / Re: Nanorod in Quantumwise-ATK
« on: June 14, 2019, 14:05 »
Nanowire plugin is available for 2017. For non-cubic crystals, you may try the procedure described in my previous post.

Questions and Answers / Re: Li+
« on: June 14, 2019, 14:04 »
Please could you clarify what you want to do?

It was killed caused by out-of-memory issue. I think using the 12x12x12 k-point grid for a pretty large supercell might be a bit overkill. You may consider reducing the grid density to 6x6x6, for example, and then see if the DOS is well-presented with this k-point sampling.. 

Did you try other tricks (different pseudopotential/basis set, different Poisson solver, e.g., PCG) suggested in these guides?

Actually, in the latter guide, the example system is Fe-based MTJ. What about trying to adopt similar computational settings to see if that would work for your Fe-based MTJ?

Installation and License Questions / Re: Running error
« on: June 12, 2019, 10:07 »
Please attach your python script. For your information, support for versions VNL-ATK 2015-2017 have already been terminated. The latest version of QuantumATK is 2019.03-SP1, see

You can do projections on groups of atoms to get layer-resolved surface band structure, see You can set projections in the GUI or in the script.

There is no standard option of saving the surface band structure data to a text file, using the NanoLab GUI. You may however always save the data to such a file through python-scripting.

Code: [Select]




for nk in range(len(kpoints)):
 for ne in range(len(energies)):
   print(kpoints[nk], energies[ne], sbs_dos[nk,ne])

This creates a log file with the data arranged in a kind of xyz format, where x->k-point, y->energy, z->density of states that quantifies the surface band structure at the (k,E) point, see for more details

Questions and Answers / Re: Nanorod in Quantumwise-ATK
« on: June 11, 2019, 11:33 »
What version of QuantumATK are you using? In principle, you must be able to use the Nanowire plugin to build nanowires/nanorods in the Builder, at least for cubic cells.

Otherwise, one needs to creative and, e.g., cleave a crystal structure in the crystallographic direction (and perhaps choosing proper in-plane lattice vectors) that is aligned with the nanowire axis. One then has to shape a nanowire of interest by manually cutting off the nanowire edges in the Builder, which can be done by selecting and deleting certain groups of atoms to make vacuum padding around the nanowire/nanorod.

Installation and License Questions / Re: Running error
« on: June 11, 2019, 11:32 »
Could you explain in a step-by-step manner what you did to get this error? Is this issue reproducible? Which version of QuantumATK are you running?

If you already have a graphene sheet, you do not need to cleave it from the graphite crystal. In fact, you do not need to do it in any way, because a single graphene monolayer can be built by just increasing the out-of-plane lattice parameter of graphite to add a sufficiently-thick vacuum padding in-between the graphite monolayers.

Setting ghost atoms is more tricky. If you use plane-wave DFT calculator of QuantumATK, you actually do not need to use any ghost atoms. Otherwise, for LCAO-DFT it involves some experimenting. You  may first start doing these calculations without ghost atoms.   

I do not see much of a difference when computing work function
 of functionalized vs. pristine graphene sheet, see the following tutorial for work function calculations,

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