wrong results got by Surface Model in 2016.0

[395235863]

why no periodic characteristic in left electrode?
Thank you very much!

[Jess Wellendorff]

Could you please attach the script you have used? Thanks.

[395235863]

I have attached it

' Surface-Mo-MoS2.py '

[Petr Khomyakov]

According to the tutorial on SurfaceConfiguration calculation, see http://docs.quantumwise.com/tutorials/gf_surface.html?highlight=surface%20configuration, one should, "in the Poisson solver settings, change the boundary condition on the right-hand C-face to Neumann".

It seems that you have not changed that setting for the boundary condition as it follows from your python script. 

[Jess Wellendorff]

1) Yes, you should use the Neumann boundary condition on the right-hand face of the surface configuration central region (towards vacuum).

2) After some testing, I think the problem you see is due to k-point sampling. As usual, the electrode should not be too thin, but I think your electrode has an OK size. But your k-point grid does not sample the Gamma point (because it is a even grid, 8x16 in kA,kB), so the electrode Fermi level may not be well determined. It is very important to accurately determine the electrode Fermi level in one- or two-probe calculations. In fact, this is the main reason to use many k-points along C for device electrodes. I suggest to use a Gamma-centered k-grid, either of the form 5x9x100, or by enabling "Shift to Gamma" in the Script Generator.

[395235863]

I changed my script in device boundary conditions and k-points.

But  the result also seems wrong!

[Jess Wellendorff]

Right, doesn't look quite right. Try to double the electrode size along C. Ought to improve things.

[395235863]

I doubled the electrode size along C.

Then the job can't  run!Maybe too large?

log file:
"
+------------------------------------------------------------------------------+
|                                                                              |
| Atomistix ToolKit 2016.0 [Build adaf9ce]                                     |
|                                                                              |
+------------------------------------------------------------------------------+

Timing:                          Total     Per Step        %

--------------------------------------------------------------------------------

Loading Modules + MPI   :       5.05 s       5.05 s      99.00% |=============|
--------------------------------------------------------------------------------
Total                   :       5.10 s

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 20293 RUNNING AT ibcu1
=   EXIT CODE: 1
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
"

[Anders Blom]

As the first step, I would remove the Grimme correction. You can add it in a second step later, once you have achieved reasonable results without it.
The error you see is indeed probably due to "out of memory", so try using fewer MPI process (or more machines).
Also the electrode of 6 Å is on the short side, about 9 would be a lot better.

[395235863]

I used other model ,still have questions.
How can I change it ?

[Jess Wellendorff]

OK, so I spent some time investigating this issue. For testing purposes, I used a small Mo(100) surface (without any S atoms at all), see attached scripts. The reason you do not find a smooth and bulk-like transition between the electrode and left-hand part of the central region is two-fold:

1) The HGH-tier4 basis functions for Mo are fairly long ranged, extending 11 Bohrs. Your electrode thickness needs to be twice this range, plus two times the range of the pseudopotential projectors. Your electrode therefore needs to be at least 12 Å along the z-axis in order to minimize overlaps with atoms in the scattering region (interactions across the electrode extension). You can use the Electrode Validator to check if a bulk configuration with a converged calculator can be used as an electrode (see http://docs.quantumwise.com/tutorials/atk_transport_calculations/atk_transport_calculations.html#check-the-electrode-geometry-and-size).

2) The HGH pseudopotential for Mo has 14 valence electrons in it. The lowest electrode Hamiltonian eigenvalues are therefore ca. -60 eV (run a band structure or DOS calculation to check this). The default semi-circle NEGF contour integral method has -1.5 Hartree (-41 eV) as the default lower bound for the integration limit. Some core electron density is therefore not captured by the default integration bound with the 14-valence electron HGH potential for Mo. This causes poor SCF convergence in the NEGF calculation and charge accumulation at the electrode-central region interface (see also the box just above the headline at this link: http://docs.quantumwise.com/tutorials/atk_transport_calculations/atk_transport_calculations.html#analyzing-the-results). There are two different ways to fix this: a) increase the semi-circle lower bound to 2.5 Ha (surface_hgh_semi-circle.py), or b) use the new Ozaki contour integral method (http://docs.quantumwise.com/manuals/Types/OzakiContour/OzakiContour.html), which does not depend on an energy bound (surface_hgh_ozaki.py). This is an extremely reliable contour integration method, but may be a little slower than the semi-circle method.

Finally, I would like to suggest you try out the SG15 pseudopotentials as an alternative to HGH, see http://docs.quantumwise.com/manuals/ATKDFT.html#sec-sg15.

[395235863]

OK, so I spent some time investigating this issue. For testing purposes, I used a small Mo(100) surface (without any S atoms at all), see attached scripts. The reason you do not find a smooth and bulk-like transition between the electrode and left-hand part of the central region is two-fold:

1) The HGH-tier4 basis functions for Mo are fairly long ranged, extending 11 Bohrs. Your electrode thickness needs to be twice this range, plus two times the range of the pseudopotential projectors. Your electrode therefore needs to be at least 12 Å along the z-axis in order to minimize overlaps with atoms in the scattering region (interactions across the electrode extension). You can use the Electrode Validator to check if a bulk configuration with a converged calculator can be used as an electrode (see http://docs.quantumwise.com/tutorials/atk_transport_calculations/atk_transport_calculations.html#check-the-electrode-geometry-and-size).

2) The HGH pseudopotential for Mo has 14 valence electrons in it. The lowest electrode Hamiltonian eigenvalues are therefore ca. -60 eV (run a band structure or DOS calculation to check this). The default semi-circle NEGF contour integral method has -1.5 Hartree (-41 eV) as the default lower bound for the integration limit. Some core electron density is therefore not captured by the default integration bound with the 14-valence electron HGH potential for Mo. This causes poor SCF convergence in the NEGF calculation and charge accumulation at the electrode-central region interface (see also the box just above the headline at this link: http://docs.quantumwise.com/tutorials/atk_transport_calculations/atk_transport_calculations.html#analyzing-the-results). There are two different ways to fix this: a) increase the semi-circle lower bound to 2.5 Ha (surface_hgh_semi-circle.py), or b) use the new Ozaki contour integral method (http://docs.quantumwise.com/manuals/Types/OzakiContour/OzakiContour.html), which does not depend on an energy bound (surface_hgh_ozaki.py). This is an extremely reliable contour integration method, but may be a little slower than the semi-circle method.

Finally, I would like to suggest you try out the SG15 pseudopotentials as an alternative to HGH, see http://docs.quantumwise.com/manuals/ATKDFT.html#sec-sg15.

Thank you very much !  Other questions need your help.

• The HGH pseudopotential for Mo has 14 valence electrons in it. The lowest electrode Hamiltonian eigenvalues are therefore ca. -60 eV (run a band structure or DOS calculation to check this).

  How to estimate the lowest electrode Hamiltonian eigenvalues roughly by the element and its valence electrons' number?
  How to run a band structure or DOS calculation to check this?to get a more accurate  eigenvalue

• the box just above the headline at this link: http://docs.quantumwise.com/tutorials/atk_transport_calculations/atk_transport_calculations.html#analyzing-the-results

  I have understand how to choose the setting Integral lower bound  by your detailed explanation above.
  But how to choose the other settings Real axis point density & Circle points & Real axis infinitesimal in Semicirclecontour ?
  Number of poles in OzakiContour ?

[Jess Wellendorff]

How to estimate the lowest electrode Hamiltonian eigenvalues roughly by the element and its valence electrons' number?
How to run a band structure or DOS calculation to check this?to get a more accurate  eigenvalue

Simply run an ordinary bandstructure or DOS analysis for the (bulk) electrode alone, using the pseudopotential you are gonna use for the 1-probe device calculation. See e.g. http://docs.quantumwise.com/tutorials/crystal_bandstructure/crystal_bandstructure.html.

I have understand how to choose the setting Integral lower bound  by your detailed explanation above.
But how to choose the other settings Real axis point density & Circle points & Real axis infinitesimal in Semicirclecontour ?
Number of poles in OzakiContour ?

- When changing the integral lower bound for the equilibrium contour, you don't need to worry about the settings for the non-equilibrium contour. So just leave them as they are. But when increasing the equilibrium contour integral lower bound you may also need to increase the number of circle points for the equilibrium contour (in order to preserve the density of points on the cirlce).
- For the Ozaki contour, I recommend to use the "Estimate" tool to estimate the number of poles needed to obtain some user-specified accuracy (which you can most likely leave at default value).