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1
sorry i missed the Webinar: Introduction to Molecular Dynamics Simulations with VNL and ATK

where can i downloads references about Molecular Dynamics Simulations Webinar,like slice ?

Thank you very much

2
is there any way to calculate the transmission spectrum gap from the transmissionspectrum.nc?

a script maybe better :)

Thank you very much!

3
But in paper http://dx.doi.org/10.1103/PhysRevB.86.075149 ,Table I gives the energy in mGGA.

Can ATK do this ? Thank you!

4
How to calculate the energy by DFT-mGGA?
Thank you!

5
Case Studies » Modeling metal–semiconductor contacts: The Ag–Si interface
http://docs.quantumwise.com/casestudies/ag_si_interface/ag_si_interface.html

In Projected local density of states part, it mentioned that
Quote
Moreover, the averaged potential nicely follows the conduction band minimum, both at the interface and far from it.

My question is how draw the line of valence band max maximum along the C direction ?

Thank you very much!

Any one can help me? Thank you very much !

6
Case Studies » Modeling metal–semiconductor contacts: The Ag–Si interface
http://docs.quantumwise.com/casestudies/ag_si_interface/ag_si_interface.html

In Projected local density of states part, it mentioned that
Quote
Moreover, the averaged potential nicely follows the conduction band minimum, both at the interface and far from it.

My question is how draw the line of valence band max maximum along the C direction ?

Thank you very much!

7
r_pot is the value of the potential obtained from the HartreeDifferencePotential whereas CBmin is the value of the conduction band minimum obtained from the DeviceDensityOfStates.

Ideally the two should match, but in practice there is always some small uncertainty, since one has to decide the threshold under which the DDOS is equal to zero. In the script the threshold is set to 0.01 eV^-1:

# Threshold under which the DOS is considered zero (Band gap region)
thr = 0.01


Regards,
Daniele.

Is HartreeDifferencePotential in ATK 2016 the same to ElectrostaticDifferencePotential in ATK 2015?

8
Hello,

r_pot gives the value of the averaged potential at the rightmost side of the interface, e.g., at Z = 400,200,80 Ang of Fig.6 in PRB 93 155302 (2016).

In fact, few lines later in the script you can see that the Schottky barrier at the interface is evaluated as:
schottky = max(av_pot-r_pot)

Regards,
Daniele.
Thank you very much!
What the difference betweet r_pot and CBmin(The conduction band minimum in the right electrode)?

9
What are the detailed differents between Optimize Geometry in Device Configuration and Optimize Geometry in Bulk Configuration?

Thank you very much!

11
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.

  • Quote
    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
  • Quote
    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 ?

12
I used other model ,still have questions.
How can I change it ?

13
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
===================================================================================
"

14
I changed my script in device boundary conditions and k-points.

But  the result also seems wrong!

15
I have attached it

' Surface-Mo-MoS2.py '

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