Messages

16

General Questions and Answers / Re: How can I use a different number of valence electrons for a specific atom

« on: April 29, 2018, 14:45 »

Hi Guang-Ping,

In ATK this can be achieved by using atomic compensation charges:
https://docs.quantumwise.com/manuals/Types/AtomicCompensationCharge/AtomicCompensationCharge.html
https://docs.quantumwise.com/manuals/technicalnotes/doping_methods/doping_methods.html

I am not sure of what you did in SIESTA, but from the ATK error it looks like that you are trying use a pseudo and a basis that have different number of valence electrons, N for the pseudo, N-1 for the basis. This can also be done in ATK, but in this case you have to generate a pseudopotential with N-1 electrons by yourself, to be consistent with the number of electrons specified in the basis. An atomic compensation charge placed on the nitrogen atom will give essentially the same result, without the need to modify the pseudo/basis.

Regards,
Daniele

Dear Daniele,

AtomicCompensationCharge works.

In SIESTA, I just use

%block ChemicalSpeciesLabel
  5   6    N+       
%endblock ChemicalSpeciesLabel

combined with a N+.psf that is copied from a normal N.psf file, and also a basis set for N+ that copied from a normal N.

%block PAO.Basis                 # Define Basis set
N+                    2                    # Species label, number of l-shells
 n=2   0   2                         # n, l, Nzeta
   4.071      2.905   
   1.000      1.000   
 n=2   1   2 P   1                   # n, l, Nzeta, Polarization, NzetaPol
   4.973      3.054   
   1.000      1.000         
%endblock PAO.Basis

I think this is equivalent to

compensation_charge = AtomicCompensationCharge([('N+', -1.0)])
molecule_configuration.setExternalPotential(compensation_charge)

With best regards,
/Guang-Ping Zhang

17

General Questions and Answers / Re: How can I use a different number of valence electrons for a specific atom

« on: April 29, 2018, 14:00 »

Hi Guang-Ping,

In ATK this can be achieved by using atomic compensation charges:
https://docs.quantumwise.com/manuals/Types/AtomicCompensationCharge/AtomicCompensationCharge.html
https://docs.quantumwise.com/manuals/technicalnotes/doping_methods/doping_methods.html

I am not sure of what you did in SIESTA, but from the ATK error it looks like that you are trying use a pseudo and a basis that have different number of valence electrons, N for the pseudo, N-1 for the basis. This can also be done in ATK, but in this case you have to generate a pseudopotential with N-1 electrons by yourself, to be consistent with the number of electrons specified in the basis. An atomic compensation charge placed on the nitrogen atom will give essentially the same result, without the need to modify the pseudo/basis.

Regards,
Daniele

Dear Daniele,

Thanks very much for your reply, especially on weekends. I will try the method you mentioned.
As I understand,

compensation_charge = AtomicCompensationCharge([[Silicon, -0.0005]])
bulk_configuration.setExternalPotential(compensation_charge)

will make the pseudo potential of Silicon more repulsive (the core ion looses 0.0005 |e| charge), which leads to the number of valence electrons for each Silicon atom decreases by 0.0005. And hence a p-doping is simulated.

With best regards,

/Guang-Ping Zhang

18

General Questions and Answers / How can I use a different number of valence electrons for a specific atom

« on: April 29, 2018, 10:15 »

Dear ATK supporters,

I now wonder how can I use a different number of valence electrons for a specific atom. To be specific, I want to use 4/5 valence electrons for nitrogen atom that uses the basis set and pseudopotential of a normal nitrogen (that is N+/N- atom). This trick will be a little different from charging this system, and it will localize this charge to the N+/N- atom. However, in ATK, I got the following WARNING and the code stops:

Exception: The number of electrons (4.000000) specified is not equal to the number of electrons in the pseudo-potential (5.000000).

However, I can do this in SIESTA code, and get an expected result, where the N+ atom has 3.941 valence electrons while N- has 5.513 valence electrons).

In some calculation, it is necessary to calculate a charged system, where the net charge spatially localized on a specific atom. So, how can I do such calculations in ATK?

With best regards,

/Guang-Ping Zhang

19

General Questions and Answers / Re: How to remove all the basis set for a specific atom in a calculation

« on: November 28, 2017, 12:45 »

I do not think so, the basis set and the potential has to be used together.
Also, I don't understand why you want to do it. It would be great if you could provide some more details.

Dear Daniele,

By the ghost atom, one can use the floating orbitls. However, I want to place a local charge near the molecule. So I want to remove the basis set of an atom while keeping the potential of it.

With best regards,

/Guang-Ping Zhang

20

General Questions and Answers / How to remove all the basis set for a specific atom in a calculation

« on: November 28, 2017, 11:08 »

Dear ATK developer,

Here, I want to remove the basis set for a atom while just using it potential, which is on the opposite to the ghost atom. Is there a way to achieve it in ATK-2015.1?

Thanks very much.

With best regards,

/Guang-Ping Zhang

21

General Questions and Answers / Re: Can not understand the results by using ghost atom

« on: November 28, 2017, 09:58 »

Dear Guang-Ping Zhang

in graphene-M(111), with M being a noble metal, the interaction between the graphene and the metal is mediated mainly by charge transfer to/from the metal surface state.
It is very likely that, by including the ghost atom, you (i) improve the description of the Cu(111) surface state, and (ii) reduce somehow the effect of the basis set superimposition error at typical binding distances.

For relevant literature, see:
Phys. Rev. B 79, 075441
Phys. Rev. B 94, 155431   

Regards,
Daniele.

Dear Daniele,

Thanks a lot for your reply.

With best regards,

/Guang-Ping Zhang

22

General Questions and Answers / Re: Can not find the "search" button in docs

« on: November 27, 2017, 13:32 »

Perhaps Google search is partially blocked on your end?

Dear Jess,

That is what your have said. The google search is blocked by my network SP. When I use a network agent abroad, I can get the google search (see the attached).

Thanks very much for your help.

With best regards,

/Guang-Ping Zhang

23

General Questions and Answers / Re: Can not find the "search" button in docs

« on: November 27, 2017, 10:01 »

The search bar uses a tool provided by Google, so maybe you have a very aggressive adblocker that has blocked it?

Dear Ulrik,

Maybe it is the reason. Before, I can find it and use it. Not long ago, I can not find it. All people around can not find it. Maybe, it is from the network SP.

With best regards,

/Guang-Ping Zhang

24

General Questions and Answers / Re: Can not understand the results by using ghost atom

« on: November 27, 2017, 09:55 »

A ghost atom is nothing but a local basis set positioned some place in space. The DZP/SZP basis set you use is relatively short-ranged (which is sometimes very good), but may not be accurate enough for the study you do. Adding the ghost atom appears to "enlarge" the effective basis set range, which changes your result. I suggest you try to use the default SG15 pseudopotentials and basis sets, which should be both more accurate and longer ranged.

Dear Jess,

My question is that since the ghost atoms are very close to the surface atoms the basis set should not be essentially enlarged and a very similar result should be expected to  that without ghost atoms. But the results are very different. You mean both my results are unreliable?

With best regards,

Guang-Ping Zhang

25

General Questions and Answers / Re: Can not find the "search" button in docs

« on: November 27, 2017, 09:47 »

Just checked; the search box appears on my PC using both Firefox and Chrome.

Dear Jess,

I tried two other kinds of browsers including IE, all failed.

With best regards,

/Guang-Ping Zhang

26

General Questions and Answers / Can not understand the results by using ghost atom

« on: November 27, 2017, 06:00 »

Dear ATK developer and ATK user,

I use ATK to investigate the distance between graphene and the Cu(111) surface. In the calculation, there are five layers of Cu(111) with the leftmost three layers fixed and the two surface layers optimzed.  During the optimization, the graphene is also relaxed. I used GGA functional and a SZP basis set for Cu atoms/DZP for C atoms. The result shows that the distance between graphene and the surface is only 2.4 Angstrom, which is much smaller to that of 3.5 Angstrom reported by other studies. So, I used a layer of ghost atom to do the optimization again, where the ghost atom layer is also optimized. The optimized positions of ghost atoms are very close to the surface layer. In this way, I would expect a very similar distance between graphene and the surface. However, the optimized distance is 3.38 Angstrom, which is close to the ones in literatures. How to understand it?

With best regards,

Guang-Ping Zhang

27

General Questions and Answers / Re: Can not find the "search" button in docs

« on: November 27, 2017, 02:41 »

It was not disabled; it should still be there. I have checked that it works, at least in Chrome and Mozilla.

Dear Petr,

I also tried Chrome and Mozilla, but all failed. Please see the attached capture of the page. Before, it was just below the icon of QuantumWise. Could you please show me where can I find the "search" slot on the page? Thanks so much.

Kind regards,

Guang-Ping Zhang

28

General Questions and Answers / Can not find the "search" button in docs

« on: November 26, 2017, 15:31 »

Dear ATK team,

Before, I can find the "search" function on the page of https://docs.quantumwise.com so that I can quick find some relevant links in the docs section by some keys words. However, it disappear now. Is there a plan to active this function again?

With best regards,

Guang-Ping Zhang

29

Future Releases / Re: Reordering for coordinate list

« on: April 16, 2017, 05:10 »

Your method works, but I think I see an easier approach (although it requires a little bit longer computation...). Couldn't you just use Conf 1 and make the left 5 layers fixed, and the right-most 5 layers rigid?

Dear Anders Blom,

Yes, your method is much easier, but it require a bit more computations, what is I want to reduced.

With best regards,

/Guangping Zhang

30

Future Releases / Re: Reordering for coordinate list

« on: April 15, 2017, 12:01 »

Glad it works for you, however it's good practice, and actually more or less required, that you constrain the electrode copy part of the central region when you optimize the device. Even if your approach works, there is a risk that you don't have a precisely crystalline geometry in the electrodes, which introduces additional scattering.

The procedure I do is as follows.
1) First, I contructed a junction with six layers of, for example Au(111), at each side, and a moleucle sandwiched between in (configuration I).  2) And then, copy configuration I for twice. There, I will have three configuaration I.
3) For the first one, I remove the two outermost Au(111) layers at each side to contructed a "extend molecule" consisting a molecule and four Au(111) layers at each side for the following geometric optimizing (configuration II).
4) For the second one, I remove all the atoms except the two lelftmost layers of Au(111) (configuration III).
5) For the third one, I remove all atoms except the two rightmost layers of Au(111) (configuration IV).
6) During the optimization of configuration II, the two leftmost layers of Au(111) will be fixed and the two rightmost layers of Au(111) will set to be rigid. All other atoms will be fully relaxed, the optimized geometry is called configuration II-opt.
7) After the optimization, I will recover the removed two layers of Au(111) at leftmost using "Drop" function by droping configration III on configuaration II-opt, and get configuration V).
8 ) Figure out the tranlation in xyz directions for the two rightmost layer of Au(111) in configuration II-opt with respect to configuration II.
9) Applied the the tranlation got in step ( 8 ) to configuration IV, and get configuration IV-trans.
10) Recover the two rightmost layers of Au(111) by droping configuration IV-trans on configuration II-opt. Then get configuration VI.

At last, I need to use "Device from bulk" to construct a real two probe system based on configuration VI. But, usually it fails due to the destruction of the peridic condition in C direction from a rearrangement of the atoms (I do not know at which step it occurs, maybe during the "Drop" step). In order to make VNL get the periodic condition in C direction, a reorder of the atoms in configuration VI will be needed. But, the "reorder" in "Coordinate List" will only make a sort for one componet. However, "Sort" function will make it.

I think the procedure above will be simple and quick one for constructing a two probe system in VNL, and is there a risk to have a precisely crystalline geometry in the electrodes, that introduces additional scattering?

With best regards,

/Guangping Zhang

I currently find that strictly following steps 1-10 can give a good basis for the two-probe system construction and it does not need a sort action.

With best regards,

/Guangping Zhang