Author Topic: How to "shift surface" in "Interface" plugin?  (Read 3900 times)

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Offline lknife

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How to "shift surface" in "Interface" plugin?
« on: May 21, 2017, 16:44 »
Dear all,

When building an interface using the "Interface" plugin, I am always confused by the usage of "shift surfaces" menu.

In the tutorial "Building an interface between Ag(100) and Au(111)", it is said that "From this menu it is possible to either adjust the relative position of the two crystal manually, or compute the optimal distance using the ATK-Classical calculator." For the Ag(100)/Au(111) interface, the “EAM_Zhou_2004” potential was used to find the optimal distance.

However, for many systems, there is no classical potential to use. Then, how to adjust the position manually? Do we just need to adjust the distance along z direction or the shifting of the lattice along x and y directions are also needed? What's the criterion for the shifting of the relative position of the two crystal?

Thanks a lot for your kind help!

Offline Jess Wellendorff

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Re: How to "shift surface" in "Interface" plugin?
« Reply #1 on: May 22, 2017, 12:01 »
The interface plugin allows you to manually tune the relative positions of the two crystals. The objective is to make the interface as realistic as possible (physically and chemically). This is sometimes not an easy task, so if suitable force fields are available one can also use those to determine the (x,y,z)-shift that minimizes interface forces. But no, force fields are not available for all possible combinations of elements and materials. In that case you need to build the interface as well as possible (using intuition for the (x,y,z)-shift), and you may then relax the interface using DFT to get the actual minimum-force interface.

Offline lknife

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Re: How to "shift surface" in "Interface" plugin?
« Reply #2 on: May 22, 2017, 16:31 »
Thank your for your kind reply! However, it's really a hard work to use "intuition" for the shifting of the two crystal! Also, the relaxation of the interface using DFT for a relative large interface (normally with a lot of atoms) is very time consuming!

Attached is the .py file for an interface of Td-WTe2 and 2H-WS2. After finishing matching the lattice, I determined the interlayer distance along z direction by scanning the total energy vs. interlayer distance. For the total energy calculation, GGA-SG15-high was used without considering the van der Waals interaction. (I am not sure if the parameters were well set because the interlayer distance with minimum total energy is a little bit large I think). After that, the interface was geometry optimized using GGA-SG15-high with the optimal interlayer distance. It's really time consuming. It has been running for more than 2 days on my local computer.

For this calculation, could you please give me some valuable advises?

Thank you very much for your time and your kind help!

Offline Anders Blom

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Re: How to "shift surface" in "Interface" plugin?
« Reply #3 on: May 22, 2017, 17:57 »
The "high" basis set is probably overkill and contributes to the very long calculation time - I would first use "low" to get a reasonable idea of the position of the minimum, then perhaps recalculate a few points with "medium" (possibly "high") for verification. But there is no alternative to DFT for these materials.

Offline Anders Blom

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Re: How to "shift surface" in "Interface" plugin?
« Reply #4 on: May 22, 2017, 17:59 »
Additionally you are optimizing the strain in all directions, and you have turned off "constrain_bravais_lattice", which is a bad idea - you want to keep the system hexagonal. At least also disable stress optimization in C.

The FastFourier2DSolver is slower than the usual FFT, which is the default and almost always most suitable choice for pure periodic calculations.

Offline lknife

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Re: How to "shift surface" in "Interface" plugin?
« Reply #5 on: May 23, 2017, 01:53 »
Thank you for your kind reply.

There are some questions about your reply:

(1)  what's the meaning of "recalculate a few points with "medium" (possibly "high") for verification." How to do so?

(2) as to your reply "Additionally you are optimizing the strain in all directions, and you have turned off "constrain_bravais_lattice", which is a bad idea - you want to keep the system hexagonal. At least also disable stress optimization in C.", normally, I will optimize the strain in all directions and turn off "constrain_bravais_lattice" to obtain a full relaxed structure. Is it not necessary? By the way, the lattice of the interface is not hexagonal. One of the angle is about 121 degree, so I can only treat it as a unit cell.

Thank you very much for you time and kind help!


Offline Anders Blom

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Re: How to "shift surface" in "Interface" plugin?
« Reply #6 on: May 23, 2017, 06:20 »
I mean one you know roughly where the minimum is, you can make the same curve but with fewer points for high and see if they agree reasonably.
Or you can reoptimize from the minimum obtained with medium, then you are already close.
I missed the fact that the cell is not hexagonal, so in that case maybe it's a good idea to not constrain the lattice. On the other hand, do you really expect the composite cell to have such a strange symmetry...? These are two hexagonal materials brought into contact - isn't it reasonable to expect the symmetry to be maintained, only the materials are strained? I don't know, just asking :)

Offline lknife

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Re: How to "shift surface" in "Interface" plugin?
« Reply #7 on: May 23, 2017, 20:18 »
Thank you for your reply!

As to the procedure of finding the optimized interlayer distance (shifting the lattice along z direction), what you said to use a relatively lower setting first is really a good idea. After that, I can use higher settings with fewer points to recalculate it and  verify it. However, it is not very time consuming as to this procedure.

The most time consuming procedure is the geometry optimization of the interface because of the large number of atoms of the interface. In your opinion, can I get a reliable result with lower settings (such as SG15-medium) for the optimized configuration? Or after I finish the geometry optimization with lower settings, I need to redo the procedure with higher settings (SG15-high) from the result of the previous calculation? Do you think that the total time consuming of the two-step calculation is less than that of the one-step calculation with higher settings?

The Td-WTe2/2H-WS2 interface was obtained from Td-WTe2 monolayer and 2H-WS2 monolayer. The lattice symmetry of Td-WTe2 monolayer is not hexagonal but simple orthorhombic. That is why the composite cell has a strange symmetry like this. I don't know how to make other composite cells with higher symmetry together with small unit cell. Could you please give me some valuable advises?

Thank you very much again for your kind help!
 

Offline lknife

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Re: How to "shift surface" in "Interface" plugin?
« Reply #8 on: May 23, 2017, 21:56 »
Another question: As to the two-step calculations, such as geometry optimization, can I use the result from the calculation with settings LDA-FHI-singlepolarized to be the initial of the following calculation with settings GGA-SG15-high? Or I need to use the result from the calculation with settings GGA-SG15-medium as the initial state? Which initial state is better for the final calculation and the time saving?

Thank you very much for your time!

Offline Jess Wellendorff

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Re: How to "shift surface" in "Interface" plugin?
« Reply #9 on: May 24, 2017, 08:33 »
None of those will work. You cannot use a ground state calculated with combination #1 of pseudopotentials+basis-sets (e.g. FHI-DZP or SG15-M) as initial state for a calculation with combination #2 of pesudopotential+basis-sets (e.g. SG15-H). The numerical representation of the electronic structure problem is different between those combinations, so they are not compatible with each other as initial guess for the ground state. Technically, you can do it, but ATK will complaint that the initial state is not usable and will therefore just not use it. The calculation will therefore start from scratch.

However, for calculations such as geometry optimization, what you can use from one combination to another is the final relaxed configuration: If you want to run geometry optimization with SG15-H, which is a high-quality calculation and therefore also slower than many others, it is sometimes useful to first run the optimization with a smaller basis set, e.g. FHI-DZP, and then start the SG15-H relaxation from that. Might save some BFGS steps in the SG15-H calculations, especially if the starting configuration is far from equilibrium.

Offline lknife

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Re: How to "shift surface" in "Interface" plugin?
« Reply #10 on: May 24, 2017, 20:31 »
That is what I wanted to say. I am sorry for my poor expression of that. As to the initial state I mentioned, what I want to do is to use LDA-FHI-DZP for the geometry optimization first. After I get the optimized configuration, I can re-optimize it using GGA-SG15-high. I wish these two-step calculation will same me some time.

I got the information from the ATK tutorial that SG15 is a newer pseudopotential type with higher accuracy and medium efficiency. Thus, I used to do all the calculations with SG15. Here I want to have your valuable opinion: is LDA-FHI-DZP sufficient enough for geometry optimization of most of the configurations?

Offline Anders Blom

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Re: How to "shift surface" in "Interface" plugin?
« Reply #11 on: May 24, 2017, 20:41 »
It depends on the material. FHI-DZP is for instance really good for C and Si, but very bad for Te. See http://docs.quantumwise.com/technicalnotes/atk_pseudo_basis/atk_pseudo_basis.html (the DZP delta-test results for Te are misleading, I think, I recall we got bad results for "real" systems, although it may be ok for atomic properties...)

Offline lknife

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Re: How to "shift surface" in "Interface" plugin?
« Reply #12 on: May 25, 2017, 05:12 »
Did you mean that if we are calculating a system containing several kinds of elements, we can choose the proper pseudopotential and basis set according to the delta-test results---choose the one with smaller delta value?

For example, if I am studying WTe2 monolayer, I'd better choose OMX-high(optimal) with delta value of W (4.32) and Te (1.93) or choose SG15-high with delta value of W (0.39) and Te (4.02)?

or on the other hand, if I am studying Si, FHI-SZP with a delta value of 4.36 is sufficient , is it correct ? 

Thank you very much for your kind help!

Offline Anders Blom

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Re: How to "shift surface" in "Interface" plugin?
« Reply #13 on: May 25, 2017, 05:47 »
It's ok to mix pseudopotentials from different sets. Generally we don't recommend the OMX sets, they are very heavy and hard. I agree WTe2 is a tricky case, with competing values, but you could pick W from SG15 and Te from OMX. However, both 2 and 4 meV are small values, and I doubt the difference has any significant impact. You can however quite easily test on bulk WTe2 or monolayer (very few atoms in both cases).

For Si, we recommend FHI-DZP or SG15 Medium (in particular with the projector-shifted pseudos or DFT+1/2 if the band gap is of importance). SZP is ok for test runs but not production calculations.

Offline lknife

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Re: How to "shift surface" in "Interface" plugin?
« Reply #14 on: May 25, 2017, 15:58 »
I appreciate you for your valuable reply! I think I have had a clearer understanding of the pseudopotentials. I wish if I have other questions about ATK in the future , I can also seek for your kind help!

Thank you very much again!