[QE-users] How to handle slab calculations (Leon Luntadila Lufungula)

Sun Sep 11 14:52:42 CEST 2022

Dear Kazume,

First of all, thanks for the quick reply! The explanation on why the dipole correction is needed really helped me understand the problem better.

In my system the surface consists of three trilayers with the bottom layer ’s positions fixed and situated at the bottom of the unit cell, so adsorbing the same molecule on the other end of the slab will require changing the basis of my system which I would rather avoid.

Some follow up questions:

  1.  From what I understand from the explanation of Dr. C. Wolf, the dipfield keyword and the assume_isolated=2d keyword work in the same manner. Is it okay to just use the assume_isolated=2d keyword? The dipfield keyword seems to be quite cumbersome in its parametrization and prone to applying it wrongully…
  2.  Is the dipole correction always required or does it depend on the adsorbate? I am using 3-mercaptopropylphosphonic acid as an adsorbate, so it has a thiol tail group + propyl backbone  + phosphonic acid head group which interacts with the surface.
  3.  So to see if any of the applied methods work as intended, I should just plot the electrostatic potential (plot_num=11 in pp.x) and check if it becomes flat in the vacuum region right?
  4.  Is there a difference between assume_isolated=2d and assume_isolated=martyna-tuckerman? If so, which would be the best option to use?

MY apologies if these are stupid questions to ask, but I’ve been trying to figure it out on my own and haven’t made any significant progress in understanding the differences between the different methods...

Kind regards,
Leon Luntadila Lufungula
Master student
University of Antwerp

P.S. I noticed that any special characters in my text turn into question marks, so I will try to avoid using any special characters in the future. Unfortunately, my name has an accent which is also turned into a question mark, so I will just use a normal e from now on.

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Today's Topics:

   1. How to handle slab calculations (L?on Luntadila Lufungula)
   2. Re: How to handle slab calculations (Kazume NISHIDATE)

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

Message: 1
Date: Sat, 10 Sep 2022 12:27:11 +0000
From: L?on Luntadila Lufungula  <Luntadilatiti at hotmail.com>
To: "users at lists.quantum-espresso.org"
        <users at lists.quantum-espresso.org>
Subject: [QE-users] How to handle slab calculations
Message-ID:
        <PA4PR04MB78374B80B3F8AE6D377FE1DEAD429 at PA4PR04MB7837.eurprd04.prod.outlook.com>

Content-Type: text/plain; charset="utf-8"

Dear QE users,

I have been performing calculations on surface-modified TiO2 for some time now, as I took over a research project from a previous PhD student who quit his PhD. The project was already running for some time so I based my calculations on his input files as I started to learn how to use QE. Now I?m reading a lot of stuff online about performing QE calculations and I start to notice that my input files might be wrong...

I am performing calculations on a 3-layer anatase (101) slab with a 20 ? vacuum width above it and adsorbing different adsorbates onto the surface. I just found out that apparently when you are adsorbing molecules onto a slab you should use a dipole correction (dipfield = .TRUE.), which I did not do... I also read that for slab calculations it is recommended to use the assume_isolated keyword to cut off the Coulomb interaction in the z-direction and that the dipfield and assume_isolated keyword should not be used simultaneously.

I tried reading the papers on dipfield and the different assume_isolated options but I?m still pretty new to QE and periodic calculations so I found them hard to understand completely... Therefore, I would be most grateful if somebody could elaborate on the following questions:

  1.  Is it correct that you should use either dipfield or assume_isolated and not both at the same time? If so, which one is the best one to use?
  2.  I don?t quite understand why you have to do a dipole correction when adsorbing a molecule on the surface, is this just due to the fact that you induce a dipole upon binding and the PBC enlarge this effect?
  3.  If assume_isolated is the way to go, which option should I use? From what I understand, I cannot use Makov-payne as it is ?ONLY FOR CUBIC SYSTEMS? and my cell is monoclinic (a=b?c, ?=?=90???), esm is also not an option as it ?Requires cell with a_3 lattice vector along z, normal to the xy plane, with the slab centered around z=0.? which is not the case for my system. So this leaves 2D and martyna-tuckerman as possible options, but I can?t seem to find a straight answer which is best or what the differences are.
  4.  What about the calculations I have already performed? Are they useless without applying a dipole and/or coulomb correction?

Thanks in advance!

L?on Luntadila Lufungula
Master student
University of Antwerp

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Message: 2
Date: Sat, 10 Sep 2022 22:41:36 +0900
From: Kazume NISHIDATE <nisidate at iwate-u.ac.jp>
To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
Subject: Re: [QE-users] How to handle slab calculations
Message-ID: <F11BD694-2647-48EF-8693-94A7295C5000 at iwate-u.ac.jp>
Content-Type: text/plain;       charset=utf-8

Hi, L?on;

> I don?t quite understand why you have to do a dipole correction
> when adsorbing a molecule on the surface, is this just due to the
> fact that you induce a dipole upon binding and the PBC enlarge this
> effect?

Modern DFT codes assume the PBC for the systems. If you put a dipole
bar (a molecule) in the system, something like (+)=(-), then the (+) pole will
directory interact with the (-) pole over the PBC. It causes
artificial effects on its energy, and therefore it brings about a
wrong result on the structural relaxations too.

> what I understand, I cannot use Makov-payne as it is ?ONLY FOR CUBIC
> SYSTEMS? and my cell is monoclinic (a=b?c, ?=?=90???), esm is
> also not an option as it ?Requires cell with a_3 lattice vector along

Alternately, you can put the same molecules on the othe side of the
slab. In this case, the dipole effect from the one side will be
eliminated by the dipole effect from the other side if you set correctly
the molecules.

> Are they useless without applying a dipole and/or coulomb correction?

You can check the effectiveness of the dipole correction by plotting
the potential energies averaged over x-y plane.

Dr. C. Wolf gave a detailed explanation on the issue.

https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fchristoph-wolf.at%2Ftag%2Fdipfield%2F&data=05%7C01%7C%7Cd436b5a39d984783bcea08da93dc83be%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637984872634912852%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=o0oZydThbYbb0P2W8sEJCFcb8PtZGhqiDs2hVXLNIGY%3D&reserved=0

> 2022/09/10 21:27?L?on Luntadila Lufungula <Luntadilatiti at hotmail.com>????:
>
> Dear QE users,
>
> I have been performing calculations on surface-modified TiO2 for some time now, as I took over a research project from a previous PhD student who quit his PhD. The project was already running for some time so I based my calculations on his input files as I started to learn how to use QE. Now I?m reading a lot of stuff online about performing QE calculations and I start to notice that my input files might be wrong...
>
> I am performing calculations on a 3-layer anatase (101) slab with a 20 ? vacuum width above it and adsorbing different adsorbates onto the surface. I just found out that apparently when you are adsorbing molecules onto a slab you should use a dipole correction (dipfield = .TRUE.), which I did not do... I also read that for slab calculations it is recommended to use the assume_isolated keyword to cut off the Coulomb interaction in the z-direction and that the dipfield and assume_isolated keyword should not be used simultaneously.
>
> I tried reading the papers on dipfield and the different assume_isolated options but I?m still pretty new to QE and periodic calculations so I found them hard to understand completely... Therefore, I would be most grateful if somebody could elaborate on the following questions:
>
>        ? Is it correct that you should use either dipfield or assume_isolated and not both at the same time? If so, which one is the best one to use?
>        ? I don?t quite understand why you have to do a dipole correction when adsorbing a molecule on the surface, is this just due to the fact that you induce a dipole upon binding and the PBC enlarge this effect?
>        ? If assume_isolated is the way to go, which option should I use? >From what I understand, I cannot use Makov-payne as it is ?ONLY FOR CUBIC SYSTEMS? and my cell is monoclinic (a=b?c, ?=?=90???), esm is also not an option as it ?Requires cell with a_3 lattice vector along z, normal to the xy plane, with the slab centered around z=0.? which is not the case for my system. So this leaves 2D and martyna-tuckerman as possible options, but I can?t seem to find a straight answer which is best or what the differences are.
>        ? What about the calculations I have already performed? Are they useless without applying a dipole and/or coulomb correction?
>
> Thanks in advance!
>
> L?on Luntadila Lufungula
> Master student
> University of Antwerp
>
>

????
Kazume NISHIDATE Ph.D

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