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. From: [email protected]<mailto:[email protected]> Sent: zondag 11 september 2022 12:01 To: [email protected]<mailto:[email protected]> Subject: users Digest, Vol 182, Issue 11 Send users mailing list submissions to [email protected] To subscribe or unsubscribe via the World Wide Web, visit https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.quantum-espresso.org%2Fmailman%2Flistinfo%2Fusers&data=05%7C01%7C%7Cd436b5a39d984783bcea08da93dc83be%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637984872634912852%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=mQCD0raGusXiZ%2F%2FEHSzoya2G%2FcVkOm4xxeInI%2FIIpa4%3D&reserved=0 or, via email, send a message with subject or body 'help' to [email protected] You can reach the person managing the list at [email protected] When replying, please edit your Subject line so it is more specific than "Re: Contents of users digest..." 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 <[email protected]> To: "[email protected]" <[email protected]> Subject: [QE-users] How to handle slab calculations Message-ID: <pa4pr04mb78374b80b3f8ae6d377fe1dead...@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 -------------- next part -------------- An HTML attachment was scrubbed... URL: <https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.quantum-espresso.org%2Fpipermail%2Fusers%2Fattachments%2F20220910%2F2fce36ff%2Fattachment-0001.html&data=05%7C01%7C%7Cd436b5a39d984783bcea08da93dc83be%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637984872634912852%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Nv2BrqAa882vDK6YknaDO1h18tW11ZFHaULjvywEHT8%3D&reserved=0> ------------------------------ Message: 2 Date: Sat, 10 Sep 2022 22:41:36 +0900 From: Kazume NISHIDATE <[email protected]> To: Quantum ESPRESSO users Forum <[email protected]> Subject: Re: [QE-users] How to handle slab calculations Message-ID: <[email protected]> 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 <[email protected]>????: > > 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 ------------------------------ Subject: Digest Footer _______________________________________________ The Quantum ESPRESSO community stands by the Ukrainian people and expresses its concerns about the devastating effects that the Russian military offensive has on their country and on the free and peaceful scientific, cultural, and economic cooperation amongst peoples. _______________________________________________ Quantum ESPRESSO is supported by MaX (https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.max-centre.eu%2F&data=05%7C01%7C%7Cd436b5a39d984783bcea08da93dc83be%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637984872634912852%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=IEvrJJu6TRNrl8%2BD%2BarbJxee7kxX1J975663IP%2B6FIo%3D&reserved=0) users mailing list [email protected] https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.quantum-espresso.org%2Fmailman%2Flistinfo%2Fusers&data=05%7C01%7C%7Cd436b5a39d984783bcea08da93dc83be%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637984872634912852%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=mQCD0raGusXiZ%2F%2FEHSzoya2G%2FcVkOm4xxeInI%2FIIpa4%3D&reserved=0 ------------------------------ End of users Digest, Vol 182, Issue 11 **************************************
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