Questions tagged [surfaces]

For questions around the modeling and description of materials surfaces

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26 votes
3 answers
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What does B3LYP do well? What does it do badly?

I have seen a general criticism of B3LYP in computational chemistry (especially with the 6-31G* basis set). I would like to know some of the more/less obvious problems that occur when using it and ...
Tristan Maxson's user avatar
21 votes
3 answers
1k views

Generating special quasirandom structures (SQS) for surface calculations?

Given that most of the available codes for performing DFT calculations work with periodic boundary conditions, there are tools like mcsqs as a part of the Alloy ...
Mythreyi's user avatar
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20 votes
1 answer
410 views

Are plane-wave basis sets reliable for modeling adsorption processes?

Plane-wave basis sets are useful in the calculation of periodic systems and can be used in combination with pseudopotentials. However, when dealing with surfaces the system is no longer periodic in, ...
Verktaj's user avatar
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19 votes
4 answers
1k views

How to explain Miller indices to someone outside nanomaterials?

I often find that when talking to experimentalists outside of the field of nanomaterials, it is nearly impossible to explain Miller indices concisely. As this often comes up during talks from other ...
Tristan Maxson's user avatar
19 votes
2 answers
203 views

How to model heterogeneous catalysis?

Heterogeneous catalysis is known to be very important: Approximately 35% of the world's GDP is influenced by catalysis. The production of 90% of chemicals (by volume) is assisted by solid catalysts....
Cody Aldaz's user avatar
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17 votes
3 answers
1k views

Computational tools for automatic creation of surface slab models of complex systems

I am looking for computational tools that can be used to automatize the generation surface slab models of latices of oxides, layered oxides, perovskites etc. I have found a promising Python package, ...
Greg's user avatar
  • 1,807
17 votes
1 answer
271 views

Fermi level change in surfaces with adsorbed molecules

In a DFT standard calculation of a solid 3D material (i.e. bulk metal), one of the properties that can be obtained is the Fermi level $E_F$. This feature is related with the required work to add an ...
SalvaCardona's user avatar
  • 1,590
16 votes
3 answers
440 views

How to model a random distribution of molecules attached to a surface?

In the same aspect as some of my previous questions, I am interested in modeling molecules on different surfaces and to study the interfacial effect on them. One of the most important problems that ...
SalvaCardona's user avatar
  • 1,590
16 votes
2 answers
134 views

The upper limit for the atomic adsorption energy value on a slab surface?

I want to adsorb atomic oxygen on a slab surface. The adsorption energy I am calculating is around -10 eV. Which seems higher to me than I expected. My question is this: Is this value reasonable ...
nisarmuhammad131's user avatar
16 votes
1 answer
99 views

Protein cavities - methodological starting point for basic characterization

Characterizing surface properties is important for understanding how proteins execute their function by interacting with other molecules. This includes characterizing cavities. Perhaps the simplest ...
Buck Thorn's user avatar
14 votes
1 answer
398 views

How do I know if the reconstruction in the picture is a 2x2 reconstruction?

How do I know if the reconstruction in the picture is a 2x2 reconstruction or not?                                     I believe that this corresponds to a 2x2 reconstruction because there's an even ...
user7077252's user avatar
13 votes
1 answer
175 views

What are the steps to prepare a surface for molecular adsorption simulations on it?

I want to study the interaction of a given surface with some molecules. How should I prepare the surface for that kind of simulation? By prepare the surface I mean how many atom layers, how many of ...
Camps's user avatar
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13 votes
1 answer
133 views

What progress has been made in modelling photocatalytic reactions on semiconductor surfaces?

For example, are there any methods to allow for modeling of photo-oxidation or photo-reduction of a compound on a semiconductor surface? It appears there has been a lot of work on the bulk properties ...
Tristan Maxson's user avatar
13 votes
0 answers
444 views

Sample LAMMPS file for graphene growth on a metal surface [closed]

I am working with graphene growth on metal substrates. But I need some sample files to know if I am doing it in the right way because running multiple simulations in LAMMPS takes a lot of time. Can ...
Abdullah Arafat's user avatar
12 votes
2 answers
2k views

What is Surface termination and how to make surface termination of a crystal structure?

I want to calculate the surface energy of CuO and for that, I've asked CuO (monoclinic) crystallographic plane and their relaxed surface energy. But for the lack of knowledge of the surface ...
Shafayet Rahat's user avatar
11 votes
1 answer
87 views

How can I properly attach ligands to a surface?

The main aim of my venture is to study the effect of the presence of surface ions on the band structure of Si slab using Quantum ESPRESSO. I've tried to use iQmol to attach ligands to the surface. The ...
Atom's user avatar
  • 945
10 votes
1 answer
1k views

How to build the [111] slab model of NiSe2 with different terminations with ASE tool?

The following figure is the bulk structure of NiSe$_2$ downloaded from the materials project database. Now I want to study the properties of its [111] plane. In detail, I cut the slab with atomic ...
Jack's user avatar
  • 15.1k
10 votes
1 answer
626 views

Simulation of charged species with plane-waves in Quantum Espresso

I am using Quantum Espresso to simulate a platinum surface with ligands, so far everything is working ok. I now need to introduce a solvated hydronium $\ce{H_3O^+(H_2O)_2}$. Is there something I ...
Okano's user avatar
  • 1,232
9 votes
1 answer
675 views

Where to get Tersoff and SW potentials for LAMMPS

I want to do some molecular dynamics simulations for silicene with hydrogen and halogen atoms deposited at the surface. Where can I find Stillinger-Weber potentials to use for this? There doesn't seem ...
jboy's user avatar
  • 1,131
9 votes
0 answers
107 views

DIY molecular dynamics for Xenes on crystal surfaces; where can I get applicable open-source force field parameters that I can use in my scripts?

The linked question(s) below describes a DIY project to simulate how Xenes (honeycomb nets of atoms like graphehe) behave on single crystal surfaces. Behaviors include rotation, strain, and heigh ...
uhoh's user avatar
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9 votes
0 answers
108 views

How to calculate the thickness of the slab when simulating a bulk surface? [closed]

The method I found, which seems to be the most commonly used for simulating surfaces, involves constructing a slab and doing a structural optimization by freezing a few of its lowermost layers. What ...
Ashique Lal's user avatar
  • 1,621
8 votes
1 answer
716 views

Electron Affinity of Semiconductors via DFT

Can we calculate electron affinity of a semiconductor (e.g., for Si) using density functional theory calculations in VASP? Which calculations are needed to compute electron affinity and band offsets?
Shahid Sattar's user avatar
8 votes
1 answer
82 views

Quantum mechanical antireflection coating; what quantity would be analogous to index of refraction?

Background Quasiparticle interference (QPI) is a technique that can be used to study 2D surface state band structure; carrier reflections at boundaries or impurity sites will interfere producing ...
uhoh's user avatar
  • 1,964
8 votes
1 answer
101 views

Working with charged surfaces

A previous question addressed how to deal with charge defects in bulk materials. What can be done to treat a 2D surface with respect to charge? For example, how can an absorption energy of OH- on Pt(...
Tristan Maxson's user avatar
8 votes
0 answers
94 views

How do I identify an oblique surface mesh?

I have drawn three surface meshes from a hexagonal material for the $(0001)$, $(1\bar{1}00)$ and $(1\bar{1}01)$. The first one would be the top horizontal surface of the hexagonal structure, the ...
user7077252's user avatar
7 votes
2 answers
236 views

What software can be used for Crystal Surface Calculations?

I have been unable to find software for making surface calculations, so I currently perform surface calculations in LAMMPS by creating crystal structures in python, before rotating and cutting them ...
Connor's user avatar
  • 929
7 votes
1 answer
530 views

How to calculate the energy of a surface?

I want to study the interaction of a surface with some molecules (green house effect gases). To obtain the binding energy, the procedure is to calculate the energy of both systems separately $E_\...
Camps's user avatar
  • 23.3k
7 votes
1 answer
649 views

ESP of molecule with charge

I like to plot with GaussView 5 the ESP surface of a charged molecule. The charge is +2, the molecule is paraquat. The problem is when I generate a cube with GaussView with the total density and as ...
Andrea's user avatar
  • 856
7 votes
1 answer
226 views

How can scanning tunneling microscopy images (constant current and dI/dV conductivity) be simulated? What's under the hood in software packages?

Scanning tunneling microscopy comes in several flavors; vanilla (traditional STM) is constant current where the tip height is varied to maintain a constant current at a set constant bias1 and the ...
uhoh's user avatar
  • 1,964
7 votes
1 answer
222 views

Which atoms should be fixed when simulating metal oxides surface relaxation?

I am trying to model the surface relaxation on the TiO2(Anatase-101) surface, but it confuses me that when I try to set some atoms as fixed, unlike the crystal that only contains one element, there is ...
Jack's user avatar
  • 2,027
7 votes
1 answer
139 views

Confused about Effective Screening Medium for surfaces

Using Quantum ESPRESSO I want to perform a slab calculation with a charged ligand ($\ce{H3O+}$), in order to avoid dipole effects across the cell I am using the "Effective Screening Medium": ...
Okano's user avatar
  • 1,232
7 votes
1 answer
268 views

Changing orientation of SQS structure generated from ATAT

I generated the following SQS cell using ATAT (the sructure is converted to POSCAR format) ...
Aman's user avatar
  • 71
7 votes
0 answers
66 views

Is it necessary to terminate the surface ions in a quantum dot? [closed]

I was trying to study quantum dots of ZnO. But I'm pretty new to creating and passivating 0-dimensional particles. Is it always necessary to passivate the free surface of the quantum dot? Regarding ...
Anoop A Nair's user avatar
  • 4,476
6 votes
1 answer
2k views

How to generate a 3D electron density surface from fchk file using GaussView 6 without Gaussian

I tried to generate a density surface (the one from red to blue) for Clothianidin, but GaussView 6 gives me errors. I am using GaussView 6.0 without Gaussian installed on the same machine. Gaussian16 ...
el-rapho's user avatar
  • 141
6 votes
1 answer
71 views

Interstitial adsorbates

I have a poscar that I would like to place oxygen atoms as adsorbates in the subsurface. I have tried with Shaun's acat code but appears is not working for me. The posccar is shown below. ...
Nana Kofi Boakye's user avatar
6 votes
1 answer
921 views

Calculating the surface state with Wannier tools

Currently I met a problem when I calculate the surface state of a topologically non-trivial thin film system. I did a DFT calculation and fit the result with wannier function. The fitting looks pretty ...
JensenPang's user avatar
  • 2,863
6 votes
1 answer
85 views

Repository of Common Surfaces

Are there any repositories of crystal surfaces? Due to orientation / termination of surfaces, occasionally it is non-trivial to decide how exactly to cut a surface for things such as oxides. I ...
Tristan Maxson's user avatar
6 votes
0 answers
456 views

How to calculate the surface area of a stepped surface slab in a unit cell? [closed]

I am trying to calculate the surface energies of Ni fcc (111) and (311) surfaces, therefore I need to calculate the surface areas. I use periodic slabs to model these surfaces. For a flat fcc (111) ...
Shaun Han's user avatar
  • 1,845
6 votes
0 answers
261 views

Spin-orbit coupling in Siesta [closed]

I am going to simulate the electronic structure of the Au 111 surface including Fe-centered porphyrin on top. Since the molecule includes Fe, I first did spin-polarized calculations. Using converged ...
masoud's user avatar
  • 61
5 votes
1 answer
89 views

SiC surface reconstruction

I know how to cleave surfaces with integer Miller indices, however I wonder how I could cleave a $(\sqrt{3} \times \sqrt{3}) R30$ reconstruction of $(001)\,\, 4H-SiC$. I have found a nice link to O-...
Roozbeh's user avatar
  • 161
5 votes
1 answer
128 views

How to model a doped surface?

I want to start studying some single-atom catalysts doping with a transition metal. However, I do not what protocol I should follow. Based on the articles that I read, I should dope my surface only ...
Everson Gomes's user avatar
5 votes
1 answer
187 views

Fix layers of a slab

How do you fix the bottom layers of a slab to mimic a bulk material in ASE? Any functional that takes the slab object and writes a POSCAR with selective dynamics will be deeply appreciated. Thank you.
Nana Kofi Boakye's user avatar
5 votes
1 answer
910 views

Adsorption calcs using Quantum ESPRESSO

I already built a copper surface using BURAI and I used an SCF calculation to find the total energy of this surface. Now, what is the next step to finding the adsorption energy of one H2 molecule on ...
Everson Gomes's user avatar
5 votes
1 answer
330 views

Using DFT to study Hydrogen Evolution Reaction on a surface?

How well can DFT, as implemented in VASP, describe surface reactions? For example, I want to study the hydrogen evolution reaction (HER) on the $(111), (110), (100) \text{ and } (011)$ surface planes ...
thehereandnow's user avatar
5 votes
1 answer
116 views

Divergence behaviour of surface energy

By definition, the surface energy of a thin film or a slab model is defined as $$ \sigma = \frac{1}{2A}(E_{slab} - N\cdot E_{bulk}) $$ where $N$ is the number of atoms in the thin film and $E_{bulk}$ ...
JensenPang's user avatar
  • 2,863
5 votes
0 answers
35 views

What is best way to get lowest adsorption site at subsurface of high entropy alloys?

I am currently studying diffusion of oxygen in high entropy alloys. I want to calculate the activation energy from an adsorption site on the surface to the subsurface. I placed the oxygen atom below ...
Nana Kofi Boakye's user avatar
5 votes
0 answers
168 views

Help regarding Geometry Optimization of a bimetallic surface

I am trying to perform a geometry optimization (GEO_OPT) of a FCC 111 Pt$_{0.5}$Au$_{0.5}$ bimetallic surface (10x10x3) generated from ASE, with a lattice parameter of 3.9 $\overset{\circ}{\mathrm{A}}$...
ARKA PRAVA SARKAR's user avatar
5 votes
0 answers
83 views

Packages that can model effects of intense electric fields from femtosecond compressed IR and EUV laser pulses on surfaces?

Laser-based and time-resolved ARPES are relatively1 new techniques to study atomic and especially electronic structure (necessarily) near crystal surfaces and of adsorbed 2D materials on those ...
uhoh's user avatar
  • 1,964
5 votes
0 answers
44 views

How to transform a perturbed surface structure to a reference surface structure?

Say I have a bulk FCC Pt structure obtained from Materials Project with a lattice constant a = 3.94 Å. I first did DFT to relax the bulk structure, and the optimized lattice constant becomes for ...
Shaun Han's user avatar
  • 1,845
5 votes
0 answers
51 views

How to find the polarity of a surface (such as ZnO 000-1)?

The 0001 and 000-1 surfaces of ZnO are polar, while the other surfaces like 101̅0 and 112̅0 are nonpolar (see here). How can one determine what is the polarity of any surface?
ansonthms's user avatar
  • 961