Questions tagged [surfaces]

For questions around the modeling and description of materials surfaces

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19 views

How would surface state affect the band gap value of semiconductors?

I am struggling to figure out the relationship between bandgap value and surface states. To my understanding, when considering the material that includes surface, there would be some surface states in ...
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25 views

Database of surface electronic structure

I'd like to compare my simulation result of a TiO2-110 surface's electronic structure, but all the literature shows too many different results, so I'd like to look for a database for surface ...
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37 views

How to compare the band structure of a slab and a bulk phase primitive cell

I am trying to simulate the band structure of a slab, and compare it to the original band structure of the bulk phase. but I got confused when seeing the different K spaces between the slab model and ...
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2answers
109 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 ...
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45 views

What are the challenges in using DFT to study the Hydrogen Evolution Reaction of (111), (110), (100) and (011) planes of Cobalt (III) Phosphide (CoP)

What are the challenges in using DFT (implemented in the VASP code) to study the hydrogen evolution reaction (HER) of the (111), (110), (100) and (011) surface planes of Cobalt (III) Phosphide CoP.
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1answer
91 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 ...
8
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1answer
62 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 ...
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68 views

Spin-orbit coupling in Siesta

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 ...
7
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1answer
47 views

Changing orientation of SQS structure generated from ATAT

I generated the following SQS cell using ATAT (the sructure is converted to POSCAR format) ...
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60 views

Simple Pt111 slab not converging using Quantum Espresso [closed]

I would like to perform a "vc-relax" calculation on a simple 3x4x5 $\ce{Pt}111$ slab, this calculation is running well but as soon as I add the ESM ...
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48 views

Building the surface for Special Quasi-random Structure (SQS) [closed]

I understand that my question is similar to what Mythreyi asked here: Generating special quasirandom structures (SQS) for surface calculations?, but based on the rules this website specifies, I ...
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27 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": ...
4
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1answer
47 views

Are all the atom tags equal to 0 for ase.build.surface() objects?

I'm looking to build a surface slab in Atomic Simulation Environment (ASE) for CeO2 (fluorite structure). Using ase.build.surface( ) allowed modelling the surface. I would now like to run a relaxation ...
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65 views

Molecular dynamics with surfaces [closed]

I want to run molecular dynamics with LAMMPS, the aim is to simulate a platinum surface with a gas phase consisting of simple molecules. I would like to use periodic boundary conditions in order to ...
8
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1answer
120 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 ...
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80 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 ...
6
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1answer
65 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 ...
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3answers
1k views

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 ...
5
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1answer
63 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 $E_{bulk}$ ...
6
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1answer
218 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 ...
5
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1answer
46 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-...
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1answer
52 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 ...
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58 views

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

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 ...
7
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1answer
191 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 detial, I cut the slab with atomic ...
12
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0answers
142 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 ...
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80 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 ...
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4answers
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 ...
8
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1answer
211 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?
8
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1answer
67 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(...
12
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2answers
719 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 ...
13
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1answer
120 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 ...
12
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0answers
174 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 ...
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0answers
54 views

Key points for studying surfaces intended for researchers on gas phase [closed]

A common situation is that researches move slightly from their expertise area. In those cases, the tutorials for beginners are not suitable. A common doubt is "This is reasonable, I am sure but: ...
7
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1answer
109 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_\...
13
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1answer
145 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 ...
16
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1answer
79 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 ...
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2answers
123 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 ...
17
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1answer
166 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 ...
19
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2answers
153 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....
16
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3answers
496 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, ...
16
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2answers
89 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 ...
21
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3answers
317 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 ...
19
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1answer
122 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, ...