Questions tagged [surfaces]

For questions around the modeling and description of materials surfaces

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How to terminate a surface with hydrogens

I am trying to study surface reconstructions of metal oxides using Quantum Espresso. For this, I am creating slabs using python tools: ASE, Pymatgen, and catgen. However, I am unable to terminate the ...
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3 votes
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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 (https://doi.org/10.1021/acs.chemmater.7b01487). What is the difference between polar and non-...
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Can you Calculate Magnetism at a Material's Surface?

I'm doing some research on FePt L10 nanoparticles, and I'd like to know how their surfaces affect their magnetic properties. However, I can't seem to find any papers on this topic. Specifically, I ...
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electronic structure of (110) Nb

I need to get the optimal number of layers of (110) niobium that is a good representative of the behavior of the material, but I am facing two problems using Quantum Espresso, I Keep getting the ...
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3 votes
1 answer
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Units of SASA generated from GROMACS gmx_sasa?

I'm wanting to use gmx sasa. I've done this on some residues I'm interested in analyzing. When I look at the output, I expect some value of $\pu{nm^2}$ or maybe $\pu{\unicode[.8,0]{x212B}^2}$. Instead,...
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6 votes
1 answer
100 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 ...
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7 votes
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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 ...
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How to calculate the surface area of a stepped surface slab in a unit cell?

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) ...
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7 votes
1 answer
186 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 ...
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6 votes
1 answer
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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 ...
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How to build [11-20] and [10-10] surfaces of hexagonal 2H, 1T and 1T’ monolayers? [closed]

I couldn’t find any software. Does anyone have any free software suggestions. I tried to do it with vesta but couldn’t figure out and for polytypes other than the 2H there are not any sources. Thanks ...
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2 votes
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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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2 votes
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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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7 votes
2 answers
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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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5 votes
1 answer
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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 ...
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9 votes
1 answer
153 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 ...
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8 votes
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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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6 votes
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99 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 ...
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7 votes
1 answer
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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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3 votes
0 answers
142 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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4 votes
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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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7 votes
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45 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": ...
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4 votes
1 answer
80 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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9 votes
0 answers
75 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 ...
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8 votes
1 answer
232 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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9 votes
0 answers
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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 ...
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6 votes
1 answer
90 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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24 votes
3 answers
2k 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 ...
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5 votes
1 answer
66 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 $E_{bulk}$ ...
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6 votes
1 answer
349 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 ...
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5 votes
1 answer
56 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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11 votes
1 answer
58 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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7 votes
0 answers
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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 ...
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7 votes
1 answer
316 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 ...
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13 votes
1 answer
218 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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8 votes
0 answers
83 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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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 ...
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8 votes
1 answer
280 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?
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8 votes
1 answer
73 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(...
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12 votes
2 answers
941 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 ...
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13 votes
1 answer
124 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 ...
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13 votes
0 answers
246 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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5 votes
0 answers
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: ...
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7 votes
1 answer
139 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_\...
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13 votes
1 answer
148 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 ...
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16 votes
1 answer
84 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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15 votes
2 answers
138 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 ...
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  • 1,560
17 votes
1 answer
188 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 ...
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  • 1,560
19 votes
2 answers
159 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....
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16 votes
3 answers
646 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, ...
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