Questions tagged [surfaces]
For questions around the modeling and description of materials surfaces
71
questions
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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 ...
- 575
5
votes
1
answer
101
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.
- 367
3
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1
answer
120
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Python code for combining two surfaces to form an interface
I have two surfaces named POSCAR1 and POSCAR2. I want to stack the surface of POSCAR2 on POSCAR1 to form an interface and also to match their lattice constants. I tried a solution here by adding it ...
- 367
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0
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52
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How to model an interface between two solids
I have two solid surfaces that I want to combine to study the interface as seen in the attached image. What I know is the lower part of the bottom structure is fixed to mimic the bulk. However, do I ...
- 367
2
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40
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Segregation Energy calculation
I am trying to calculate the segregation energy of an element in a slab. The literature I have consulted all says I should calculate the formation energy of the impurity element in the bulk and ...
- 367
2
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1
answer
55
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What is the meaning of a "free energy per unit surface area" vs "pressure" plot?
I don't understand this graph. From the graph, does it mean that at high pressures the oxide layer is stable and this stability reduces at low pressures and temperatures?
- 367
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80
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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 ...
- 1,894
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41
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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 ...
- 1,550
2
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85
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Generate a bimetallic surface in ASE
I am trying to generate a 50-50 Pt-Au fcc(111) bimetallic surface in ASE for DFT calcualtions. However, I am unable to figure out the procedure. Any help regarding the procedure will be great. Thanks
2
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How to read a poscar file which is a surface and add adsorbates using ASE
I have a POSCAR file containing Co, Cr, Fe, Ni elements. It is a slab of 6 layers. The first 3 layers are mobile whiles the last three layers are fixed. I would like to add adsorbates at the FCC ...
- 367
3
votes
1
answer
107
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VASP - suggestion on optimization of interfaced slabs
I am currently trying to create a CeO2 (100) / CoO (200) interface for a bulk oxide.
Unlike what I usually see, slabs stacked on the z-axis ("vertically"), I would like to stack the two &...
- 63
3
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How to make a relaxation of a 2D surface with LAMMPS [closed]
I would like to perform an energy minimization of a 2D surface without changing the c parameter. I run a :
fix 1 all box/relax iso 0.0 vmax 0.001
with
boundary p p f
but it was not ...
- 31
3
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0
answers
36
views
How are reconstructed surfaces named? [closed]
I am trying to understand the terminology of reconstructed surfaces.
Simple surfaces such as 2x2 or 1x1 make sense to me. For instance, figure 1 of the paper https://doi.org/10.1063/1.1574798 shows a ...
- 911
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votes
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answer
253
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Optimzation for Large supercell
I am trying to optimize a copper supercell for the study of chalcones adsorption using Quantum ESPRESSO, however, the size of my supercell is large (>200 atoms) and QE can not handle it.
What is an ...
- 575
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685
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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 ...
- 575
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Basic principles (and vocabulary) necessary to begin modeling the rate of atom surface diffusion and thermal planarization of ground metal surfaces?
Background:
Surface science experiments very often start with atomically smooth crystal surfaces as substrates. After one experiment ends the surface is sputter cleaned with cycles of keV energy argon ...
- 1,894
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194
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Did my Lennard-Jones potential LAMMPS simulation of a metal island on an FCC crystal surface find an energy minimum? (don't understand output)
I'm starting to learn LAMMPs with the intention of replacing my simple Python model for equilibrium configurations of adatoms on a crystal surface. Here's an example of what I do now, using a Lennard-...
- 1,894
6
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1
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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 ...
- 10.8k
2
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0
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98
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Slab rotation with ASE, unexpected behaviour [closed]
I am trying to generate the $\sqrt{3}\times\sqrt{3}R30^\circ$ representation of a Pt111 slab, I start by generating the $1\times1$ using ASE:
...
- 1,222
2
votes
1
answer
244
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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 ...
- 911
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47
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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 (see here).
How can one determine what is the polarity of any surface?
- 911
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59
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Can you Calculate Magnetism at a Material's Surface? [closed]
I'm researching FePt L10 nanoparticles and want to know how their surfaces affect their magnetic properties. However, I can't seem to find any papers on this topic.
Specifically, I would like to know ...
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210
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electronic structure of (110) Nb [closed]
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 ...
- 161
3
votes
1
answer
610
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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,...
7
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1
answer
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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 ...
- 1,977
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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 ...
- 1,894
6
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0
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381
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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) ...
- 1,550
7
votes
1
answer
586
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 ...
- 816
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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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answers
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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 ...
2
votes
0
answers
109
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How would surface state affect the band gap value of semiconductors? [closed]
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 ...
- 1,977
2
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81
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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 ...
- 1,977
7
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2
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221
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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 ...
- 929
5
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286
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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 ...
- 119
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1
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539
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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 ...
- 1,222
8
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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 ...
- 1,894
6
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0
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227
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
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1
answer
226
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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)
...
- 71
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0
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318
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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 ...
- 1,222
4
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0
answers
175
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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 ...
- 41
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1
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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":
...
- 1,222
4
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254
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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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608
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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 ...
- 1,131
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106
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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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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 ...
- 1,894
26
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3
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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 ...
- 10.8k
5
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1
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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 $E_{bulk}$ ...
- 2,793
6
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1
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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 ...
- 2,793
5
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1
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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-...
- 161
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1
answer
85
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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 ...
- 957