Questions tagged [surfaces]
For questions around the modeling and description of materials surfaces
80 questions
2
votes
0
answers
29
views
Error while doing ESM in QuantumEspresso/7.3.1
I am trying to do charged surface calculations using Quantum Espresso/7.3.1. I have a copper slab and am trying to adsorb CO2 molecule on one of the adsorption sites. Later, I will compare the ...
- 41
2
votes
0
answers
27
views
Surface atoms concentration
I have a bulk crystal that contains 4 different elements. I want to cut the crystal in such a way that the atoms at the surface still obey the concentration of each atom in the bulk. At least close. ...
- 609
4
votes
1
answer
75
views
Issue in Converging a FCC Pd crystal on VASP, errors in body text
I have been struggling optimizing a specific structure in VASP. But I keep getting errors, and it only runs for like 3 seconds. These are a few errors I get. Sometimes it doesn't have the final one ...
- 71
5
votes
0
answers
49
views
What's wrong with Lithium BCC(100) slab and implicit solvation?
A colleague is having a rough time getting his Lithium slab BCC(100) to converge when using QuantumEspresso + Environ, so I decided to give it a shot but I can't make it converge neither. SCF seems to ...
- 1,467
6
votes
1
answer
162
views
Do the bottom layers of the slab need to be fixed when we use DFPT or finite displacement methods to compute the phonon spectrum of a surface?
When using DFPT or the finite displacement (also known as the frozen phonon) method to compute surface phonon spectra, it is generally necessary to perform high-precision optimization on the slab ...
- 65
5
votes
1
answer
89
views
How to convert all structure coordinates in .traj file to separate .txt files (e.g. POSCAR format files)?
I am using the ACAT code for generating the structures.
...
- 617
5
votes
0
answers
42
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 ...
- 609
5
votes
0
answers
231
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 $\overset{\circ}{\mathrm{A}}$...
6
votes
1
answer
75
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.
...
- 609
5
votes
1
answer
173
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 ...
- 595
5
votes
1
answer
393
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.
- 609
4
votes
1
answer
189
views
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 ...
- 609
3
votes
1
answer
138
views
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 ...
- 609
2
votes
0
answers
65
views
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 ...
- 609
2
votes
1
answer
58
views
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?
- 609
5
votes
0
answers
86
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 ...
- 2,074
5
votes
0
answers
47
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 ...
- 1,970
2
votes
1
answer
236
views
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
4
votes
1
answer
730
views
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 ...
- 609
4
votes
1
answer
202
views
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 &...
- 83
3
votes
0
answers
173
views
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
votes
0
answers
42
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 ...
- 1,003
4
votes
1
answer
425
views
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 ...
- 595
5
votes
1
answer
1k
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 ...
- 595
4
votes
0
answers
65
views
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 ...
- 2,074
3
votes
0
answers
292
views
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-...
- 2,074
7
votes
1
answer
103
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 ...
- 11.6k
3
votes
0
answers
156
views
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:
...
- 1,467
2
votes
1
answer
384
views
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 ...
- 1,003
5
votes
0
answers
58
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?
- 1,003
3
votes
0
answers
61
views
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 ...
- 959
5
votes
0
answers
287
views
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
934
views
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,...
8
votes
1
answer
253
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 ...
- 2,107
9
votes
0
answers
118
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 ...
- 2,074
6
votes
0
answers
568
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) ...
- 1,970
7
votes
1
answer
783
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 ...
- 866
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 ...
- 141
3
votes
0
answers
80
views
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
156
views
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 ...
- 2,107
2
votes
0
answers
85
views
Database of surface electronic structure [closed]
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 ...
- 2,107
7
votes
2
answers
284
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 ...
- 959
5
votes
1
answer
387
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 ...
- 119
11
votes
1
answer
827
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 ...
- 1,467
8
votes
1
answer
90
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 ...
- 2,074
6
votes
0
answers
316
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 ...
- 61
7
votes
1
answer
311
views
Changing orientation of SQS structure generated from ATAT
I generated the following SQS cell using ATAT (the sructure is converted to POSCAR format)
...
- 71
3
votes
0
answers
403
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 ...
- 1,467
4
votes
0
answers
245
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 ...
- 41
7
votes
1
answer
230
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":
...
- 1,467