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Questions tagged [adsorption]

For questions about modeling the adsorption, the process of molecules attaching to a solid surface.

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5 votes
1 answer
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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. ...
Rubi Agrawal's user avatar
7 votes
1 answer
102 views

Calculated adsorption energy is too high in VASP

I am trying to calculate the adsorption energy of benzoic acid into a PtRu surface, but the energy that I am finding is too high (around 40eV). The reported values are around -2.0eV for this. Also, I ...
César Catizane's user avatar
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
2 votes
1 answer
89 views

Reproducing ZPE corrections to adsorption from literature

Background In this paper by Lee, et al., they are looking at different functionals and dispersion corrections and how they change the predicted value of CO$_2$ chemisorption on an amine-functionalized ...
Adsorptioneer's user avatar
4 votes
0 answers
30 views

Primary source for recovery time equation?

I am working with nanostructure used as gas sensor/filters. Reading the literature, I found that one of the properties that can be calculated to characterize the (re)usability of a sensor is the ...
Camps's user avatar
  • 23.4k
5 votes
1 answer
84 views

Large energy differences across successive geometry optimization steps in SIESTA

I am trying to calculate adsorption energies of acetophenone on a 6x6x3 nickel surface with about 12 Angstrom of vacuum above it using SIESTA 5. I have arranged the molecule so that the ring plane is ...
user1420303's user avatar
3 votes
1 answer
60 views

Adsorption of Li on GeC (optimization problem)

Actually I am trying to study the adsorption of Li or K on the sheet starting from the hexagon centre the system optimises with Li or (K) adsorbed over one of the Ge atoms and not remain at the centre....
Mas's user avatar
  • 31
4 votes
1 answer
118 views

Can adsorption energy be upto -8 eV for VOC adsorption in MoS2 layer?

I've been using VASP for DFT calculations and came across with an adsorption energy value over $-8\,eV$. Is this a reasonable value for S-H bond?
Surya's user avatar
  • 101
3 votes
2 answers
127 views

Adsorption of naphthalene on graphene oxide sheets with gmx

How to set up a molecular dynamics (MD) simulation for the adsorption of naphthalene on graphene oxide sheets using GROMACS?
Mohamed El-amine's user avatar
2 votes
0 answers
47 views

What is the Miller index of the highest site?

I am trying to use Pymatgen adsorption module for my adsorption site calculations. While going through the documentation, I had a small confusion. It says the following Determine “surface sites” by ...
Ezio's user avatar
  • 21
6 votes
1 answer
525 views

How to calculate Gibbs free energy of adsorption at constant temperature with varying pressures

I want to calculate the Gibbs free energy of adsorption for an oxidized surface. The literature I consulted used the equations attached to this post. I am trying hard to find my way through. Any idea ...
Nana Kofi Boakye's user avatar
4 votes
1 answer
473 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 ...
Nana Kofi Boakye's user avatar
4 votes
1 answer
201 views

Can CP2K be used for slab calculations?

I am trying to map out potential energy of a slab surface + cation interaction, since VASP has been giving me very not-so-reliable results I wanted to know if CP2K have the ability to do such ...
Xdrake's user avatar
  • 541
6 votes
1 answer
133 views

How the adsorption energies calculated at DFT level, is valid at finite temperatures?

The adsorption energies of atoms or molecules on any surface in a standalone DFT are inherently devoid of any temperature influence. so, let's say an atom/molecule has very weak binding, in ...
Alukaar's user avatar
  • 343
4 votes
1 answer
156 views

Adsorption of Zn2+ on the metallic surface in VASP

I am trying to model the adsorption of charged atom (Zn2+) on the metallic surface using VASP. Since NELECT assumes total charge (metallic surface + Zn), is it the right flag to use? Or are there any ...
Abhishek's user avatar
3 votes
0 answers
107 views

Is there a way to estimate the energy of desorption of an adsorbed molecule? [closed]

I'm studying the adsorption of several molecules in metal organic frameworks (MOFs) using both experimental and computational methods. Experimetally I can easily obtain the temperature at which a ...
manuelpb's user avatar
  • 453
7 votes
1 answer
110 views

XANES simulation software/code besides FEFF for Pt L3 edge?

I need to generate the XANES region spectra of the Pt L3 edge of a theoretical Pt6 crystal with adsorbed atoms/molecules, such as $\ce{Pt(H^*), Pt(O^*), Pt(OH^*),Pt(CO^*)}$. It is for generating ...
quantum.puppy's user avatar
7 votes
1 answer
742 views

How to estimate adsorption energy of Li atom on graphene?

I would like to reproduce the data of adsorption energies published in paper. For example, they say the adsorption energy for Li atom on graphene is -1.19 eV (estimated by GGA-PBE). I used vasp (5.4) ...
Binh Thien's user avatar
  • 2,095
5 votes
1 answer
99 views

How can I find the area of an overlayer structure?

What sources would you recommend (or if you could instead explain it to me that would be great). I have never studied crystallography but must do a module on it and in some of the questions we were ...
user7077252's user avatar
10 votes
0 answers
93 views

Converge number of layers of atoms or number of unit cells for adsorption calculations? [closed]

I'm trying to calculate the adsorption energies of various adsorbates on Fe2O3 surfaces (although, with there being many possible surfaces for Fe2O3 it is quite complex, but that's for another time...)...
Charlie A's user avatar
  • 411
21 votes
2 answers
358 views

Semi-infinite surfaces for adsorption: a valid approach?

I'm currently trying to surface reaction of small molecules on metal oxides in VASP. Several papers I've read have approached surface energy calculations in a variety of ways. I first began looking at ...
Charlie A's user avatar
  • 411
12 votes
1 answer
160 views

What are the steps to prepare a solid-solid interface for adsorption studies in plane-wave DFT?

Please, how may one simulate a solid-solid interface that one can carry out adsorption studies from. I tried using virtual nanolab in Quantum ATK but didn't get a hand of it.
ABDULMUJEEB's user avatar
17 votes
1 answer
275 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