24
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What does B3LYP do well? What does it do badly?
B3LYP is still a decent functional at its level of theory (single-hybrid functional), but you're right that there's a general criticism of it, which I largely hear in the form of people saying things ...
22
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What does B3LYP do well? What does it do badly?
I think this review¹ by Head-Gordon is a useful supplement to Nike's answer. Its combines a review of functional development, a benchmarking of various functionals, and an explanation of the design ...
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19
votes
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How to explain Miller indices to someone outside nanomaterials?
You can see it with VESTA software. For example, we can see the different lattice planes of NaCl crystal.
[001] plane of NaCl:
[101] plane of NaCl:
[111] plane of NaCl:
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17
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What does B3LYP do well? What does it do badly?
I don't have too much to add to the answers of Nike Dattani and Tyberius, but I think the crux is that its capabilities have been historically overestimated.
One particular failing of B3LYP is that it ...
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16
votes
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Computational tools for automatic creation of surface slab models of complex systems
I highly recommend using pymatgen for this.
I coded a surface slab generator for Avogadro and in addition to being slow (since it generates a supercell before ...
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13
votes
How to explain Miller indices to someone outside nanomaterials?
Assuming a generic chemistry background I wouldn't assume that knowledge of crystal structure would be too in depth at an undergraduate level. It is definitely encountered, but depending on the type ...
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13
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Are plane-wave basis sets reliable for modeling adsorption processes?
In the example you highlighted and indeed in most plane-wave DFT codes, there is periodicity in all three dimensions including for surface slab calculations. In the case of a surface slab, vacuum ...
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11
votes
Protein cavities - methodological starting point for basic characterization
The identification of cavities, for drug design, is beyond the geometric characterization (aka volume).
The server and individual software, beside the geometrical cavity determination, characterize ...
- 23.9k
11
votes
The upper limit for the atomic adsorption energy value on a slab surface?
To address the question in the title, I went to Catalysis-Hub and sorted the computed energies from most exothermic to most endothermic. Ignoring the C (g) entries adsorbing onto surfaces (which have ...
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10
votes
How to build the [111] slab model of NiSe2 with different terminations with ASE tool?
There is currently no tool built into ASE to do this sort of detective work on surface terminations. I highly suggest that you take the approach of trying to eliminate dangling bonds first (for ...
- 11.4k
10
votes
Generating special quasirandom structures (SQS) for surface calculations?
First of all, it's better to define the terms here because probably not all the people here are familiar with SQS right away. SQS is an abbreviation for special quasirandom structures. The ...
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10
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What is Surface termination and how to make surface termination of a crystal structure?
Determining a surface energy requires a few steps.
Calculate a bulk structure
Cut a surface termination manually or using a tool
Calculate the surface structure
Calculate the surface energy
I will ...
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9
votes
What are the steps to prepare a surface for molecular adsorption simulations on it?
I'll try to outline an approach in plane-wave DFT. The main idea is to build up the system step-wise and reuse previous results as the number of atoms and therefore the computational burden will grow ...
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9
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How to model a random distribution of molecules attached to a surface?
As mentioned by @GeoffHutchison, PACKMOL is probably the most used one for random dense packing of molecules.
Sometimes this might however not suit your needs, e.g. if the shape you want to fit ...
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9
votes
Where to get Tersoff and SW potentials for LAMMPS
Generally, if you want to perform simulations with some force field, you will have to search the literature for published FFs tailored for your problem. The Stillinger-Weber (SW) model is very popular ...
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8
votes
How to model heterogeneous catalysis?
I did some work during my rotation in the Brooks group on surfaces that could act as abiogenesis sources (self-sustaining chemical reactions that become living organisms).
Key considerations for ...
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8
votes
Computational tools for automatic creation of surface slab models of complex systems
I have used ASE to create slaps of complex, anisotropic materials in the past. However, ase.lattice is not for creating slabs, it's a module containing functions ...
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8
votes
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How to generate a 3D electron density surface from fchk file using GaussView 6 without Gaussian
Finally found the solution:
After optimizing the structure I needed to generate an electron density cube like this:
...
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7
votes
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What software can be used for Crystal Surface Calculations?
Atomsk
Creating surface based on Miller indices is tough work if it is not cubic lattice. for example $\langle011\rangle$ direction and $(011)$ plane normal in case of $c>a$ is not same. So, in ...
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6
votes
What is Surface termination and how to make surface termination of a crystal structure?
What is surface termination?
The following figure should give you a clear understanding of the surface termination. Note that the vacuum should be large enough to avoid the interaction between slabs.
...
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6
votes
How to calculate the energy of a surface?
For calculating the energy of a surface, we need to split the contribution of the surface and the contribution of the bulk to the total energy.
$$E_\mathrm{total} = E_\mathrm{surface} + E_\mathrm{...
- 1,359
6
votes
How to model a random distribution of molecules attached to a surface?
I might be late to the party, but I have recently developed a Python package ACAT that can help people with similar problems of building surface adsorption models. The package is interfaced with the ...
- 1,970
6
votes
How to model a random distribution of molecules attached to a surface?
If your molecules form not too many types of adsorption complexes on your surfaces, then you can built a lattice model with SuSMoST ( http://SuSMoST.com/ ) and run a short Monte Carlo simulation at ...
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6
votes
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How to read a poscar file which is a surface and add adsorbates using ASE
I remember running into exactly the same issue like you when I just started my PhD. In ASE, there is this ase.build.add_adsorbate() function that allows placing a ...
- 1,970
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Interstitial adsorbates
To allow identifying subsurface interstitial sites (a.k.a. "6fold" sites in ACAT), you need to set allow_6fold=True when identifying adsorption sites. ...
- 1,970
6
votes
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How to convert all structure coordinates in .traj file to separate .txt files (e.g. POSCAR format files)?
You can use the following code to write the generated images to xyz files
...
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5
votes
Computational tools for automatic creation of surface slab models of complex systems
Also, you can use Atomsk and Nanocut. Both are free.
Atomsk info (from the site):
A free, Open Source command-line program dedicated to the creation, manipulation, and conversion of data files for ...
- 23.9k
5
votes
Electron Affinity of Semiconductors via DFT
This may be a bit of a rough answer, so apologies in advance...
Since the eigenvalues obtained using non-energy-consistent pseudopotentials (i.e. the situation in VASP as far as I know) do not ...
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5
votes
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How do I know if the reconstruction in the picture is a 2x2 reconstruction?
Start by constructing 1×1 and 2×2 reciprocal space lattices; the latter case has the real space lattice constant twice as big, so its reciprocal lattice unit cell will be half the size, and square. ...
- 316
5
votes
How to explain Miller indices to someone outside nanomaterials?
I would propably explain that there are different planes within a crystal, show some of them in an animation or pyhsical prop and depending on the depth of the presentation just omit the numbering and ...
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