14
votes
How to calculate DFT energy with density from another level of theory?
Incidentally, I initiated some discussions along these lines in these questions for HF-DFT (also called 'density-corrected' DFT) here,
and here. I'm familiar with Quantum ESPRESSO, so I can detail a ...
- 2,506
13
votes
How to start with the optical properties of 2D materials with the VASP code?
Due to the enhanced coulomb interaction and the quantum confinement effect in the two-dimensional limit, the optical properties should be investigated with the GW+BSE method.
The practical calculation ...
- 15.3k
12
votes
How to start with the optical properties of 2D materials with the VASP code?
The VASP manual is always the first resource to check, you can find it here. As a beginner, following "Getting Started" should help you greatly, from how to install the code, some details of ...
- 11.2k
12
votes
Accepted
How to run single point energy calculation on Mg2Si in VASP
I assume that you have relaxed your geometry structure. The single point energy calculation also called the self-consistent field calculation (SCFC), the central quantities outputted by it are:
Total ...
- 15.3k
9
votes
Convert .xyz format to Gaussian Input file (.gjf)
If you have a python installation, you can use ASE to do this in one line.
ase-gui structure.xyz -o structure.gjf
(I have always seen it as gjf not gif)
If you don'...
- 11.4k
9
votes
Accepted
How do I build and run a simulation of water molecules in NAMD?
One way could be as follow.
Download software PACKMOL.
Download the examples files (tar.gz or zip).
Modify the file solvprotein-comment.inp: removing the info about the protein, and the ions and ...
- 24k
7
votes
Study of supercell after creating vacuum
The common feature of a surface is that interlayer distance changes near the surface. For relaxation of atom and calculating surface energy in vasp ISIF=2 and ...
- 4,366
7
votes
Accepted
what do I need to change about typical VASP input file to calculate the energy of a single atom?
Isolated atom itself mean that there is no interaction from other nuclei , Hence box needs to be large enough so that atom doesn't interact with periodic image. In general 10-15 Angstrom size of box ...
- 4,366
7
votes
Accepted
How do I create geometry files for carbon nanoribbons and molecular junctions for DFTB+?
Since you know how to use Avogadro to create XYZ files, a very simple solution to your problem is to simply create the XYZ file then use an xyz2gen script to ...
6
votes
Accepted
Advice on converging a restricted open-shell DFT (rob3lyp/LANL2DZ) single point Gaussian09 calculation for a triplet spin-state molecule?
Before introducing solutions to solve this problem, let us analyze unnecessary keywords:
pop=full IOp(3/33=1) use=L506 does not affect the SCF convergence at all, ...
- 806
5
votes
Convert .xyz format to Gaussian Input file (.gjf)
There are two independent issues here: (1) How to convert XYZ to Gaussian input file and (2) How to make Windows to not associate it with Graphics Interchange ...
- 24k
5
votes
Accepted
How to calculate DFT energy with density from another level of theory?
So this question is related to the recent discussion in Procedure to classify errors in Kohn-Sham DFT where I already gave the general procedure: get the density from some level of theory, and use it ...
- 20k
5
votes
Accepted
How to edit the first line of XYZ file?
You could do this by just modifying the first line of the file.
But here are some more general purpose utilities you could use (note it requires the re module)
<...
- 8,015
5
votes
Accepted
How to use VEDA to analyze vibrational energy distribution?
After some experimentation, I was able to track down the problem.
Your output files tell me that you are using Gaussian 16. Upon inspection, the formchk utility in that version seems to put an "...
- 546
5
votes
How to select the projections and inner/outer window for Wannier90 calculations?
Notes on my answer: I'll mainly link to arXiv versions of papers, but will also link the peer-reviewed version if the arXiv page doesn't do that itself. DFA means "density functional ...
- 1,026
5
votes
How to add atom attribute molecule for each layer in LAMMPS?
I accepted Andrey Poletayev's answer and upvoted it because it gives me the right direction, although it needs to be corrected (see my comment).
However, I couldn't do it with the python package ASE, ...
4
votes
Need INCAR equivalent Quantum Espresso input file
I notice you are using Hubbard U in your input file and you are not using the same Hubbard U in both, which is probably good. However, you might consider if using a larger U value does give you the ...
- 11.4k
4
votes
How to create an input file for band calculation
A general idea is:
Determine the crystal symmetry of your system.
Select the path between high symmetry points to calculate the bands (follow one of these links: 1, 2, 3 or read this paper).
Use a ...
- 24k
4
votes
Accepted
How to add atom attribute molecule for each layer in LAMMPS?
The 'molecule' identifier will need be a separate column field for each atom. In your case, each layer will count for one molecule. So layer 1 will have a 1 in that column and so on.
From the ...
- 1,658
3
votes
Convert .xyz format to Gaussian Input file (.gjf)
One could do such a conversion online with this tool. The user could start uploading of an xyz file. After upload, an interactive ball-and-stick model is shown, the unit cell parameters are reported ...
- 161
3
votes
Accepted
How to write the REBO force field
If I remember correctly, the CHO extension of the REBO force field (which was further updated in a later publication) also introduces some changes in formalism, which in turn are not implemented in ...
- 1,401
3
votes
How to create an input file for band calculation
Using Quantum ESPRESSO, you can follow one of several routes to calculate the band structure of your material. The number of input files depends on the specific path that you follow. All routes have ...
3
votes
How to edit the first line of XYZ file?
It should be easy to achieve what you want with a bash script. For a file named test.xyz, it can be achieved with:
...
- 1,144
3
votes
How to edit the first line of XYZ file?
More a comment than an answer, note that e.g., for methane
...
- 1,589
3
votes
Accepted
VASP input file for formation energy calculation
If your structure is relaxed. The total energy can be calculated with a self-consistent calculation.
An INCAR template you may refer to:
...
- 15.3k
3
votes
Quantum ESPRESSO: how to calculate mobility?
A simple equation for the electron mobility is $\mu=e\tau/m^*$.
Here, $e$ is the electron charge, and the effective mass $m^*$ can be obtained by fitting a parabola to a band minimum/maximum as ...
- 2,719
2
votes
How do I build and run a simulation of water molecules in NAMD?
Another way is to use Amber file with NAMD!
Amber tleap is more user friendly, you can set the box size with box mol {x y z}. The only difference is you need to use ...
2
votes
How to edit the first line of XYZ file?
This is a strange type question. First, there is something wrong with the xyz file having total 5 columns.
For you answer,
Find total row number (let it be r)
calculate r-2 (since the format of the ...
- 1,056
2
votes
How to call VASP input files from parent directory
For VASP it is best to just copy over the duplicate files. You can use a tool like ASE which allows you to move just a single script (that will end up generating these duplicate files) or you can ...
- 11.4k
2
votes
Convert .xyz format to Gaussian Input file (.gjf)
The easiest way to convert .xyz to .gif(Gaussian input file) without being interfered by .GIF(Graphics Interchange) is to use Gaussian 09W (or your version of Gaussian software) and excel.
open your ....
- 331
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