13 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 ...
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  • 2,306
11 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 ...
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  • 13.6k
11 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 ...
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  • 10k
8 votes
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Single point energy calculation 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 ...
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  • 13.6k
7 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 ...
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  • 18.5k
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 ...
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  • 3,054
6 votes
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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 ...
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  • 3,054
6 votes
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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 ...
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  • 27.8k
5 votes

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) <...
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  • 7,744
5 votes
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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 "...
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  • 556
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 ...
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4 votes
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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 ...
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  • 14.2k
3 votes
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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: ...
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  • 13.6k
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: ...
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3 votes

How to edit the first line of XYZ file?

More a comment than an answer, note that e.g., for methane ...
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  • 1,457
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 ...
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1 vote

Which software can I use to model a nanotube with a triangular lattice shape and extract from it the lammps input file?

You can build your nanotube with the recent versions of the CRYSTAL code (see their tutorial). Using the pycrystal Python library you then extract an ASE Atoms object and convert it into the LAMMPS ...
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1 vote
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Steps to obtain ionic diffusivity using AIMD

Here is an example from vaspwiki
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  • 1,450
1 vote

Reading complex potential into CP2K

If I'm interpreting the manual correctly, it is not possible to define a complex external potential in CP2K. It specifies that the VALUES keyword to define the ...
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