Questions tagged [python]

For questions about materials modeling scripts written in the Python programming language. Questions should focus on interfacing with existing packages and aspects related to modeling, not general debugging.

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19
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263 views

What are the tools available for point defects calculations?

As far as I know, there are mainly PyCDT, PyDEF, pylada and some part of pymatgen. As a new user to those tools, which one would be a good choice? It would be appreciated if you could explain one of ...
11
votes
0answers
90 views

What are good protocols for creating a database based on python?

I am aware of software tools such as atomate, but that is quite specific to crystals. There are other equally specific workflows - I think we all have our own... What I am interested in is making my ...
9
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0answers
46 views

Is there a script that will suggest (hkl) indices based on distances in an electron diffraction pattern for a known crystal structure?

I am looking for a script (preferably in Python) that will suggest (hkl) indices based on distances in an electron diffraction pattern. The crystal structure is known,i.e. I have the CIF file and know ...
7
votes
0answers
49 views

Convert standard image file format to py4DSTEM datacube?

I want to analyze a diffraction pattern. Py4dSTEM is asking for a datacube to start with. I thought it might be able to convert an image to this format: ...
6
votes
0answers
85 views

How to calculate radial distribution functions for MD trajectories without PBC, directly from coordinates with python?

I have been running MD simulations on water droplets with an ion in them. I am trying to implement a python program that could calculate the radial distribution function from ion to oxygen (or ion to ...
6
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0answers
41 views

Error when using pycotem to index an electron diffraction pattern?

In the pycotem code, this error comes up when using the Diffraction GUI. ...
6
votes
0answers
70 views

How to interpret WannierTools Python code that generates tight-binding model in the wannier90_hr.dat format?

I am getting myself acquainted with Wannier Tools. Wannier Tools requires two inputs, a wt.in file, and a .dat file. This .dat file should have the structure explained in the manual here. This file ...
4
votes
0answers
45 views

RDkit parse zero-order bonds (python)

I'm a computer scientist, helping with a chemistry project in python. I have been working with the library pysmiles in order to parse ...
4
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0answers
67 views

Error while installing ShengBTE

I am trying to install the thirdorder script that is mean to work in tandem with ShengBTE on an Ubuntu OS, but I'm getting the following error: ...
2
votes
0answers
46 views

How to plot a charge density from a CHGCAR file in Python?

I can convert a CHGCAR file on the NxNxN grid into a 3D array of shape (N,N,N) for better handling, if that helps. At the end of the day, I want plot/visualize the ...