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.

11 questions with no upvoted or accepted answers
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19
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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
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0answers
83 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 ...
8
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0answers
41 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
35 views

Bloch wave function extraction for the specific k points and specific band from QE calculation

I would like to use QE to obtain u_K(r), which is the Bloch wave function of spin-up maximum valance band at K point. If I define the K point in the input file and do a scf calculation by QE including ...
7
votes
0answers
81 views

What are open source options to simulate kinematical electron diffraction patterns?

I tried using the python package diffsims. I get an image, but not a diffraction pattern I was expecting. ...
6
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0answers
44 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
57 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 ...
5
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0answers
35 views

Error when using pycotem to index an electron diffraction pattern?

In the pycotem code, this error comes up when using the Diffraction GUI. ...
4
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0answers
34 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
59 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
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0answers
44 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 ...