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41 votes
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How to write my own density functional theory (DFT) code in Python?

Understanding, deriving, writing, testing and debugging an ab initio code can be a lenghty and tedious task. I'd like to provide a starting point for you here. If you just to it for pedagocial reasons,...
pmu2022's user avatar
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36 votes
Accepted

How is Julia used in matter modeling?

(Disclaimer: As one of the main authors of a Julia-based DFT code, DFTK, my opinion is definitely biased) The community of people employing Julia for materials modelling is still small, but a couple ...
Michael F. Herbst's user avatar
33 votes

What is a good programming language for matter modeling?

Julia The answers above allude to what some call the "two-language problem". In materials science it takes the form of writing your code in Fortran for speed, and writing an interface to it ...
Antoine Levitt's user avatar
32 votes

What is a good programming language for matter modeling?

Fortran A large part of materials modelling involves density functional theory and molecular mechanics. From this compilation of quantum chemistry software, the most widely used programming language ...
TheSimpliFire's user avatar
24 votes

What is a good programming language for matter modeling?

Julia Okay, I have to add Julia. Everyone is saying Fortran or Python, and I love them both, but they both have issues. Fortran is easy for a compiled language to write, but I still have ...
B. Kelly's user avatar
  • 4,376
24 votes

What is a good programming language for matter modeling?

It depends on what you want to do I'll go first. For context: I do mostly Monte Carlo simulations, especially quantum Monte Carlo. My work has focused on spin systems, using techniques like the ...
taciteloquence's user avatar
24 votes

What is a good programming language for matter modeling?

Python @taciteloquence has already mentioned Python for data analysis and visualization, but let me add one more angle: automation. Simulation nowadays often means high-throughput, automated ...
Greg's user avatar
  • 1,807
20 votes

What is a good programming language for matter modeling?

It depends on what you want to do I think one major question that needs to be asked is "What do you want to do?". Develop new quantum chemistry codes? Use them more efficiently? Automate ...
DetlevCM's user avatar
  • 621
20 votes

What is a good programming language for matter modeling?

It depends on what you want to do It depends on what you want to do. As a couple of others have pointed out, many of the computer programs used in computational chemistry and theoretical solid state ...
Fuzzy's user avatar
  • 928
19 votes

What is a good programming language for matter modeling?

Python Python is definitely a good language for scientific calculation. The syntax is very simple. It is not hard to implement some novel method and conduct preliminary tests. The library is ...
Paulie Bao's user avatar
  • 3,973
17 votes

What is a good programming language for matter modeling?

Cython There are currently two answers suggesting Python (by Paulie Bao and Greg). Python is a high-level, interpreted, dynamically typed, garbage collected, and general-purpose programming language. ...
schneiderfelipe's user avatar
17 votes

How to write my own density functional theory (DFT) code in Python?

For molecular DFT, there are definitely several tutorials around for major pieces. The Psi4 code has a set of Jupyter notebooks called Psi4Numpy, working through each element of a quantum chemical ...
Geoff Hutchison's user avatar
17 votes

How to find Young's Modulus using stress strain curve using Python?

I designed the Python program a few years back but haven't looked at it in some time. The __init__.py line can be commented out for your usage. That "model" was for my team's use case, and ...
Enusi's user avatar
  • 296
17 votes

Convert XYZ coordinates to Z-matrix

ASE The ASE library has an atom object with built-in get_angle, get_dihedral and ...
16 votes
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How to find Young's Modulus using stress strain curve using Python?

I was able to run the code on your data and got a Young's Modulus of $2.08236\times10^{-5}$. This clearly doesn't seem right for an aluminum system, though I don't know the units you are using. To get ...
Tyberius's user avatar
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16 votes
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How to "get my feet wet" in Density Functional Theory by simulating a water molecule using Python

SlowQuant In your question from 2015, you mentioned PyQuante and PySCF, but I saw no mention of SlowQuant in the question or in the multiple answers. I see that while writing this, someone else ...
Nike Dattani - No Free Time's user avatar
16 votes

How to "get my feet wet" in Density Functional Theory by simulating a water molecule using Python

If you're set on using Python here are some options. I haven't used these codes so I can't speak to their ease of use. PyQyante PyQuante is a suite of programs that can not only do DFT but also ...
Kevin J. May's user avatar
  • 3,171
16 votes

Convert XYZ coordinates to Z-matrix

Easiest free tool to do this (no download necessary): What you are describing, is the conversion from XYZ format to ZMAT format. How to do this, has been asked here on the Chemistry Stack Exchange, ...
Nike Dattani - No Free Time's user avatar
16 votes

Convert XYZ coordinates to Z-matrix

Open Babel First, the command-line version: obabel c60.xyz -oreport Yields: All interatomic distances All bond angles All connected torsions Also, partial charges ...
Geoff Hutchison's user avatar
15 votes

What is a good programming language for matter modeling?

Compiled Languages Since all simulations are CPU and memory consuming, I recommend to not use interpreted language like Java, Julia*, Python, etc. Compiled languages are converted directly into ...
Camps's user avatar
  • 23.6k
15 votes

How to generate the high symmetry paths for band structure calculations?

If you are really interested in learning how to generate the path, I strongly advice you to avoid using any automatic tool like suggested in previous answers. In the Wiki page entitle Brillouin zone ...
Camps's user avatar
  • 23.6k
15 votes
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How can I use a GUI on a supercomputer?

I prefer to just download the data from the remote disks and then do the plots on my own local machine, which has all of my favorite tools for post-processing my data. I understand that this can be ...
Nike Dattani - No Free Time's user avatar
14 votes

Python script for convergence test

Here is the simple bash script for testing kpoint energy convergence for VASP you can use same logic in python but you can also use this. ...
Pranav kumar's user avatar
  • 4,278
14 votes
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Python script for convergence test

There is an example in the pyiron documentation to calculate energy volume curves: https://pyiron.readthedocs.io/en/latest/source/notebooks/energy_volume_curve.html And the corresponding jupyter ...
Jan's user avatar
  • 256
14 votes

How to generate the high symmetry paths for band structure calculations?

If the crystal unit cell is in a format readable by ASE, then you can use code that looks approximately like so: ...
Anubhab Haldar's user avatar
14 votes

How to start a Machine Learning project for chemical properties prediction?

Admittedly, there are tons of materials on the chemistry + machine learning topics. Let me give one: An introductory text I find useful is Machine Learning in Chemistry from Janet and Kulik in ACS in ...
Greg's user avatar
  • 1,807
14 votes
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Easy ways to generate "teaching" band structures in Python?

I'd suggest having a look at PythTB by Sinisa Coh and David Vanderbilt, which I found very useful and easy to use. Here's a stab at recreating the band structure of the 2d square lattice shown above <...
leopold.talirz's user avatar
13 votes

How can I use a GUI on a supercomputer?

It would probably be easier to use some software such as WinSCP. It allows you to select the location on your remote system and synchronise with the local system by matching either the time stamp or ...
PBH's user avatar
  • 2,653
12 votes

What is a good programming language for matter modeling?

Bash Scripting I have used bash scripts to automate materials modelling workflows. You can use online resources to learn more about bash commands and bash scripting. The idea is simple. If you have a ...
Anoop A Nair's user avatar
  • 4,506

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