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34 votes
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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 ...
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32 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,...
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31 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 ...
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29 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 ...
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23 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 ...
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  • 3,810
23 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 ...
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22 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 ...
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  • 1,638
19 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 ...
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  • 611
18 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 ...
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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 ...
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  • 27.8k
15 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 ...
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15 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 ...
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  • 2,881
15 votes

How to make a python code that can read a .xyz file and find the distance between atoms?

ASE The ASE library has an atom object with built-in get_angle, get_dihedral and ...
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  • 1,363
15 votes

How to make a python code that can read a .xyz file and find the distance between atoms?

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, ...
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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 ...
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  • 27.8k
14 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. ...
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14 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 ...
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  • 266
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. ...
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  • 3,064
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 ...
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  • 256
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 ...
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  • 1,638
13 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 ...
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13 votes

How to make a python code that can read a .xyz file and find the distance between atoms?

Open Babel First, the command-line version: obabel c60.xyz -oreport Yields: All interatomic distances All bond angles All connected torsions Also, partial charges ...
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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 ...
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  • 2,454
12 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 ...
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12 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 ...
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12 votes

How to make a python code that can read a .xyz file and find distance, angle and dihedral angle between atoms?

It helps to know that in computational chemistry the collection of distance, angle and dihedral coordinates is collectively known as "z-matrix coordinates". Unless you care to reinvent the ...
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12 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: ...
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12 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 ...
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11 votes

Is python sufficient for serious tensor network or DMRG calculations?

There probably are good Python bindings to various DMRG implementations, which allow one to run DMRG from Python. Since the implementations typically rely on lower-level C/C++/Fortran routines, the ...
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