36
votes
Accepted
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,...
- 578
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 ...
- 2,364
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 ...
- 646
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 ...
- 1,607
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 ...
- 4,306
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 ...
- 6,569
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 ...
- 1,797
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 ...
- 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 ...
- 898
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 ...
- 3,751
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. ...
- 1,700
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
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 ...
- 286
16
votes
Accepted
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 ...
- 33.1k
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 ...
- 3,061
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, ...
- 33.1k
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
...
- 8,655
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 ...
- 22k
15
votes
Accepted
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 ...
- 15k
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 ...
- 22k
15
votes
Accepted
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 ...
- 33.1k
14
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 ...
- 8,655
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.
...
- 3,836
14
votes
Accepted
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 ...
- 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:
...
- 1,416
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 ...
- 1,797
14
votes
Accepted
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
<...
- 2,484
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 ...
- 2,583
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 ...
- 4,388
Only top scored, non community-wiki answers of a minimum length are eligible