Thermostats

[jaketanderson]

Hi there, are you planning on writing a page about thermostats? I see there's already code written to support Berendsen thermostats and barostats. Would you be open to the idea of including/mentioning Nosé–Hoover thermostats?

[simongravelle]

Hi Jake,

Yes, definitely, there should eventually be a Nosé-Hoover and probably a Langevin too. Currently, I am focussing more on having a clean basic code + doc for Monte Carlo, so I don't focus so much on molecular dynamics aspect at the moment, but if you are interested in implementing it, that would be great. Note that since I haven't worked on the MD part for a while, and have made a lot of modifications to the rest of the code, I am sure that the MD part is currently broken.

Sidenote

I will also need to write a guideline for contributors. The way it works, currently, is that I have a code-generator that reads the documentation and generate the most recent code from the doc, and test it systematically (here: https://github.com/mdcourse/mdcourse.github.io/tree/main/tests). This makes things a bit convoluted, but my goal was to make sure that the website was always 100% up to date and always contains the last and a working version of the code. I don't know if you noticed, but there is also a secondary repository (https://github.com/mdcourse/python-codes) that will eventually host only the code as generated from the doc.

Please let me know if you have questions, or if the structure of the project is really too confusing.

Simon

[jaketanderson]

Simon,

I'd be happy to put some work toward a page for thermostats in MD! Fair warning, though, that I will not be very fast in implementing it :). If in the future anyone wants to join me in working on thermostats they are more than welcome to.

I did see the second repository -- it should not be edited directly, then? Thanks.

[simongravelle]

I'd be happy to put some work toward a page for thermostats in MD! Fair warning, though, that I will not be very fast in implementing it :).

Its completely fine. I think that the first step is to work on the code part. Once we have a working code, and once I will have re-integrated the MD inside the main part of the doc, we can decide how to integrate it. A page dedicated to thermostat is certainly a good possibility.

I did see the second repository -- it should not be edited directly, then?

Yes… I realize that this is not ideal, but I don't know a better system that would avoid having duplicated code and doc.... That being said, the code in here:

https://github.com/mdcourse/python-codes/tree/main/python-codes

is the current last version of the code, and you can use it to make tests and development. Then, when you have a working version for a NH thermostat, we can add it to the documentation, so its getting automatically included to the code.

Simon