[WIP] Add draft post introducing distopia #269
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
orbeckst
reviewed
Apr 21, 2023
|
|
||
| Calculating Euclidian distances under periodic boundary conditions is a core component in both running and analysing molecular simulations. For example, the calculation of radial distribution functions, hydrogen bonds, structure factors, and many other common analyses require calculation of one or more pairwise Euclidian distances. | ||
|
|
||
| The Euclidian distance formula under periodic boundary conditions can be expressed as: |
| title: Introducing Distopia | ||
| --- | ||
|
|
||
| Calculating Euclidian distances under periodic boundary conditions is a core component in both running and analysing molecular simulations. For example, the calculation of radial distribution functions, hydrogen bonds, structure factors, and many other common analyses require calculation of one or more pairwise Euclidian distances. |
There was a problem hiding this comment.
perhaps link to a wiki page on PBC or cite a paper ... making it more scholarly
comment on different "simulation boxes" would be helpful
Image illustrating PBC (at least in 2D) would be icing on the cake.
|
|
||
| ## Conclusion | ||
|
|
||
| In this post we have seen how we can use the `distopia` library to accelerate distance calculations. Distopia is available as a backend to some MDAnalysis distiance functions right now, with support for more to be added in the future. |
|
|
||
| Many molecular mechanics engines have highly optimised code for calculating distances that often make use of specialised code paths and/or accelerators to achieve maximal performance. However this functionality is often heavily "baked-in" and is not able to be used as a standalone component. | ||
|
|
||
| We at MDAnalysis wanted to bring some of this blazing speed to our distance calculations without sacrificing the modularity of MDAnalysis by introducing heavyweight dependencies on a simulation engine. |
There was a problem hiding this comment.
Say early on how to use it in MDA and from which release onwards it is available.
The detail below is really informative and it's great to have technical blog posts. I would just make sure that our general users get the message that (1) we have fast distance calculations and (2) you can use them right away.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Fixes #265.
Still quite WIP, missing figures and inline math.
Would love some inital feedback and possibly help @richardjgowers.