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Task #2396

Refactor trajectoryanalysis module to allow handling of trajectory frame manipulation

Added by Paul Bauer over 1 year ago. Updated 9 months ago.

Status:
New
Priority:
Normal
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Category:
analysis tools
Target version:
Difficulty:
uncategorized
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Description

The trajectoryanalysis module works currently with the assumption that all data sets are of a type such as

  • index , value , deviation

This makes it more difficult to use the machinery for something like trajectory file manipulation or internal manipulation of coordinate frames.

A proposed change is to move the declaration of the per-frame data structures to the individual analysis modules, so that each module could declare different kinds of data handlers that are distinct from the currently implemented types in analysisdata.h.

One issue that Teemu has already raised is that this would remove the option to run the analysis in parallel, which should be avoided. I don't know if there would be a way around this by keeping the original structure and adding a different abstraction layer between the different kinds of data handled during the analysis.

History

#1 Updated by Gerrit Code Review Bot over 1 year ago

Gerrit received a related patchset '4' for Issue #2396.
Uploader: Paul Bauer ()
Change-Id: gromacs~master~I6bbb5c803c246cbea66470bccbd0d00d0bad0931
Gerrit URL: https://gerrit.gromacs.org/7529

#2 Updated by Teemu Murtola over 1 year ago

I don't understand what your problem is. Using any of analysisdata, or even the per-frame data objects, is completely opt-in in the framework. You can perfectly well put arbitrary objects in your analysis module, or in a custom per-frame data structure, and at most you will lose the ability to run that particular tool with the simple parallelism scheme that is in the background (but has never been implemented). None of this should require removing any existing code or functionality.

#3 Updated by Paul Bauer over 1 year ago

ok, then I didn't understand the code good enough for this, sorry.
I'll remove the linked change then again and will upload a proposal for a change that will introduce coordinate data handling and internal storage to the general framework.
Thanks for your advice and for setting me right on this.

#4 Updated by Gerrit Code Review Bot over 1 year ago

Gerrit received a related DRAFT patchset '1' for Issue #2396.
Uploader: Paul Bauer ()
Change-Id: gromacs~master~I9d8717c7a6a708f9bdd83e3a8cc478b5a8725be6
Gerrit URL: https://gerrit.gromacs.org/7561

#5 Updated by Gerrit Code Review Bot over 1 year ago

Gerrit received a related patchset '3' for Issue #2396.
Uploader: Paul Bauer ()
Change-Id: gromacs~master~Ib9040c37d4b3b3d7ff2a83bfe356dbedc32b6403
Gerrit URL: https://gerrit.gromacs.org/7627

#6 Updated by Gerrit Code Review Bot 9 months ago

Gerrit received a related patchset '13' for Issue #2396.
Uploader: Paul Bauer ()
Change-Id: gromacs~master~I1413721faa1383a9d3b8f14cdbea2bcc3089273f
Gerrit URL: https://gerrit.gromacs.org/8285

#7 Updated by Mark Abraham 9 months ago

  • Target version changed from 2019 to 2020

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