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Task #2133

gmx traj needs reform

Added by Mark Abraham over 2 years ago. Updated over 2 years ago.

Status:
New
Priority:
Low
Assignee:
-
Category:
analysis tools
Target version:
-
Difficulty:
uncategorized
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Description

gmx traj does too many things that conflict with each other.

The xvg written by -av and -ax does not describe the Y axis adequately.

The implementations of things like -av and -cv are conflated to the point that you can't dump the average velocities of a group per frame to .xvg unless you provide a topology (because you need that for implementing -cv). Same for -af and -cf.

There should not be a distinct implementation of PBC handling in remove_jump.

The -vd option should probably not roll its own histogram implementation

Associated revisions

Revision a2d8c56c (diff)
Added by Mark Abraham over 2 years ago

Fix minor issues in gmx traj -av -af

Made the description of the xvg y-axis more useful. Also works for
option -af.

Refs #2133

Change-Id: If3796ddbd9841fc442b765afab9ad249954f9316

History

#1 Updated by Mark Abraham over 2 years ago

  • Description updated (diff)

#2 Updated by Gerrit Code Review Bot over 2 years ago

Gerrit received a related patchset '1' for Issue #2133.
Uploader: Mark Abraham ()
Change-Id: gromacs~release-2016~If3796ddbd9841fc442b765afab9ad249954f9316
Gerrit URL: https://gerrit.gromacs.org/6500

#3 Updated by Teemu Murtola over 2 years ago

This should also be compared with gmx trajectory. Probably some of the existing functionality in gmx traj would fit there (I just put the bare minimum to support writing out trajectories from selections), but some of the existing options would probably better fit into a separate tool. And generic abilities like removing jumps would probably better go into the framework instead of individual tools.

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