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Task #2727

Move non-analysis functions out of gmxana

Added by Kevin Boyd 5 months ago. Updated 2 months ago.

Status:
In Progress
Priority:
Low
Assignee:
-
Category:
analysis tools
Target version:
Difficulty:
simple
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Description

Several files/tools sitting in the gmxana folder seem more suited for gmxpreprocess, e.g.

-gmx genion
-gmx editconf
-gmx genpr

-gmx tune_pme probably shouldn't be bundled with the analysis tools either, though I'm not sure where it should go.

A few others whose purpose is not solely analysis, but it could be argued they belong here

-gmx make_ndx
-gmx eneconv
-gmx trjconv

Associated revisions

Revision f9c7a4ee (diff)
Added by Kevin Boyd 2 months ago

Move non-analysis tools from gmxana to gmxpreprocess

Renamed genpr to genrestr to align with actual gmx <tool> call

refs #2727

Change-Id: I83a1dc6b39915372c4178768354d334c7e911ae2

History

#1 Updated by Gerrit Code Review Bot 5 months ago

Gerrit received a related patchset '1' for Issue #2727.
Uploader: Joe Jordan ()
Change-Id: gromacs~master~I9a87f642482f84770e2cad19f76b21f807184b0f
Gerrit URL: https://gerrit.gromacs.org/8645

#2 Updated by Gerrit Code Review Bot 2 months ago

Gerrit received a related patchset '1' for Issue #2727.
Uploader: Kevin Boyd ()
Change-Id: gromacs~master~I83a1dc6b39915372c4178768354d334c7e911ae2
Gerrit URL: https://gerrit.gromacs.org/8995

#3 Updated by Mark Abraham 2 months ago

Kevin Boyd wrote:

Several files/tools sitting in the gmxana folder seem more suited for gmxpreprocess, e.g.

-gmx genion
-gmx editconf
-gmx genpr

Sure

-gmx tune_pme probably shouldn't be bundled with the analysis tools either, though I'm not sure where it should go.

src/gromacs/tools I guess

A few others whose purpose is not solely analysis, but it could be argued they belong here

-gmx make_ndx
-gmx eneconv
-gmx trjconv

They could move to tools too, perhaps.

#4 Updated by Kevin Boyd 2 months ago

  • Status changed from New to In Progress

#5 Updated by Gerrit Code Review Bot 2 months ago

Gerrit received a related patchset '1' for Issue #2727.
Uploader: Kevin Boyd ()
Change-Id: gromacs~master~Idf8375b672fbb6e4676fa22b9eb9c33d1b347166
Gerrit URL: https://gerrit.gromacs.org/9002

#6 Updated by Kevin Boyd 2 months ago

Joe pointed out that some of the functionality I was trying to move out of gmxana is deprecated and will be changed / removed in the near future, and so maybe shouldn't be moved now. I see 7 tools that don't belong in gmxana still.

Superseded by gmx select but not officially deprecated:
gmx make_ndx
gmx mk_angndx

Should be moved:
gmx tune_pme
gmx pme_error

Work being done on these:
gmx trjconv
gmx trjcat
gmx eneconv

#7 Updated by Joe Jordan 2 months ago

Any script that currently uses make_ndx can trivially be updated by using the -on flag on select. There is a cost to having multiple tools to do the same job, and select has better index writing functionality than make_ndx such as dynamic selections, so I think it would be reasonable to remove make_ndx.

#8 Updated by Kevin Boyd 2 months ago

Joe Jordan wrote:

Any script that currently uses make_ndx can trivially be updated by using the -on flag on select. There is a cost to having multiple tools to do the same job, and select has better index writing functionality than make_ndx such as dynamic selections, so I think it would be reasonable to remove make_ndx.

That seems reasonable to me, but since we haven't officially deprecated it, should we do that for the 2020 release and then remove for 2021?

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