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Task #1805

Difficult to find gmx select documentation

Added by Viveca Lindahl about 2 years ago. Updated over 1 year ago.

Status:
Closed
Priority:
Normal
Category:
selections
Target version:
Difficulty:
uncategorized
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Description

I find it difficult to find the gmx select syntax. I end up googling it and wind up here: http://www.gromacs.org/Documentation/Gromacs_Utilities/g_select where I read that

g_select -select 'help all'

should give me the docs. On my (master-based) gmx doing

gmx select -select 'help all'

gives a syntax error.

To get to the docs I need a tpr and do 'gmx select -s topol.tpr' and then 'help' and then e.g.'help syntax'. It would be much better if 1) I get info about how to reach the docs directly from 'gmx select -h' and 2) if I can go through the docs without providing any input.

Associated revisions

Revision b8019378 (diff)
Added by Mark Abraham about 2 years ago

Make it easier to find selection help

Fixes #1805

Change-Id: Ie09baa75601f6ba3e8e514f78e3bae34e7327f86

Revision c99cdd50 (diff)
Added by Mark Abraham about 2 years ago

Make it easier to find selection help

Now the command-line reference part of the user guide has a TOC entry
that has the magic work "selection" in it.

Fixes #1805

Change-Id: Ib99840ab1f3fd72a52f28ffa1e06ee1242fa4310

History

#1 Updated by Justin Lemkul about 2 years ago

The "problem" (if it can be called that) is that the selection mechanism is gradually being introduced into multiple tools; the help info is no longer unique to gmx select, which in old versions as g_select, was the only tool that used the selection syntax. Now, others (e.g. gmx distance) use it, too. So what you want is

gmx help selections

which can then be used to find syntax, examples, etc. Much of the information on the wiki is getting outdated, and I haven't had time to keep up with that as I once did, but of course others can add to it with new information that they learn :)

#2 Updated by Mark Abraham about 2 years ago

gmx help selections is the new magic thing. Let me see if I can make this easier in both 5.0 and 5.1 branches

#3 Updated by Gerrit Code Review Bot about 2 years ago

Gerrit received a related patchset '1' for Issue #1805.
Uploader: Mark Abraham ()
Change-Id: Ie09baa75601f6ba3e8e514f78e3bae34e7327f86
Gerrit URL: https://gerrit.gromacs.org/4990

#4 Updated by Gerrit Code Review Bot about 2 years ago

Gerrit received a related patchset '1' for Issue #1805.
Uploader: Mark Abraham ()
Change-Id: Ib99840ab1f3fd72a52f28ffa1e06ee1242fa4310
Gerrit URL: https://gerrit.gromacs.org/4991

#5 Updated by Teemu Murtola about 2 years ago

Note that in 5.1, you can just read all the information that is available in the selection help directly from the user guide.

#6 Updated by Mark Abraham about 2 years ago

Teemu Murtola wrote:

Note that in 5.1, you can just read all the information that is available in the selection help directly from the user guide.

Indeed, although 4991 makes it easier to find it in the TOC

#7 Updated by Mark Abraham about 2 years ago

  • Status changed from New to Resolved
  • % Done changed from 0 to 100

#8 Updated by Teemu Murtola over 1 year ago

  • Status changed from Resolved to Closed
  • Target version set to 5.1.2

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