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Bug #2114

gmx trjconv -pbc cluster claims to have -clustercenter option but does not (5.1.2)

Added by Chris Neale about 4 years ago. Updated almost 4 years ago.

Status:
Closed
Priority:
Low
Assignee:
Category:
documentation
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

gmx trjconv -h contains the text:
The separate option -clustercenter can be used to specify an approximate
center for the cluster. This is useful e.g. if you have two big vesicles,
and you want to maintain their relative positions.

However, that (useful) option doesn’t seem to actually exist:

Command line:
gmx trjconv -pbc cluster -f EMet.gro -s EM.tpr -o aha.gro -n aha.ndx -clustercenter

-------------------------------------------------------
Program:     gmx trjconv, VERSION 5.1.2
Source file: src/gromacs/commandline/cmdlineparser.cpp (line 234)
Function:    void gmx::CommandLineParser::parse(int *, char **)

Error in user input:
Invalid command-line options
    Unknown command-line option -clustercenter

Also, searching the 5.1.2 source code for gmx_trjconv.c doesn't have any mention of "clustercenter" except in the help file.


Related issues

Related to GROMACS - Task #2115: trjconv does too many things, and combinations of them work poorlyNew

Associated revisions

Revision 9c7dfd2f (diff)
Added by Mark Abraham about 4 years ago

Remove docs for unimplemented trjconv -clustercenter

2d8b8dd16d8 introduced a partial implementation, which was removed in
73b83321 because it introduced variables that were unused. However,
the matching documentation was not removed then.

Fixes #2114

Change-Id: Iedddf99b0254b772ffaebfcb27bec862493d920d

History

#1 Updated by Mark Abraham about 4 years ago

  • Related to Task #2115: trjconv does too many things, and combinations of them work poorly added

#2 Updated by Aleksei Iupinov about 4 years ago

The file has been moved and renamed to gmx_trjconv.cpp.

This specific option was removed in revision 73b83321.
Looking at commit history, this and other similar commits at that moment removed quite a few command line options without amending the documentation at the same time.

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

Gerrit received a related patchset '1' for Issue #2114.
Uploader: Mark Abraham ()
Change-Id: gromacs~release-2016~Iedddf99b0254b772ffaebfcb27bec862493d920d
Gerrit URL: https://gerrit.gromacs.org/6458

#4 Updated by Mark Abraham about 4 years ago

  • Target version set to 2016.3

Thanks Aleksei, I looked through Alexey's commits and didn't see any other cases of command-line options that were removed despite having documentation. Did you have anything particular in mind?

#5 Updated by Mark Abraham about 4 years ago

  • Description updated (diff)

#6 Updated by Mark Abraham about 4 years ago

  • Category set to documentation
  • Status changed from New to Fix uploaded
  • Assignee set to Mark Abraham

#7 Updated by Aleksei Iupinov about 4 years ago

I did not look closely, but just grepping changes for "opt2" shows line

bQuad = opt2bSet("-q", NFILE, fnm);

being removed, for example. Many slight changes, all without touching the docs.

So I have no clue, of course, if it was the old code catching up with the documentation, or the other way round :-)

#8 Updated by Mark Abraham about 4 years ago

  • Status changed from Fix uploaded to Resolved

#9 Updated by Mark Abraham almost 4 years ago

  • Status changed from Resolved to Closed

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