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Bug #1954

gmx order requires -nr input option even when the (default) -noradial option is selected

Added by Chris Neale over 3 years ago. Updated over 3 years ago.

Status:
Closed
Priority:
Low
Assignee:
-
Category:
analysis tools
Target version:
Affected version - extra info:
5.1-5.1.2
Affected version:
Difficulty:
uncategorized
Close

Description

In addition to the fact that the -nr input should not be required with -noradial, the -nr input option is not explained at all in gmx order -h output. I had to go into the source code to get any idea of what this was:

{ efNDX, "-nr", NULL,  ffREAD },              /* index for radial axis calculation        */

Note that I did get the program to run simply by passing the same .ndx file to -n and -nr where without the -radial option turned on I presume that the input to -nr is not actually used to do anything.

There's a post on the list from March 2016 that highlights this issue, but I didn't see an answer:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2016-March/104466.html

Associated revisions

Revision 9f4f3141 (diff)
Added by Teemu Murtola over 3 years ago

Mark optional input/output files in gmx order

Mark files that are not always read, or which are not written if the
user does not ask for them, with ffOPTRD/ffOPTWR instead of using
ffREAD/ffWRITE. With changes in 5.1, files marked with ffREAD are
really mandatory, since we check already during command-line parsing
that the file actually exists (so that we can give a good error
message). This change also improves the understandability of the help.

Fixes #1954.

Change-Id: I6a991786b8cc48a61eedad9f855a93559bb8a5a0

History

#1 Updated by Gerrit Code Review Bot over 3 years ago

Gerrit received a related DRAFT patchset '1' for Issue #1954.
Uploader: Teemu Murtola ()
Change-Id: I6a991786b8cc48a61eedad9f855a93559bb8a5a0
Gerrit URL: https://gerrit.gromacs.org/5840

#2 Updated by Teemu Murtola over 3 years ago

  • Category set to analysis tools
  • Status changed from New to Fix uploaded
  • Target version set to 5.1.3
  • Affected version - extra info set to 5.1-5.1.2

#3 Updated by Teemu Murtola over 3 years ago

  • Status changed from Fix uploaded to Resolved

#4 Updated by Erik Lindahl over 3 years ago

  • Status changed from Resolved to Closed

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