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Bug #2143

Pull group 0 shows up in logs, states one more group than actually exists

Added by James Barnett over 2 years ago. Updated over 1 year ago.

Status:
Closed
Priority:
Low
Assignee:
Berk Hess
Category:
mdrun
Target version:
2018
Affected version - extra info:
Affected version:
2016.3
Difficulty:
uncategorized
Close

Description

In md.log when using the pull code, there is always a "pull-group 0" output with no atoms. grompp does not accept "pull-group0-name", etc, so the count should start at 1. Additionally, pull-ngroups always is set to one number higher than the actual number of pull groups set. For example, setting "pull-ngroups" to 2 in the mdp file results in the md.log stating that "pull-ngroups" is 3; the processed mdp file has the correct number. Additionally later in the log it states (using to virtual sites in this one, so no masses):

Will apply potential COM pulling
with 1 pull coordinate and 3 groups
Pull group 1:     1 atoms, mass     0.000
Pull group 2:     1 atoms, mass     0.000

Associated revisions

Revision fba92a59 (diff)
Added by Erik Lindahl almost 2 years ago

Don't write reference pull group 0 to log

This is an internal group used for absolute
references, which cannot be set by users, so
printing it just leads to confusion.

Fixes #2143.

Change-Id: I89ee3a0e3a65855735b745f4ed7615ca47bfd36a

Revision 3891bbbb (diff)
Added by Berk Hess over 1 year ago

Do not calculate COM for pull group 0

Pull group 0 is an absolute reference with coordinates 0,0,0,
so it is clearer to never compute its center of mass.

Refs #2143

Change-Id: Ifa974ab84afe303594c3b65e9567e0568bb151a9

History

#1 Updated by Mark Abraham over 2 years ago

Looks like there are some minor errors with starting counting from 0 vs 1 here, Berk.

#2 Updated by Berk Hess over 2 years ago

  • Category set to mdrun
  • Status changed from New to Accepted
  • Assignee set to Berk Hess
  • Priority changed from Normal to Low

Group 0 is (only) used for absolute reference. It's coordinates are 0,0,0. I did this to avoid having to add a group and changing the user numbering. I suppose we should simply avoid printing it.

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

Gerrit received a related patchset '1' for Issue #2143.
Uploader: Erik Lindahl ()
Change-Id: gromacs~release-2018~I89ee3a0e3a65855735b745f4ed7615ca47bfd36a
Gerrit URL: https://gerrit.gromacs.org/7410

#4 Updated by Erik Lindahl almost 2 years ago

  • Status changed from Accepted to Fix uploaded

#5 Updated by Erik Lindahl almost 2 years ago

  • Status changed from Fix uploaded to Resolved

#6 Updated by Erik Lindahl almost 2 years ago

  • Status changed from Resolved to Closed

#7 Updated by Gerrit Code Review Bot over 1 year ago

Gerrit received a related patchset '1' for Issue #2143.
Uploader: Berk Hess ()
Change-Id: gromacs~master~Ifa974ab84afe303594c3b65e9567e0568bb151a9
Gerrit URL: https://gerrit.gromacs.org/7718

#8 Updated by Mark Abraham over 1 year ago

  • Target version set to 2018

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