Bug #2143
Pull group 0 shows up in logs, states one more group than actually exists
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
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 almost 4 years ago
Looks like there are some minor errors with starting counting from 0 vs 1 here, Berk.
#2 Updated by Berk Hess almost 4 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 about 3 years ago
Gerrit received a related patchset '1' for Issue #2143.
Uploader: Erik Lindahl (erik.lindahl@gmail.com)
Change-Id: gromacs~release-2018~I89ee3a0e3a65855735b745f4ed7615ca47bfd36a
Gerrit URL: https://gerrit.gromacs.org/7410
#4 Updated by Erik Lindahl about 3 years ago
- Status changed from Accepted to Fix uploaded
#5 Updated by Erik Lindahl about 3 years ago
- Status changed from Fix uploaded to Resolved
Applied in changeset fba92a59628c0fb04f7c2b6f110ab357fe6861ef.
#6 Updated by Erik Lindahl about 3 years ago
- Status changed from Resolved to Closed
#7 Updated by Gerrit Code Review Bot almost 3 years ago
Gerrit received a related patchset '1' for Issue #2143.
Uploader: Berk Hess (hess@kth.se)
Change-Id: gromacs~master~Ifa974ab84afe303594c3b65e9567e0568bb151a9
Gerrit URL: https://gerrit.gromacs.org/7718
#8 Updated by Mark Abraham almost 3 years ago
- Target version set to 2018
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