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Issue created by Paul Bauer@acmnpvMaintainer

Core dump with gmx rdf with some selections - Redmine #2951

Archive from user: Dallas Warren

When running some selections with gmx rdf 2019.2 get:
‘Segmentation fault (core dumped)’

Exact same files and command, but using 2016.3 the program executes fine.

‘gmx rdf -f md_001_short.xtc -s md_001.tpr -bin 0.01 -n index.ndx -seltype part_res_com -selrpos part_res_com -o ’
Select 11 and 11

‘gmx rdf -f md_001_short.xtc -s md_001.tpr -bin 0.01 -n index.ndx -seltype dyn_res_com -selrpos dyn_res_com -o ’
Select 11 and 11

This one works fine with 2019.2:
‘gmx rdf -f md_001_short.xtc -s md_001.tpr -bin 0.01 -n index.ndx -seltype whole_res_com -selrpos whole_res_com -o ’

(from redmine: issue id 2951, created on 2019-05-14 by gmxdefault, closed on 2019-06-11)

  • Changesets:
    • Revision a822b10a by Paul Bauer on 2019-06-11T12:55:14Z:
Fix residue and molecule indexing in selections

The residue and molecule indexing did not account for the global
indices when building blocks from selections.

Also fixed a docs formatting issue noticed while working on the fix.

Fixes #2951

Change-Id: Ifa16f032822f5d96b6ff747333a7aed60b9a414d
  • Revision 6d0ed8b7 by Mark Abraham on 2019-07-05T08:09:02Z:
Improve tests of index block construction

Only trivial topologies were tested, and bugs have been
identified. Some test code is commented out until the fix lands.

Added missing Doxygen

Improved some assertions hit while investigating the issue.

Refs #2951

Change-Id: Ia03e38aca42be43efa1fd548c32e522d97e13e94