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Feature #1619

gangle add x and y axis to second vector group options

Added by Dallas Warren about 5 years ago. Updated over 4 years ago.

Status:
Closed
Priority:
Low
Assignee:
Category:
analysis tools
Target version:
Difficulty:
uncategorized
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Description

Currently the second vector group that can calculate the angle with only includes the z axis. Would be very handy if was also able to calculate the angle of the vector with the x and y axes.

i.e. current options are
-g2 <enum> (none)
Type of second vector group: none, vector, plane, t0, z, sphnorm

Addition of two:
-g2 <enum> (none)
Type of second vector group: none, vector, plane, t0, x, y, z, sphnorm

Associated revisions

Revision bd72a865 (diff)
Added by Teemu Murtola almost 5 years ago

Support more complex fixed position selections

Make it possible to create selections like
[0,0,0] plus [0,1,0]
to specify a fixed set of positions. This can be useful at least for
'gmx gangle' to calculate angles from a fixed reference vector.
Such selections were already understood properly by the parser, but
caused various crashes elsewhere in the code. Fixed those crashes by
consistently managing the memory for the involved t_block structures
(always allocate one value in the index array, even if the block is
empty), and by not assuming that a plus-like keyword always has a child
element in the evaluation tree.

Fixes #1619.

Change-Id: I513cddbe882f269ad867c726a54583ee48b41b4d

History

#1 Updated by Teemu Murtola almost 5 years ago

  • Status changed from New to In Progress
  • Assignee set to Teemu Murtola
  • Target version set to 5.1

I'll implement this in a slightly different manner than originally requested, but the functionality should be there: it should be possible to run

gmx gangle ... -g2 vector -group2 '[0,0,0] plus [0,1,0]'

to calculate angles with respect to the Y axis (and equally well with respect to any arbitrary fixed vector, by just modifying the selection). This syntax is already a valid selection, but unfortunately it causes a crash in the selection engine. That should be relatively easily fixable, though.

#2 Updated by Gerrit Code Review Bot almost 5 years ago

Gerrit received a related patchset '2' for Issue #1619.
Uploader: Teemu Murtola ()
Change-Id: I513cddbe882f269ad867c726a54583ee48b41b4d
Gerrit URL: https://gerrit.gromacs.org/4424

#3 Updated by Teemu Murtola almost 5 years ago

  • Status changed from In Progress to Fix uploaded

#4 Updated by Mark Abraham almost 5 years ago

Dallas, does Teemu's patch scratch your itch? It'd be good to know for upcoming GROMACS 5.1...

#5 Updated by Teemu Murtola almost 5 years ago

  • Status changed from Fix uploaded to Resolved

#6 Updated by Mark Abraham over 4 years ago

  • Status changed from Resolved to Closed

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