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ChangeLog
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ChangeLog
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2013-05-17 Olaf Lenz
* ChangeLog: This ChangeLog is discontinued. If you are interested
in the history of pbctools, refer either to NEWS or to the git
log.
2010-04-26 Olaf Lenz <olenz@qwghlm>
* pbcjoin.tcl: Small fix to allow pbc join to be used on several
frames in one command.
2010-04-21 Olaf Lenz <[email protected]>
* pbcwrap.tcl: Reintroduced Tcl code (get_connected) to determine
connected compounds that contain all atoms that are
connected ("fragment" only does this if all atoms are in the same
segment and chain).
* pbcjoin.tcl: Added compound type "connected". Extended verbosity.
2010-02-16 Olaf Lenz <olenz@qwghlm>
* pbctools.tcl: Fixed email address of olenz.
* pbcwrap.tcl: Added compound type "fragment".
2009-11-04 Olaf Lenz <olenz@qwghlm>
* pbcset.tcl: Incorporated Jan Saams commits to the VMD CVS, log
message:
Fixed a bug reported by Olaf Lenz:
> % pbc readxst kiley.xst -alignx
> atomselection move:: need a 4x4 matrix
Now xst files containing PBC vectors that don't follow the
standard alignment (A||x, B in x-y plane) are read and the
molecule is aligned accordingly when using -alignx option.
Fixed indentation in a few places.
2009-10-09 Olaf Lenz <[email protected]>
* doc/pbctools.tex (subsection{\texttt{set}}): Fixed small error
in the documentation of "pbc set", thanks to Axel Kohlmeier and
Lan He.
2009-06-26 Olaf Lenz <[email protected]>
* doc/pbctools.tex: Added note that -centersel only has an effect
when -center bb/com is used. Thanks to Alberto Sergio Saray.
2009-05-14 Olaf Lenz <olenz@qwghlm>
* pbctools.tcl: Applied Axel Kohlmeyer's docfix patch.
* doc/pbctools.tex: Restructured introduction, abstract and basic
usage section.
* pbcjoin.tcl (pbcjoin): Added option "-[no]border", which allows
to specify the maximal depth were atoms of a broken compound can
be found inside the unit cell. Currently works only for orthorhombic
unit cells.
* pbcwrap.tcl (pbcwrap): "-center" now understands a selection as
argument again, for backward compatibility. However, a deprecation
warning is printed.
2009-05-11 Olaf Lenz <olenz@qwghlm>
* pbcjoin.tcl (pbcjoin): Some more improvements, added more
detailed progress report.
2009-04-30 Olaf Lenz <[email protected]>
* pbcjoin.tcl (pbcjoin): Some more improvements to "pbc
join". Im my tests, I got a performance gain of about 50%.
2009-04-23 Olaf Lenz <olenz@qwghlm>
* pbcjoin.tcl: Thanks to Dan Lussier: significantly reduced memory
footprint of "pbc join".
2009-02-10 Olaf Lenz <olenz@true>
* pbcjoin.tcl: Thanks to Axel Kohlmeyer, join now checks whether the pbc cell
parameters are reasonable.
* pbctools.tcl: Added implementation of vmdcon for VMD version
before 1.8.7.
* *.tcl: All functions use vmdcon now instead of "puts".
2009-01-21 Olaf Lenz <olenz@true>
* Advanced to version 2.5.
* pbcbox.tcl, pbcwrap.tcl, pbctools.tex: Commands pbcwrap and
pbcbox: Added option "-centersel" that takes a selection. The
option "-center" does not take the $sel argument anymore, instead
the keywords "com", "centerofmass", "bb" or "boundingbox" can be
used to denote that the center of the box/wrapping is in the
center of mass or the center of the bounding box of the given
selection.
2008-11-20 Olaf Lenz <[email protected]>
* Advanced to version 2.4.
* maintainer/: Added maintainer directory that contains scripts
and notes for the maintainer.
* pbcwrap.tcl, pbcunwrap.tcl, pbcjoin.tcl: Added option
"-noverbose" for completeness.
* doc/index.html: Now contains only link to the pbctools gfroge
home page: http://www.espresso-pp.de/projects/pbctools/
* doc/pbctools.tex: Translated doc/index.html to LaTeX.
2008-10-27 Olaf Lenz <olenz@true>
* doc/index.html: History and credits will be included from the
NEWS and AUTHORS file in the future.
* doc/ChangeLog: Moved one directory up.
* NEWS, README, AUTHORS: Created files with release notes, basic
docs and credits.
2008-10-04 Olaf Lenz <olenz@qwghlm>
* Advanced to version 2.3.
* pbcbox.tcl, pbcwrap.tcl: Renamed option -rectangular to
-orthorhombic (-rectangular still works).
* doc/index.html: Updated docs.
2008-09-04 Olaf Lenz <[email protected]>
* doc/index.html: Updated history.
2008-06-14 Olaf Lenz <olenz@qwghlm>
* pbcjoin.tcl, doc/index.html: Replaced homemade "bonded" keyword
and implementation by VMDs native "fragment".
2008-06-10 Olaf Lenz <olenz@qwghlm>
* pbcwrap.tcl, pbcjoin.tcl: Bugfix: "pbcwrap -compound segment"
didn't work: Used wrong keyword "segment" for segment selection,
instead of "segid". Reported by Chris Maffeo <[email protected]>.
2008-03-27 Olaf Lenz <[email protected]>
* Advanced to version 2.2.
* pbcwrap.tcl (pbcwrap), index.html: Changed default of option
"-compound" to "-nocompound".
* index.html: Some doc fixes.
2007-07-30 Olaf Lenz <[email protected]>
* Advanced to version 2.1.
* index.html: Added history and table of contents.
2007-06-01 Olaf Lenz <[email protected]>
* pbcjoin.tcl, pbcwrap.tcl, pbcunwrap.tcl, pbcset.tcl, pbcbox.tcl:
Improved error handling.
* pbcwrap.tcl, pbcunwrap.tcl, pbcjoin.tcl: Added -verbose option
to wrap, unwrap and join.
* pbcset.tcl: Added -check option to pbcget: checks the cell
parameters for validity.
* pbcunwrap.tcl: Use generic function from pbcwrap.
* pbcwrap.tcl: Added generic pbcwrap_coordinates function to wrap
coordinates into a unit cell around another coordinate.
* pbcjoin.tcl, pkgIndex.tcl, doc/index.html: First implementation
of pbc join.
2007-03-01 Olaf Lenz <[email protected]>
* pbcjoin.tcl: Added. Will contain a function to join wrapped atom
compounds.
* pbcbox.tcl (pbcbox): Bugfix: handling of errors in pbcbox when
tracing is activated and pbcbox_draw returns with an
error. Reported by Axel Kohlmeyer.
2007-02-28 Olaf Lenz <[email protected]>
* all: Made all files into a single package pbctools, version
2.0.
Removed docs from the Tcl files, to reduce redundancy and
maintenance overhead.
RELEASE 2.0
* pbcwrap.tcl, index.html: Added option "-compoundref" to "pbc
wrap".
2007-02-26 Olaf Lenz <[email protected]>
* Created the ChangeLog.