VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Feb 10 2015 - 09:15:46 CST

On Feb 10, 2015 9:22 AM, "Ben Hanson" <ben19q_at_hotmail.com> wrote:
>
> Thanks! That worked great! I have one last quick question. I was
wondering if there is some reason when I import a lammps data file with
topotools it generates a 0 volume.

How do you determine this?

>
> Thanks again
> Ben
>
> > Date: Mon, 9 Feb 2015 14:25:36 -0500
> > Subject: Re: vmd-l: topo guessatom
> > From: akohlmey_at_gmail.com
> > To: ben19q_at_hotmail.com
> > CC: vmd-l_at_ks.uiuc.edu
> >
> > On Mon, Feb 9, 2015 at 2:07 PM, Axel Kohlmeyer <akohlmey_at_gmail.com>
wrote:
> > > On Mon, Feb 9, 2015 at 1:43 PM, Ben Hanson <ben19q_at_hotmail.com> wrote:
> > >> The vmd version is 1.9.2 and I am unsure how to check the topotools
version.
> > >
> > > package require topotools
> > >
> > > it will return the version number of the topotools plugin. however, if
> > > you have VMD 1.9.2, you also have the latest plugin.
> > >
> > >> I have attached the simple data file.
> > >
> > > thanks. there has to be something about it that is different from
> > > others and thus makes it trigger the bug you are reporting.
> > >
> > > hopefully i can get back to you soon with a bugfix.
> >
> > ok. here we are. you have to edit the file topoatoms.tcl in
> > /usr/local/lib/vmd/plugins/noarch/tcl/topotools1.5/ (or in the
> > corresponding directory, if you didn't install VMD into the default
> > location).
> >
> > in line 43, you have to replace the [ptefrommass $idx] call with
> > [ptefrommass $a] so that it reads:
> >
> > $s set element [lindex $elements [ptefrommass $a]]
> >
> > that should take care of this bug. as far as i can tell, this was
> > changed only recently during some cleaning up of the code. i will also
> > upload a corrected version to the topotools section of my homepage.
> >
> > axel.
> >
> > >
> > > more later,
> > > axel.
> > >
> > >>
> > >> Thanks
> > >> Ben
> > >>
> > >>
> > >>> Date: Mon, 9 Feb 2015 13:37:07 -0500
> > >>> Subject: Re: vmd-l: topo guessatom
> > >>> From: akohlmey_at_gmail.com
> > >>> To: ben19q_at_hotmail.com
> > >>> CC: vmd-l_at_ks.uiuc.edu
> > >>
> > >>>
> > >>> On Mon, Feb 9, 2015 at 1:03 PM, Ben Hanson <ben19q_at_hotmail.com>
wrote:
> > >>> > I have imported a lammps data file using topotools, but when I
attempt
> > >>> > to
> > >>> > change types to elements using the command
> > >>> >
> > >>> > topo guessatom lammps data
> > >>> >
> > >>> > I get the error "can't read "idx": no such variable", with
previous
> > >>> > versions
> > >>> > I have not had this issue. Any help would be greatly appreciated
> > >>>
> > >>> which version of topotools? which version of VMD? are both the
latest?
> > >>>
> > >>> if both are the latest, can you provide a (simple) test file to
> > >>> reproduce the issue?
> > >>>
> > >>> axel.
> > >>>
> > >>> >
> > >>> > Ben Hanson
> > >>>
> > >>>
> > >>>
> > >>> --
> > >>> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> > >>> College of Science & Technology, Temple University, Philadelphia
PA, USA
> > >>> International Centre for Theoretical Physics, Trieste. Italy.
> > >
> > >
> > >
> > > --
> > > Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> > > College of Science & Technology, Temple University, Philadelphia PA,
USA
> > > International Centre for Theoretical Physics, Trieste. Italy.
> >
> >
> >
> > --
> > Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> > College of Science & Technology, Temple University, Philadelphia PA, USA
> > International Centre for Theoretical Physics, Trieste. Italy.