VMD-L Mailing List

From: Ben Hanson (ben19q_at_hotmail.com)
Date: Tue Feb 10 2015 - 08:22:02 CST

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.
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.