VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jan 04 2019 - 12:10:52 CST

Hey,
  To date, VMD has been compiled with the classic NetCDF 3.x versions
that have no additional library dependencies. I'm guessing based on
what you've said below that LAMMPS is using NetCDF 4.x, which as I
understand it depends on HDF5 now, and it can supposedly use
HDF5 as a container file format that is totally incompatible with
the classic NetCDF format. I haven't recently re-read the details about
thet NetCDF 4.x features since AMBER has always used the classic
NetCDF 3.x format AFAIK. If you can provide me with some sample file(s)
I should be able to chase this down on my side. Now that I've been asked
to start supporting HDF5 files for a new VMD plugin, it may become practical
to update VMD's NetCDF builds to encompass the newer NetCDF4+HDF5 build
strategy required by the current NetCDF lib.

Best,
  John

On Fri, Jan 04, 2019 at 12:43:06PM -0500, Axel Kohlmeyer wrote:
> John,
>
> the LAMMPS netcdf files are supposed to be compatible with amber. it
> uses Conventions = AMBER. i can easily produce example files. source
> code is available here:
> https://github.com/lammps/lammps/blob/master/src/USER-NETCDF/dump_netcdf.cpp#L222
>
> from what i can tell, it doesn't even get to the point of checking
> which conventions it follows, but fails in the nc_open() function.
>
> which version of netcdf do you compile the plugin/VMD with?
>
> axel.
>
> On Fri, Jan 4, 2019 at 12:34 PM John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> > Hi,
> > The NetCDF reader in VMD currently understands NetCDF files written
> > by AMBER, MMTK, and some others, but as of yet there is no reader for
> > LAMMPS data there. If someone has documentation about LAMMPS NetCDF
> > files and some example files, I would be interested in implementing
> > the required changes to add the necessary support.
> >
> > Best,
> > John
> >
> > On Wed, Jan 02, 2019 at 12:52:35AM -0500, Axel Kohlmeyer wrote:
> > > On Tue, Jan 1, 2019 at 1:40 AM LIGESH B <ligeshkannur178_at_gmail.com> wrote:
> > > >
> > > > Dear Users,
> > > > I have done a simulation of polymers in LAMMPS. The output file format is netcdf type (file.nc) but when I try to load it VMD using Ubuntu OS. It is showing a error as could not read the file.
> > >
> > > > Why it is showing this error?
> > >
> > > impossible to say from remote. possibly, because it cannot read the
> > > file, or the format is not compatible.
> > >
> > > > What may be the possible solution?
> > >
> > > use a different file format?
> > >
> > > axel.
> > > >
> > > > Thanks in advance
> > > >
> > > > -Ligesh
> > > >
> > >
> > >
> > > --
> > > 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.
> >
> > --
> > NIH Center for Macromolecular Modeling and Bioinformatics
> > Beckman Institute for Advanced Science and Technology
> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> > http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> > http://www.ks.uiuc.edu/Research/vmd/
>
>
>
> --
> 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. 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/