VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Jan 04 2019 - 12:36:22 CST

On Fri, Jan 4, 2019 at 1:10 PM John Stone <johns_at_ks.uiuc.edu> wrote:
>
> 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 am not an netcdf expert, but my understanding is, that the API is
mostly compatible.
for instance i was able to compile the VMD netcdf plugin against the
netcdf 4 headers.
it didn't change anything on reading, as it just looks like the ABI is
still imported from VMD and not from external shared libraries when i
load the custom compiled plugin (on Linux x86_64) and then try to load
a netcdf-4 format file. but i may be misreading things. its been a
(too) long time, since i was able to do some serious VMD hacking.
managing the LAMMPS github repo is consuming a lot of my time.

> 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.

there is a contributed HDF5 based (non-netCDF) format available in
LAMMPS as well. perhaps there is a connection. if you want to go down
the HDF5 rabbit hole, perhaps, you can get two for the price of one.
;-)
please see:
https://github.com/lammps/lammps/tree/master/src/USER-H5MD
https://github.com/lammps/lammps/tree/master/lib/h5md

LAMMPS has a long list of examples and the information that is stored
in LAMMPS generated trajectory files.
see the (native, text mode trajectory) LAMMPS plugin for some
background. basically, you can have the same kind of information and
then some:
https://lammps.sandia.gov/doc/dump.html
https://lammps.sandia.gov/doc/dump_netcdf.html

we should probably continue this off-list. you give me some idea what
you would like and then i'll set up a cloud folder with some files for
you, best also with the corresponding native LAMMPS trajectories to
compare to. ;-)

axel.

>
> 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/ 

-- 
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.