VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jan 04 2019 - 12:47:28 CST

Axel,
  Thanks, I will dig into this when I'm back from travel next week.
I'll let you know if I need more example files/trajectories, etc.

Best,
  John

On Fri, Jan 04, 2019 at 01:36:22PM -0500, Axel Kohlmeyer wrote:
> 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. 

-- 
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/