[lammps-users] Trajectory files from simulations involving multiple processors

Steve, LAMMPS users,
After running LAMMPS simulations on a single processor, I have been able to load a dump file from LAMMPS into VMD (as LAMMPS trajectory file) and view the animations without problems. However, after I run the LAMMPS simulation on multiple processors, there are errors with reading the dump file into VMD.

As an alternative, I was advised to try the dcd format for outputting the coordinates from LAMMPS; however, I believe a structure file (psf?) is required to be input in VMD prior to loading the dcd file. I was unsure of how to create this structure (psf) file within the framework of LAMMPS.

If possible, please advise on the appropriate way to proceed.

Thanks,
Sreekant

2009/7/3 Sreekant Narumanchi <[email protected]…24…>

Steve, LAMMPS users,
After running LAMMPS simulations on a single processor, I have been able to load a dump file from LAMMPS into VMD (as LAMMPS trajectory file) and view the animations without problems. However, after I run the LAMMPS simulation on multiple processors, there are errors with reading the dump file into VMD.

As an alternative, I was advised to try the dcd format for outputting the coordinates from LAMMPS; however, I believe a structure file (psf?) is required to be input in VMD prior to loading the dcd file. I was unsure of how to create this structure (psf) file within the framework of LAMMPS.

If possible, please advise on the appropriate way to proceed.

If you have an existing input file and dump file, you can use the lammps2pdb.pl tool in the tools subdirectory of the LAMMPS installation to create a PDB/PSF file combo suitable for viewing in VMD.

Alternatively, if you get the beta version of VMD now available, LAMMPS dump files are directly readable, even if they are from multiprocessor runs.

–AEI

Steve, LAMMPS users,
After running LAMMPS simulations on a single processor, I have been
able to load a dump file from LAMMPS into VMD (as LAMMPS trajectory
file) and view the animations without problems. However, after I run
the LAMMPS simulation on multiple processors, there are errors with
reading the dump file into VMD.

sreekant,

please tell us what the errors _are_?

there is no principle problem in VMD with reading
trajectory files from parallel runs. the difference
has to be elsewhere.
please note that the LAMMPS dump file format had some
changes recently, and those break the LAMMPS trajectory
reader in VMD 1.8.6. this has been corrected and the
LAMMPS reader in VMD greatly enhanced. the latest beta
version for VMD 1.8.7 has all those changes included.

As an alternative, I was advised to try the dcd format for outputting
the coordinates from LAMMPS; however, I believe a structure file
(psf?) is required to be input in VMD prior to loading the dcd file. I
was unsure of how to create this structure (psf) file within the
framework of LAMMPS.

.dcd files only contain coordinates, so they have no
information about atom types, bond and so on. in CHARMM
(and NAMD) the .psf file more-or-less is the equivalent
of the data file in LAMMPS and thus contains the missing
information (data files in LAMMPS can contain more data).

again, in this case you would benefit a lot from trying
out the latest VMD-1.8.7 beta. this contains a package
called topotools, that can read quite a few variants of
LAMMPS data files and thus can be used to create a .psf
file or to load a .dcd file on topo of it.

this has to be done from the VMD command terminal window:

package require topotools
topo readlammpsdata data.file atom_style

(please replace data.file with your data file name
and atom_style with the atom style used).

mol addfile file.dcd waitfor all

(to load a .dcd on top of it)

or to save a .psf you can do (with or without the .dcd):

animate write psf file.psf

if you have some files that don't work with the
last VMD beta, i would be _very_ interested in
getting a copy of those, so the code in VMD can
be fixed before the release.

cheers,
   axel.

Axel, Ahmed,
I will try out the VMD 1.8.7 beta version. I have been using the VMD 1.8.6 version upto this point.

Thanks,
Sreekant

Axel,
I wanted to mention that in the dump file that is generated with LAMMPS simulation run on multiple processors, the atom numbers do not appear to be sequential (they are sequential for a LAMMPS simulation on a single processor). I was not sure if this is a concern.

Thanks,
Sreekant

Axel,
I wanted to mention that in the dump file that is generated with
LAMMPS simulation run on multiple processors, the atom numbers do not
appear to be sequential (they are sequential for a LAMMPS simulation
on a single processor). I was not sure if this is a concern.

sreekant,

that is the way lammps dump files always have been.
it is explained in detail in the documentation of
the dump command. this is done for memory and communication
efficiency and a side effect of the domain decomposition.

what would be _much_ more useful, if you would actually
go ahead and answer _my_ question, i.e. what is the error
message that you get in VMD exactly?

cheers,
   axel.

Axel,
Sorry for the delayed response on this.
I have attached (Word file) the specific error message I get when I load a LAMMPS dump file into VMD 1.8.6.

However, I do not get this error message when I load the LAMMPS dump file into VMD 1.8.7 beta version, and I am able to visualize the atoms in the simulation domain.

Thanks,
Sreekant

errormessagewithVMD1.8.6.doc (49 KB)

Axel,

sreekant,

Sorry for the delayed response on this.
I have attached (Word file) the specific error message I get when I

please don't send word files when for example a simple .jpg image
serves the same purpose. not everybody uses word, but every web
browser can handle .jpg.

load a LAMMPS dump file into VMD 1.8.6.

However, I do not get this error message when I load the LAMMPS dump
file into VMD 1.8.7 beta version, and I am able to visualize the atoms
in the simulation domain.

ok. that error means, that you have using a version of LAMMPS that
generates the improved dump format and for that you need the improved
parser in VMD 1.8.7.

apropos, the final release of VMD 1.8.7 will appear in the next days
and contains a few additional bugfixes in its support for LAMMPS.

axel.