Input file format for the latest VMD version 1.9

Hi,

Please find attached my LAMMPS input script file. My dump command is as follows.

dump myDump2 all custom 20 dump.movie id type x y z vx vy vz

1: dump.movie file’s contents are in the format mentioned above. My objective is to run this file with the particle velocities in the VMD latest version 1.9 which is supposed to have the capability of taking in atom velocities too. The VMD input file format does not seem to be recognized by the latest VMD version. Could anybody please provide me with a sample VMD input script with velocities.

2: The dump.movie file is spit out by LAMMPS which reads the input script NEWTADSI.txt attached. I read a restart binary file through the input script. I observed that the atom coordinates are not in serial order of index. This file is originally around 430MB. Attached dump.movie has 2 timesteps only.

1 1 0 0 0 0 0 0

5 1 1.35947 1.35947 1.35947 0 0 0

9 1 5.4379 0 0 0 0 0

13 1 6.79737 1.35947 1.35947 0 0 0

193 1 10.8577 0.0673323 0.0909179 -1.20692 -1.08158 -3.13772

4 1 2.71895 2.71895 0 0 0 0

12 1 8.15685 2.71895 0 0 0 0

17 1 0 5.4379 0 0 0 0

8 1 4.07843 4.07843 1.35947 0 0 0

What is causing this problem? Could anybody please help me with these issues.

Regards,

Saketh.

University of Toledo.

NEWTADSI.txt (1.95 KB)

dump.movie (34.6 KB)

Hi,

Please find attached my LAMMPS input script file. My dump command is as
follows.

dump myDump2 all custom 20 dump.movie id type x y z vx vy vz

1: dump.movie file’s contents are in the format mentioned above. My
objective is to run this file with the particle velocities in the VMD latest
version 1.9 which is supposed to have the capability of taking in atom
velocities too. The VMD input file format does not seem to be recognized by
the latest VMD version. Could anybody please provide me with a sample VMD
input script with velocities.

all you have to do is to pay attention to error messages!

this is the output that VMD produces when reading your dump.

Info) Using plugin lammpstrj for structure file dump.movie
Info) lammpsplugin) New style dump with 8 data fields. 0x21
Info) lammpsplugin) Using absolute atomic coordinates directly.
Info) lammpsplugin) Importing atomic velocities.
Info) Using plugin lammpstrj for coordinates from file dump.movie
Info) lammpsplugin) Importing velocities from custom LAMMPS dump file.
Info) Determining bond structure from distance search ...
Info) lammpsplugin) Importing velocities from custom LAMMPS dump file.
ERROR) lammpsplugin) Inconsistent number of atoms in timestep.
Info) Finished with coordinate file dump.movie.

so it _does_ read your dump, but you are adding atoms,
and _that_ is not supported by VMD.

2: The dump.movie file is spit out by LAMMPS which reads the input script
NEWTADSI.txt attached. I read a restart binary file through the input
script. I observed that the atom coordinates are not in serial order of
index. This file is originally around 430MB. Attached dump.movie has 2
timesteps only.

please pay more attention to the lammps documentation.
atom order is not preserved unless sorting of atoms is
explicitly requested, since this comes at an extra performance
penalty and larger memory consumption.

axel.

Hi,

Please find attached my LAMMPS input script file. My dump command is as follows.

dump myDump2 all custom 20 dump.movie id type x y z vx vy vz

1: dump.movie file’s contents are in the format mentioned above. My objective is to run this file with the particle velocities in the VMD latest version 1.9 which is supposed to have the capability of taking in atom velocities too. The VMD input file format does not seem to be recognized by the latest VMD version. Could anybody please provide me with a sample VMD input script with velocities.

2: The dump.movie file is spit out by LAMMPS which reads the input script NEWTADSI.txt attached. I read a restart binary file through the input script. I observed that the atom coordinates are not in serial order of index. This file is originally around 430MB. Attached dump.movie has 2 timesteps only.

1 1 0 0 0 0 0 0

5 1 1.35947 1.35947 1.35947 0 0 0

9 1 5.4379 0 0 0 0 0

13 1 6.79737 1.35947 1.35947 0 0 0

193 1 10.8577 0.0673323 0.0909179 -1.20692 -1.08158 -3.13772

4 1 2.71895 2.71895 0 0 0 0

12 1 8.15685 2.71895 0 0 0 0

17 1 0 5.4379 0 0 0 0

8 1 4.07843 4.07843 1.35947 0 0 0

What is causing this problem? Could anybody please help me with these issues.

Regards,

Saketh.

University of Toledo.