[lammps-users] Only one frame of lammpstrj file is read by VMD

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1

I saved my simulation dump file as a “.lammpstrj”, and it have worked well so far.

But for one of my dump file, only one frame is read in VMD. (The others work)

The difference of the dump file (the problem thing) from others has some changes in input file.

In my guess, it is because the input file which has the problem has two “run” command.

Could you check the two input file, and let me know how to fix it? (Is the first run command really necessary for equilibrium? If it is necessary, what should I do?)

Thanks

The problem

# LAMMPS input - silicon nitride with reaxff

#----------------------------- Initial setup -------------------------------

boundary p p f

units real

atom_style charge

read_data practice1

molecule SiN SiH2NH221.data

group ADD type 2

velocity ADD create 500 12345

run 0

timestep 0.1

pair_style reax/c lmp_control

pair_coeff * * ffield.reax.SiN N Si

#----------------------------- Grouping --------------------------------

region bulk prism 0 30.336407 0 26.272099 1.14 8.46 -15.168203 0 0

group bulk region bulk

region surface prism 0 30.336407 0 26.272099 8.46 9.35 -15.168203 0 0

group surface region surface

region addarea prism 10 20 10 20 15 20 -15.168203 0 0

group addarea region addarea

neigh_modify delay 0

#--------------------------------- Minimization -----------------------------

fix mynve all nve

fix Temp all temp/berendsen 500.0 500.0 100.0

fix qeq all qeq/reax 1 0.0 10.0 1e-6 param.qeq

minimize 1.0e-4 1.0e-6 500 1000

unfix Temp

thermo 100

run 4000

reset_timestep 0

# For making the system in temperature equilibrium

#------------------------------- Simulation start --------------------------

fix Temp1 bulk temp/berendsen 500.0 500.0 100.0

fix please ADD deposit 1 0 1000 12345 region addarea near 1.0 &

mol SiN vz -0.05 -0.05

compute mytemp ADD temp

dump dp1 all atom 50 ADD.lammpstrj

thermo 100

run 10000

The well-working input file

# LAMMPS input - silicon nitride with reaxff

# --------------------- Initialize Simluation -------------------------

boundary p p f

units real

atom_style charge

read_data CONTCAR1

timestep 0.1

pair_style reax/c lmp_control

pair_coeff * * ffield.reax.SiN C H N Si

# --------------------- Initialize minimization to relax surface -------------------------

minimize 1.0e-4 1.0e-6 500 1000

reset_timestep 0

# --------------------- Define groups -------------------------

region bulk prism 0 30.33640671 0 26.27209887 0 8 -15.16820335 0 0

group bulk region bulk

fix mynve all nve

fix Temp bulk temp/berendsen 500.0 500.0 100.0

fix qeq all qeq/reax 1 0.0 10.0 1e-6 param.qeq

dump dp1 all atom 50 CONTCAR.lammpstrj

neb 0.0 0.001 2000 2000 50 final

thermo 100

run 10000

2

two things:

  1. this is really a question about VMD, not about LAMMPS, so you should be asking it on the VMD mailing list, not here.
  2. you guess is wrong. your “failing” LAMMPS trajectory does not conform to the “normal” requirements of VMD: every frame has to have the same number of atoms. there are some workarounds for it, but as mentioned under 1) this is not the place to discuss it. you may want to consider using some other visualization tool if you plan to frequently visualize trajectories with a variable number of atoms or use dump image or dump movie in LAMMPS.

axel.

3

Thanks Axel.

It works on Ovito visualization tool, but not on VMD. I will use Ovito, but it doesn’t support “ball and stick” style.

Anyway, thank you for letting me know that input file cause the problem.