Dear all,
I read about visualizing of LAMMPS outputs and about corresponding tools including pizza.py but I could not really figure out how can I look at the geometry before running any simulation, i.e. if my in.geometry file contains only:
dimension 2
boundary s s p
lattice hex 0.93
region box block 0 100 0 40 -0.25 0.25
create_box 5 box
create_atoms 1 box
mass 1 1.0
mass 2 1.0
mass 3 1.0
mass 4 1.0
mass 5 1.0
and my log.lammps includes only this information. I thought the option could be lmp2cfg but it requires dump file in its input.
I am probably the wrong person to answer this question, but I'll try
to post a quick message before I have to catch my ride home.
(I'm sure there are alternative ways to do this.)
I would recommend that you generate a LAMMPS data file ("data" format).
(If you run your simulation for a short time, you can generate a
restart file. Then use the "restart2data" program, [distributed with
the LAMMPS source code], to create a data file.)
Once you have a "data" file, we find topotools to be extremely useful
for visualising LAMMPS output.
http://www.ks.uiuc.edu/Research/vmd/plugins/topotools/
Use "topotools" (and VMD) to generate a PSF file. The PSF file is
especially useful when you want to visualize trajectories in VMD and
other molecular visualisation programs. (Viewing trajectories is
something you are going to want to do anyway.)
Here's a brief example:
just generate a dump of the initial coordinates by defining a suitable
dump and then do a “run 0”
axel
And use the dump image command and “presto”
you will have an image of your initial config.
Steve
Thank you, I did as you suggested and it works for xyz or ppm output perfectly but I have problems with dump image. I linked JPEG library as discussed in the manual and rebuilt LAMMPS, however, I get error: cannot dump JPEG file. The error itself does not give much information, I’m run out of options what the reason could be, I guess this is not a linking error. Here is my in.test:
dimension 2
boundary s s p
atom_modify sort 0 0.0.
atom_style atomic
neighbor 0.3 nsq
neigh_modify delay 5
lattice hex 0.93
region box block 0 100 0 40 -0.25 0.25
create_box 5 box
create_atoms 1 box
mass 1 1.0
mass 2 1.0
mass 3 1.0
mass 4 1.0
mass 5 1.0
dump myDump all image 1 dump.myexp.*.jpeg type type
run 0
Did you define -DLAMMPS_JPEG in your Makefile.foo for LMP_INC?
If not, please read the build doc pages again.
Steve
Yes, I did, and indicated all the paths. Is there any other way to check if it’s correctly linked to LAMMPS?
P.S. I just managed to solve the problem, there was an error in the name of the library name, now I got it.