[lammps-users] simulating granular particles

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1

Hi Steve and Lammps users,

I'm using lammps-21Dec09 to run simulations for my project.
I want to simulate a horizontal box filled with granular particles which
is skinny in z-dimension. Also I need to add an oscillatory force(in
x-dimension) on each particle and my boundary conditions are peridic in x
and y dimensions. I considered the frictional inter action between
particles and lower z-plane. I used these commands.

# my first program

units metal
dimension 3
boundary p p f
atom_style granular

region cell block -1000 1000 -100 100 -0.7 0.7 units box
create_box 1 cell
fix ins all pour 100 1 300719 region cell diam 1.0 1.0
fix 1 all gravity 1.0 spherical 0.0 -180.0

pair_style gran/hooke 400.0 NULL 100.0 NULL 0.5 0
pair_coeff * *
neighbor 0.2 bin
neigh_modify every 2 delay 10 check yes
communicate single vel yes

timestep 0.001
fix 2 all nve/sphere
fix 3 all gran/wall 400.0 NULL 100.0 NULL 0.5 0 zplane -0.7 NULL wiggle x
1.0 0.5

compute 1 all erotate/sphere
thermo_style custom step atoms ke
thermo 100
thermo_modify lost ignore norm no
compute_modify thermo_temp dynamic yes

dump id all atom 100 dump.pour
run 5000

My questions are as follows:

1) When I run these command, I get these error:
"ERROR: Invalid fix style"

2) Are these commands correct for my problem and nothing would be correct?

3) communicate single

4) when I run examples/pour/in.pour.2d or in.pour, it doesn't show
anything and I get this error:

"rlwrap: Command not found.
Info) VMD for LINUX, version 1.8.7 (August 1, 2009)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to [email protected]...
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 2 CPUs detected.
Info) Free system memory: 2746MB (90%)
Info) No CUDA accelerator devices available.
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this optional X server feature.
Info) OpenGL renderer: Software Rasterizer
Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (4096x4096), 3-D (256x256x256), Multitexture (8)
Info) File loading in progress, please wait.
ERROR) Unable to determine file type for file 'dump.pour'. Assuming pdb.
PDB file 'dump.pour' contains no atoms.
ERROR) Could not read file dump.pour
"

Your helps would be very useful for me:)
Robabeh

2

For the invalid fix style error, run with -echo screen and you
will see what command is offending. Compare your syntax
to the doc page.

I don't know what the rlwrap error is. Can you run all
the other example problems?

Steve

3

Dear Steve,

When I want to visualize dump files with vmd package, I got this error anh
I have this problem with all the other example problems. What the lines
mean which prfixed with ERROR? And how can I remove them?

rlwrap: Command not found.
Info) VMD for LINUX, version 1.8.7 (August 1, 2009)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to [email protected]...
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 2 CPUs detected.
Info) Free system memory: 2531MB (83%)
Info) No CUDA accelerator devices available.
Warning) Detected X11 'Composite' extension: if incorrect display occurs
Warning) try disabling this optional X server feature.
Info) OpenGL renderer: Software Rasterizer
Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
Info) Full GLSL rendering mode is available.
Info) Textures: 2-D (4096x4096), 3-D (256x256x256), Multitexture (8)
Info) File loading in progress, please wait.
ERROR) Unable to determine file type for file 'dump.vibration'. Assuming
pdb.
PDB file 'dump.vibration' contains no atoms.
ERROR) Could not read file dump.vibration
ERROR) Loading of startup molecule files aborted.
vmd > Info) VMD for LINUX, version 1.8.7 (August 1, 2009)

4

Dear Steve,

please use the right forum for your questions.
this is a VMD question and should be posted on
the VMD list as you already did.

When I want to visualize dump files with vmd package, I got this error anh
I have this problem with all the other example problems. What the lines
mean which prfixed with ERROR? And how can I remove them?

by using your brain and some common sense.
i already told you on the VMD mailing list to read
the VMD documentation and i'm doing it again.

do *read* those lines. they tell you what problem
with what you are doing. VMD has no built in
6th sense that can tell it where those files came
from and how to read them. how should it? it
is a computer program and only does what
you tell it to do. so instead of filling up people's
mailboxes, please do yourself the favor and
learn how VMD works. the solution is rather
simple, but it will be much more educational
if you find it yourself.

cheers,
    axel.