Dear All
It is my first week since I started using LAMMPS and my question can be so silly.
I created nanowire by cutting from a box and I want to see the cylinder created but
got stucked.
Regards,
Zeru
Dear All
It is my first week since I started using LAMMPS and my question can be so
silly.
I created nanowire by cutting from a box and I want to see the cylinder
created but
got stucked.
try adding:
write_dump all image snap*.jpg type type
to your input (you may have to switch to .ppm, if you don't have jpeg
support included).
axel.
p.s.: this needs a *very* new LAMMPS executable to work.
for older versions, you need to create dump (image or trajectory file)
and do a run 0 and then undump.
p.p.s: also check out: http://lammps.sandia.gov/viz.html
I am not familiar with the write_dump command. However using VMD
allows you to rotate and move the system using the mouse (which is
nice). You can also extensively customize the way it is displayed.
http://www.ks.uiuc.edu/Research/vmd/
Axel Kohlmeyer created a plugin for VMD which can read and write
LAMMPS data files (and dump files) named topotools.
To use this, you must have a DATA file. If you don't have one, you
can use the "write_data" command. In your input script, insert the
following line after you have created your nanowire:
write_data nanowire.data
Then run LAMMPS on this input script. This will create a file named
"nanowire.data".
Then you can load this file into VMD:
1) Start VMD
2) From the menu, select: Extensions->Tk Console
3) Type:
topo readlammpsdata nanowire.data full
# (If you are not using "atom_style full", then change the line above)
# It is a good idea to create a PSF file you can use later for
viewing DUMP files:
animate write psf nanowire.psf
Cheers
Andrew
P.S.
I attached some quickly-written instructions for viewing LAMMPS data
files and dump files using VMD. "README_visualize.txt" There are
also many tricks for making the atoms and molecules look pretty, but I
did not explain that in that document. Once you can see your
molecule, (after typing the commands above into the Tk Console), try
the the Graphics->Representations menu option and change the drawing
method to "VDW". "CPK", or "Licorice" (for example).
More information:
http://lammps.sandia.gov/doc/write_data.html
http://sites.google.com/site/akohlmey/software/topotools
http://www.ks.uiuc.edu/Research/vmd/
README_visualize.txt (2.85 KB)
I am not familiar with the write_dump command. However using VMD
it is a new feature. it can write on a single frame dump similar to
write_restart, but as a dump file. and with the "image" style dump,
you can do a very quick visualization of the current system without
the need to use any external tool. this and the - equally new - dump
movie option are wrappers to make things like what is show here even
easier (particularly on windows machines, where a lot of the linux
script magic doesn't work).
https://sites.google.com/site/akohlmey/news-and-announcements/thehiddengemoflammps
allows you to rotate and move the system using the mouse (which is
nice). You can also extensively customize the way it is displayed.
yeah, VMD is one of the tools to look at for ambitious visualizations,
but seeing all the steps that you need to do, there is something to be
said for the quick route, if all you want to know is whether your
input works ok and generates the right kind of structure.
axel.
Dear Axel
I tried 'write_dump wire image ’ but its giving error.
regard,
Zeru
Dear Axel
I tried 'write_dump wire image ' but its giving error.
and? it works for me.
Dear Axel
I dont know why its not working for me its gives ‘unknown command’. The place i insert it is highlighted below.
#!!!
units real
variable T equal 200
variable V equal vol
variable dt equal 4.0
variable p equal 200 # correlation length
variable s equal 5 # sample interval
variable d equal $p*$s # dump interval
#!!!1
convert from LAMMPS real units to SI
variable kB equal 1.3806504e-23 # [J/K] Boltzmann
variable kCal2J equal 4186.0/6.02214e23
variable A2m equal 1.0e-10
variable fs2s equal 1.0e-15
variable convert equal {kCal2J}*{kCal2J}/{fs2s}/{A2m}
#!!!1
setup problem
dimension 3
boundary p p p
atom_style atomic
lattice diamond 5.43
region whole block 0 200 0 200 0 200 units box
create_box 1 whole
region wire cylinder z 100 100 75 INF INF units box
lattice hcp 5.43 orient x 1 0 0 orient y 0 1 0 orient z 0 0 1
create_atoms 1 region wire
mass 1 28.8
pair_style tersoff
pair_coeff * * …/potentials/Si.tersoff Si
timestep ${dt}
thermo $d
write_dump all image snap*.jpg
#!!!1
equilibration and thermalization
velocity all create $T 102486 mom yes rot yes dist gaussian
fix NVT all nvt temp $T $T 10 drag 0.2
run 4000
thermal conductivity calculation, switch to NVE if desired
#unfix NVT
#fix NVE all nve
reset_timestep 0
compute myKE all ke/atom
compute myPE all pe/atom
compute myStress all stress/atom virial
#!!!1
compute flux all heat/flux myKE myPE myStress
variable Jx equal c_flux[1]/vol
variable Jy equal c_flux[2]/vol
variable Jz equal c_flux[3]/vol
fix FLX all ave/correlate $s $p $d &
c_flux[1] c_flux[2] c_flux[3] type auto file argon.dat ave running
variable scale equal {convert}/{kB}/$T/$T/$V*s*{dt}
variable k11 equal trap(f_FLX[3]){scale}
variable k22 equal trap(f_FLX[4])*{scale}
variable k33 equal trap(f_FLX[5])${scale}
thermo_style custom step temp v_k11 v_k22 v_k33
run 10000 #00
variable JJ equal v_Jxv_Jx+v_Jyv_Jy+v_Jz*v_Jz
#!!!1
variable k equal (v_k11+v_k22+v_k33)/3.0
variable ndens equal count(all)/vol
#print $JJ
print “average conductivity: $k[W/mK] @ T K, {ndens} /A^3”
regards,
Zeru
...and i already told you:
p.s.: this needs a *very* new LAMMPS executable to work.
for older versions, you need to create dump (image or trajectory file)
and do a run 0 and then undump.
so your LAMMPS executable may not be new enough. i also pointed out a
link to other alternatives for visualization as well as andrew gave
you a very detailed reply with multiple options and a tutorial.
how much *more* information do you need? all you have to do is to read
and act on it.
axel.