(no subject)

I tried to do it like this:

region nanowire prism 0.0 25.0 -1.267 25.0 -2.6137 3049.700 -8.772 0 0

create_atoms 1 region nanowire

delete_atoms porosity nanowire 0.2 9800

fix 1 all npt temp 300 300 0.1 iso 0.0 0.0 1000.0

dump 1 all atom 1 vmd.dat
restart 1 deg90.*.restart
timestep 0.001
thermo 1
thermo_style custom step temp pe ke press epair etotal
run 10

I created another nanowire with the dimensions for 8x8x80 and then to cut 20% from it.

I got an error:

Another transport will be used instead, although this may result in
lower performance.

I tried to do it like this:

region nanowire prism 0.0 25.0 -1.267 25.0 -2.6137 3049.700 -8.772 0 0

create_atoms 1 region nanowire

delete_atoms porosity nanowire 0.2 9800

fix 1 all npt temp 300 300 0.1 iso 0.0 0.0 1000.0

dump 1 all atom 1 vmd.dat
restart 1 deg90.*.restart
timestep 0.001
thermo 1
thermo_style custom step temp pe ke press epair etotal
run 10

I created another nanowire with the dimensions for 8x8x80 and then to cut 20% from it.

I got an error:

Another transport will be used instead, although this may result in
lower performance.

This is a message from OpenMPI indicating some problem with your cluster. Not a lammps issue.

LAMMPS (26 May 2013)
Reading data file ...
  triclinic box = (0 -1.267 -2.6137) to (35.088 303.9 3049.7) with tilt
(-8.772 0 0)
  1 by 1 by 1 MPI processor grid
ERROR on proc 0: Unexpected end of data file (../read_data.cpp:568)

This message got split up, so I don't think I have the complete
conversation. (Isabela, please include a subject with your (first)
post.)

Anyway it looks like Isabela put a "read_data" command somewhere in
her input script, and the data file she is reading has too few lines
in one of its sections. (This can conflict with the number at the top
of the data file. This is easy to do if you are making your own data
file by hand.)

...That could be the problem, or...

Perhaps LAMMPS does not like it when you combine a "read_data" and
"create_atoms" together in the same lammps input script? I have not
seen people do this before.

-------- suggestions --------

I'm not an expert on using the create_atoms command. If instead, you
want to create your entire system using a DATA file (not using
create_atoms), there are several tools for building DATA files:
http://lammps.sandia.gov/prepost.html

You can delete the atoms you want to delete using those tools, and
then create a DATA file which has only the atoms you want to keep.

I am also not a VMD expert, but when I google "VMD delete atoms", it
brings up links like these:
http://www.ks.uiuc.edu/Research/vmd/plugins/molefacture/
http://www.ks.uiuc.edu/Research/vmd/vmd-1.7/ug/node17.html
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/4672.html
  for psfgen (not vmd):
http://www.ks.uiuc.edu/Research/namd/2.6/ug/node18.html

Anyway, once you have built or loaded your final system into VMD, it
should be possible to save it as a LAMMPS DATA file using topotools,
and that data file should not have these kinds of errors.

Cheers
Andrew

PS.
You can delete atoms (and bonds, etc) using moltemplate too:
http://moltemplate.org/images/translocation/solvent.jpg
http://moltemplate.org/examples/translocation/solvent.lt
http://moltemplate.org/images/translocation/walls.jpg
http://moltemplate.org/examples/translocation/walls.lt
http://lammps.sandia.gov/threads/msg34435.html

This is a message from OpenMPI indicating some problem with your cluster.
Not a lammps issue.

I got an error:

Another transport will be used instead, although this may result in
lower performance.

This is a message from OpenMPI indicating some problem with your cluster.

true but