I made a simulation box of 0 6 0 1 0 2
then I deleted INF 2 0 2 0 5 4 INF 0 2 0 5 this region
:
I read documentation I come with some “fix pour” “fix deposit”
“molecule” command, can u help to use it appropriately.
I recommend you build a LAMMPS “data” file instead. LAMMPS data files contain atom positions, and bond topology. LAMMPS input scripts contain force-field parameters (i.e. “_coeff” commands) and other settings. (LAMMPS data files can contain force-field parameters, but I recommend you leave this information in the input script instead.) There are several molecule building programs which will create these LAMMPS files:
http://montecarlo.sourceforge.net
http://www.moltemplate.org/
https://sites.google.com/site/akohlmey/software/topotools
https://sourceforge.net/projects/moleculardynami/
http://avogadro.cc/wiki/Main_Page
If you decide to use “moltemplate” (one of these programs), then you can create a 3-D array of O2 molecules and move them to the region of interest.
-------- example file “system.lt” --------------
You must create a file (gg “O2mol.lt”) which defines the O2 molecule
type. To see how this is done (for water), see this example. For more
complicated molecules, you can use one of the built in force-fields
(eg: OPLSAA or AMBER)
import “O2mol.lt”
Then create a rectangular array of 5x20x10 oxygen molecules
of size 15x60x30 nm^3
O2mols = new O2
[5].move(0, 0, 3.0)
[20].move(0, 3.0, 0)
[10].move(3.0, 0, 0)
Then move this array 20.0 nm in the +x direction:
O2mols[][][*].move(20, 0, 0)