# Diffusion Examples

Hello,
I'm a LAMMPS neophyte trying to figure my way around.
I've played with a number of example inputs and tutorials but haven't found any that get at what I'd like to do (which seems odd). I'm looking for any examples out there of simple diffusion; basically atoms A diffusing into atoms B.
I know this is probably a trivial thing for LAMMPS using a MSD calculation. I have looked through the LAMMPS documentation but haven't come by what I'm looking for; yet.
I come from the GAMESS and NWChem world so I'm trying get my bearings with input structure, nomenclature etc.
Thanks for any help or pointers you can provide!
Tom

Hello,
I'm a LAMMPS neophyte trying to figure my way around.
I've played with a number of example inputs and tutorials but haven't found any that get at what I'd like to do (which seems odd). I'm looking for any examples out there of simple diffusion; basically atoms A diffusing into atoms B.
I know this is probably a trivial thing for LAMMPS using a MSD calculation. I have looked through the LAMMPS documentation but haven't come by what I'm looking for; yet.

that is to be expected. the documentation mostly describes the tools,
not how to build scientific studies. that is the equivalent going to a
DIY store and getting explanations for use a hammer and a saw and a
drill and glue, but to build a birdhouse, you better talk with
somebody that has done it or look up descriptions and pictures (i.e.
publications or text books)

I come from the GAMESS and NWChem world so I'm trying get my bearings with input structure, nomenclature etc.
Thanks for any help or pointers you can provide!

your description is *far* too vague to provide any meaningful help.
you can observe atoms of type 1 diffusing into type 2 very easily by
just modifying, e.g. the "melt" example like this:

# 3d Lennard-Jones melt

units lj
atom_style atomic

lattice fcc 0.8442
region box block 0 10 0 10 0 10

# define a second region covering half the box
region half block 0 10 0 10 5.1 10.1

# need to reserve space for two atom types.
create_box 2 box

# fill box with atoms of type 1...
create_atoms 1 box

# ... and change those in the half region to type 2. and set their masses.
set region half type 2
mass 1 1.0
mass 2 1.0

# initialized velocities, so the system melts.
velocity all create 3.0 87287

pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0 2.5

neighbor 0.3 bin
neigh_modify every 5 delay 0 check yes

fix 1 all nve

#dump id all atom 50 dump.melt

#dump 2 all image 25 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30