# thermostat and atom trajectory

Hi Dears
I have two question:
1: what do we mean when we say that "apply thermostat on the group" ,
in other words, how can I interpert meaning of "thermostating"?

2: how can I include "trajectory of a single atom" for my simulation?
Is there any command for a "single atom" trajectory?

any discussion will be appreciated.
Elena

Hi Dears
I have two question:
1: what do we mean when we say that "apply thermostat on the group" ,
in other words, how can I interpert meaning of "thermostating"?

You best read up on this topic in your favorite MD text book. In short
it means to manipulate the system to represent a desired target
temperature.

2: how can I include "trajectory of a single atom" for my simulation?
Is there any command for a "single atom" trajectory?

The dump command is per group, so you can define a group containing
only one atom.

Axel

Thanks alot Dear Axel…
for dumping trajectory of a special atom via dump command, for example in the “flow” example of lammps, how Can I extract one single atom from many atoms in it???
because it arranges number of atoms in “lower” ,“upper” ," flow" ,“boundary” groups according to lattice spacing.
How can I seperate a special atom near the solid boundary and show its trajectory during run???
Cheers
Elena

# 2-d LJ flow simulation

dimension 2
boundary p s p
atom_style atomic
neighbor 0.3 bin
neigh_modify delay 5

# create geometry

lattice hex 0.7
region box block 0 20 0 10 -0.25 0.25
create_box 3 box
create_atoms 1 box
mass 1 1.0
mass 2 1.0
mass 3 1.0

# LJ potentials

pair_style lj/cut 1.12246
pair_coeff * * 1.0 1.0 1.12246

# define groups

region 1 block INF INF INF 1.25 INF INF
group lower region 1
region 2 block INF INF 8.75 INF INF INF
group upper region 2
group boundary union lower upper
group flow subtract all boundary
set group lower type 2
set group upper type 3

# initial velocities

compute mobile flow temp
velocity flow create 1.0 482748 temp mobile
fix 1 all nve
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
fix_modify 2 temp mobile

# Couette flow

velocity lower set 0.0 0.0 0.0
velocity upper set 3.0 0.0 0.0
fix 3 boundary setforce 0.0 0.0 0.0
fix 4 all enforce2d

# Run

timestep 0.003
thermo 500
thermo_modify temp mobile
dump 1 all xyz 50 flow.xyz
run 10000

Thanks alot Dear Axel...
for dumping trajectory of a special atom via dump command, for example
in the "flow" example of lammps, how Can I extract one single atom
from many atoms in it???

just like i told you. define a group.

because it arranges number of atoms in "lower" ,"upper" ,"
flow" ,"boundary" groups according to lattice spacing.

so what?

How can I seperate a special atom near the solid boundary and show its
trajectory during run???

now _that_ is a completely different question.
this is most conveniently done from inside a
visualization program. VMD for example allows
to select atoms in very complex (but also simple)
ways and overlay multiple representations of
you system and so on. many other viz tools have
similar features; i just mention VMD, since
that is the one that i know best.

axel.