using an output as the input of another simulation

Hello,

I have faced a problem in my simulation which needs changing the boundary condition from periodic condition into non-periodic one during a specific simulation. When I reuse the boundary command, lammps gives me this error: boundary command after simulation box is defined.
So I have to do something else. Now I have to use the output( each atoms’ position and velocity, x y z vx vy vz ) of a part of my simulation as the input of another simulation. This another simulation is actually the second part of the first simulation.
Is it possible to do this? If so, how can I do?

Your help is highly appreciated,
Ezel

See the change_box command. You can change
from periodic to non in the middle of a script.

Steve

Dear Steve,

Thanks for your answer.
At first I have boundary p p p. in the middle of the simulation I want to change it to boundary p p s. So I used " change_box all boundary p p s remap " and also " change_box all boundary z s “. But I got this error” Illegal change_box command.
would you please tell me what its problem is?

Ezel

I have even tested the example of the manual " change_box all xy final -2.0 z final 0.0 5.0 boundary p p f remap units box " by 21dec2011 but I have got the illegal change_box command error!

Either of these commands work when you add them to bench/in.lj

change_box all boundary p p s remap
change_box all x final -20 20 z final 0.0 5.0 boundary p p f remap units box

Note that the 2nd one (from the examples on the doc page)
was missing one number after "final".

The first one is what you said didn't work for you. I'm guesing
you are not running the current version of LAMMPS.

Steve

Correct that - the one with x final -20 20 is listed
as xy final -2.0 on the doc page, which is correct
for a triclinic box. Xy only takes one numeric arg.
X takes 2.

Steve

Dear Steve,

I have downloaded the current version (21dec2011) again from the lammps website. But unfortunately it still does not work.
This is a part of my input script:

units metal
boundary p p p

lattice bcc 3.015
variable lx equal 30
variable ly equal 30
variable lz equal 90

region box block 0 {lx} 0 {ly} 0 ${lz} units box
region box2 block 1 28 1 28 1 88 units box

create_box 2 box
create_atoms 1 region box basis 2 2

group box2 region box2

#Potential
pair_style eam/fs
pair_coeff * * NiTi.FS Ni Ti
timestep 0.001

thermo_style custom step temp pe press lx ly lz
thermo 100

initial velocities

velocity all create 350.0 5812775 units box
fix 1 all npt temp 350 350 0.01 aniso 0.0 0.0 10 drag 0.2

dump a box2 atom 1000 dump.indent

variable s equal step
variable t equal temp
variable v equal vol
variable p equal pe
fix def2 all print 10 “{s} {v} {p} {t}” file melt.dat screen no

equilibrium

run 10000
unfix 1
undump a
dump 2 box2 atom 1000 dump-change.indent

change_box all x final -20 20 z final 0.0 5.0 boundary p p f remap units box
#change_box all x scale 1.1 y volume z volume remap

Thanks,
Ezel

I have downloaded the current version (21dec2011) again from the lammps website.

That's not the current version, by 6 months. Try clearing
your browser cache, and download it again.

Steve

I did what you said but surprisingly there was nothing except 21dec2011 !!! I know I am making mistake but I absolutely need the current version.
I use lammps on windows. Can anyone do me a favor and send the current version of lammps to me by attachment?

Your help would be so appreciated.
Ezel

Paul updates the Windows versions periodically.
He is CCd.

Steve

I've updated the LAMMPS Windows executables to the 1 July 2012 version of LAMMPS.

Paul

wwwooooowww!!!

many thanks!! it was really kind of you…

Best,
Ezel