Load a file sphere positions in LIGGGTHS

JF's picture
Submitted by JF on Fri, 06/11/2010 - 11:48

Hi everyone,

I would like to know, How I can integrate the position of spheres into my simulation ?
I have ready created a sphere packing and I want to use it.

I know that I must add this line into the fle in.mysimulation
# Read data

read_data position.sys

The file position.sys need to be writen like that ? (look the line under)
Please, can you correct ( position.sys) it in order that it works.
Thanks
Regards
Jf

LIGGGHTS Description

1 spheres # number of spheres

T atom types
# type of atom = granular ?

0.000000 150.000000 xlo xhi #box

0.000000 150.000000 ylo yhi #box

0.000000 150.000000 zlo zhi #box

Masses

T xxxxxxxx

Atoms

1 T X Y Z R # number type position(X Y Z) radius (R)

Velocities

1 VX VY VZ

JF's picture

JF | Fri, 06/11/2010 - 20:08

Hi Christoph,

Thanks for your reply. In following your indication, I read the doc of read_data and I wrote this file to position 8 spheres into my simulation.

LIGGGHTS Description

8 atoms
1 atom types
0 bond types
0 angle types

0.000000 150.000000 xlo xhi
0.000000 150.000000 ylo yhi
0.000000 150.000000 zlo zhi

Atoms

1 1 0.0009 40 0.0 0.0 0.02
2 1 0.0009 40 0.0 0.0 0.04
3 1 0.0009 40 0.0 0.0 0.06
4 1 0.0009 40 0.0 0.0 0.08
5 1 0.0009 40 0.0 0.0 0.1
6 1 0.0009 40 0.0 0.0 0.12
7 1 0.0009 40 0.0 0.0 0.14
8 1 0.0009 40 0.0 0.0 0.16

Velocities

1 0.0 0.0 0.0 0.0 0.0 0.0
2 0.0 0.0 0.0 0.0 0.0 0.0
3 0.0 0.0 0.0 0.0 0.0 0.0
4 0.0 0.0 0.0 0.0 0.0 0.0
5 0.0 0.0 0.0 0.0 0.0 0.0
6 0.0 0.0 0.0 0.0 0.0 0.0
7 0.0 0.0 0.0 0.0 0.0 0.0
8 0.0 0.0 0.0 0.0 0.0 0.0

In the file mysimulation.in, I wrote these sentences in first:

units si

atom_style granular
atom_modify map array
boundary m m m
newton off

# Read data
read_data liggghts.sys
#####################

But I have this error, when I run my simulation: ERROR: Cannot create_box after simulation box is defined.
It is a mystery for me.

Have a nice weekend !!!
Jf

raguelmoon's picture

raguelmoon | Sat, 06/12/2010 - 14:25

Hi,
Have you defined create_box in your input-file? If yes then remove it... read_data command reads dimension of box from the file "liggghts.sys"..
cheers,
Ram

Ram

JF's picture

JF | Sun, 06/13/2010 - 22:03

Hi Ram,

Thanks for your reply. Effectively, I didn't realize that the box was created with the file"liggghts.sys".
Now it works well, thanks again for your help.
Actually, I try to make a simulation of compression simple. So, see you soon on the forum.

Regards
Jf

ckloss's picture

ckloss | Mon, 06/14/2010 - 09:13

Hi JF,

fine to hear it worked out. Just a hint: Section 9 comprises the most common error messages - in this case it says

"Cannot create_box after simulation box is defined": The create_box command cannot be used after a read_data, read_restart, or create_box command.

Cheers,
Christoph

JF's picture

JF | Mon, 06/14/2010 - 09:39

Hi Christoph,

Thanks for your advice. I discovered this new section yesterday evening with google, because I had this error "Too many atom sorting bins".
So, I decreased the size of the box and now it works fine.

Thanks again.
Jf