回复： How to create atoms after read data

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1

Hi Axel,

The following is the part in the in.file:

units metal
dimension 3
boundary p p s

atom_style atomic
#neighbor 3.0 bin
#neigh_modify delay 5.0
newton on

#create geometry

read_data data.c

region 6 block INF INF INF INF INF 377 units box

region 8 plane 178.906 276.078 377 0.707 -0.408 0.577 units box
region 9 plane 178.906 276.078 377 -0.707 -0.408 0.5770 units box
region 10 plane 93.206 127.645 377 0 0.816 0.577 units box

region indenter intersect 4 6 8 9 10

lattice diamond 3.57
create_atoms 3 region indenter

group indenter region indenter

fix 41 indenter rigid single

This is the output.file,

units metal
dimension 3
boundary p p s

atom_style atomic
#neighbor 3.0 bin
#neigh_modify delay 5.0
newton on

#create geometry

read_data data.c
orthogonal box = (0 0 0) to (357.812 354.196 500)
1 by 1 by 1 MPI processor grid
reading atoms …
3264591 atoms
reading velocities …
3264591 velocities

region 6 block INF INF INF INF INF 377 units box

region 8 plane 178.906 276.078 377 0.707 -0.408 0.577 units box
region 9 plane 178.906 276.078 377 -0.707 -0.408 0.5770 units box
region 10 plane 93.206 127.645 377 0 0.816 0.577 units box

region indenter intersect 4 6 8 9 10

lattice diamond 3.57
Lattice spacing in x,y,z = 3.57 3.57 3.57
create_atoms 3 region indenter
Created 0 atoms

group indenter region indenter
0 atoms in group indenter

fix 41 indenter rigid single
ERROR: One or zero atoms in rigid body (…/fix_rigid.cpp:534)

The new region is also in the box, so I dont know why.

Best wishes!

2

create_atoms 3 region indenter
Created 0 atoms

group indenter region indenter
0 atoms in group indenter

fix 41 indenter rigid single
ERROR: One or zero atoms in rigid body (…/fix_rigid.cpp:534)

3

FWIW, with the latest version of LAMMPS (30 Nov 2016) atoms *are* created.

perhaps this issue is due to a bug that was fixed (quite) some time ago.

axel.

LAMMPS (30 Nov 2016)
  using 1 OpenMP thread(s) per MPI task

units metal
region box block 0 357.812 0 354.196 0 500 units box
create_box 3 box
Created orthogonal box = (0 0 0) to (357.812 354.196 500)
  1 by 1 by 1 MPI processor grid
lattice diamond 3.57
Lattice spacing in x,y,z = 3.57 3.57 3.57
region 6 block INF INF INF INF INF 377 units box

region 8 plane 178.906 276.078 377 0.707 -0.408 0.577 units box
region 9 plane 178.906 276.078 377 -0.707 -0.408 0.5770 units box
region 10 plane 93.206 127.645 377 0 0.816 0.577 units box

region indenter intersect 4 6 8 9 10
#region indenter intersect 6 8 9 10
create_atoms 3 region indenter
Created 52309 atoms

4

Hi Alex and Steve,

Thank you for your suggest. I used another version of LAMMPS, it can create as that you said. Maybe this is the bug .

Best wishes!