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Re: [lammps-users] Lost atoms while atoms are still in the box
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Re: [lammps-users] Lost atoms while atoms are still in the box


From: Axel Kohlmeyer <akohlmey@...24...>
Date: Thu, 10 Aug 2017 11:13:29 -0400



On Thu, Aug 10, 2017 at 12:13 AM, Trung Phung <clone.1.trung@...24...> wrote:
Dear LAMMPS users,

I created 2 atoms in simulation box, and moved them to new positions using "set" command. Even though I placed atoms to new positions inside the box, LAMMPS warned me of lost atoms. And this warning was, to my surprise, dependent on where I created my atoms in the beginning. Here is my input script:

​i cannot reproduce this with the current LAMMPS version 24 Jul 2017.

axel.​

 

#------------------------------------------INPUT---------------------------------------------
units                  metal
atom_style        charge

region                box block  0 120   0 20   0 20 units box
create_box        2 box

mass                 1   65
mass                 2   16

create_atoms    1 single  5    5    5
create_atoms    2 single  4  10  10
# If in "create_atoms 2", I change "4 10 10" to "40 10 10" then there is no atom lost

pair_style           lj/cut 2.5
pair_coeff           * * 1 1

neighbor             1.0 bin

thermo                1
thermo_style       custom  step atoms
#thermo_modify   lost warn

run 0
set       atom  1  x 10  y 10  z 10
run 0
set       atom  2  x 40  y 10  z 10
run 10

#---------------------------------------------LOG---------------------------------------------
(1) If I use "create_atoms  2   single  4  10  10 " then:
...
set         atom  2  x 40  y 10  z 10
  1 settings made for x
  1 settings made for y
  1 settings made for z
run 10
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
Per MPI rank memory allocation (min/avg/max) = 0.442 | 0.7623 | 3.192 Mbytes
Step Atoms
ERROR: Lost atoms: original 2 current 1 (../thermo.cpp:433)
Last command: run 10

(2) If I use "create_atoms  2   single 40 10 10" then:
...
set         atom  2  x 40  y 10  z 10
  1 settings made for x
  1 settings made for y
  1 settings made for z
run 10
WARNING: No fixes defined, atoms won't move (../verlet.cpp:55)
Per MPI rank memory allocation (min/avg/max) = 0.442 | 0.8873 | 2.817 Mbytes
Step Atoms
       0        2
       1        2
       2        2
       3        2
       4        2
       5        2
       6        2
       7        2
       8        2
       9        2
      10        2
Loop time of 0.000372484 on 16 procs for 10 steps with 2 atoms

Could anyone tell where the problem lies, please?

Best regards,
Trung Quoc Phung

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--
Dr. Axel Kohlmeyer  akohlmey@...12...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.