[lammps-users] What might be wrong with removing the atoms?

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1

Hi, Steve:

Thanks for your suggestion. Now I’m testing the scheme. However, the removing atoms doesn’t seemt to work like I expected.

The test system is a slab of diamond atoms. All the atoms starts with a 10,000K initial temperature plus a -3A/ps initial speed in center of mass. Then the system is going NVE so that the atoms will move towards the left end of the box. I was expecting to see the atoms get removed when they hit the left end. However, the program stops when this happens.

I wish the program continues to run. What shall I do? Thanks,

Here’s the input of my lammps run:

variable x index 6
variable y index 6
variable z index 6

units metal
atom_style atomic
boundary p p f

lattice diamond 3.5657
region sbox block 0 $x 0 $y 0 $z
region mbox block 0 $x 0 $y 5 $z
create_box 1 sbox
create_atoms 1 region mbox basis 1 1

neighbor 0.5 bin
neigh_modify delay 1

pair_style rebo 0.0 0 0
pair_coeff * * potentials/ch.airebonew C

mass * 12.01

velocity all set NULL NULL -3 loop geom
velocity all create 10000.0 376847 sum yes loop geom
compute T_ALL all temp/com

fix LNVT all nve

timestep 0.0001
thermo 1
thermo_modify format float %.10f
dump Dump2 all custom 10000 xyzFxyz-*.bin tag x y z fx fy fz vx vy vz

run 50000

2

I presume you got an error? Did it say, lost atoms? If
so, then you need to set thermo_modify lost ignore. The
default is to throw an error and stop.

Steve

3

Hi, Steve:

I tried to run a system of diamond using langevin thermostat by the following command.

4

I don't know. You don't really need to unfix and then re-fix for
Langevin. You should just be able to apply it to all atoms at
any time. I think it will just work on whatever atoms are currently
in group all. I also wouldn't mess with temp/com initially. I would
just see if you can thermostat with Langevin.

Steve