error lost atoms in thermo

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1

Hi I want to decrease the temperature of my system. I;m using following lines :

variable t equal 1
thermo_style custom step temp etotal
thermo 10000

velocity all create $t 5898 dist gaussian mom no rot no
fix 1 all nvt temp $t 0.02 100.

timestep 0.001

run 100000000

run 10000000

but I’m getting the following error :

58820000 0.38752275 16.426996
58830000 0.40476363 16.422477
58840000 0.37155634 16.422245
58850000 0.39115889 16.414839
58860000 0.38386821 16.414015
ERROR: Lost atoms: original 155 current 0 (…/thermo.cpp:392)

I’m using periodic boundaries so it doesn’t make sense to have lost atoms.
In addition, I think that I have understood the “fix nvt Tdamp”
I set Tdam equal 100 as the documents suggested. I expected that my system’s temperature reach to 0.02 after 100 step but as you can see above the temperature is equal 0.4 in 58860000th step. Why?

thanks

2

Recommended temperature damping factor from the doc page is 100 times the timestep size, which should be 0.1 in your example.

You can still lose atoms with periodic boundary conditions – this is a frequently discussed topic on the mailing list. I suggest you do a little search.

Hope this helps,
Ray

3

Thanks,
So can you tell me in which step I get my final temperature which is 0.02? I’m still confused what does 0.1 mean here? Is it the timre required to pass or it is 0.1 of run steps?