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Re: [lammps-users] Fix Deposit and Particle Insertion Discrepancy
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Re: [lammps-users] Fix Deposit and Particle Insertion Discrepancy


From: "T. Majdi" <majdit@...1849...>
Date: Sun, 27 May 2018 16:17:34 -0400

Hi Masato,

I suggest adding

thermo_style custom step time atoms
thermo 1

only during deposition of a shorter test run. The output will show you the number of atoms in each step. Then you can see exactly in which time step the number of atoms in your system increased.

Is the total number of atoms at the end of your simulation what you expect it to be based on your script?

Regards,
Tara 



On Sun, May 27, 2018 at 3:54 AM, MASATO KOIZUMI <mkoizumi@...3709...> wrote:
Dear LAMMPS Users,

Hello. I was curious if I could ask a question regarding the fix deposit command.

I understand that fix deposit command inserts a single atom or molecule into the simulation domain every M timesteps until N atoms or molecules have been inserted. 

In my MD simulation, I have 

fix    4 addatoms deposit 10 0 1000 12345 region mobile near 0.0 mol dimer vz -1 -1

My simulation runs for 10000 and my simulation box is changing in size with periodic boundary conditions.

I output a dump file every 50 timesteps, and when I look at my dump file that was generated at 50 timestep, I see that the molecule has already been inserted. I check with OVITO, which confirmed that the first molecule was inserted at 50 timesteps when in fact, the first molecule should have been inserted at 1000 timesteps. The second molecule was inserted at 1000 timesteps consistent with the parameters I specified in my fix deposit command

I would greatly appreciate if I could request an advice on why the first molecule is being inserted at 50 timestep and not at 1000 timesteps. 

Thank you.

Sincerely,

Masato Koizumi

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--
Tahereh Majdi, B.Eng., M.A.Sc.
PhD candidate, Engineering Physics
McMaster University

e:majdit@...1849...
t: (905)-541-3814