How to output only the atoms positions after equilibrium?

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1

Hello All,

I am using write_data command after minimizing the emergy of my system, to output the after equilibrium data. This command gives me all the bond, angle data. How can I tell it to write only the atom positions (x,y,z) of one type of atoms?

I only need the position of my carbon atoms after equilibrium.

Thanks a lot.

2

Can use a custom data file instead, see dump command — LAMMPS documentation
e.g. something like this:
dump 1 all custom 100 dump.mypos.* id x y z

3

Thank you so much, but this also gives me the data in every 100 * timesteps. Is there any way to out put the last timestep data only to get just the last position of atoms in that moment that the system is relaxed?
(I know that I can increase the N=100 and delet some information in the data file, but wanted to know if there is more neat way to ask LAMMPS to print the last time step data)

4

Just check the documentation for the write_dump command — LAMMPS documentation
It is listed right next to write_data in the command overview: 5.5. General commands — LAMMPS documentation
:wink:

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5

Thanks a lot

6

Dear Axel,

my time step is 0.01 and I am running for 5000 times. I used "write_dump CNT custom cntrelx.* id type x y z " to output the cnt relaxed atom positions, and I am getting a file with the name : “cntrelx.100”. I am not sure where 100 comes from since I am not asking for repetetive outputs. I want to make sure that the data I am outputting is the relaxed data. Could you please explain this to me and tell me how to use the command properly?

I noticed 100 in “cntrelx.100” means data belongs to timestep 100,
when the time step is 0.01, timestep 100 is 100*0.01=1, does that mean this data belongs to the last timestep of last run?

Thanks a lot

7

The * means append the timestep to the file. So whatever timestep the dump file was created on will match the file name.

8

Thank you, I noticed that 100 in “cntrelx.100” means data belongs to timestep 100,
My time step is 0.01, so timestep 100 is the total time 100*0.01=1, does that mean this data belongs to the last timestep of last run?

9

Not sure, how many timesteps did you run for? Did you use the reset_timestep 0 or similar command? reset_timestep command — LAMMPS documentation

If you put the write_dump command after the last run command then yes it is for the last timestep.

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10

yes I ran 5000 times and then wrote write_dump command. that is why i was confused . 0.01 is my timestep and I was expecting 0.01*5000 =50

11

Can you post your exact commands from the input? It should be 5000 not 100 unless you used reset_timestep. It is the number of timesteps completed not simulation time in the file name for *

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12

Why don’t you just use cntrelx.final as file name for the write_dump command?
No more puzzling over timesteps and simulation length needed.

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