Zn and O are replaced by H and He inside pdb file

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1

Dear lammps users,
I am simulating ZnO using reax force field in lammps. I faced some difficulty inside the output pdb file. I save the pdb file from lammps trajectory file and see that Zn and O are replaced by H and He, inside the pdb file. How’s it possible? any help.
Regards

Sasthi

2

Does your trajectory dump file actually contain information which elements your system has? If there is just the numerical atom type, there will be a 1 and a 2. How should a visualization software know what those stand for? best guess would be element number in the periodic table, which corresponds to H and He.

Have a look at the documentation for the dump custom and dump_modify commands for how to output and assign element information to a dump file.

Axel

3

Hi
dump ID …should be followed by
dump_modify ID element Zn O (if type 1 is Zn and O is type 2) or reverse)

Regards

4

Thank you Axel and Pascal sir.

5

Dear Axel and Pascal sir,
I am sorry to say that again I got error of putting ID element in input script. The error is saying that: ERROR: Cound not find dump_modify ID (…/output.cpp:621)
Last command: dump_modify ID element ZN O.

6

Hi
Your ID should be the same for dump and dump_modify command.
See dump_modify command in the LAMMPS documentation by googlizing « LAMMPS pair_modify »
Pascal

Dear Axel and Pascal sir,
I am sorry to say that again I got error of putting ID element in input script. The error is saying that: ERROR: Cound not find dump_modify ID (…/output.cpp:621)
Last command: dump_modify ID element ZN O.