A question about the final files of LAMMPS CI-NEB simulation

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1

Hi,all

Here I have a question on LAMMPS CI-NEB simulation: I noticed that in the example code, the

‘final.hop1’ and ‘final.sivac’ show only the atoms for simulation are included. Can we included all the atoms

in the system in such final files? If the system itself is dynamic (other atoms also move) , we have to put the coordinates of all

atoms in the final files, right?

Thanks for help~

2

Hi,

     Here I have a question on LAMMPS CI-NEB simulation: I noticed that in
the example code, the

'final.hop1' and 'final.sivac' show only the atoms for simulation are
included. Can we included all the atoms
in the system in such final files? If the system itself is dynamic (other
atoms also move) , we have to put the coordinates of all
atoms in the final files, right?

I don't know the details of the simulations. Still, the command that manages the
output of coordinates to a file is 'dump'.

Requesting the dump for 'all' particles will do what you want.

dump MyDumpID all /rest of command/

Pierre

3

Hi,all

     Here I have a question on LAMMPS CI-NEB simulation: I noticed that in
the example code, the

'final.hop1' and 'final.sivac' show only the atoms for simulation are
included. Can we included all the atoms in the system in such final files?

why not do this with a simple script in post-processing?
just load a frame of the initial complete systems and then loop over
the various images and overwrite the respective coordinates and write
out the processed system as a whole.

axel.

4

Hi, Dr.Axel,

Thank you for your advice!! That’s what exactly I have done. The frame of the initial complete systems I created was loaded by my

“read_data” command in the “in.* file”. And my whole operation was almost in accordance to your procedure. I did write a python code

to get the processed system as a whole~

But what I cared was the simulation itself: there were two input files( starting atoms coordinates of the whole box and end

coordinates of the reagent atom).

As you can see in the example code in Lammps/examples/neb: the input file ‘final.hop’ code only includes the end coordinates

of the atoms they focus on. In that case, they study surface atoms hopping so they might only include the hopping H atom. While in my

case, I study the atoms diffusion in bulk material, then bonds breaking and generating may happen with system. Thus I think they were

different situations. So I feel puzzled whether to put all the end coordinates of the system in the initial input “final.*” files

Thank you for you help very much~