Reading additional bonds for system from additional data file

Dear all,

I am trying to modify a system, consisting of a molecule and a zeolite structure, so that bonds are added to the system. The situation starts of as follows:

I obtained these structures by treating the zeolite atoms as frozen with “setforce” so I did not need bonds or angles between the Si and O atoms. Then a molecule (which of course can bonds, angles, etc) was inserted into the pores and the adsorption goemetry was optimized. Now I want to investigate the effect of framework relaxation, so bonds and angles for the zeolite have to be added to the system. My approach was to use “read_data add append” but I am getting the error
“Invalid atom ID in Bonds section of data file: 1 1 1 447 (src/atom.cpp:1318)”
Here you find the input file, the structure of the molecule in the zeolite and the bonds and angles of the zeolite.

flex_zeo_emami_add-data.in (796 Bytes)
low-E_ACA-in-MOR.lmp (42.9 KB)
data.MOR_emami-bond_no_atoms (69.4 KB)

I suspect, that the error occurs because the datafile that contains the bonds is appended, so the atomIDs are appended aswell and thus exceed maxID. Using “merge” instead of append does not solve this and gives the error “Bonds assigned incorrectly”.

Could anyone suggest a solution here?
Kind regards
Jakob

Why trying to add bonds and angles only? Why not just delete the original atoms and then add the system with bonds and angles?

That is the kind of advise I come here for!
Works like a charm, thanks a lot!