fix bond/react position of created atoms

LAMMPS LAMMPS General Discussion
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1

Hello,

I have a simple question about the position of created atoms in fix bond/react. I have read the documentation but not found the explanation or didn’t understand fully.

I try to implement the reaction below:

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In the course of reaction a new atom must be created (red hydrogen atom). I identified a molecule fragment as shown in blue (frag1) in the post reaction template. I want the newly created hydrogen atom to be created in relation to this fragment, not the whole molecule template. So, I am using “modify_create” with below fix:

fix myrxn all bond/react stabilization yes statted_grp 0.3 react rxn12 all 10 0.5 6.0 molpre molpost reaction_map.txt prob 0.006 33254 modify_create fit fragment-ID frag1

But I keep getting below error:

ERROR on proc 0: Fix bond/react: Molecule fragment for ‘modify_create’ keyword does not exist (src/REACTION/fix_bond_react.cpp:423)

I am missing something obvious but couldn’t figure out what it is?

Any help will be appreciated. Thanks in advance

2

The bond/react command should probably read:
… modify_create fit frag1

Please let me know if that helps.

3

It worked! Now position of newly created atoms are in the proper places.

Thank you very much @jrgissing.