Does any of you know how I can get the bond order ReaxFF calculates for a specific pair of atoms which I’m interested in ?
I have an organic molecule crystal lattice that undergoes some reactions during heating. I’d like to find out what’s the bond order ReaxFF assigned the pair of atoms with ID’s $X and $Y to learn about the covalent
character of the bond between these two pairs of atoms.
I know that all bonding information is stored in bonds.reax, but I couldn’t understand the structure of this file. What does each column mean ?
How can I extract from there the desired bond order according to requested ID’s ?
Best Regards,
David Furman, MSc. student The Fritz Haber Research Center for Molecular Dynamics Institute of Chemistry The Hebrew University of Jerusalem Jerusalem, ISRAEL
By the bonds.reax file do you mean the output
generated by the fix bond/reax command?
If so, ask a Q about a specific quantity(s) in that file.
If not, then I think that is all the info the ReaxFF pair
style can generate. So you will have to go into the
code and print out the bond-order param if that is
what you want. If that's the case, post again,
and possibly Aidan will have a suggestion.
Yes. I mean the bonds.reax file generated by the fix bonds/reax command.
My question is about how this file is structured. What each column of
numbers in it means ?
Yes. I mean the bonds.reax file generated by the fix bonds/reax command.
My question is about how this file is structured. What each column of
numbers in it means ?
have you _looked_ at the file? it doesn't really need a
lot of imagination to figure out what each column means:
# Particle connection table and bond orders
# id type nb id_1...id_nb mol bo_1...bo_nb abo nlp q
id: atom id
type: atom type
nb: number of bonds
id_1...id_nb: atom ids of bonded atoms (nb columns)
mol: molecule id
bo_1...bo_nb: bond order of bonds (nb columns)
abo: accumulated bond order (sum of all bond orders)
nlp: number of lone pairs
q: charge
(and this is from somebody who has not used reax seriously
for anything and just looked at the file)