Dear community,
My question is: is there a way in LAMMPS to map atomic indices (as they appear in the data file) to indices based on reaction product structures? See below for details.
I’m trying to employ LAMMPS to study the denamic mechanism of a pretty known and widely discussed reaction between two or more NO2 molecules. To do that I employ reax.chon2019 ff and NVT experimental conditions. As an example the intermediate results for the box that containes 900 NO2 molecules is shown on the picture, where the interested products are colored in red. To analyze the results I use dump files altogether with “fix reaxff/species” and "fix reaxff/bonds " commands as follows:
fix NO2spcs NO2 reaxff/species 10 100 5000 spcsNPT2K.out cutoff * * 0.5 element N O position 10000 posNPT2K.pos delete spc_delNPT2K.del masslimit 46.005 46.005
fix NO2bnd NO2 reaxff/bonds 5000 bndsNPT2K.out
As a result , there is a statistics of the reaction products as a function of time.
To analyze the mechanism of the reaction it would be great to know the indices of the atoms that undergo the reactions. I could obtain the indecices of atoms from the dump file and the reaction statistics from species.out file. What I don’t know is to find is the indices of atoms of the products as a function of time.
Thus, there is a question, is there any option in LAMMPS to
correlate atomic indices (as their appears in the data file) to those based on the reaction products structures.
Thank you and kind regards,
Victor
