I run a simulation with water and methane molecules using reaxff and I am trying to monitor what reaction are taking place. So I’d like to be able to follow each atom individually and see how bonds are changing.
To do that I use the command reaxff/atom with the line:
compute rffat all reaxff/atom bonds yes
But then when I am no able to dump the information I get with this command in a file to be able to use it after. I tried several things with fix and dump, the latest command line I tried is:
dump 1 all custom 100 rffatom.out c_rffat
but it says:
ERROR: Dump custom compute rffat does not calculate per-atom vector
Do you know how I could dump information from reaxff/atom in a text file?
If I remember correctly compute reaxff/atom calculates a per-atom array. In order for dump to access it you should specify the desired column(s) by indexing it. For example c_rffat[1] will retrieve the first column or, using the wildcard notation, c_rffat[*] will get you all three columns.
I do access to the 3 columns containing atoms bond order, number of lone pairs and number of bonds, but I also asked to compute a local array with all the bonds with they keyword “bonds yes” and this one is not getting dumped. Do you (or anyone else) happen to know how to access this array? I don’t find the information on the reaxff/atom manual page nor anywhere else.