How to analyze the results of reaxff

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1

Dear lammps users

I have used Reaxff forcefiled in LAMMPS to perform MD simulation and I want to observe bond breaking and formation during the simulation. I heated the system to 1800 K with the fixed heating rate to see whether there is bond breaking. I got the trajectory from the lammps, and then I exported the trajectory to VMD to observe the bond breaking. However, I got strange results. The first picture is the initial structure; the second picture is the structure from specific temperature. It seems that there is bond breaking in second one, but it looks so strange. My question is

(1) Whether VMD can be used to analyze results from Reaxff forcefiled in LAMMPS

(2)If not, is there other tools can be used to analyze results from Reaxff forcefiled in LAMMPS

Sincerely

Fan Li

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2

It seems VMD drew bonds that are wrapped around the periodic boundary condition. I am not familiar with VMD so I do not know how to draw bonds correctly using it. Note VMD uses a pure distance based criterion to draw bonds, while ReaxFF bonds are based on analytical bond order values.

You can use fix reax/c/bonds and/or fix reax/c/species to write out bonding information. Please see their doc pages for more info.

Ray

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3

I am not that familiar with ReaxFF or VMD, but to me it seems like a part of the atoms moved across a periodic boundary. If you make VMD display the unwrapped atom positions it will probably look better.

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