how to determine "extra/bond/per/atom"


I’m using the molecule command to add a new molecule. I’m trying to figure out how to use the “extra/bond/per/atom” and the other “extra” per atom keywords. If I have a molecule such as methanol, carbon has 4 bonds, oxygen has 2 bonds and each of the hydrogen have 1 bond, so would I set the “extra/bond/per/atom” keyword to 4 since it’s the largest?


Under normal circumstances, there is no problem in using even larger numbers like 20 or more. It would only make a difference with very large systems and extremely large “extra” values on a machine with limited RAM, as those settings increase the memory use.

Also, if you write out a data file of the resulting system with molecules added, then use the clear command to start over, and read that generated data file back into LAMMPS, no more “extra” parameters are needed and LAMMPS will automatically pick the optimum values.