LAMMPS Element Mapping

LAMMPS LAMMPS General Discussion
1

#Use Tersoff potential
pair_style tersoff
pair_coeff * * SiO.tersoff Si O Si

In the above command in LAMMPS, it says 3rd element in LAMMPS is mapping to Si in the tersoff file but the tersoff file contains Si Si O , Si O, Si as attached snapshot.

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But the third element refers to which Si in the tersoff file as shown in snapshot because file contains many Si Si O, Si O Si upto 8 permutations of Si, SI and O.

2

Any of them.

The pair_coeff command maps atom types to elements and the Tersoff file has parameters for all permutations of triples of elements. You can have multiple atom types referring to the same element.

More details are in the documentation for the pair_style, pair_coeff and pair_style tersoff commands.