1. The phrases in the manual you mentioned implies that in the cases of C Si

C and Si C Si, the Tersoff code will ignore whatever the values are in the

place for two-body interactions?

Yes

2. For such entries as C Si C and Si C Si, the parameters for two-body

interaction are same with corresponding values in C Si Si or Si C C because

the bond between 1st and 2nd atom are C-Si, equivalently Si-C? If so, the

required values for the two-body interaction bring from other entries such

as C Si Si or Si C C?

The parameters following C Si C specify the values of the threebody

parameters m, gamma, lambda3, c, d, and costheta0, and the cut-off paramters

R and D which are needed. All these parameters appear in the sum over k that

defines zeta_ij. Hence, they are depend on the types of atoms i, j and k.

Conversely, the twobody parameters n, beta, lambda2, B, lambda1, and A only

depend on the types of atoms i and j. For historic reasons, we chose to

handle this by arbitrarily defining the two-body parameters in the line

where j = k.

It would have been less confusing to the new user if we had defined all the

twobody parameters in lines starting with two elements, say C Si, followed

by values for n, beta, lambda2, B, lambda1, A, R and D, and all the twobody

parameters in line starting with three elements, say C Si Si, followed by

values for the threebody parameters m, gamma, lambda3, c, d, costheta0, R

and D. But the existing scheme is more straight-forward to code up and is

actually simpler to use as well, once you understand it.

Aidan