Code:
$ cat file
Geometry "geometry" -> "geometry"
1 Pd 46.0000 -0.19290971 0.00535260 0.02297606
2 P 15.0000 -0.14710910 -2.36148276 0.03834032
3 P 15.0000 -0.15274409 2.36634164 -0.06817369
4 C-t 6.0000 -2.28301257 -0.04175538 0.06012368
5 H-t 1.0000 -2.64711929 -0.61127738 -0.80775979
6 H-t 1.0000 -2.59746921 -0.53769963 0.98862569
7 H-t 1.0000 -2.72455591 0.96040010 0.02865251
8 O-t 8.0000 2.07206484 -0.64945821 -0.99276006
9 H-t 1.0000 2.35209406 -0.10074612 -1.74408343
10 H-t 1.0000 2.22690284 -0.00778417 0.03690656
11 O-t 8.0000 2.04896854 0.63726649 1.06014962
12 H-t 1.0000 2.29703540 0.08837100 1.82240885
Atomic Mass
$ nawk 'NR == 1 {
split("H, He, Li, Be, B, C, N, O, F, Ne, Na, Mg, Al, Si, P, S, Cl, Ar, K, Ca, Sc, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Ga, Ge, As, Se, Br, Kr, Rb, Sr, Y, Zr, Nb, Mo, Tc, Ru, Rh, Pd, Ag, Cd, In, Sn, Sb, Te, I ,Xe, Cs, Ba, La, Ce, Pr, Nd, Pm, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu, Hf, Ta, W, Re, Os, Ir, Pt, Au, Hg, Tl, Pb, Bi, Po, At, Rn, Fr, Ra, Ac, Th, Pa, U, Np, Pu, Am, Cm, Bk, Cf, Es, Fm, Md, No, Lr, Rf, Db, Sg, Bh, Hs, Mt",pse,", ") }
{ $3 = int($3) in pse ? pse[int($3)] : $3
}1' file
Geometry "geometry" -> "geometry"
1 Pd Pd -0.19290971 0.00535260 0.02297606
2 P P -0.14710910 -2.36148276 0.03834032
3 P P -0.15274409 2.36634164 -0.06817369
4 C-t C -2.28301257 -0.04175538 0.06012368
5 H-t H -2.64711929 -0.61127738 -0.80775979
6 H-t H -2.59746921 -0.53769963 0.98862569
7 H-t H -2.72455591 0.96040010 0.02865251
8 O-t O 2.07206484 -0.64945821 -0.99276006
9 H-t H 2.35209406 -0.10074612 -1.74408343
10 H-t H 2.22690284 -0.00778417 0.03690656
11 O-t O 2.04896854 0.63726649 1.06014962
12 H-t H 2.29703540 0.08837100 1.82240885
Atomic Mass