list%nnl for H is 0, in LiH hamiltonian testcase

[tornikeo]

Dear all,
When testing get_hamiltonian function with Li H testcase, I couldn't understand why is it that Li in this molecule has number of neighbors list%nnl equal to 0? Specifically:

! print number of neighbors, nnl
print list%nnl 

Prints 0 for Li and 1 or H. I can't understand why this is correct.

[awvwgk]

For the Hamiltonian calculation a symmetric adjacency list is used and only one half of the list is stored, i.e. the Li-H adjacency is stored for the second atom and the first atom is considered to not have any entries.

For more details on the logic behind the adjacency list construction and format, see https://tblite.github.io/tblite/namespacetblite__adjlist.html or

tblite/src/tblite/adjlist.f90

Lines 22 to 42 in fd0e7ca

	!> A symmetric neighbour map given in dense format like
	!>
	!> | | 1 | 2 | 3 | 4 | 5 | 6 |
	!> |---|---|---|---|---|---|---|
	!> | 1 | | x | | x | x | |
	!> | 2 | x | | x | | x | x |
	!> | 3 | | x | | x | | x |
	!> | 4 | x | | x | | x | x |
	!> | 5 | x | x | | x | | |
	!> | 6 | | x | x | x | | |
	!>
	!> Is stored in two compressed array identifying the neighbouring atom `nlat`
	!> and its cell index `nltr`. Two index arrays `inl` for the offset
	!> and `nnl` for the number of entries map the atomic index to the row index.
	!>
	!> ```
	!> inl = 0, 3, 7, 10, 14, 17, 20
	!> nnl = | 2 -> | 3 -> | 2 -> | 3 -> | 2 -> | |
	!> nlat = 2, 4, 5, 1, 3, 5, 6, 2, 4, 6, 1, 3, 5, 6, 1, 2, 4, 2, 3, 4
	!> nltr = 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1
	!> ```