Do you use the simulation cell to generate the .dat?

[Leticia-maria]

Hi! Great project! I have a question: do you use the simulation cell to generate the data file? I didn't what the utility of the simulation cell here.

[stefanbringuier]

Thanks for your interest!

So I think your question is referring to the cell line in the input file:

#Hydrogen molecule
#Angstroms
cell 10.0 10.0 10.0
natoms 2
#Atoms Z ,x , y, z in Angstroms
positions 1 0.00 0.00 0.00 &
1 4.4 0.00 0.00
#Basis definition
basistype 6-31
basisfile ../../examples/basissets/H.6-31G.mod

So this is there because I initially intended to extend the code to enable various transformations and allow for periodic systems. I never got around to this, and so it adds no utility.

[Leticia-maria]

Thank you for your reply, @stefanbringuier . I was talking about the type: SystemOfAtoms

struct SystemOfAtoms
    natoms::Integer;
    atoms::Array{Atom,1};
    cell::Array{Float64,2};
    function SystemOfAtoms(natoms=1,
                    atoms=[Atom()],
                    cell=zeros(3,3))
            if natoms < 0
                error("Simulation cell cannot have negative atoms.")
            end
            if size(cell) != (3,3)
                error("Simulation cell is not a 3x3 array.")
            end
            if typeof(atoms) != Array{Atom,1}
                error("Atomic entries are not of the typeof() == Atom.")
            end
            new(natoms,atoms,cell)
    end
end #SystemOfAtoms

[Leticia-maria]

I didn't get why have you used it @stefanbringuier

[Leticia-maria]

Any updates, @stefanbringuier ?

[stefanbringuier]

@Leticia-maria so the cell field in SystemOfAtoms is not used, but the idea was that if the code base get's extended to allow for various transformations of the simulation, the cell info will be required. In addition if support is added for planewave basis the cell with periodic boundary conditions provides numerical conveniences.