Extensions of the siesta dft code for simulation of molecules

We describe extensions to the siesta density functional theory (dft) code [30], for the simulation of isolated molecules and their absorption spectra. The extensions allow for: - Use of a multi-grid solver for the Poisson equation on a finite dft mesh. Non-periodic, Dirichlet boundary conditions are computed by expansion of the electric multipoles over spherical harmonics. - Truncation of a molecular system by the method of design atom pseudo- potentials of Xiao and Zhang[32]. - Electrostatic potential fitting to determine effective atomic charges. - Derivation of electronic absorption transition energies and oscillator stren- gths from the raw spectra produced by a recently described, order O(N3), time-dependent dft code[21]. The code is furthermore integrated within siesta as a post-processing option.