yambo is an ab initio code for calculating quasiparticle energies and optical properties of electronic systems within the framework of many-body perturbation theory and time-dependent density functional theory. Quasiparticle energies are calculated within the GW approximation for the self-energy. Optical properties are evaluated either by solving the Bethe-Salpeter equation or by using the adiabatic local density approximation. yambo is a plane-wave code that, although particularly suited for calculations of periodic bulk systems, has been applied to a large variety of physical systems. yambo relies on efficient numerical techniques devised to treat systems with reduced dimensionality, or with a large number of degrees of freedom. The code has a user-friendly command-line based interface, flexible I/O procedures and is interfaced to several publicly available density functional ground-state codes. 71.45.Gm, 71.15.Qe

We present a reciprocal space analytical method to cut off the long range interactions in supercell calculations for systems that are infinite and periodic in one or two dimensions, generalizing previous work to treat finite systems. The proposed cutoffs are functions in Fourier space, that are used as a multiplicative factor to screen the bare Coulomb interaction. The functions are analytic everywhere except in a subdomain of the Fourier space that depends on the periodic dimensionality. We show that the divergences that lead to the nonanalytical behavior can be exactly canceled when both the ionic and the Hartree potential are properly screened. This technique is exact, fast, and very easy to implement in already existing supercell codes. To illustrate the performance of the scheme, we apply it to the case of the Coulomb interaction in systems with reduced periodicity ͑as one-dimensional chains and layers͒. For these test cases, we address the impact of the cutoff on different relevant quantities for ground and excited state properties, namely: the convergence of the ground state properties, the static polarizability of the system, the quasiparticle corrections in the GW scheme, and the binding energy of the excitonic states in the Bethe-Salpeter equation. The results are very promising and easy to implement in all available first-principles codes.

yambo is an open source project aimed at studying excited state properties of condensed matter systems from first principles using many-body methods. As input, yambo requires ground state electronic structure data as computed by density functional theory codes such as Quantum ESPRESSO and Abinit. yambo's capabilities include the calculation of linear response quantities (both independentparticle and including electron-hole interactions), quasi-particle corrections based on the GW formalism, optical absorption, and other spectroscopic quantities. Here we describe recent developments ranging from the inclusion of important but oft-neglected physical effects such as electron-phonon interactions to the implementation of a real-time propagation scheme for simulating linear and nonlinear optical properties. Improvements to numerical algorithms and the user interface are outlined. Particular emphasis is given to the new and efficient parallel structure that makes it possible to exploit modern high performance computing architectures. Finally, we demonstrate the possibility to automate workflows by interfacing with the yambopy and AiiDA software tools. CONTENTS

We performed first-principles calculations of the optical response of the green fluorescent protein (GFP) within a combined quantum-mechanical molecular-mechanics and time-dependent density-functional theory approach. The computed spectra are in excellent agreement with experiments assuming the presence of two, protonated and deprotonated, forms of the photoreceptor in a approximately 4:1 ratio, which supports the conformation model of photodynamics in GFP. Furthermore, we discuss charge transfer, isomerization, and environment effects. The present approach allows for systematic studies of excited-state electron-ion dynamics in biological systems.