Ralph Gebauer

QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials

QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.

Advanced capabilities for materials modelling with Quantum ESPRESSO

Quantum ESPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudo-potential and projector-augmented-wave approaches. Quantum ESPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement theirs ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.Quantum EXPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudopotential and projector-augmented-wave approaches. Quantum EXPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement their ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.

Turbo charging time-dependent density-functional theory with Lanczos chains

We introduce a new implementation of time-dependent density-functional theory which allows the entire spectrum of a molecule or extended system to be computed with a numerical effort comparable to that of a single standard ground-state calculation. This method is particularly well suited for large systems and/or large basis sets, such as plane waves or real-space grids. By using a superoperator formulation of linearized time-dependent density-functional theory, we first represent the dynamical polarizability of an interacting-electron system as an off-diagonal matrix element of the resolvent of the Liouvillian superoperator. One-electron operators and density matrices are treated using a representation borrowed from time-independent density-functional perturbation theory, which permits us to avoid the calculation of unoccupied Kohn-Sham orbitals. The resolvent of the Liouvillian is evaluated through a newly developed algorithm based on the nonsymmetric Lanczos method. Each step of the Lanczos recursion essentially requires twice as many operations as a single step of the iterative diagonalization of the unperturbed Kohn-Sham Hamiltonian. Suitable extrapolation of the Lanczos coefficients allows for a dramatic reduction of the number of Lanczos steps necessary to obtain well converged spectra, bringing such number down to hundreds (or a few thousands, at worst) in typical plane-wave pseudopotential applications. The resulting numerical workload is only a few times larger than that needed by a ground-state Kohn-Sham calculation for a same system. Our method is demonstrated with the calculation of the spectra of benzene, C(60) fullerene, and of chlorophyll a.

Efficient approach to time-dependent density-functional perturbation theory for optical spectroscopy.

Using a superoperator formulation of linearized time-dependent density-functional theory, the dynamical polarizability of a system of interacting electrons is represented by a matrix continued fraction whose coefficients can be obtained from the nonsymmetric block-Lanczos method. The resulting algorithm, which is particularly convenient when large basis sets are used, allows for the calculation of the full spectrum of a system with a computational workload only a few times larger than needed for static polarizabilities within time-independent density-functional perturbation theory. The method is demonstrated with calculation of the spectrum of benzene, and prospects for its application to the large-scale calculation of optical spectra are discussed.

turboTDDFT – A code for the simulation of molecular spectra using the Liouville–Lanczos approach to time-dependent density-functional perturbation theory☆

We introduce turboTDDFT, an implementation of the Liouville-Lanczos approach to linearized time-dependent density-functional theory, designed to simulate the optical spectra of molecular systems made of up to several hundred atoms. turboTDDFT is open-source software distributed under the terms of the GPL as a component of Quantum ESPRESSO. As with other components, turboTDDFT is optimized to run on a variety of di erent platforms, from laptops to massively parallel architectures, using native mathematical libraries (LAPACK and FFTW) and a hierarchy of custom parallelization layers built on top of MPI.

Proton Transfer and Structure-Specific Fluorescence in Hydrogen Bond-Rich Protein Structures.

Protein structures which form fibrils have recently been shown to absorb light at energies in the near UV range and to exhibit a structure-specific fluorescence in the visible range even in the absence of aromatic amino acids. However, the molecular origin of this phenomenon has so far remained elusive. Here, we combine ab initio molecular dynamics simulations and fluorescence spectroscopy to demonstrate that these intrinsically fluorescent protein fibrils are permissive to proton transfer across hydrogen bonds which can lower electron excitation energies and thereby decrease the likelihood of energy dissipation associated with conventional hydrogen bonds. The importance of proton transfer on the intrinsic fluorescence observed in protein fibrils is signified by large reductions in the fluorescence intensity upon either fully protonating, or deprotonating, the fibrils at pH = 0 or 14, respectively. Thus, our results point to the existence of a structure-specific fluorophore that does not require the presence of aromatic residues or multiple bond conjugation that characterize conventional fluorescent systems. The phenomenon may have a wide range of implications in biological systems and in the design of self-assembled functional materials.

Water adsorption and dissociation on α-Fe2O3(0001): PBE+U calculations.

Adsorption and dissociation of water on different oxygen- and iron-terminated hematite(0001) surfaces at monolayer coverage have been studied by density-functional theory calculations, including a Hubbard-like+U correction. We considered six possible surface terminations, including four oxygen- and two iron-terminations. Binding energy of water on these terminations can be as large as 1.0 eV. On these terminations the energy barrier for the dissociation of the molecularly adsorbed water is less than 0.3 eV, and in few cases the dissociation is even spontaneous, i.e., without any detectable barrier. Our results thus suggest that water can be adsorbed on the α-Fe2O3(0001) surface dissociatively at room temperature, as previously found by experiment. This study also presents a very first theoretical insight into the adsorption and dissociation of water on all known terminations of the hematite(0001) surface.

Ultrasoft pseudopotentials in time-dependent density-functional theory

We describe an efficient formulation allowing the use of ultrasoft pseudopotentials (USPPs) in plane wave based time-dependent density-functional theory. The practical steps required to implement USPP functionality within real time propagation schemes and linear-response schemes based on Lanczos algorithms are provided. The functioning of the methodology is demonstrated by calculations of the optical absorption spectra of the fullerene C(60), using both real time propagation and the Lanczos/linear-response approaches. Comparisons between the rates of convergence of the optical spectra with the number of applications of the Hamiltonian required in calculations with ultrasoft pseudopotentials and norm-conserving pseudopotentials show clearly the benefits provided by the use of USPP.

Dielectric and thermal effects on the optical properties of natural dyes: a case study on solvated cyanin.

The optical properties of the flavylium state of the cyanin dye are simulated numerically by combining Car-Parrinello molecular dynamics and linear-response time-dependent density functional theory calculations. The spectrum of the dye calculated in the gas phase is characterized by two peaks in the yellow and in the blue (green and violet), using a GGA-PBE (hybrid-B3LYP) DFT functional, which would bring about a greenish (bright orange) color incompatible with the dark purple hue observed in nature. Describing the effect of the water solvent through a polarizable continuum model does not modify qualitatively the resulting picture. An explicit simulation of both solvent and thermal effects using ab initio molecular dynamics results instead in a spectrum that is compatible with the observed coloration. This result is analyzed in terms of the spectroscopic effects of the molecular distortions induced by thermal fluctuations.

Photo-driven oxidation of water on α-Fe2O3 surfaces: An ab initio study

Adopting the theoretical scheme developed by the Nørskov group [see, for example, Nørskov et al., J. Phys. Chem. B 108, 17886 (2004)], we conducted a density functional theory study of photo-driven oxidation processes of water on various terminations of the clean hematite (α-Fe2O3) (0001) surface, explicitly taking into account the strong correlation among the 3d states of iron through the Hubbard U parameter. Six best-known terminations, namely, Fe−Fe−O3− (we call S1), O−Fe−Fe−(S2), O2−Fe−Fe−(S3), O3−Fe−Fe− (S4), Fe−O3−Fe− (S5), and O−Fe−O3−(S6), are first exposed to water, the stability of resulting surfaces is investigated under photoelectrochemical conditions by considering different chemical reactions (and their reaction free energies) that lead to surfaces covered by O atoms or/and OH groups. Assuming that the water splitting reaction is driven by the redox potential for photogenerated holes with respect to the normal hydrogen electrode, UVB, at voltage larger than UVB, most 3-oxygen terminated substrates are stable. These results thus suggest that the surface, hydroxylated in the dark, should release protons under illumination. Considering the surface free energy of all the possible terminations shows that O3–S5 and O3–S1 are the most thermodynamically stable. While water oxidation process on the former requires an overpotential of 1.22 V, only 0.84 V is needed on the latter.