Paolo Giannozzi

Bio: Paolo Giannozzi is an academic researcher from University of Udine. The author has contributed to research in topics: Density functional theory & Ab initio. The author has an hindex of 38, co-authored 122 publications receiving 44408 citations. Previous affiliations of Paolo Giannozzi include Nest Labs & École Polytechnique Fédérale de Lausanne.

Zn induced structural aggregation patterns of β-amyloid peptides by first-principle simulations and XAS measurements

Abstract: We show in this paper that in the presence of Zn ions a peculiar structural aggregation pattern of β-amyloid peptides in which metal ions are sequentially coordinated to either three or four histidines of nearby peptides is favored. To stabilize this configuration a deprotonated imidazole ring from one of the histidines forms a bridge connecting two adjacent Zn ions. Though present in zeolite imidazolate frameworks, remarkably in biological compounds this peculiar Zn–imidazolate–Zn topology is only found in enzymes belonging to the Cu,Zn-superoxide dismutase family in the form of an imidazolate bridging Cu and Zn. The results we present are obtained by combining X-ray absorption spectroscopy experimental data with detailed first-principle molecular dynamics simulations.

Reconstruction of frozen-core all-electron orbitals from pseudo-orbitals

Abstract: We investigate the numerical feasibility of reconstructing frozen-core all-electron molecular orbitals from corresponding pseudo-orbitals. We perform density-functional calculations on simple atomic and molecular model systems using ultrasoft pseudopotentials to represent the atomic cores. We apply a transformation due to Blochl [Phys. Rev. B 50, 17953 (1994)] to each calculated pseudo-orbital to obtain a corresponding frozen-core all-electron molecular orbital. Our model systems include the reconstruction of the 5d orbital of a gold atom, and the occupied valence states of the TiO2 molecule. Comparison of the resulting all-electron orbitals to corresponding ones that were obtained from calculations in which the core electrons were explicitly included indicates that all-electron molecular orbital reconstruction is a feasible and useful operation in reproducing the correct behavior of molecular orbitals in the nuclear core regions.

Fast hybrid density-functional computations using plane-wave basis sets

Abstract: A new, very fast, implementation of the exact (Fock) exchange operator for electronic structure calculations within the plane-wave pseudopotential method is described in detail for both molecular and periodic systems, and carefully validated. Our method combines the recently proposed Adaptively Compressed Exchange approach, to reduce the number of times the exchange is evaluated in the self-consistent loop, with an orbital localization procedure that reduces the number of exchange integrals to be computed at each evaluation and potentially the compute time of each of them. The new implementation, already available in the Quantum ESPRESSO distribution, results in a speedup that is never smaller than 3-4x and that increases with the size of the system, according to various realistic benchmark calculations.

Fast parallel algorithms for short-range molecular dynamics

Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

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

Abstract: 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.

First-principles simulation: ideas, illustrations and the CASTEP code

Abstract: First-principles simulation, meaning density-functional theory calculations with plane waves and pseudopotentials, has become a prized technique in condensed-matter theory. Here I look at the basics of the suject, give a brief review of the theory, examining the strengths and weaknesses of its implementation, and illustrating some of the ways simulators approach problems through a small case study. I also discuss why and how modern software design methods have been used in writing a completely new modular version of the CASTEP code.

Phonons and related crystal properties from density-functional perturbation theory

Abstract: This article reviews the current status of lattice-dynamical calculations in crystals, using density-functional perturbation theory, with emphasis on the plane-wave pseudopotential method. Several specialized topics are treated, including the implementation for metals, the calculation of the response to macroscopic electric fields and their relevance to long-wavelength vibrations in polar materials, the response to strain deformations, and higher-order responses. The success of this methodology is demonstrated with a number of applications existing in the literature.