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.

Fast parallel algorithms for short-range molecular dynamics

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.

/pdf/quantum-espresso-a-modular-and-open-source-software-project-4t6vlupbeh.pdf

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

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.

https://iopscience.iop.org/article/10.1088/0953-8984/14/11/301/pdf

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

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.

/pdf/phonons-and-related-crystal-properties-from-density-3mdybdn8w1.pdf

Phonons and related crystal properties from density-functional perturbation theory

https://repository.kulib.kyoto-u.ac.jp/dspace/bitstream/2433/202086/1/j.scriptamat.2015.07.021.pdf

First principles phonon calculations in materials science

Phonon spectra of ultrathin (GaAs${)}_{\mathrm{n}}$(AlAs${)}_{\mathrm{n}}$ (001) superlattices are studied theoretically using linear-response density-functional techniques. Results are presented for n=1,2,3 superlattices, along with prototype supercell calculations aimed at simulating a completely disordered (alloy) as well as some partially disordered superlattices. Besides interfacial disorder, which modifies the effective confinement length of low-order longitudinal-optic phonons, we find that\char22{}in the ultrathin regime\char22{}some degree of cationic mixing must also affect inner planes in order to explain experimental findings.

/pdf/phonon-spectra-of-ultrathin-gaas-alas-superlattices-an-ab-185y7tozhi.pdf

Phonon spectra of ultrathin GaAs/AlAs superlattices: An ab initio calculation.

We present first-principles calculations of the properties of atomic and molecular hydrogen in pure bulk GaAs. Our results indicate that H penetrates into GaAs in atomic form. Inside GaAs, atomic H tends to form ${\mathrm{H}}_{2}$ molecules in tetrahedral sites, which are deep energy wells for ${\mathrm{H}}_{2}$. The ${\mathrm{H}}_{2}^{\mathrm{*}}$ defect, formed by one H in a bond-center site and one H in an adjacent tetrahedral position, has higher energy than ${\mathrm{H}}_{2}$ but lower-energy barriers for diffusion. Isolated H could be present as a metastable species. We compute the stable charge state of isolated H as a function of the Fermi energy. Our results suggest that H behaves as a negative-U defect. As a consequence, isolated H is expected to be present only as a charged species (positively charged in p-doped samples, negatively charged in undoped and n-doped samples). Our conclusions are compared with experimental results and with the results of calculations for H in other semiconductors. The main features of H in GaAs are quite similar to what has been found in Si.

Atomic and molecular hydrogen in gallium arsenide: A theoretical study.

The vibrational properties of ${\mathrm{Ga}}_{\mathit{x}}$${\mathrm{Al}}_{1\mathrm{\ensuremath{-}}\mathit{x}}$As alloys have been studied using large supercells to simulate the disorder and ab initio interatomic force constants. In agreement with recent experimental evidence, our results indicate that well defined GaAs-like and AlAs-like phonon dispersions exist for any concentration. Besides broadening phonon states with definite wave vector, alloying narrows the optic branches and lowers the longitudinal modes more than the transverse ones, thus reducing the LO-TO splitting. The acoustic bands are instead rather insensitive to the composition.

Phonon dispersions in Ga x Al 1 − x As alloys

The calculation of vibrational properties of materials from their electronic structure is an important goal for materials modeling. A wide variety of physical properties of materials depend on their lattice-dynamical behavior: specific heats, thermal expansion, and heat conduction; phenomena related to the electron‐phonon interaction such as the resistivity of metals, superconductivity, and the temperature dependence of optical spectra, are just a few of them. Moreover, vibrational spectroscopy is a very important tool for the characterization of materials. Vibrational frequencies are routinely and accurately measured mainly using infrared and Raman spectroscopy, as well as inelastic neutron scattering. The resulting vibrational spectra are a sensitive probe of the local bonding and chemical structure. Accurate calculations of frequencies and displacement patterns can thus yield a wealth of information on the atomic and electronic structure of materials. In the Born‐Oppenheimer (adiabatic) approximation, the nuclear motion is determined by the nuclear Hamiltonian H:

Density-functional perturbation theory

An intercalation compound of azafullerene, K6C59N, was prepared and structurally characterized. It is isostructural with the fullerene compound K6C60, adopts a body-centered- cubic structure (lattice constant a = 11.31 angstroms), and consists of quasi-spherical monomeric (C59N)6− ions. Density functional calculations of the structural and electronic properties confirm the similarity to K6C60 but also suggest a sizable deformation, principally confined in the vicinity of the nitrogen atom, of both the molecular structure and the electron states. These results show that study of the intercalation chemistry of azafullerene promises to reveal a rich family of both n- and p-doped systems with novel conducting and magnetic properties, like their fullerene antecedents.

https://science.sciencemag.org/content/sci/271/5257/1833.full.pdf

Paolo Giannozzi

Papers

Phonon spectra of ultrathin GaAs/AlAs superlattices: An ab initio calculation.

Atomic and molecular hydrogen in gallium arsenide: A theoretical study.

Phonon dispersions in Ga x Al 1 − x As alloys

Density-functional perturbation theory

Isolation, Structure, and Electronic Calculations of the Heterofullerene Salt K6C59N