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.

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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

Quantum ESPRESSO is an open-source distribution of computer codes for quantum-mechanical materials modeling, based on density-functional theory, pseudopotentials, and plane waves, and renowned for its performance on a wide range of hardware architectures, from laptops to massively parallel computers, as well as for the breadth of its applications. In this paper we present a motivation and brief review of the ongoing effort to port Quantum ESPRESSO onto heterogeneous architectures based on hardware accelerators, which will overcome the energy constraints that are currently hindering the way towards exascale computing.

Quantum ESPRESSO toward the exascale.

We study the binding of molecular oxygen to a graphene sheet and to a (8,0) single walled carbon nanotube, by means of spin-unrestricted density-functional calculations. We find that triplet oxygen retains its spin-polarized state when interacting with graphene or the nanotube. This leads to the formation of a weak bond with essentially no charge transfer between the molecule and the sheet or tube, as one would expect for a physisorptive bond. This result is independent on the approximation used for the exchange-correlation functional. The binding strength, however, depends strongly on the functional, reflecting the inability of current approximation functionals to deal correctly with dispersion forces. Gradient-corrected functionals yield very weak binding at distances around 4 A, whereas local density functional results yield substantially stronger binding for both graphene and the nanotube at distances of less than 3 A. The picture of oxygen physisorption is not substantially altered by the presence of topological defects such as 5–7 Stone–Wales pairs.

/pdf/oxygen-adsorption-on-graphite-and-nanotubes-52k9lh9en8.pdf

Oxygen adsorption on graphite and nanotubes

Computer simulations allow for the investigation of many materials properties and processes that are not easily accessible in the laboratory. This is particularly true in the Earth sciences, where the relevant pressures and temperatures may be so extreme that no experimental techniques can operate at those conditions. Computer modeling is often the only source of information on the properties of materials that, combined with indirect evidence (such as seismic data), allows one to discriminate among competing planetary models. Many computer simulations are performed using effective interatomic potentials tailored to reproduce some experimentally observed properties of the materials being investigated. The remoteness of the physically interesting conditions from those achievable in the laboratory, as well as the huge variety of different atomic coordination and local chemical state occurring in the Earth interior, make the dependability of semi-empirical potentials questionable. First-principles techniques based on density-functional theory (DFT) (Hohenberg and Kohn 1964; Kohn and Sham 1965) are much more predictive, not being biased by any prior experimental input, and have demonstrated a considerable accuracy in a wide class of materials and variety of external conditions. The importance of thermal effects in the range of phenomena interesting to the Earth sciences makes a proper account of atomic motion essential. Traditionally, this is achieved using molecular dynamics techniques which have been successfully combined with DFT in the first-principles molecular dynamics technique of Car and Parrinello (1985). Well below the melting temperature, the numerical efficiency of molecular dynamics is limited by the lack of ergodicity, which would require long simulation times, and by the importance of long-wavelength collective motions (phonons), which would require large simulation cells. Both difficulties are successfully dealt with in the quasi-harmonic approximation (QHA) where the thermal properties of solid materials are traced back to those of a system of non-interacting …

Density-Functional Perturbation Theory for Quasi-Harmonic Calculations

This paper gives a short overview of the calculation of thermal properties of materials from first principles, using the Quasi-Harmonic Approximation (QHA) We first introduce some of the thermal properties of interest and describe how they can be calculated in the framework of the QHA; then we briefly recall Density-Functional Perturbation Theory as a tool for calculating phonons from first principles, and present some codes that implement it; finally we review recent applications of first-principle QHA

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Thermal properties of materials from ab-initio quasi-harmonic phonons

We present a first-principles calculation of lattice dynamical properties of diamond. Our calculations have been performed using density-functional perturbation theory together with plane-wave expansion and nonlocal pseudopotentials. As a first step we have evaluated the equilibrium structure of diamond via the minimization of the total energy. Then, harmonic phonon dispersion curves and phonon eigenvectors have been evaluated within the linear-response framework. As a by-product of the calculation we have also obtained the internal-strain parameter. Furthermore, we have also tested the validity of the ab initio calculation for describing properties beyond the harmonic approximation. Using the quasiharmonic approximation we have calculated the thermal expansion coefficient and the mode Gr\"uneisen parameter dispersion curves. Where experimental data are available, good agreement is found with our theoretical predictions.

Paolo Giannozzi

Papers

Quantum ESPRESSO toward the exascale.

Oxygen adsorption on graphite and nanotubes

Density-Functional Perturbation Theory for Quasi-Harmonic Calculations

Thermal properties of materials from ab-initio quasi-harmonic phonons

Ab initio lattice dynamics of diamond