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

We have developed and implemented a selfconsistent density functional method using standard norm-conserving pseudopotentials and a flexible, numerical linear combination of atomic orbitals basis set, which includes multiple-zeta and polarization orbitals. Exchange and correlation are treated with the local spin density or generalized gradient approximations. The basis functions and the electron density are projected on a real-space grid, in order to calculate the Hartree and exchange-correlation potentials and matrix elements, with a number of operations that scales linearly with the size of the system. We use a modified energy functional, whose minimization produces orthogonal wavefunctions and the same energy and density as the Kohn-Sham energy functional, without the need for an explicit orthogonalization. Additionally, using localized Wannier-like electron wavefunctions allows the computation time and memory required to minimize the energy to also scale linearly with the size of the system. Forces and stresses are also calculated efficiently and accurately, thus allowing structural relaxation and molecular dynamics simulations.

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The SIESTA method for ab initio order-N materials simulation

I. Introduction: Conceptual vs Fundamental andComputational Aspects of DFT1793II. Fundamental and Computational Aspects of DFT 1795A. The Basics of DFT: The Hohenberg−KohnTheorems1795B. DFT as a Tool for Calculating Atomic andMolecular Properties: The Kohn−ShamEquations1796C. Electronic Chemical Potential andElectronegativity: Bridging Computational andConceptual DFT1797III. DFT-Based Concepts and Principles 1798A. General Scheme: Nalewajski’s ChargeSensitivity Analysis1798B. Concepts and Their Calculation 18001. Electronegativity and the ElectronicChemical Potential18002. Global Hardness and Softness 18023. The Electronic Fukui Function, LocalSoftness, and Softness Kernel18074. Local Hardness and Hardness Kernel 18135. The Molecular Shape FunctionsSimilarity 18146. The Nuclear Fukui Function and ItsDerivatives18167. Spin-Polarized Generalizations 18198. Solvent Effects 18209. Time Evolution of Reactivity Indices 1821C. Principles 18221. Sanderson’s Electronegativity EqualizationPrinciple18222. Pearson’s Hard and Soft Acids andBases Principle18253. The Maximum Hardness Principle 1829IV. Applications 1833A. Atoms and Functional Groups 1833B. Molecular Properties 18381. Dipole Moment, Hardness, Softness, andRelated Properties18382. Conformation 18403. Aromaticity 1840C. Reactivity 18421. Introduction 18422. Comparison of Intramolecular ReactivitySequences18443. Comparison of Intermolecular ReactivitySequences18494. Excited States 1857D. Clusters and Catalysis 1858V. Conclusions 1860VI. Glossary of Most Important Symbols andAcronyms1860VII. Acknowledgments 1861VIII. Note Added in Proof 1862IX. References 1865

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Conceptual density functional theory.

In the past ten years we have witnessed a revival of, and subsequent rapid expansion in, the research on zinc oxide (ZnO) as a semiconductor. Being initially considered as a substrate for GaN and related alloys, the availability of high-quality large bulk single crystals, the strong luminescence demonstrated in optically pumped lasers and the prospects of gaining control over its electrical conductivity have led a large number of groups to turn their research for electronic and photonic devices to ZnO in its own right. The high electron mobility, high thermal conductivity, wide and direct band gap and large exciton binding energy make ZnO suitable for a wide range of devices, including transparent thin-film transistors, photodetectors, light-emitting diodes and laser diodes that operate in the blue and ultraviolet region of the spectrum. In spite of the recent rapid developments, controlling the electrical conductivity of ZnO has remained a major challenge. While a number of research groups have reported achieving p-type ZnO, there are still problems concerning the reproducibility of the results and the stability of the p-type conductivity. Even the cause of the commonly observed unintentional n-type conductivity in as-grown ZnO is still under debate. One approach to address these issues consists of growing high-quality single crystalline bulk and thin films in which the concentrations of impurities and intrinsic defects are controlled. In this review we discuss the status of ZnO as a semiconductor. We first discuss the growth of bulk and epitaxial films, growth conditions and their influence on the incorporation of native defects and impurities. We then present the theory of doping and native defects in ZnO based on density-functional calculations, discussing the stability and electronic structure of native point defects and impurities and their influence on the electrical conductivity and optical properties of ZnO. We pay special attention to the possible causes of the unintentional n-type conductivity, emphasize the role of impurities, critically review the current status of p-type doping and address possible routes to controlling the electrical conductivity in ZnO. Finally, we discuss band-gap engineering using MgZnO and CdZnO alloys.

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Fundamentals of zinc oxide as a semiconductor

We have performed a comprehensive first-principles investigation of native point defects in ZnO based on density functional theory within the local density approximation (LDA) as well as the $\mathrm{LDA}+U$ approach for overcoming the band-gap problem. Oxygen deficiency, manifested in the form of oxygen vacancies and zinc interstitials, has long been invoked as the source of the commonly observed unintentional $n$-type conductivity in ZnO. However, contrary to the conventional wisdom, we find that native point defects are very unlikely to be the cause of unintentional $n$-type conductivity. Oxygen vacancies, which have most often been cited as the cause of unintentional doping, are deep rather than shallow donors and have high formation energies in $n$-type ZnO (and are therefore unlikely to form). Zinc interstitials are shallow donors, but they also have high formation energies in $n$-type ZnO and are fast diffusers with migration barriers as low as $0.57\phantom{\rule{0.3em}{0ex}}\mathrm{eV}$; they are therefore unlikely to be stable. Zinc antisites are also shallow donors but their high formation energies (even in Zn-rich conditions) render them unlikely to be stable under equilibrium conditions. We have, however, identified a different low-energy atomic configuration for zinc antisites that may play a role under nonequilibrium conditions such as irradiation. Zinc vacancies are deep acceptors and probably related to the frequently observed green luminescence; they act as compensating centers in $n$-type ZnO. Oxygen interstitials have high formation energies; they can occur as electrically neutral split interstitials in semi-insulating and $p$-type materials or as deep acceptors at octahedral interstitial sites in $n$-type ZnO. Oxygen antisites have very high formation energies and are unlikely to exist in measurable concentrations under equilibrium conditions. Based on our results for migration energy barriers, we calculate activation energies for self-diffusion and estimate defect-annealing temperatures. Our results provide a guide to more refined experimental studies of point defects in ZnO and their influence on the control of $p$-type doping.

Native point defects in ZnO

The convergence of the electrostatic energy in calculations using periodic boundary conditions is considered in the context of periodic solids and localized aperiodic systems in the gas and condensed phases. Conditions for the absolute convergence of the total energy in periodic boundary conditions are obtained, and their implications for calculations of the properties of polarized solids under the zero-field assumption are discussed. For aperiodic systems the exact electrostatic energy functional in periodic boundary conditions is obtained. The convergence in such systems is considered in the limit of large supercells, where, in the gas phase, the computational effort is proportional to the volume. It is shown that for neutral localized aperiodic systems in either the gas or condensed phases, the energy can always be made to converge as O(${\mathit{L}}^{\mathrm{\ensuremath{-}}5}$) where L is the linear dimension of the supercell. For charged systems, convergence at this rate can be achieved after adding correction terms to the energy to account for spurious interactions induced by the periodic boundary conditions. These terms are derived exactly for the gas phase and heuristically for the condensed phase.

Periodic boundary conditions in ab initio calculations.

Density functional theory(DFT) is one of the most widely used methods for ab initio calculations of the structure of atoms, molecules, crystals, surfaces, and their interactions. Unfortunately, the customary introduction to DFT is often considered too lengthy to be included in various curricula. An alternative introduction to DFT is presented here, drawing on ideas which are well-known from thermodynamics, especially the idea of switching between different independent variables. The central theme of DFT, i.e., the notion that it is possible and beneficial to replace the dependence on the external potential v(r) by a dependence on the density distribution n(r), is presented as a straightforward generalization of the familiar Legendre transform from the chemical potential μ to the number of particles N. This approach is used here to introduce the Hohenberg–Kohn energy functional and to obtain the corresponding theorems, using classical nonuniform fluids as simple examples. The energy functional for electronic systems is considered next, and the Kohn–Sham equations are derived. The exchange-correlation part of this functional is discussed, including both the local density approximation to it, and its formally exact expression in terms of the exchange-correlation hole. A very brief survey of various applications and extensions is included.

http://www.giovannibachelet.it/AJP-Argaman-DFT.pdf

Density functional theory: An introduction

The ionization potential of small metal and dielectric spheres is considered in different frameworks: classical, semiclassical, and quantum mechanical density functional approach. Classical calculations give conflicting results, and the generally accepted result for the ionization potential of a metal sphere of radius R: WI(R)=bulk work function+(3/8)q2/R is shown to be wrong, resulting from the classical image potential too close to the metal surface. Using appropriate cutoff to the image potential, the result WI(R)=bulk work function+(1/2)q2/R (previously obtained from solvation energy considerations) is recovered. Experimental results on relatively large particles are in agreement with the latter result. For very small clusters, deviations of experimental results from this classical behavior are shown by a density functional calculation to arise from quantum mechanical effects. These are first the spilloff of the electronic wave functions beyond the cluster edge and secondly from exchange and correlati...

On the ionization potential of small metal and dielectric particles

We report on the synthesis of the newly discovered cubic phase of tin sulfide π-SnS and compare its properties to the well-known phase of tin sulfide, α-SnS. Shape control was achieved by the variation of synthesis parameters, resulting in cubic, rhombic dodecahedral and tetrahedral shapes of the π-SnS nanoparticles. X-ray diffraction provided authentication of the proposed model and refined determination of the lattice parameter a = 11.595 A. Raman spectroscopy showed a substantial shift towards higher energies and peak splitting for π-SnS. Optical absorption spectroscopy indicated an indirect band gap of 1.53 eV, in good agreement with density functional theory (DFT) calculations indicating a band gap greater than that of α-SnS. DFT total energy calculations show that the π-SnS phase is energetically similar to α-SnS, and is significantly more stable than the hypothetical ideal rocksalt structure of SnS.

Guy Makov

Papers

Periodic boundary conditions in ab initio calculations.

Density functional theory: An introduction

On the ionization potential of small metal and dielectric particles

Synthesis and properties of nanocrystalline π-SnS – a new cubic phase of tin sulphide

Chemical Hardness in Density Functional Theory