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

In the present study, an extensive investigation of the molecule−surface interaction in hybrid systems formed by phthalocyanines (Pcs) and inorganic semiconductors (IS) has been performed by using ...

/pdf/ab-initio-theoretical-investigation-of-phthalocyanine-144amk621m.pdf

Ab initio Theoretical Investigation of Phthalocyanine−Semiconductor Hybrid Systems

The effects of external and internal strains and of defect charges on the formation of gallium vacancies and arsenic antisites in GaAs and ${\mathrm{In}}_{0.5}{\mathrm{Ga}}_{0.5}\mathrm{As}$ have been investigated by ab initio density functional methods. Present results show that a proper understanding of strain and defect charge permits the development of a defect engineering of semiconductors. Specifically, they predict that arsenic antisites in InGaAs ternary alloys can form, upon $p$-type doping in the presence of an arsenic overpressure, even in the case of high-temperature epitaxial growths.

Effects of strain and local charge on the formation of deep defects in III-V ternary alloys

First-principles pseudopotential calculations are reported for the lattice distortion and electronic properties of the Al substitutional defect in $\ensuremath{\alpha}$ quartz. We determine microscopical properties of the center such as Al coordination, symmetry of the distorted lattice and defect-induced electronic states. The localization properties of the electronic spin density of this paramagnetic color center are investigated. Our results show that the spin density is evenly distributed on the four oxygen nearest neighbors to Al in contrast to phenomenological model results.

Microscopic structure of the substitutional Al defect in α quartz

Previous theoretical studies on N-H complexes in GaAsN have been extended here to new di-hydrogen complex configurations and to N-H complexes in the In 0 . 2 5 Ga 0 . 7 5 As 0 . 9 7 N 0 . 0 3 alloy. Moreover, a deeper analysis has been performed on the structure, formation energies, chemical bonding and electronic properties of old and new N-H complexes in the above alloys. On the ground of the achieved results, the existence of a novel di-hydrogen complex is predicted that is characterized by a C 2 v symmetry and peculiar vibrational properties. Complexes with this symmetry are not stable in N-free GaAs. Further, we propose a sound model for the N passivation founded on the characteristics of the electronic states and the local atomic relaxations induced by the N-H complexes. This model explains why the N passivation is not achieved in the case of monohydrogen complexes and realized through the formation of the N-H* 2 dihydrogen complexes. Finally, it is suggested that different N-H complexes (and different vibrational spectra) should be observed in hydrogenated p-type and n-type N-containing alloys.

Nitrogen passivation by atomic hydrogen in GaAs y N 1 − y and In x Ga 1 − x As y N 1 − y alloys

Ab initio calculations of the phonon spectrum of ${\mathrm{K}}_{6}{\mathrm{C}}_{60}$ are presented, based on the local-density approximation of density-functional theory and on linear response theory. The effects of doping on frequencies and infrared intensities are identified and their physical origin discussed in detail for optically allowed modes. Whereas structural relaxation is primarily responsible for the frequency changes, and especially for the softening of tangential modes, the change in infrared relative intensities is a direct consequence of the electron transfer. The potassium vibrations are found to lie within $60--100{\mathrm{cm}}^{\ensuremath{-}1}$ and are well decoupled from ${\mathrm{C}}_{60}$ intramolecular modes.

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Paolo Giannozzi

Papers

Ab initio Theoretical Investigation of Phthalocyanine−Semiconductor Hybrid Systems

Effects of strain and local charge on the formation of deep defects in III-V ternary alloys

Microscopic structure of the substitutional Al defect in α quartz

Nitrogen passivation by atomic hydrogen in GaAs y N 1 − y and In x Ga 1 − x As y N 1 − y alloys

Effects of Doping on the Vibrational Properties of C60 from First Principles: K6C60.