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

Metallo-organic molecules with highly conjugated pi-electrons, like phthalocyanines (Pc's), are widely investigated for usage in electronic and electro-optic devices. However, their weak coupling with semiconductors is an obstacle to technological applications. Here we report a first-principle theoretical study of some fundamental features of the Pc-semiconductor interaction. Our results shed light on the general problem of organic-inorganic coupling and show that an effective coupling can be achieved by a careful choice of the Pc-substrate system and the semiconductor doping. Our results also reveal a universal alignment of the Pc electronic levels to the semiconductor band gap and suggest a general procedure for designing efficiently coupled organic-inorganic systems.

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Theoretical design of coupled organic-inorganic systems.

We study the interactions of NO2 gas molecules with Rh nanoparticles supported on graphene, using first-principles molecular dynamics in the Car–Parrinello scheme. The stability, morphology, adsorption energies of various models of Rhx nanoparticles (x = 1, 3, 10, 20) supported on graphene, and the binding of NO2 molecules to the Rh clusters, together with its effect on the graphene properties, are reported. Metastable flat structures anchored to the substrate that can bind NO2 to Rh via both N and O atoms are identified, with adsorption energies in the range 60–70 kcal per mole per molecule.

The interactions of nitrogen dioxide with graphene-stabilized Rh clusters: a DFT study.

Improved understanding of metal–graphene contacts

The classical moment problem for continued fraction expansion of relaxation functions is surveyed. The theory is then extended to the moment problem associated to relaxation operators or super-operators. Numerical aspects and sensitivity of algorithms to round-off errors are also examined. A new convenient approach is developed exploiting a product-difference recursive scheme, within the memory function formalism.



Nous examinons ici le probleme classique des moments pour l'expansion en fraction continue des fonctions de relaxation. La theorie est en outre etendu au probleme des moments associe a operateurs ou super-operateurs de relaxation. Nous examinons aussi les aspects numeriques et la sensibilite d'algorithmes a erreurs „round-off”. Nous developpons une nouvelle et convenable approche qui utilise un schema de recurrence produit-difference, dans le contexte du formalisme de la fonction de memoire.

The Classical and Generalized Moment Problem in the Theory of Relaxation

Quantum ESPRESSO (QE) starts in 2002 as a DEMOCRITOS initiative, in collaboration with SISSA, CINECA and with research groups in Princeton University, MIT, EPF Lausanne [1]. The name “ESPRESSO” stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization, while “Quantum” stresses its scope: first-principle (i.e. based on the electronic structure) calculations within DensityFunctional Theory (DFT) in a plane-wave (PW) pseudopotential (PP) approach. Building upon pre-existing codes, QE is evolving into a distribution, open to external contributions: QE is released under the terms of the General Public License (GPL). Different categories of scientists may find QE useful for their research work:

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Paolo Giannozzi

Papers

Theoretical design of coupled organic-inorganic systems.

The interactions of nitrogen dioxide with graphene-stabilized Rh clusters: a DFT study.

Improved understanding of metal–graphene contacts

The Classical and Generalized Moment Problem in the Theory of Relaxation

Large-scale computing with Quantum ESPRESSO