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

The two low-energy isomers of C{sub 61}H{sub 2} are the parent molecules of fulleroids and methanofullerenes. We present a thorough study of their structural and electronic properties within the density functional theory, in the local-density approximation and also including gradient corrections to the exchange and correlation functionals. Calculations are performed both on the isolated molecules and on the solid phases. Changes with respect to C{sub 60} as well as differences between the two C{sub 61}H{sub 2} isomers are described with regard to geometrical characteristics, bond patterns, valence charge distribution, and electronic energy bands. Our results can be considered a paradigm for the study of fulleroids and methanofullerenes. 37 refs., 7 figs., 6 tabs.

/pdf/c61h2-in-molecular-and-solid-phases-density-functional-sb3gup4yy0.pdf

C61h2 in molecular and solid phases : density-functional approach to structural and electronic properties

We present the theory and the application of a first-principle transport model employing a basis set obtained directly from the ab initio Bloch functions. We use a plane-wave density functional theory Hamiltonian and show that a judicious choice of the reduced basis set can effectively suppress the potentially thorny problem of the unphysical solutions. Our methodology enables ab initio transport simulations with a huge reduction of the size of the problem compared to the original ab initio formulation. Moreover, the approach can also be used for local and nonlocal empirical pseudopotential Hamiltonians, thus promising a wide range of possible applications. We report results for ab initio simulations of ${\mathrm{MoS}}_{2}$ field effect transistors, where the transport and electrostatics equations are solved self-consistently for channel lengths up to about 20 nanometers. The simulation results rapidly converge with the size of the basis set, so that the blocks of the Hamiltonian matrix can be reduced to a size below 100. Our methodology is a viable approach for ab initio and semiempirical quantum transport simulations and, in particular, it offers an alternative to the use of maximally localized Wannier functions.

/pdf/unit-cell-restricted-bloch-functions-basis-for-first-1ek5ty7oav.pdf

Unit cell restricted Bloch functions basis for first-principle transport models: Theory and application

Alexis Amezaga,1,2 Erik Holmstrom,3 Raquel Lizarraga,3 Eduardo Menendez-Proupin,2 P. Bartolo-Perez,4 and Paolo Giannozzi5,6 1Instituto de Matematicas, Facultad de Ciencias, Universidad Austral de Chile, Casilla, Valdivia, Chile 2Departamento de Fisica, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, 780-0024 Nunoa, Santiago, Chile 3Instituto de Fisica, Facultad de Ciencias, Universidad Austral de Chile, Casilla 567, Valdivia, Chile 4Departamento de Fisica Aplicada, CINVESTAV-IPN, Unidad Merida, A.P. 73 Cordemex, 97310 Merida, Yucatan, Mexico 5Department of Physics, University of Udine, via delle Scienze 208, I-33100 Udine, Italy 6CNR-INFM DEMOCRITOS National Simulation Center, I-34014 Trieste, Italy Received 13 September 2009; revised manuscript received 10 December 2009; published 27 January 2010

/pdf/quantitative-local-environment-characterization-in-amorphous-gzjnuiciwt.pdf

Quantitative local environment characterization in amorphous oxides

Raman cross section for the pentagonal-pinch mode in buckminsterfullerene C60

The weak-chemisorption/charge-transfer picture for adsorption of aromatic molecules over carbon nanotubes, proposed in the commented paper, is criticized.

/pdf/comment-on-noncovalent-functionalization-of-carbon-nanotubes-4th8uhez4t.pdf

Paolo Giannozzi

Papers

C61h2 in molecular and solid phases : density-functional approach to structural and electronic properties

Unit cell restricted Bloch functions basis for first-principle transport models: Theory and application

Quantitative local environment characterization in amorphous oxides

Raman cross section for the pentagonal-pinch mode in buckminsterfullerene C60

Comment on “Noncovalent functionalization of carbon nanotubes by aromatic organic molecules” [Appl. Phys. Lett. 82, 3746 (2003)]