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.

/pdf/quantum-espresso-a-modular-and-open-source-software-project-4t6vlupbeh.pdf

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

Carbonyl group generation on single-wall carbon nanotubes with nitric acid: A theoretical description

Theory of electronic states in lattices and superlattices

This papers resolves a long standing experimental paradox in one of the most promising hydrogen storage materials. The authors use an innovative simulation technique to show that rapid molecular rotations explain how a molecule with a three-fold rotational axis crystallizes at room temperature into a form with a four-fold symmetry about the same axis.

/pdf/positional-disorder-in-ammonia-borane-at-ambient-conditions-147z41ked2.pdf

Positional disorder in ammonia borane at ambient conditions

The structural, electronic and magnetic properties of the MIL-47(Mn) metal–organic framework are investigated using first principles calculations. We find that the large-pore structure is the ground state of this material. We show that upon transition from the large-pore to the narrow-pore structure, the magnetic ground-state configuration changes from antiferromagnetic to ferromagnetic, consistent with the computed values of the intra-chain coupling constant. Furthermore, the antiferromagnetic and ferromagnetic configuration phases have intrinsically different electronic behavior: the former is semiconducting, the latter is a metal or half-metal. The change of electronic properties during breathing posits MIL-47(Mn) as a good candidate for sensing and other applications. Our calculated electronic band structure for MIL-47(Mn) presents a combination of flat dispersionless and strongly dispersive regions in the valence and conduction bands, indicative of quasi-1D electronic behavior. The spin coupling constants are obtained by mapping the total energies onto a spin Hamiltonian. The inter-chain coupling is found to be at least one order of magnitude smaller than the intra-chain coupling for both large and narrow pores. Interestingly, the intra-chain coupling changes sign and becomes five times stronger going from the large pore to the narrow pore structure. As such MIL-47(Mn) could provide unique opportunities for tunable low-dimensional magnetism in transition metal oxide systems.

/pdf/investigation-of-structural-electronic-and-magnetic-3srqxk1uwa.pdf

Investigation of structural, electronic and magnetic properties of breathing metal─organic framework MIL-47(Mn): a first principles approach

We used Density Functional Theory (DFT) to study the Fermi level pinning and Schottky barrier height in metal-MoS2 contacts. We showed that the Fermi level de-pinning could be attained by controlling the distance between the metal and MoS2. In particular, with proper buffer layers and the use of back-gated structures, the Schottky barrier height can be practically zeroed in some metal-MoS2 stacks, which is important to attain Ohmic contacts.

Paolo Giannozzi

Papers

Carbonyl group generation on single-wall carbon nanotubes with nitric acid: A theoretical description

Theory of electronic states in lattices and superlattices

Positional disorder in ammonia borane at ambient conditions

Investigation of structural, electronic and magnetic properties of breathing metal─organic framework MIL-47(Mn): a first principles approach

Simulation study of Fermi level depinning in metal-MoS2 contacts