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

http://experimentationlab.berkeley.edu/sites/default/files/AFMImages/butt_AFM.pdf

Force measurements with the atomic force microscope: Technique, interpretation and applications

Simple rules for the understanding of Heusler compounds

: The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

High-throughput computational materials design is an emerging area of materials science. By combining advanced thermodynamic and electronic-structure methods with intelligent data mining and database construction, and exploiting the power of current supercomputer architectures, scientists generate, manage and analyse enormous data repositories for the discovery of novel materials. In this Review we provide a current snapshot of this rapidly evolving field, and highlight the challenges and opportunities that lie ahead.

The high-throughput highway to computational materials design

Here, we review the basic concepts and applications of the phase-field-crystal (PFC) method, which is one of the latest simulation methodologies in materials science for problems, where atomic- and microscales are tightly coupled. The PFC method operates on atomic length and diffusive time scales, and thus constitutes a computationally efficient alternative to molecular simulation methods. Its intense development in materials science started fairly recently following the work by Elder et al. [Phys. Rev. Lett. 88 (2002), p. 245701]. Since these initial studies, dynamical density functional theory and thermodynamic concepts have been linked to the PFC approach to serve as further theoretical fundamentals for the latter. In this review, we summarize these methodological development steps as well as the most important applications of the PFC method with a special focus on the interaction of development steps taken in hard and soft matter physics, respectively. Doing so, we hope to present today's state of the...

/pdf/phase-field-crystal-models-for-condensed-matter-dynamics-on-1gju86z5x3.pdf

Phase-field-crystal models for condensed matter dynamics on atomic length and diffusive time scales: an overview

Here, we review the basic concepts and applications of the phase-field-crystal (PFC) method, which is one of the latest simulation methodologies in materials science for problems, where atomic- and microscales are tightly coupled. The PFC method operates on atomic length and diffusive time scales, and thus constitutes a computationally efficient alternative to molecular simulation methods. Its intense development in materials science started fairly recently following the work by Elder et al. [Phys. Rev. Lett. 88 (2002), p. 245701]. Since these initial studies, dynamical density functional theory and thermodynamic concepts have been linked to the PFC approach to serve as further theoretical fundaments for the latter. In this review, we summarize these methodological development steps as well as the most important applications of the PFC method with a special focus on the interaction of development steps taken in hard and soft matter physics, respectively. Doing so, we hope to present today's state of the art in PFC modelling as well as the potential, which might still arise from this method in physics and materials science in the nearby future.

/pdf/phase-field-crystal-models-for-condensed-matter-dynamics-on-415vrp3ta1.pdf

Half-Heusler compounds $XYZ$ crystallize in the space group $F\overline{4}3m$ and can be viewed as a zinc-blende-like ${(YZ)}^{\ensuremath{-}}$ lattice partially filled with He-like ${X}^{+}$ interstitials. In this work, we investigated I-II-V (eight-electrons) half-Heusler compounds by first-principles calculations in order to find suitable semiconductors for optoelectronics such as Cd-free buffer layer materials for chalcopyrite-based thin-film solar-cell devices. We report a systematic examination of band gaps and lattice parameters, depending on the electronegativities and the ion radii of the involved elements. Half-Heusler buffer materials should have a band gap of more than 2 eV to avoid absorption losses and a lattice constant of about $5.9\text{ }\text{\AA{}}$ to match the crystal structure of the absorber material. With these criteria we selected seven half-Heusler compounds as candidates for a buffer layer material.

I-II-V half-Heusler compounds for optoelectronics: Ab initio calculations

For the advancement of optoelectronic applications, such as thin-film solar cells or laser diodes, there is a strong demand for new semiconductor materials with tailored structural and electronic properties. The eight-electron half-Heusler compounds include many promising materials with a big variety of lattice constants and band gaps. So far only a small number of them have been investigated. With the help of ab initio calculations, we have studied all possible configurations of ternary 1:1:1 compounds in the half-Heusler structure. We have investigated 648 half-Heusler materials, including compounds of the types I-I-VI, I-II-V, I-III-IV, II-II-IV, and II-III-III. For all compounds, we have optimized the lattice constant and determined the most stable arrangement of elements on the half-Heusler lattice sites. Preferred configurations and semiconductivities are compared for the different half-Heusler types. A discussion of the lattice geometries provides a parameter-free function for estimating the lattice constants. The calculated band gaps and lattice constants are used to select potential substitute materials for CdS in the buffer layer of ${\text{CuInSe}}_{2}$ and $\text{Cu}(\text{In},\text{Ga}){\text{Se}}_{2}$ thin-film solar cells.

Thomas Gruhn

Papers

Phase-field-crystal models for condensed matter dynamics on atomic length and diffusive time scales: an overview

Phase-field-crystal models for condensed matter dynamics on atomic length and diffusive time scales: an overview

I-II-V half-Heusler compounds for optoelectronics: Ab initio calculations

Comparative ab initio study of half-Heusler compounds for optoelectronic applications

Microscopic structure of molecularly thin confined liquid-crystal films