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

We report the observation and analysis of the low frequency vibrational modes of green fluorescent proteins (GFPs). Our study exploits the surface enhanced Raman scattering technique, which allowed the analysis of the vibrational modes of the proteins down to 300 cm � 1 . Here we present results on two GFP mutants, namely S65T/F64L GFP (EGFP) and S65T/F64L/T203Y GFP (E 2 GFP). These particularly bright mutants display almost inverted population ratio of anionic (B) to neutral (A) forms of the chromophore. By comparing the vibrational spectrum of the proteins with that of a synthetic model chromophore in solution and with the aid of first principle calculations based on density functional theory, we identify the Raman active bands in this region of frequencies. A dominant collective mode at 720 cm � 1 is found and assigned to a collective planar deformation of the chromophore. Low frequency vibrational modes belonging specifically to A and/or Bstructural configurations are also identified. This work demonstrates the possibility of monitoring the structural sub-states of GFPs through vibrational spectroscopy in a range of frequencies where collective modes peculiar of the double ring structure of the chromophore lie. 2002 Elsevier Science B.V. All rights reserved.

/pdf/the-low-frequency-vibrational-modes-of-green-fluorescent-4fm30sggr2.pdf

The low frequency vibrational modes of green fluorescent proteins

We present the results of local-density-approximation-based Car-Parrinello calculations of orientationally ordered phases of ${\mathrm{K}}_{3}$${\mathrm{C}}_{60}$ and ${\mathrm{K}}_{6}$${\mathrm{C}}_{60}$. Our investigation focuses on the following points: the effects of alkali-mental intercalation on the structural and electronic properties of ${\mathrm{C}}_{60}$, the chemical bonding, the inhomogeneity of the electron distribution, and the degree of freedom of the potassium atoms in the interstitial region. The results are discussed in view of experimental data, such as x-ray and neutron-diffraction data as well as nuclear magnetic resonance spectroscopy.

Molecular structure and chemical bonding in K 3 C 60 and K 6 C 60

We present the results of pseudopotential density-functional supercell calculations of the properties of neutral hydrogen in bulk GaAs. The equilibrium sites are determined, and the electronic properties for the equilibrium positions are studied. We find that the equilibrium site for unrelaxed GaAs:H is in the low-valence-charge-density region, whereas if the relaxation of the whole lattice is allowed, a shallow equilibrium minimum occurs at an antibonding site near an As ion. The diffusion path is in the high-valence-charge-density region around the As ions with a barrier as low as 0.1 eV. From our results, we suggest that H behaves as a deep acceptor in n-type GaAs and as a deep donor in p-type GaAs, and occupies different positions. Hence passivation of dopants occurs by neutralization.

Amphoteric behavior of H 0 in GaAs

Static and dynamical density functional theory calculations have been carried out to investigate the coordination and haptotropic rearrangement of the Cr(CO)3 fragment on the (6,0) carbon nanotube sidewalls. Geometry optimizations have been performed on the Cr(CO)3−(C72H12) complex, pointing out the preferred coordination sites of the metal fragment on the nanotube sidewalls. We find a hole site configuration of the Cr(CO)3 to be the global energy minimum of the Cr(CO)3−(C72H12) system, with a binding energy of 143 kJ mol-1. The shifting of the Cr(CO)3 complex between two coordination sites on adjacent hexagonal rings of (6,0) carbon nanotubes has been investigated by means of Car−Parrinello simulations, from which the transition state structure for the haptrotropic rearrangement has been localized and found to be 68 kJ mol-1 above the global minimum structure.

Paolo Giannozzi

Papers

The low frequency vibrational modes of green fluorescent proteins

Molecular structure and chemical bonding in K 3 C 60 and K 6 C 60

Amphoteric behavior of H 0 in GaAs

Coordination and Haptotropic Rearrangement of Cr(CO)3 on (n,0) Nanotube Sidewalls: A Dynamical Density Functional Study

The ordinary and matrix continued fractions in the theoretical analysis of Hermitian and relaxation operators