Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set

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

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

We present ab initio quantum-mechanical molecular-dynamics simulations of the liquid-metal--amorphous-semiconductor transition in Ge. Our simulations are based on (a) finite-temperature density-functional theory of the one-electron states, (b) exact energy minimization and hence calculation of the exact Hellmann-Feynman forces after each molecular-dynamics step using preconditioned conjugate-gradient techniques, (c) accurate nonlocal pseudopotentials, and (d) Nos\'e dynamics for generating a canonical ensemble. This method gives perfect control of the adiabaticity of the electron-ion ensemble and allows us to perform simulations over more than 30 ps. The computer-generated ensemble describes the structural, dynamic, and electronic properties of liquid and amorphous Ge in very good agreement with experiment. The simulation allows us to study in detail the changes in the structure-property relationship through the metal-semiconductor transition. We report a detailed analysis of the local structural properties and their changes induced by an annealing process. The geometrical, bonding, and spectral properties of defects in the disordered tetrahedral network are investigated and compared with experiment.

Ab initio molecular-dynamics simulation of the liquid-metal-amorphous-semiconductor transition in germanium.

By including a fraction of exact exchange (EXX), hybrid functionals reduce the self-interaction error in semilocal density functional theory (DFT) and thereby furnish a more accurate and reliable d...

Enabling Large-Scale Condensed-Phase Hybrid Density Functional Theory Based Ab Initio Molecular Dynamics. 1. Theory, Algorithm, and Performance.

A first-principles molecular-dynamics study of liquid NaSn alloy is presented. The structural properties (static structure factor, bond angle distribution) are discussed. The calculated static structure factor is in good agreement with that from neutron diffraction experiments. The calculations show a tendency of network formation of threefold and fourfold coordinated tin atoms in the liquid. Tetrahedral Sn4 complexes-Zintl anions (Sn44)-which are typical structural units in solid NaSn are nearly absent in the liquid. As a consequence of the network formation there is an indication of a bimodal bond angle distribution for the tin atoms.

https://iopscience.iop.org/article/10.1088/0953-8984/4/11/002/pdf

Ab initio molecular dynamics simulation of liquid NaSn alloy

We explore how anharmonicity, nuclear quantum effects (NQE), many-body dispersion interactions, and Pauli repulsion influence thermal properties of dispersion-bound molecular crystals. Accounting for anharmonicity with ab initio molecular dynamics yields cell parameters accurate to within $2%$ of experiment for a set of pyridinelike molecular crystals at finite temperatures and pressures. From the experimental thermal expansion curve, we find that pyridine-I has a Debye temperature just above its melting point, indicating sizable NQE across the entire crystalline range of stability. We find that NQE lead to a substantial volume increase in pyridine-I $(\ensuremath{\approx}40$% more than classical thermal expansion at 153 K) and attribute this to intermolecular Pauli repulsion promoted by intramolecular quantum fluctuations. When predicting delicate properties such as the thermal expansivity, we show that many-body dispersion interactions and more sophisticated density functional approximations improve the accuracy of the theoretical model.

Thermal expansion in dispersion-bound molecular crystals

Les fonctions de distribution radiale obtenues par ces deux procedures sont coherentes avec l'experience. On predit que la coordination evolue du seuil au degre six quand on augmente la densite

Liquid arsenic: Comparison of ab initio and pair-potential predictions of molecular structure.

We study diffusion of self-interstitial atoms (SIAs) in vanadium via molecular-dynamics simulations. The ⟨111⟩-split interstitials are observed to diffuse one-dimensionally at low temperature, but rotate into other ⟨111⟩ directions as the temperature is increased. The SIA diffusion is highly non-Arrhenius. At $Tl600\phantom{\rule{0.3em}{0ex}}\mathrm{K}$, this behavior arises from temperature-dependent correlations. At $Tg600\phantom{\rule{0.3em}{0ex}}\mathrm{K}$, the Arrhenius expression for thermally activated diffusion breaks down when the migration barriers become small compared to the thermal energy. This leads to Arrhenius diffusion kinetics at low $T$ and diffusivity proportional to temperature at high $T$.

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Roberto Car

Papers

Enabling Large-Scale Condensed-Phase Hybrid Density Functional Theory Based Ab Initio Molecular Dynamics. 1. Theory, Algorithm, and Performance.

Ab initio molecular dynamics simulation of liquid NaSn alloy

Thermal expansion in dispersion-bound molecular crystals

Liquid arsenic: Comparison of ab initio and pair-potential predictions of molecular structure.

Strongly Non-Arrhenius Self-Interstitial Diffusion in Vanadium