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.

We present a quantum-kinetic scheme for the calculation of non-equilibrium transport properties in nanoscale systems. The approach is based on a Liouville-master equation for a reduced density operator and represents a generalization of the well-known Boltzmann kinetic equation. The system, subject to an external electromotive force, is described using periodic boundary conditions. We demonstrate the feasibility of the approach by applying it to a double-barrier resonant tunneling structure.

Kinetic theory of quantum transport at the nanoscale

A combination of low-energy electron diffraction, x-ray and ultraviolet photoelectron spectroscopy, and scanning-tunneling microscopy studies, in conjunction with ab initio calculations leads us to suggest a model for the carbon (C)-induced $\mathrm{Si}(001)c(4\ifmmode\times\else\texttimes\fi{}4)$ atomic structure. This surface superstructure is obtained in a defined range of ${\mathrm{C}}_{2}{\mathrm{H}}_{4}$ exposures at 600 \ifmmode^\circ\else\textdegree\fi{}C. Experimental probes show that the $c(4\ifmmode\times\else\texttimes\fi{}4)$ superstructure involves C atoms in both surface and subsurface sites. This is reflected in well-marked features in photoemission valence- and core-level spectra. Surface carbon atoms are stabilized in Si-C heterodimers, with a surface density of about 0.25 monolayer (ML) [i.e., two C atoms per $c(4\ifmmode\times\else\texttimes\fi{}4)$ unit cell of eight atoms]. In the subsurface region, carbon atoms substitute for Si atoms in well-defined sites of the third or fourth layers of the Si substrate. The subsurface C density increases with ${\mathrm{C}}_{2}{\mathrm{H}}_{4}$ exposure time up to a limit value of about 0.5 ML, within the $c(4\ifmmode\times\else\texttimes\fi{}4)$ surface structure. Further exposure disrupts the $c(4\ifmmode\times\else\texttimes\fi{}4)$ reconstruction and leads to a $(2\ifmmode\times\else\texttimes\fi{}1)$ low-energy electron diffraction pattern. Interaction with atomic hydrogen shows that the surface contains a mixture of heterodimers (Si-C) and homodimers (Si-Si), with an 1:1 proportion. These assignments are supported by first-principle calculations, which yield valence band and core level states in fairly good agreement with the experiment. Furthermore, total energy calculations strongly favor C incorporation in surface Si-C dimers and in third and fourth layer sites, and rule out C incorporation in sites of the second Si layer. The most stable $c(4\ifmmode\times\else\texttimes\fi{}4)$ surface configuration, suggested by our calculations, consists of alternate Si-C and Si-Si dimer lines. In such a configuration, surface carbon atoms in Si-C dimers induce a surface stress that leads to charge redistribution and atomic relaxation of the adjacent Si-Si dimers, consistent with scanning-tunneling microscopy images. Additional C atoms (in excess of those accommodated in surface sites) are forced in selected compressive (\ensuremath{\alpha}) sites of the third and fourth layers. This model is discussed with respect to the previous models published in the literature.

Atomic structure of carbon-induced Si(001)c(4x4) reconstruction as a Si-Si homodimer and C-Si heterodimer network

Structural transitions in aluminum clusters

We introduce the notion of a band-inverted, topological semimetal in two-dimensional nonsymmorphic crystals. This notion is materialized in the monolayers of MTe$_2$ (M $=$ W, Mo) if spin-orbit coupling is neglected. We characterize the Dirac band touching topologically by the Wilson loop of the non-Abelian Berry gauge field. An additional feature of the Dirac cone in monolayer MTe$_2$ is that it tilts over in a Lifshitz transition to produce electron and hole pockets, a type-II Dirac cone. These pockets, together with the pseudospin structure of the Dirac electrons, suggest a unified, topological explanation for the recently-reported, non-saturating magnetoresistance in WTe$_2$, as well as its circular dichroism in photoemission. We complement our analysis and first-principle bandstructure calculations with an $\textit{ab-initio}$-derived-derived tight-binding model for the WTe$_2$ monolayer.

Tilted Dirac Fermions

Time-dependent DFT calculations reveal a strong dependence of low-lying excited states on the <Fe−O−O angle of a model O2-heme adduct and ready access to a metastable side-on isomer. The predicted state crossings provide a pathway for internal conversion to the ground state and account for the low quantum yield for O2 dissociation, while the side-on isomer can account for the observation of an unphotolyzable fraction at low temperature. For CO-heme, the angle-sensitive states lie above the photoaccessed Q state and do not participate in photodissociation.

Roberto Car

Papers

Kinetic theory of quantum transport at the nanoscale

Atomic structure of carbon-induced Si(001)c(4x4) reconstruction as a Si-Si homodimer and C-Si heterodimer network

Structural transitions in aluminum clusters

Tilted Dirac Fermions

Role of ligand bending in the photodissociation of O2 vs CO-heme: a time-dependent density functional study.