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 develop a plane-wave pseudopotential scheme for noncollinear magnetic structures, based on a generalized local spin-density theory in which the direction of the magnetization is a continuous variable of position. We allow the atomic and magnetic structures to relax simultaneously and self-consistently. Application to small Fe clusters yields noncollinear magnetic structures for Fe-3 and Fe-5. The components of the magnetization density vary smoothly with position. The spin direction undergoes sizable changes only in the regions of small charge and spin density between the atoms and is generally uniform in the magnetic regions of the atoms.

Fully Unconstrained Approach to Noncollinear Magnetism: Application to Small Fe Clusters

We introduce a scheme for molecular simulations, the deep potential molecular dynamics (DPMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data. The neural network model preserves all the natural symmetries in the problem. It is first-principles based in the sense that there are no ad hoc components aside from the network model. We show that the proposed scheme provides an efficient and accurate protocol in a variety of systems, including bulk materials and molecules. In all these cases, DPMD gives results that are essentially indistinguishable from the original data, at a cost that scales linearly with system size.

Deep Potential Molecular Dynamics: a Scalable Model with the Accuracy of Quantum Mechanics

An amorphous carbon structure is obtained with a computer simulation based on a first-principles molecular-dynamics method, in which the interatomic potential is constructed directly from the electronic ground state, using density-functional techniques. From our results, which agree well with the limited experimental information available, we analyze the short-range order, particularly the fractions of $s{p}^{2}$ and $s{p}^{3}$ sites, together with the electronic properties.

Structural and electronic properties of amorphous carbon.

Design principles and predictions of new three-dimensional (3D) Dirac semimetals are presented and placed in the context of currently known materials. Three different design principles are presented (cases I, II, and III), each of which yields predictions for new candidates. For case I, 3D Dirac semimetals based on charge-balanced compounds BaAgBi, SrAgBi, YbAuSb, ${\mathrm{PtBi}}_{2}$, and ${\mathrm{SrSn}}_{2}{\mathrm{As}}_{2}$ are identified as candidates. For case II, 3D Dirac semimetals in analogy to graphene, ${\mathrm{BaGa}}_{2}$ is identified as a candidate, and BaPt and ${\mathrm{Li}}_{2}\mathrm{Pt}$ are discussed. For case III, 3D Dirac semimetals based on glide planes and screw axes, ${\mathrm{TlMo}}_{3}{\mathrm{Te}}_{3}$ and the $A{\mathrm{Mo}}_{3}{X}_{3}$ family, in general ($A=\text{K}$, Na, In, Tl; $X=\text{Se}$,Te), as well as the Group IVb trihalides such as ${\mathrm{HfI}}_{3}$, are identified as candidates. Finally, we discuss conventional intermetallic compounds with Dirac cones and identify ${\mathrm{Cr}}_{2}\mathrm{B}$ as a potentially interesting material.

Three-dimensional Dirac semimetals: Design principles and predictions of new materials

The uncatalyzed edge growth of carbon nanotubes was investigated by first-principles molecular dynamics simulations. At experimental temperatures the open end of single-walled nanotubes closed spontaneously into a graphitic dome, which may explain why these nanotubes do not grow in the absence of transition metal catalysts, On the other hand, chemical bonding between the edges of adjacent coaxial tubes (''lip-lip'' interactions) trapped the end oi a double-walled nanotube in a metastable energy minimum, thus preventing dome closure. These calculations show that this end geometry exhibits a high degree of chemical activity and easily accommodates incoming carbon fragments, supporting a model of growth by chemisorption from the vapor phase.

Roberto Car

Papers

Fully Unconstrained Approach to Noncollinear Magnetism: Application to Small Fe Clusters

Deep Potential Molecular Dynamics: a Scalable Model with the Accuracy of Quantum Mechanics

Structural and electronic properties of amorphous carbon.

Three-dimensional Dirac semimetals: Design principles and predictions of new materials

Microscopic growth mechanisms for carbon nanotubes