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.

The growth of carbon (C) and boron nitride (BN) nanotubes cannot be directly observed and the underlying microscopic mechanism is a controversial subject. Transition metal catalysts are necessary to produce single-walled nanotubes (SWNT) of carbon, but they are not needed in the multi-walled (MWNT) case, suggesting different growth mechanisms. Here we report on the results of first-principles dynamical simulations of both single- and double-walled carbon nanotube edges. We find that the open end of carbon SWNTs spontaneously closes by forming a graphitic dome in the 2500-3000 K temperature range of synthesis experiments. On the other hand, "lip-lip" interactions, consisting of chemical bonding between the edges of adjacent coaxial tubes, trap the end of the double-walled carbon nanotube into a metastable energy minimum, preventing dome closure. The resulting end geometry is highly chemically active, and can easily accommodate incoming carbon fragments? thus allowing growth by chemisorption from the vapour phase. The growth mechanisms of boron nitride SWNTs is studied as well, and is compared to the case of pure carbon tubes. In the experimental temperature conditions, the behavior of growing BN nanotubes strongly depends on the nanotube network helicity. In particular, we find that open-ended "zigzag" SWNTs close rapidly into an amorphous like tip? preventing further growth. In the case of "armchair" SWNTs, the formation of sro squares traps the tip into a flat cap presenting a large central even-member ring. This structure is metastable and able to revert to a growing hexagonal framework by incorporation of incoming atoms. These findings are directly related to frustration effects, namely that B-N bonds are energetically favored over B-B and N-N bonds.

Microscopic growth mechanisms for carbon and boron-nitride nanotubes

We show that a dissipative current component is present in the dynamics generated by a Liouville-master equation, in addition to the usual component associated with Hamiltonian evolution. The dissipative component originates from coarse graining in time, implicit in a master equation, and needs to be included to preserve current continuity. We derive an explicit expression for the dissipative current in the context of the Markov approximation. Finally, we illustrate our approach with a simple numerical example, in which a quantum particle is coupled to a harmonic phonon bath and dissipation is described by the Pauli master equation.

https://arxiv.org/pdf/cond-mat/0410105.pdf

Current in Open Quantum Systems

We report simulated infrared (IR) spectra of deuterated water and ice using Car--Parrinello molecular dynamics with maximally localized Wannier functions. Experimental features are accurately reproduced within the harmonic approximation. By decomposing the line shapes in terms of intramolecular and intermolecular dipole correlation functions, we find that short-range intermolecular dynamic charge fluctuations associated to hydrogen bonds are prominent over the entire spectral range. Our analysis reveals the origin of several spectral features and identifies network bending modes in the far IR range.

Role of dipolar correlations in the infrared spectra of water and ice

Structure and dynamics of small metallic clusters on an insulating metal-oxide surface : copper on mgo(100)

A first-principle molecular dynamics study on liquid GeSe2 yields structural properties in good agreement with detailed neutron scattering data. The short range order is accurately described by a variety of bonding configurations, in which regular tetrahedra coexist with an important fraction of homopolar bonds and threefold centers. The first sharp diffraction peak in the total structure factor, which characterizes order over intermediate range distances, is also well reproduced. However, this level of theory does not yield concentration fluctuations over such distances as observed in experiment.

Roberto Car

Papers

Microscopic growth mechanisms for carbon and boron-nitride nanotubes

Current in Open Quantum Systems

Role of dipolar correlations in the infrared spectra of water and ice

Structure and dynamics of small metallic clusters on an insulating metal-oxide surface : copper on mgo(100)

Microscopic structure of liquid GeSe2: The problem of concentration fluctuations over intermediate range distances