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.

/pdf/quantum-espresso-a-modular-and-open-source-software-project-4t6vlupbeh.pdf

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.

Migration of a carbon adatom on a charged single-walled carbon nanotube

We illustrate a method for performing first-principles free-energy calculations within the Kohn-Sham scheme. We show that the method can be used in cases in which electrons have to be decoupled from the system and illustrate it with results for the formation free energy of the Si vacancy. The results agree well with the available data from experiments and ab initio calculations. \textcopyright{} 1996 The American Physical Society.

First-principles free-energy calculations on condensed-matter systems: Lattice vacancy in silicon.

We investigate atomic and molecular nanostructures on metal surfaces by variable low-temperature scanning tunnelling microscopy. In combination with molecular dynamics calculations we achieve a detailed understanding of the stability of these structures.¶Atomic nanostructures in homoepitaxial metallic systems are thermodynamically only metastable. Two-dimensional islands on Ag(110) decay above a threshold temperature of Tl=175 K. Caused by the anisotropy of the surface, distinct decay behaviours exist above and below a critical temperature of Tc=220 K. Calculations based on effective medium potentials of the underlying rate limiting atomic processes allow us to identify the one-dimensional decay below Tc as well as the two-dimensional decay above Tc.¶In contrast to atoms, the intermolecular electrostatic interaction of polar molecules leads to thermodynamically stable structures. On the reconstructed Au(111) surface, the pseudo-chiral 1-nitronaphthalin forms two-dimensional supermolecular clusters consisting predominantly of ten molecules. Comparison of images with submolecular resolution to local density calculations elucidates the thermodynamical stability as well as the internal structure of the decamers.

Stability of two-dimensional nanostructures

This is a self-contained discussion of a recently proposed theoretical approach for off-resonance tunneling transport. The final result is an analytic formula for the asymptotic tunneling conductance involving the overlap of three well-defined physical quantities that can be easily evaluated with the standard electronic structure codes. We argue that the formula can be used to gain fresh insight into the tunneling transport characteristics of various systems. The formalism is applied to molecular devices consisting of planar phenyl chains connected to gold electrodes via amine linkers.

Theory of tunneling transport in periodic chains

In this work, an investigation of supercritical water is presented combining inelastic and deep inelastic neutron scattering experiments and molecular dynamics simulations based on a machine-learned potential of ab initio quality. The local hydrogen dynamics is investigated at 250 bar and in the temperature range of 553-823 K, covering the evolution from subcritical liquid to supercritical gas-like water. The evolution of libration, bending, and stretching motions in the vibrational density of states is studied, analyzing the spectral features by a mode decomposition. Moreover, the hydrogen nuclear momentum distribution is measured, and its anisotropy is probed experimentally. It is shown that hydrogen bonds survive up to the higher temperatures investigated, and we discuss our results in the framework of the coupling between intramolecular modes and intermolecular librations. Results show that the local potential affecting hydrogen becomes less anisotropic within the molecular plane in the supercritical phase, and we attribute this result to the presence of more distorted hydrogen bonds.

Roberto Car

Papers

Migration of a carbon adatom on a charged single-walled carbon nanotube

First-principles free-energy calculations on condensed-matter systems: Lattice vacancy in silicon.

Stability of two-dimensional nanostructures

Theory of tunneling transport in periodic chains

Hydrogen Dynamics in Supercritical Water Probed by Neutron Scattering and Computer Simulations.