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.

An active learning procedure called deep potential generator (DP-GEN) is proposed for the construction of accurate and transferable machine learning-based models of the potential energy surface (PES) for the molecular modeling of materials. This procedure consists of three main components: exploration, generation of accurate reference data, and training. Application to the sample systems of Al, Mg, and Al-Mg alloys demonstrates that DP-GEN can produce uniformly accurate PES models with a minimal number of reference data.

https://link.aps.org/accepted/10.1103/PhysRevMaterials.3.023804

Active learning of uniformly accurate interatomic potentials for materials simulation

We show than an ab initio molecular-dynamics scheme based on Vanderbilt ultrasoft pseudopotentials and a plane-wave expansion for the electronic orbitals allows one to perform accurate calculations for large systems containing tightly bound d-electron states. We use a novel real-space double-grid technique to deal efficiently with the localized augmentation functions in the core region. We apply our scheme in a full molecular-dynamics simulation of liquid copper at a temperature of 1500 K and find structural and dynamical properties that are in excellent agreement with experimental data.

/pdf/ab-initio-molecular-dynamics-for-d-electron-systems-liquid-x0v1rojg9o.pdf

Ab initio molecular dynamics for d -electron systems: Liquid copper at 1500 K

In this work, we report the results of a series of density functional theory (DFT) based ab initio molecular dynamics (AIMD) simulations of ambient liquid water using a hierarchy of exchange-correlation (XC) functionals to investigate the individual and collective effects of exact exchange (Exx), via the PBE0 hybrid functional, non-local van der Waals/dispersion (vdW) interactions, via a fully self-consistent density-dependent dispersion correction, and an approximate treatment of nuclear quantum effects, via a 30 K increase in the simulation temperature, on the microscopic structure of liquid water. Based on these AIMD simulations, we found that the collective inclusion of Exx and vdW as resulting from a large-scale AIMD simulation of (H2O)128 significantly softens the structure of ambient liquid water and yields an oxygen-oxygen structure factor, SOO(Q), and corresponding oxygen-oxygen radial distribution function, gOO(r), that are now in quantitative agreement with the best available experimental data. This level of agreement between simulation and experiment demonstrated herein originates from an increase in the relative population of water molecules in the interstitial region between the first and second coordination shells, a collective reorganization in the liquid phase which is facilitated by a weakening of the hydrogen bond strength by the use of a hybrid XC functional, coupled with a relative stabilization of the resultant disordered liquid water configurations by the inclusion of non-local vdW/dispersion interactions. This increasingly more accurate description of the underlying hydrogen bond network in liquid water also yields higher-order correlation functions, such as the oxygen-oxygen-oxygen triplet angular distribution, POOO(θ), and therefore the degree of local tetrahedrality, as well as electrostatic properties, such as the effective molecular dipole moment, that are in much better agreement with experiment.

The individual and collective effects of exact exchange and dispersion interactions on the ab initio structure of liquid water

We present an investigation of the structural and electronic properties of the sodium clusters ${\mathrm{Na}}_{\mathrm{n}}$ and ${\mathrm{Na}}_{\mathrm{n}}$${\mathrm{}}^{+}$ with n\ensuremath{\le}8 and n=13, based on self-consistent pseudopotential local-spin-density calculations. In order to obtain the equilibrium geometries without imposing any symmetry constraint, we start from randomly generated cluster geometries and let them relax under the action of the forces on the atoms, which are derived from the Hellmann-Feynman theory. We find that the clusters with up to five atoms have planar equilibrium geometries, the six-atom cluster is quasiplanar, and real three-dimensional structures only begin to occur when the number of atoms is greater than or equal to seven. We compare our results with recently obtained experimental data and find good agreement with the measured photoionization appearance potentials and the electron-spin-resonance spectra. Metallic bonding is the dominant feature of our calculated electronic structures and we show that the equilibrium geometries can be explained with a simple model having the delocalized nature of the metallic electrons and the Jahn-Teller effect as basic ingredients.

Electronic and structural properties of sodium clusters

We study the binding of molecular oxygen to a graphene sheet and to a (8,0) single walled carbon nanotube, by means of spin-unrestricted density-functional calculations. We find that triplet oxygen retains its spin-polarized state when interacting with graphene or the nanotube. This leads to the formation of a weak bond with essentially no charge transfer between the molecule and the sheet or tube, as one would expect for a physisorptive bond. This result is independent on the approximation used for the exchange-correlation functional. The binding strength, however, depends strongly on the functional, reflecting the inability of current approximation functionals to deal correctly with dispersion forces. Gradient-corrected functionals yield very weak binding at distances around 4 A, whereas local density functional results yield substantially stronger binding for both graphene and the nanotube at distances of less than 3 A. The picture of oxygen physisorption is not substantially altered by the presence of topological defects such as 5–7 Stone–Wales pairs.

/pdf/oxygen-adsorption-on-graphite-and-nanotubes-52k9lh9en8.pdf

Roberto Car

Papers

Active learning of uniformly accurate interatomic potentials for materials simulation

Ab initio molecular dynamics for d -electron systems: Liquid copper at 1500 K

The individual and collective effects of exact exchange and dispersion interactions on the ab initio structure of liquid water

Electronic and structural properties of sodium clusters

Oxygen adsorption on graphite and nanotubes