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.

The unified approach to density functional and molecular dynamics in real space

We present a first-principles study of positron trapping at a negatively charged As vacancy in GaAs Lattice relaxations induced both by the presence of the defect and of the positron have been included in a self-consistent way In the presence of a positron, the volume of the vacancy increases and its symmetry is lowered The positron wave function is well localized in the defect Calculated positron lifetime and angular correlations of annihilation photons are in good agreement with recent experiments

https://archive-ouverte.unige.ch/unige:93806/ATTACHMENT01

Ab initio study of positron trapping at a vacancy in GaAs.

An accurate treatment of the long-range electron correlation energy, including van der Waals (vdW) or dispersion interactions, is essential for describing the structure, dynamics, and function of a wide variety of systems. Among the most accurate models for including dispersion into density functional theory (DFT) is the range-separated many-body dispersion (MBD) method [A. Ambrosetti et al., J. Chem. Phys., 2014, 140, 18A508], in which the correlation energy is modeled at short-range by a semi-local density functional and at long-range by a model system of coupled quantum harmonic oscillators. In this work, we develop analytical gradients of the MBD energy with respect to nuclear coordinates, including all implicit coordinate dependencies arising from the partitioning of the charge density into Hirshfeld effective volumes. To demonstrate the efficiency and accuracy of these MBD gradients for geometry optimizations of systems with intermolecular and intramolecular interactions, we optimized conformers of the benzene dimer and isolated small peptides with aromatic side-chains. We find excellent agreement with the wavefunction theory reference geometries of these systems (at a fraction of the computational cost) and find that MBD consistently outperforms the popular TS and D3(BJ) dispersion corrections. To demonstrate the performance of the MBD model on a larger system with supramolecular interactions, we optimized the C60@C60H28 buckyball catcher host–guest complex. In our analysis, we also find that neglecting the implicit nuclear coordinate dependence arising from the charge density partitioning, as has been done in prior numerical treatments, leads to an unacceptable error in the MBD forces, with relative errors of ∼20% (on average) that can extend well beyond 100%.

/pdf/analytical-nuclear-gradients-for-the-range-separated-many-1ojhvwmp9g.pdf

Analytical nuclear gradients for the range-separated many-body dispersion model of noncovalent interactions

We present a simple and informationally efficient approach to electronic-structure-based simulations of large material science systems. The algorithm is based on a flexible embedding scheme, in which the parameters of a model potential are fitted at run time to some precise information relevant to localised portions of the system. Such information is computed separately on small subsystems by electronic-structure “black box” subprograms, e.g. based on tight-binding and/or ab initio models. The scheme allows to enforce electronic structure precision only when and where needed, and to minimise the computed information within a desired accuracy, which can be systematically controlled. Moreover, it is inherently linear scaling, and highly suitable for modern parallel platforms, including those based on non-uniform processing. The method is demonstrated by performing computations of tight-binding accuracy on solid state systems in the ten thousand atoms size scale.

A Novel Scheme for Accurate Md Simulations of Large Systems

We predict an oscillatory bias behavior of the fieldlike spin torque, T(perpendicular), in magnetic tunnel junctions, which can be selectively controlled via the asymmetry in band filling between the ferromagnetic leads. This can lead to a linear or quadratic low-bias behavior, including tuning the bias-induced reversal of T(perpendicular). These findings reconcile the apparently contradictory experimental results recently reported in the literature. The underlying mechanism for the nonequilibrium interlayer exchange coupling (IEC) of noncollinear configurations is the interplay of four independent IEC for the majority- and minority-spin bands of the leads solely in the ferromagnetic configuration.

/pdf/controlling-the-nonequilibrium-interlayer-exchange-coupling-2zwrr4qtze.pdf

Roberto Car

Papers

The unified approach to density functional and molecular dynamics in real space

Ab initio study of positron trapping at a vacancy in GaAs.

Analytical nuclear gradients for the range-separated many-body dispersion model of noncovalent interactions

A Novel Scheme for Accurate Md Simulations of Large Systems

Controlling the nonequilibrium interlayer exchange coupling in asymmetric magnetic tunnel junctions.