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.

By employing mechanical work analogies, we derive a convenient computational approach for evaluation of the free energy profile (FEP) along some discretized path defined as a sequence of hyperplanes. A hyperplane is fully specified by any of its point and a tangent vector. The FEP is obtained as an integral of two components. The translational component of the free energy is computed by integrating the hyperplane constraint force. The rotational component is evaluated via the hyperplane torque. Both ingredients—the constraint force and the hyperplane torque—are evaluated on each hyperplane independently. The integration procedure utilizes a set of reference points defining a point of rotation on each hyperplane, and these points can be chosen before or after the sampling takes place. A shift in the reference points redistributes the FEP contributions between the translational and rotational components. For systems where the FEP is dominated by the potential energy differences, reference points residing on the minimum energy path present a natural choice. We demonstrate the validity of our approach on two examples, a simple two-dimensional (2D) potential, and a seven-atom Lennard-Jones cluster. In each case, we compare the numerical FEP with the harmonic approximation estimates. Our results for the 2D potential are also verified by the data available in the literature. In both cases, the rotational component of the FEP represents a sizable contribution to the total FEP, so ignoring it would yield clearly incorrect results.

http://mcc.uiuc.edu/workshops/electronicstructure/2005/abstracts/posters/kudin_es2005.pdf

Free energy profile along a discretized reaction path via the hyperplane constraint force and torque

The equilibrium geometries of Nan clusters (n ⩽ 7) are calculated by letting randomly generated clusters relax under the action of the Hellmann-Feynman forces. We find that clusters with five atoms or less have a planar structure whereas larger clusters have closely packed three-dimensional geometries. The calculated adiabatic ionization potentials are in good agreement with the experimental appearance potentials.

Calculation of Cluster Geometries with the Help of Hellmann-Feynman Forces

We present a Monte Carlo method for computing the renormalized coupling constants and the critical exponents within renormalization theory. The scheme, which derives from a variational principle, overcomes critical slowing down, by means of a bias potential that renders the coarse grained variables uncorrelated. The two-dimensional Ising model is used to illustrate the method.

Variational Approach to Monte Carlo Renormalization Group

Metal molten salt solutions exhibit a number of interesting properties with variation of the metal concentration. In the dilute limit, the metal valence electrons are released to form F-center-like localized states. At higher concentrations, metallic behavior sets in. A theoretical approach to the properties of these systems obviously requires a correct quantum-mechanical treatment of the solvated electrons. We show here that an approach that uses a local spin density description of many electron interactions, is a powerful and efficient method for the study of the adiabatic dynamics of such systems. We apply our approach to the case of one and two solvated electrons. In the first case we confirm the F-center model and elucidate the mechanism of electron diffusion. In the case of two solvated electrons, we find that parallel spin electrons repel each other and form separate F-center-like states. Antiparallel spin electrons, instead, attract each other and coalesce into a single bipolaronic complex. The diffusion of the bipolaron, while bound, occurs on a ionic time scale. However, dissociation process occur during which the electrons can acquire a high mobility leading to a large electronic diffusion. At even higher concentrations preliminary indication of clustering and of metallic behavior are observed.

http://iopscience.iop.org/article/10.1088/0031-8949/1989/T25/048/pdf

Simulation of electrons in molten salts

We explored the reactivity of the active center of the [FeFe]-hydrogenases detached from the enzyme and immersed in acidified water by first-principles Car−Parrinello molecular-dynamics simulations...

Roberto Car

Papers

Free energy profile along a discretized reaction path via the hyperplane constraint force and torque

Calculation of Cluster Geometries with the Help of Hellmann-Feynman Forces

Variational Approach to Monte Carlo Renormalization Group

Simulation of electrons in molten salts

Hydrogen production by the naked active site of the di-iron hydrogenases in water.