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.

X-ray absorption of liquid water studied by advanced ab initio methods

Jeremy C. Palmer, ∗ Amir Haji-Akbari, † Rakesh S. Singh, Fausto Martelli, Roberto Car, Athanassios Z. Panagiotopoulos, and Pablo G. Debenedetti ‡ Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, USA Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, USA Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA (Dated: December 25, 2017)

Notes on the Hybrid Monte Carlo Method

As a promising layered electrode material, TiS2-based capacitive deionization (CDI) devices for water desalination have attracted significant attention. However, TiS2/H2O interfacial features, potentially important for device optimization, remain unidentified. Using Deep Potential Molecular Dynamics (DPMD), we characterized distinct aqueous interfaces introduced by four TiS2 terminations expected to be present as water intercalates into TiS2, namely, Armchair, Zigzag, Zigzag-L, and Zigzag-R. First, we assessed important representative physical properties of the system to validate the deep potentials (DPs). DPMD simulations agree well with experiments and first-principles simulations, suggesting the DPs are accurate and reliable. Subsequent simulations of these TiS2/water interfaces revealed how TiS2 surface termination influences the structure of interfacial water. This effect is most evident in the first and second water layers close to the TiS2 surface, and more pronounced when spontaneous dissociative adsorption of water occurs. The extent of water dissociation on each surface was evaluated using enhanced sampling. Zigzag-L is the only interface where proton transfer from adsorbed water to TiS2 surface S atoms is thermodynamically and kinetically favored. The coexistence of surface four-fold-coordinated Ti (Ti4c) and one-fold-coordinated S (S1c) is found to be essential to making proton transfer feasible on the Zigzag-L surface. Furthermore, remaining unprotonated S1c atoms can act as good proton acceptors after water dissociation. Thus, TiS2 with Zigzag-L termination may be a surface to avoid in CDI device construction, given that pH fluctuations adversely affect performance. This work provides new understanding of TiS2/H2O interfacial features that could aid future design and optimization of TiS2-based CDI devices for water desalination. 

Characterizing Structure-Dependent TiS2/Water Interfaces Using Deep-Neural-Network-Assisted Molecular Dynamics

Cu(001)表面におけるCuアドアトムの拡散機構

Roberto Car tells Nature Materials how the Car–Parrinello molecular dynamics method originated and how his research career has evolved since then.

Roberto Car

Papers

X-ray absorption of liquid water studied by advanced ab initio methods

Notes on the Hybrid Monte Carlo Method

Characterizing Structure-Dependent TiS2/Water Interfaces Using Deep-Neural-Network-Assisted Molecular Dynamics

Cu(001)表面におけるCuアドアトムの拡散機構

From ab initio onwards