Large Scale Atomistic Simulations using the Tight Binding Approach

1997 ◽  
Vol 491 ◽  
Author(s):  
M. Celino ◽  
F. Cleri ◽  
L. Colombo ◽  
M. Rosati ◽  
V. Rosato ◽  
...  
Keyword(s):  
Computer Architecture ◽  
Amorphous Materials ◽  
Large Scale ◽  
Materials Science ◽  
Tight Binding ◽  
Hamiltonian Matrix ◽  
Extended Defects ◽  
Atomistic Modelling ◽  
New Perspective ◽  
Scaling Algorithms

ABSTRACTAtomistic modelling of Materials Science problems often requires the simulation of systems with an irreducibly-large unit cell, such as amorphous materials, fullerites, or systems containing extended defects, such as dislocations, cracks or grain boundaries. Large-scale simulations with the Tight-Binding approach must face the computational obstacle represented by the O(N3)-scaling of the diagonalization of the Hamiltonian matrix. This bottleneck can be overcome by parallel computing techniques and/or the introduction of faster, O(N)-scaling algorithms. We report the activities performed in the frame of a collaboration among several research groups on the porting of TBMD codes on parallel computers. In particular, we describe the porting of a O(N3) TBMD code on different MIMD computers, with either distributed or shared memory, by using appropriate software tools. Furthermore, preliminary results obtained in the porting of an O(N) TBMD code on an experimental, hybrid MIMD-SIMD computer architecture are reported. The new perspective of using specialized platforms to deal with large-scale TBMD simulation is discussed.

A Parallel Implementation of Tight-Binding Molecular Dynamics Based on Reordering of Atoms and the Lanczos Eigen-Solver

1995 ◽  
Vol 408 ◽  
Author(s):  
Luciano Colombot ◽  
William Sawyer ◽  
Djordje Marict
Keyword(s):  
Molecular Dynamics ◽  
Parallel Machines ◽  
Materials Science ◽  
Parallel Implementation ◽  
Tight Binding ◽  
Hamiltonian Matrix ◽  
Time Step ◽  
Full Spectrum ◽  
Eigen Values ◽  
Storage Format

AbstractWe introduce an efficient and scalable parallel implementation of tight-binding molecular dynamics (TBMD) which employs reordering of the atoms in order to maximize datalocality of the distributed tight-binding (TB) Hamiltonian matrix. Reordering of the atom labels allows our new algorithm to scale well on parallel machines since most of the TB hopping integrals for a given atom are local to the processing element (PE) therefore minimizing communication. The sparse storage format and the distribution of the required eigenvectors reduces memory requirements per PE. The sparse storage format and a stabilized parallel Lanczos eigen-solver allow consideration of large problem sizes relevant to materials science. In addition, the implementation allows the calculation of the full spectrum of individual eigen-values/-vectors of the TB matrix at each time-step. This feature is a key issue when the dielectric and optical response must be computed during a TBMD simulation. We present a benchmark of our code and an analysis of the overall efficiency.

Large-Scale Molecular Dynamics Simulations of Interstitial Defect Diffusion in Silicon

2002 ◽  
Vol 731 ◽  
Author(s):  
David A. Richie ◽  
Jeongnim Kim ◽  
Richard Hennig ◽  
Kaden Hazzard ◽  
Steve Barr ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Materials Science ◽  
Tight Binding ◽  
Md Simulations ◽  
Binding Potential ◽  
Interstitial Defect ◽  
Long Time ◽  
Computational Materials ◽  
Dynamics Simulations

AbstractThe simulation of defect dynamics and evolution is a technologicaly relevant challenge for computational materials science. The diffusion of small defects in silicon unfolds as a sequence of structural transitions. The relative infrequency of transition events requires simulation over extremely long time scales. We simulate the diffusion of small interstitial clusters (I1, I2, I3) for a range of temperatures using large-scale molecular dynamics (MD) simulations with a realistic tight-binding potential. A total of 0.25 μ sec of simulation time is accumulated for the study. A novel real-time multiresolution analysis (RTMRA) technique extracts stable structures directly from the dynamics without structural relaxation. The discovered structures are relaxed to confirm their stability.

Evolution of Metastable Structures in Bimetallic Catalysts from Microscopy and Machine-Learning Molecular Dynamics

2020 ◽  
Author(s):  
Jin Soo Lim ◽  
Jonathan Vandermause ◽  
Matthijs A. van Spronsen ◽  
Albert Musaelian ◽  
Christopher R. O’Connor ◽  
...  
Keyword(s):  
Machine Learning ◽  
Molecular Dynamics ◽  
Large Scale ◽  
Materials Science ◽  
Complete Characterization ◽  
Layer By Layer ◽  
Surface Restructuring ◽  
Metastable Structures ◽  
Mechanistic Investigation ◽  
Underlying Mechanisms

Restructuring of interface plays a crucial role in materials science and heterogeneous catalysis. Bimetallic systems, in particular, often adopt very different composition and morphology at surfaces compared to the bulk. For the first time, we reveal a detailed atomistic picture of the long-timescale restructuring of Pd deposited on Ag, using microscopy, spectroscopy, and novel simulation methods. Encapsulation of Pd by Ag always precedes layer-by-layer dissolution of Pd, resulting in significant Ag migration out of the surface and extensive vacancy pits. These metastable structures are of vital catalytic importance, as Ag-encapsulated Pd remains much more accessible to reactants than bulk-dissolved Pd. The underlying mechanisms are uncovered by performing fast and large-scale machine-learning molecular dynamics, followed by our newly developed method for complete characterization of atomic surface restructuring events. Our approach is broadly applicable to other multimetallic systems of interest and enables the previously impractical mechanistic investigation of restructuring dynamics.

Research on highly parallel embedded control system design and implementation method

Impact ◽  
2019 ◽  
Vol 2019 (10) ◽  
pp. 44-46
Author(s):  
Masato Edahiro ◽  
Masaki Gondo
Keyword(s):  
Computer Architecture ◽  
Intelligent Systems ◽  
Large Scale ◽  
General Purpose ◽  
Heterogeneous Structure ◽  
Single Chip ◽  
Powertrain Control ◽  
Processing Power ◽  
Hardware Description ◽  
Many Core

The pace of technology's advancements is ever-increasing and intelligent systems, such as those found in robots and vehicles, have become larger and more complex. These intelligent systems have a heterogeneous structure, comprising a mixture of modules such as artificial intelligence (AI) and powertrain control modules that facilitate large-scale numerical calculation and real-time periodic processing functions. Information technology expert Professor Masato Edahiro, from the Graduate School of Informatics at the Nagoya University in Japan, explains that concurrent advances in semiconductor research have led to the miniaturisation of semiconductors, allowing a greater number of processors to be mounted on a single chip, increasing potential processing power. 'In addition to general-purpose processors such as CPUs, a mixture of multiple types of accelerators such as GPGPU and FPGA has evolved, producing a more complex and heterogeneous computer architecture,' he says. Edahiro and his partners have been working on the eMBP, a model-based parallelizer (MBP) that offers a mapping system as an efficient way of automatically generating parallel code for multi- and many-core systems. This ensures that once the hardware description is written, eMBP can bridge the gap between software and hardware to ensure that not only is an efficient ecosystem achieved for hardware vendors, but the need for different software vendors to adapt code for their particular platforms is also eliminated.

scholarly journals Enabling Large-Scale Simulations of Quantum Transport with Manycore Computing

Electronics ◽  
2021 ◽  
Vol 10 (3) ◽  
pp. 253
Author(s):  
Yosang Jeong ◽  
Hoon Ryu
Keyword(s):  
Quantum Transport ◽  
Large Scale ◽  
Performance Enhancement ◽  
Silicon Nanowire ◽  
Matrix Multiplication ◽  
Tight Binding ◽  
Optimization Techniques ◽  
Wide Energy Range ◽  
Processing Unit ◽  
Binding Model

The non-equilibrium Green’s function (NEGF) is being utilized in the field of nanoscience to predict transport behaviors of electronic devices. This work explores how much performance improvement can be driven for quantum transport simulations with the aid of manycore computing, where the core numerical operation involves a recursive process of matrix multiplication. Major techniques adopted for performance enhancement are data restructuring, matrix tiling, thread scheduling, and offload computing, and we present technical details on how they are applied to optimize the performance of simulations in computing hardware, including Intel Xeon Phi Knights Landing (KNL) systems and NVIDIA general purpose graphic processing unit (GPU) devices. With a target structure of a silicon nanowire that consists of 100,000 atoms and is described with an atomistic tight-binding model, the effects of optimization techniques on the performance of simulations are rigorously tested in a KNL node equipped with two Quadro GV100 GPU devices, and we observe that computation is accelerated by a factor of up to ∼20 against the unoptimized case. The feasibility of handling large-scale workloads in a huge computing environment is also examined with nanowire simulations in a wide energy range, where good scalability is procured up to 2048 KNL nodes.

scholarly journals Hydropower, Geothermal, and Ocean Energy

MRS Bulletin ◽  
2008 ◽  
Vol 33 (4) ◽  
pp. 389-395 ◽  
Author(s):  
Ralph E.H. Sims
Keyword(s):  
Renewable Energy ◽  
Large Scale ◽  
New Technologies ◽  
Materials Science ◽  
Development Stage ◽  
Design Development ◽  
Ocean Energy ◽  
Improve Design ◽  
And Performance ◽  
Improve Reliability

AbstractSome forms of renewable energy have long contributed to electricity generation, whereas others are just emerging. For example, large-scale hydropower is a mature technology generating about 16% of global electricity, and many smaller scale systems are also being installed worldwide. Future opportunities to improve the technology are limited but include upgrading of existing plants to gain greater performance efficiencies and reduced maintenance. Geothermal energy, widely used for power generation and direct heat applications, is also mature, but new technologies could improve plant designs, extend their lifetimes, and improve reliability. By contrast, ocean energy is an emerging renewable energy technology. Design, development, and testing of a myriad of devices remain mainly in the research and development stage, with many opportunities for materials science to improve design and performance, reduce costly maintenance procedures, and extend plant operating lifetimes under the harsh marine environment.

Application of High-Performance Computing to Numerical Simulation of Human Movement

1995 ◽  
Vol 117 (1) ◽  
pp. 155-157 ◽  
Author(s):  
F. C. Anderson ◽  
J. M. Ziegler ◽  
M. G. Pandy ◽  
R. T. Whalen
Keyword(s):  
Computer Architecture ◽  
High Performance ◽  
Large Scale ◽  
Optimization Problems ◽  
Optimal Solution ◽  
Human Movement ◽  
Parallel Machine ◽  
Optimal Controls ◽  
Processing Machine ◽  
Vector Processing

We have examined the feasibility of using massively-parallel and vector-processing supercomputers to solve large-scale optimization problems for human movement. Specifically, we compared the computational expense of determining the optimal controls for the single support phase of gait using a conventional serial machine (SGI Iris 4D25), a MIMD parallel machine (Intel iPSC/860), and a parallel-vector-processing machine (Cray Y-MP 8/864). With the human body modeled as a 14 degree-of-freedom linkage actuated by 46 musculotendinous units, computation of the optimal controls for gait could take up to 3 months of CPU time on the Iris. Both the Cray and the Intel are able to reduce this time to practical levels. The optimal solution for gait can be found with about 77 hours of CPU on the Cray and with about 88 hours of CPU on the Intel. Although the overall speeds of the Cray and the Intel were found to be similar, the unique capabilities of each machine are better suited to different portions of the computational algorithm used. The Intel was best suited to computing the derivatives of the performance criterion and the constraints whereas the Cray was best suited to parameter optimization of the controls. These results suggest that the ideal computer architecture for solving very large-scale optimal control problems is a hybrid system in which a vector-processing machine is integrated into the communication network of a MIMD parallel machine.

TRADITION AND INNOVATION IN MODERN KAZAKH POETRY (XX century and independence)

2021 ◽  
Vol 76 (2) ◽  
pp. 118-128
Author(s):  
Sh. Kuttybaev ◽  
◽  
Е. Abdimomynov ◽  
Keyword(s):  
20Th Century ◽  
Large Scale ◽  
Point Of View ◽  
Soviet Period ◽  
Evolutionary Development ◽  
Spiritual Values ◽  
Literary Traditions ◽  
New Perspective ◽  
National Poetry ◽  
In The Beginning

The article analyzes views on innovation in the literary science of the early twentieth century and the work of Alash representatives in an era that is a period filled with profound changes and large-scale innovations in Kazakh society. In addition, works related to freedom, enlightenment, politics, spiritual values, the position of the people as a whole and social changes are considered the idea of independence and continuity. On the way of evolutionary development of the Kazakh literature, artistic power, thematic and ideological character, substantial and stylistic features of poetry of poets in the beginning of the XX century and during the Great Patriotic War, in subsequent years and years of independence are discussed in detail. In addition, on the basis of literary traditions and novelty, the works of prominent poets of Kazakh poetry of the 20th century and Independence are considered and comprehensively characterized, i.e. internal motives, the content of life phenomena in national poetry are analyzed in close connection with the works of poets. The original vision of the traditional and differentiated in the literature of the Soviet period in the works of poets from a new perspective, from the point of view of today. In addition, the works of outstanding poets of Kazakh poetry in the period of the 20th century and independence are considered on the basis of classical tradition and novelty in literature.

Expression and Self Assembly of Cowpea Chlorotic Mottle Virus Capsid Proteins inPichia pastorisand Encapsulation of Fluorescent Myoglobin

2011 ◽  
Vol 1317 ◽  
Author(s):  
Yuanzheng Wu ◽  
Hetong Yang ◽  
Hyun-Jae Shin
Keyword(s):  
Coat Protein ◽  
Large Scale ◽  
Materials Science ◽  
Cesium Chloride ◽  
Size Exclusion ◽  
Mottle Virus ◽  
Cowpea Chlorotic Mottle Virus ◽  
Chlorotic Mottle Virus ◽  
Chlorotic Mottle

Abstract:Cowpea chlorotic mottle virus (CCMV) has been a model system for virus studies for over 40 years and now is considered to be a perfect candidate as nanoplatform for applications in materials science and medicine. The ability of CCMV to self assemblein vitrointo virus-like particles (VLPs) or capsids makes an ideal reaction vessel for nanomaterial synthesis and entrapment. Here we report expression of codon optimized CCMV coat protein inPichia pastorisand production of self assembled CCMV VLPs by large-scale fermentation. CCMV coat protein gene (573 bp) was synthesized according to codon preference ofP. pastorisand cloned into pPICZA vector. The recombinant plasmid pPICZA-CP was transformed intoP. pastorisGS115 by electroporation. The resulting yeast colonies were screened by PCR and analyzed for protein expression by SDS-PAGE. After large-scale fermentation CCMV coat protein yields reached 4.8 g L−1. The CCMV VLPs were purified by modified PEG precipitation followed by cesium chloride density gradient ultracentrifugation, and then analyzed by size exclusion fast performance liquid chromatography (FPLC), UV spectrometry and transmission electron microscopy. Myoglobin was used as a model protein to be encapsulated in CCMV VLPs. The fluorescence spectroscopy showed that inclusion of myoglobin had occurred. The results indicated the production of CCMV capsids byP. pastorisfermentation now available for utilization in pharmacology or nanotechnology fields.

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