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

[신간의 별자리x] 우리/미술, 그리고 ‘슬픔의 박물관’

The modern science of networks has brought significant advances to our understanding of complex systems. One of the most relevant features of graphs representing real systems is community structure, or clustering, i. e. the organization of vertices in clusters, with many edges joining vertices of the same cluster and comparatively few edges joining vertices of different clusters. Such clusters, or communities, can be considered as fairly independent compartments of a graph, playing a similar role like, e. g., the tissues or the organs in the human body. Detecting communities is of great importance in sociology, biology and computer science, disciplines where systems are often represented as graphs. This problem is very hard and not yet satisfactorily solved, despite the huge effort of a large interdisciplinary community of scientists working on it over the past few years. We will attempt a thorough exposition of the topic, from the definition of the main elements of the problem, to the presentation of most methods developed, with a special focus on techniques designed by statistical physicists, from the discussion of crucial issues like the significance of clustering and how methods should be tested and compared against each other, to the description of applications to real networks.

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Community detection in graphs

Developing algorithms for solving high-dimensional partial differential equations (PDEs) has been an exceedingly difficult task for a long time, due to the notoriously difficult problem known as the “curse of dimensionality.” This paper introduces a deep learning-based approach that can handle general high-dimensional parabolic PDEs. To this end, the PDEs are reformulated using backward stochastic differential equations and the gradient of the unknown solution is approximated by neural networks, very much in the spirit of deep reinforcement learning with the gradient acting as the policy function. Numerical results on examples including the nonlinear Black–Scholes equation, the Hamilton–Jacobi–Bellman equation, and the Allen–Cahn equation suggest that the proposed algorithm is quite effective in high dimensions, in terms of both accuracy and cost. This opens up possibilities in economics, finance, operational research, and physics, by considering all participating agents, assets, resources, or particles together at the same time, instead of making ad hoc assumptions on their interrelationships.

https://www.pnas.org/content/pnas/115/34/8505.full.pdf

Solving high-dimensional partial differential equations using deep learning

We present an efficient method for computing the transition pathways, free energy barriers, and transition rates in complex systems with relatively smooth energy landscapes. The method proceeds by evolving strings, i.e., smooth curves with intrinsic parametrization whose dynamics takes them to the most probable transition path between two metastable regions in configuration space. Free energy barriers and transition rates can then be determined by a standard umbrella sampling around the string. Applications to Lennard-Jones cluster rearrangement and thermally induced switching of a magnetic film are presented.

/pdf/string-method-for-the-study-of-rare-events-11twdlbcah.pdf

String method for the study of rare events

We introduce a scheme for molecular simulations, the deep potential molecular dynamics (DPMD) method, based on a many-body potential and interatomic forces generated by a carefully crafted deep neural network trained with ab initio data. The neural network model preserves all the natural symmetries in the problem. It is first-principles based in the sense that there are no ad hoc components aside from the network model. We show that the proposed scheme provides an efficient and accurate protocol in a variety of systems, including bulk materials and molecules. In all these cases, DPMD gives results that are essentially indistinguishable from the original data, at a cost that scales linearly with system size.

Deep Potential Molecular Dynamics: A Scalable Model with the Accuracy of Quantum Mechanics

We propose a deep learning-based method, the Deep Ritz Method, for numerically solving variational problems, particularly the ones that arise from partial differential equations. The Deep Ritz Method is naturally nonlinear, naturally adaptive and has the potential to work in rather high dimensions. The framework is quite simple and fits well with the stochastic gradient descent method used in deep learning. We illustrate the method on several problems including some eigenvalue problems.

The Deep Ritz Method: A Deep Learning-Based Numerical Algorithm for Solving Variational Problems

The heterogenous multiscale method (HMM) is presented as a general methodology for the efficient numerical computation of problems with multiscales and multiphysics on multigrids. Both variational and dynamic problems are considered. The method relies on an efficent coupling between the macroscopic and microscopic models. In cases when the macroscopic model is not explicity available or invalid, the microscopic solver is used to supply the necessary data for the microscopic solver. Besides unifying several existing multiscale methods such as the ab initio molecular dynamics [13], quasicontinuum methods [73,69,68] and projective methods for systems with multiscales [34,35], HMM also provides a methodology for designing new methods for a large variety of multiscale problems. A framework is presented for the analysis of the stability and accuracy of HMM. Applications to problems such as homogenization, molecular dynamics, kinetic models and interfacial dynamics are discussed.

https://www.intlpress.com/site/pub/files/_fulltext/journals/cms/2003/0001/0001/CMS-2003-0001-0001-a008.pdf

Weinan E

Papers

Solving high-dimensional partial differential equations using deep learning

String method for the study of rare events

Deep Potential Molecular Dynamics: A Scalable Model with the Accuracy of Quantum Mechanics

The Deep Ritz Method: A Deep Learning-Based Numerical Algorithm for Solving Variational Problems

The Heterognous Multiscale Methods