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

다중혈관 관상동맥 환자에서 y-문합을 이용하여 양쪽 내흉동맥만을 사용한 우회술의 조기 성적

N G van Kampen 1981 Amsterdam: North-Holland xiv + 419 pp price Dfl 180 This is a book which, at a lower price, could be expected to become an essential part of the library of every physical scientist concerned with problems involving fluctuations and stochastic processes, as well as those who just enjoy a beautifully written book. It provides an extensive graduate-level introduction which is clear, cautious, interesting and readable.

https://iopscience.iop.org/article/10.1088/0031-9112/34/4/040/pdf

Stochastic Processes in Physics and Chemistry

We explore in this chapter questions of existence and uniqueness for solutions to stochastic differential equations and offer a study of their properties. This endeavor is really a study of diffusion processes. Loosely speaking, the term diffusion is attributed to a Markov process which has continuous sample paths and can be characterized in terms of its infinitesimal generator.

Stochastic Differential Equations

Physical Review B

Field II has been a recognized simulation tool for piezoceramic medical transducer arrays for more than a decade. The program has its strength in doing fast computations of the spatial impulse response (SIR) from array elements by dividing the elements into smaller mathematical elements (ME)s from which it calculates the SIR responses. The program features predefined models for classical transducer geometries, but currently none for the fast advancing CMUTs. This work addresses the assumptions required for modeling CMUTs with Field II. It is shown that rectangular array elements, populated with cells, can be well approximated by neglecting the cells. Further, it is demonstrated that scaling of the SIR translates into better computational efficiency.

/pdf/simulating-capacitive-micromachined-ultrasonic-transducers-46jso0o17g.pdf

Simulating capacitive micromachined ultrasonic transducers (CMUTs) using field II

This paper presents a method for learning Peg-In-Hole actions with flexible objects. To learn the actions we parametrize the entire trajectory by a single point and use Kernel Density Estimation to reflect the different variations of the action and the object characteristics. The object is characterized by its elastic behaviour rather than geometric properties. Thereby an action learned for one object can be transferred to a new object that behaves similarly although it might have different elastic properties, dimensions and geometries. To bootstrap the learning mechanism, the system performs simulated actions and utilizes the detailed information obtained from the simulation environment. Subsequently Peg-In-Hole actions are tested successfully on the real life

Learning Peg-In-Hole Actions with Flexible Objects

Phase shift and attenuation characteristics of acoustic waves in a flowing gas confined by cylindrical walls

Spherical Polar Coordinates

A one-dimensional model for examining the combined influence of lattice mismatch, spontaneous polarization, piezoelectricity, strain, and nonlinear permittivity effects is described. Nonlinear permittivity effects in two-layer AlN∕GaN structures used in, e.g., heterojunction field effect transistors are shown to have a significant influence (approximately 20%) in the absence of interface charge screening due to strong electric fields in the thin-film AlN layer. Considerable reductions occur, however, in the electric field when interface charge screening is effectively reducing the importance of nonlinear permittivity effects. Determination of dynamic strain characteristics is performed for the case of a strong dc electric field in the AlN layer (due to short-circuit dc voltage conditions over the full structure) superimposed by a small ac voltage and it is shown that resonance frequencies exist being weakly affected by permittivity nonlinearities. As a corollary, it is found that a nonlinear permittivity ...

Morten Willatzen

Papers

Simulating capacitive micromachined ultrasonic transducers (CMUTs) using field II

Learning Peg-In-Hole Actions with Flexible Objects

Phase shift and attenuation characteristics of acoustic waves in a flowing gas confined by cylindrical walls

Spherical Polar Coordinates

Nonlinearities and piezoelectric fields in AlN∕GaN wurtzite heterostructures