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

Based on group theoretical arguments we derive the most general Hamiltonian for the $\text{Bi}_2\text{Se}_3$-class of materials including terms to third order in the wave vector, first order in electric and magnetic fields, first order in strain and first order in both strain and wave vector. We determine analytically the effects of strain on the electronic structure of $\text{Bi}_2\text{Se}_3$. For the most experimentally relevant surface termination we analytically derive the surface state spectrum, revealing an anisotropic Dirac cone with elliptical constant energy counturs giving rise to different velocities in different in-plane directions. The spin-momentum locking of strained $\text{Bi}_2\text{Se}_3$ is shown to be modified and for some strain configurations we see a non-zero spin component perpendicular to the surface. Hence, strain control can be used to manipulate the spin degree of freedom via the spin-orbit coupling. We show that for a thin film of $\text{Bi}_2\text{Se}_3$ the surface state band gap induced by coupling between the opposite surfaces changes opposite to the bulk band gap under strain. Tuning the surface state band gap by strain, gives new possibilities for the experimental investigation of the thickness dependent gap and optimization of optical properties relevant for, e.g., photodetector and energy harvesting applications. We finally derive analytical expressions for the effective mass tensor of the Bi$_2$Se$_3$ class of materials as a function of strain and electric field.

Symmetry analysis of strain, electric and magnetic fields in the $\text{Bi}_2\text{Se}_3$-class of topological insulators.

A method for solving exactly the Helmholtz equation in parabolic rotational coordinates is presented using separability of the eigenfunctions and the Frobenius power series expansion technique. Two examples of interest in wave physics are considered and analyzed quasi-analytically: (I) the wavefunctions of an electron in a quantum dot confined by two paraboloids (forming a lens-shaped structure) and the associated energy spectrum, and (II) the acoustic eigenmodes and eigenfrequencies of the pressure field bounded by rigid walls as defined by two paraboloids. The quantum dot (acoustic enclosure) problem is a Dirichlet (Neumann) boundary condition problem. In both cases, eigenfunctions and eigenmodes are calculated and the shape-dependence of the first eigenvalue for the groundstate in the quantum dot case (and the fundamental mode in the acoustic enclosure case) is examined.

Quantum dot and acoustic enclosure problems in lens-shaped structures

The linear acoustics problem of resonant vibrational modes in a triaxial ellipsoidal acoustic cavity with walls of arbitrary acoustic impedance has been quasi-analytically solved using the Frobenius power-series expansion method. Eigenmode results are presented for the lowest two eigenmodes in cases with pressure-release, rigid-wall, and lossy-wall boundary conditions. A mode crossing is obtained as a function of the specific acoustic impedance of the wall; the degeneracy is not symmetry related. Furthermore, the damping of the wave is found to be maximal near the crossing.

Morten Willatzen

Papers

Symmetry analysis of strain, electric and magnetic fields in the $\text{Bi}_2\text{Se}_3$-class of topological insulators.

Quantum dot and acoustic enclosure problems in lens-shaped structures

Eigenmodes of triaxial ellipsoidal acoustical cavities with mixed boundary conditions

Model Calculation of the Piezoelectric Coefficient of Hexagonal 2D Materials

Calibration of Field II using a convex ultrasound transducer