J. Mościński

The Force-Biased Algorithm for the Irregular Close Packing of Equal Hard Spheres

Abstract We present a “force-biased” algorithm for generating the irregular close packing of hard spheres. The algorithm is partly based on Jodrey and Torys ideas [9] and incorporates methods from Molecular Dynamics. Packings generated by means of the two algorithms are consistent up to final packing fraction of 0.65, which seems to be the limit density of Jodrey and Torys method. Significantly higher densities (up to 0.71) can be achieved for small numbers of spheres by the force-biased algorithm. However the shape of the radial and angle distribution functions implies that a partial short-range ordering occurs in packings of those densities.

C-language program for the irregular close packing of hard spheres

Abstract The paper presents a C-language program for the irregular close packing of equal haed spheres in a cubic box with periodic boundary conditions using Jodrey and Torys algorithm. For the nearest-neighbour searching of a given sphere the link-cell method is applied. The program has been developed for microcomputers/workstations so that it incorporates the sequential algorithm optimized for computational time demands.

“Checker Board” Periodic Boundary Conditions in Molecular Dynamics Codes

Abstract Checker board periodic boundary conditions for molecular simulation are proposed. They represent a simple geometric transformation of the well known periodic boundary conditions formulae for variety of periodic and regular computational boxes (e.g. the truncated octahedron, rhombic dodecahedron, hexagonal prism, etc.) into a shifted parallelepiped periodic grid. As a result, the choice of an optional computational box shape is equivalent to the proper choice of the basic parallelepiped sides lengths. The checker board periodic boundary conditions have been applied in a molecular dynamics (MD) code based on the link-cell method (using Lennard-Jones interactions). Simulation efficiency is approximately the same as for the classical cubic periodic boundary transformations.

C-language molecular dynamics program for the simulation of Lennard-Jones particles

Abstract The paper presents a molecular dynamics C-language program suitable for mixtures of mono-atomic molecules of different types include in a cuboid box with periodic boundary conditions. The molecules mutually interact with the short-range Lennard-Jones potential. To solve the Newtonian equations of motion the leapfrog scheme is applied. Neighbours of a particular molecule are searched using the link-cell method. The program has been developed for microcomputers/workstations so that it incorporates the sequential algorithm optimized in respect with CPU-time.

A vectorized algorithm on the ETA 10-P for molecular dynamics simulation of large number of particles confined in a long cylinder

Abstract In this paper we describe an algorithm suitable for molecular dynamics (MD) computer simulation of particles confined in a cylinder and interacting by short-ranged forces. A procedure for determining neighbours is based on sorting the particles according to values of one coordinate along the axis of a cylinder and gathering the values of the other two coordinates due to indices of the sorted list. In addition to the classical cut-off distance an integer cut-off number is introduced. This and the organization of data structures make that the calculating forces loop is completely vectorized. The algorithm has been devised for the CYBER 205 and ETA 10 computers and is specially efficient for MD simulation in cylindrical micropores.

Parallel finite element calculation of plastic deformations on Exemplar SPP1000 and on networked workstations

Abstract In this paper we present an approach to parallelization of the program for computation of axisymmetrical forging process. The parallel algorithm we have applied is based on non-overlapping domain decomposition method. A mesh of elements is divided into layers assigned to different processes. The parallel program was written in C using PVM and it was implemented on Convex Exemplar SPP1000 and on networked workstations IBM RS/6000-320. We have investigated dependence of performance of the elaborated parallel program on number of processs and on number of nodes in the mesh.

Linked Lists and the Method of Lights in Molecular Dynamics Simulation - Search for the Best Method of Forces Evaluation in Sequential MD Codes

Abstract In this paper two methods of forces evaluation used in the MD codes are presented and compared against the classical linked lists algorithm [3,4] and its modified version [5]. The first algorithm, so called the method of lights is a sequential version of the CYBER 205 vector oriented code [6]. A new algorithm of forces evaluation is also proposed, which incorporates advantages of the method of lights and the linked lists technique.

An examination of long-rod penetration in micro-scale using particles

Abstract The authors show how using particle simulations one can try to solve the problems out of reach of classical models based on the matter, momenta and energy flows continuity. Being aware about limitations of the method applied, the paper presents the perspectives of particle based simulations considering as an example the penetration mechanism investigation in micro-scale.

The results and perspectives of the particles method approach in investigations of plastic deformations I. Penetration mechanism

Abstract In the paper the assumptions of the particles method are presented and adapted to macroscopic quasi-particles and quasi-potentials. The system representing a physical object consists of a large number of mutually interacting “particles” ( N ≈ 10 5 +). The model can be used as an alternative to the model of continuous medium described by the set of partial differential equations, usually solved by the finite elements method (FEM). The advantages and disadvantages of both approaches for the simulation of shocking phenomena are discussed. The unique character of the presented method for simulation of non-continuities of the matter under stress is exemplified by the preliminary results obtained for simulation of projectile and long rod penetration.

Molecular dynamics and lattice gas parallel algorithms for transputers and networked workstations

Abstract In this paper we present parallel algorithms for molecular dynamics and lattice gas simulations for hydrodynamics phenomena at the microscopic level. Characteristics of the algorithms (execution time, efficiency and speedup) are shown for the transputer networks and for the networks of SUN SPARC and IBM RS/6000 workstations. Some of the results are compared with those obtained on the iPSC/860 multiprocessor computer.