Introduction

RYUON is a particle simulation suite, currently covering Stokesian dynamics method and hopefully more general many-body problems in the future, released under the GNU General Public License (see Chapter A).

This document describes overview of RYUON and some tutorials aiming for users. There are other documents:

• ``RYUON User's Manual'': describing overview and some tutorials of RYUON (for users).
• ``RYUON Reference Manual'': describing numerical implementations of RYUON (for developers).
• ``Theory of RYUON'': a textbook describing theoretical background of RYUON (for researchers).

My scientific interest is on ``particles in a fluid'' or between ``discrete and continuous systems.'' RYU of RYU-ON has meanings of ``grain'' and ``flow'' in Japanese and it well fits my interest, the GAP between the two.

Currently, RYUON contains the following codes and data:

• Simulators: stokes (Chapter 2)
  • Stokesian dynamics for massless particles in a viscous fluid
  • Fluidized-Beds Simulator [16,17] for heavy particles in a viscous fluid
  • Chain Simulator for bead-spring model in a viscous fluid
• Libraries
  • libstokes (Chapter 3): library for Stokesian dynamics [4,6,5,13]
  • libiter (Chapter 4): library of iterative solvers for the linear set of equations [14]
  • libexp (Chapter 5): Solver for General Many-Body Problems: including electrostatics, gravitational systems, elasticity, vortex dynamics, etc
  • FEM, BEM layer using the above.
• Data and Details
  • twobody (Chapter 6): The exact solutions for two-body problems in Stokes flows [20,18,19]
• Utilities: Analysis and Visualization
  • Molecular dynamics: utility for existing Open Source Projects such as GROMACS and TINKER [15]