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Contents
RYUON - a Particle Simulation Suite
Kengo Ichiki
1
Date:
October 12, 2008
Contents
Introduction
stokes
: Stokesian Dynamics Simulator
stokes3
: Stokesian Dynamics Simulator
Output Parameters
System Parameters
Hydrodynamic Interaction Parameters
Core
libstokes
Parameters
libiter
Parameters
Non-Brownian Dynamics Parameters
Massless Particles
Massive Particles
ODE Parameters
Brownian Dynamics Parameters
Chain Interaction Parameters
Bond Parameters
Agnle Parameters
Constraint Parameters
Excluded-Volume Parameters
Gaussian Type Excluded-Volume Parameters
Debye-Hückel Type Excluded-Volume Parameters
Lennard-Jones Type Excluded-Volume Parameters
Confinement Force Parameters
Parameter Script
xi3
: Tuning Program for the Ewald Summation
Sample Run
Help
Visualization and Other Utilities
Wrappers
C
Python
Perl
Ruby
Guile
Octave
libstokes
: Library for Stokesian Dynamics
API
System Parameters
NetCDF Interface
Solvers
Hydrodynamic Interaction in Stokes Flows
Many Body Problem
FTS formulation
Fixed Particles - Mixed Problem
Lubrication Correction
Ewald Summation
Navier Slip Boundary Condition
Brownian Dynamics
Chain Interaction among Particles
Bead-Spring Models -- Overview
Hookean Spring
Finitely Extensible Nonlinear Spring Models
Discrete Wormlike Chain Model
Bead-Rod Model
Confinements
libiter
: Library of Iterative Solvers
API
Iterative Method for Dense Matrix
Schemes
libexp
: Library for Multipole Expansion
Multipole Expansion
Ewald Summation
Fast Multipole Expansion
Linear Partial Differential Equations
twobody
: Exact Solutions of Two Rigid Spheres in Stokes Flows
Postscript
The GNU General Public License
Bibliography
About this document ...
Kengo Ichiki 2008-10-12
