Contents of the OCTA System


OCTA is an integrated simulation system for soft materials. It consists of four simulation programs (COGNAC, PASTA, SUSHI, MUFFIN), one graphical user interface program (GOURMET) and an I/O interface library.

1 Simulation programs

Coarse-grained molecular dynamics simulator -- COGNAC: COGNAC is a program of molecular dynamics. It covers a large class of molecular models, ranging from full atomistic models to bead-spring models, under various conditions(equilibrium and nonequilibrium). In addition to the usual function of molecular dynamics program, COGNAC has a special function, called zooming, which generates the equilibrium molecular configuration for given density profile of atoms

Rheology simulator -- PASTA: PASTA calculates the rheological properties of polymeric liquids from a knowledge of the molecular weight distribution and branching structure. It is based on the slip-link model, in which polymer molecules interact through the creation and release of binary entanglements. PASTA can handle polydisperse linear and star polymers, and can predict various linear and nonlinear rheological properties.

Interfacial dynamics simulator -- SUSHI: SUSHI calculates the equilibrium and non-equilibrium structures in polymer blends and block copolymers by solving the self-consistent Edwards equation. SUSHI can deal with a variety of polymers; linear polymer, branched polymers with any topology, copolymers with any monomer sequences (block, random, tapered-random) and the polymers grafted on a solid surface. SUSHI can be used to study the surface modification caused by polymer grafting or polymer adsorption, and the self-assembly of block polymers (micellar formation).

Continuum dynamics simulator -- MUFFIN: MUFFIN is a general solver for the continuum models for the dynamics of soft materials based on finite difference method (FDM) or finite element method (FEM). MUFFIN includes six packages, Elastica, ElaDyna, GelDyna, Electrolyte, MEMFluid and PhaseSeparation, and can deal with various problems in soft materials, such as the elasticity of multi-phase materials, swelling and deswelling of gels, ion transport in charged colloids, reaction and diffusion in narrow channels, phase separation and droplets deformation in shear and electric field.

2 Additional Simulation programs

Rheology simulator -- NAPLES: NAPLES is a computer code to simulate dynamics of entangled polymers based on a theoretical model called PCN (Primitive Chain Network) model. NAPLES enables us to simulate linear and non-linear viscoelastic properties of entangled polymers with various configurations, blends and copolymers, etc.

DNS simulator for colloidal/particular dispersions -- KAPSEL: KAPSEL is a software designed specially to simulate the accurate dynamics of colloidal and particular dispersions using SPM (Smoothed Particle Method), which is an unique simulation method enables us to perform DNS (Direct Numerical Simulation) by solving motions of dispersed colloids/particles and host fluids simultaneously. For example, one can use KAPSEL to simulate complex rheological properties of particular dispersions, electrophoresis of charged colloids, and sedimentation of rigid particles.

3 Modeling Platform GOURMET

GOURMET is a platform on which simulation programs run. GOURMET provides a common graphical user interface for all simulation programs. GOURMET is an editor of the input data, a viewer of the output data, a tool to make graphs and animations, and most importantly a place for various simulation programs to meet and exchange the information they have. These services can be customized and enhanced by users. New simulation programs can be easily connected to GOURMET by writing the input and output files in a certain text file format called UDF (User Definable Format).

4 I/O interface library

The UDF file is a text file, but can be viewed as a random access storage: any data in UDF can be read and written in any order. To facilitate the reading and writing of the UDF files, two service programs are provided.

libplatform: This is the library needed to read and write UDF files by C/C++ programs.

Python UDF Manager: This is the library needed to read and write UDF files by Python.