Contents of the OCTA System

1. Programs

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.

1.1 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.

1.2 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).

1.3 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.

2. Documents

The following is the list of the documents which can be downloaded in OCTA BBS.

OCTA Overview: It describes how OCTA was developed, the design policy of OCTA, and the content of the package of OCTA.

OCTA Installation Guide: An installation manual of OCTA.

GOURMET Primer Tutorial: This document is a compact tutorial book for GOURMET primers. It describes how you can use and modify GOURMET. It also summarizes a minimal reference for python and its extended feature in GOURMET. Those who want to play with GOURMET should start with this document.

GOURMET Operation's Manual: It is a manual for using GOURMET.

Coarse-grained Molecular Dynamics Program COGNAC -- User's Manual: It includes details of the COGNAC engine.

Rheology Simulator PASTA -- User's Manual: It includes details of the PASTA engine, such as theory and usage.

Simulation Utilities for Soft and Hard Interfaces SUSHI -- User's Manual: It includes details of the SUSHI engine, such as theory and usage.

Multi-Phase Dynamics Program MUFFIN -- User's Manual: It includes details of the MUFFIN engine, such as theory and usage.

GOURMET Python Script Reference: GOURMET uses a script language "Python" for data processing, data plotting and making 3D graphics. GOURMET has a special feature that all data in the UDF file can be handled like a variable in python. This manual explains these extended services of GOURMET for Python. It also contains a brief summary of the syntax of Python.

UDF Syntax Reference: UDF (User Definable Format) is a text data format which is used in OCTA. UDF file consists of the definition of the data structure, and the data itself. This manual explains the syntax of the UDF file.

Platform interface Library libplatform Reference: This manual explains the library which you need to read and write the UDF file in C++ programs. It also explains how the data can be handled in the command line of Python.

Application Report: This is a collection of the application report of OCTA to various problems in polymer science and engineering. You can have an overview on what kind of problems can be tackled by OCTA.

Application Report - AMUSE: In the OCTA project, there was a sub project called AMUSE which explored the possibility of "zooming" for a particular material. Poly-propyrene was chosen as a target material. This document is the report of this project.