Allink

Overview

Allink is a collection of analysis, visualisation and image processing tools to study the physical properties of the following systems:

• "Bilayer membrane": mechanical properties (bending, stretching and coupling energies, diffusivity, pressure tensor...).
• "Signals": statistical properties (power spectrum, autocorrelation, distribution...).
• "Images": statistical properties, filters, reconstruction of lines.

Allink is as well an integrator of equation of motion, Monte Carlo simulator and differential equation solver for the following systems:

• "Integrator": molecular dynamics for polymers, rotating rigid cylinders.
• "Simulator": Monte Carlo with configurational bias for lipid systems.
• "Solver": for a forth order differential equation in 1 or 2d lattices.

Each tools needs a configuration file inside the directory they are run to change the default options. This solution is preferred to the extensive use of menus which slows down the development of the software but makes the program less user friendly.
Some tools are still under development if they are not properly documented.
The programming style is modular, ojected oriented but not abstract (no use of friend classes, templates...). This might cause inefficiency in the program and in the source writing but is meant to furnish a clear understanding of the algorithms.
The program is still under clean up of obsolete function and conversion of some original italian variable names.

Table of contents:

• Avvis
• ElPoly
• DrEffect
• Addyn

Using Allink

• Compilation
• Getting Started
• Parameter File
• Design Overview

Data Organization