maicos 0.3

Analyse molecular dynamics simulations of interfacial and confined systems.

MAICoS - Molecular Analysis for Interfacial and Confined Systems

A Python library to analyse molecular dynamics simulations of interfacial and confined systems based on MDAnalysis.

Installation

You'll need Python3 and a C-compiler to build the underlying libraries. To install the package
for all users type

    pip3 install numpy
    pip3 install maicos

To install only on the user site use pip's --user flag. If you are using BASH you can add the autocompletion script by adding

    source $(maicos --bash_completion)

to your .bashrc or .profile file.

Usage

You can use maicos either from the command line or directly from your python code. All available modules are briefly described below.

From the command line

To run maicos from the command line use

maicos <module> <paramaters>

You can get a help page by typing maicos -h or package specific help page by typing maicos <package> -h.

From the python interpreter

To use maicos with the python interpreter create analysis object, by supplying an MDAnalysis AtomGroup then use the run method

import maicos

ana_obj = maicos.<module>(atomgroup, <paramaters>)
ana_obj.run()

Results are available through the objects results dictionary.

Modules

Currently maicos contains the following analysis modules:

Density

• density_planar: Computes partial densities or temperature profiles across the box.
• density_cylinder: Computes partial densities across a cylinder of given radius r and length l

Dielectric Constant

• epsilon_bulk: Computes dipole moment fluctuations and from this the static dielectric constant.
• epsilon_planar: Calculates a planar dielectric profile.
• epsilon_cylinder: Calculation of the cylindrical dielectric profile for axial (along z) and radial (along xy) direction.
• dielectric_spectrum: Calculates the complex dielectric function as a function of the frequency.

Structure Analysis

• saxs: Computes SAXS scattering intensities S(q) for all atom types from the given trajectory.
• debyer: Calculates scattering intensities using the debye equation. For using you need to download and build the debyer library see https://github.com/wojdyr/debyer.
• diporder: Calculates dipolar order parameters

Timeseries Analysis

• dipole_angle: Calculates the timeseries of the dipole moment with respect to an axis.
• kinetic_energy: Calculates the timeseries for the molecular center translational and rotational kinetic energy.

Transport Analysis

• velocity: Calculates a velocity profile along a given axis.

Custom modules

You can add your custom modules to the maicos library. Just create a .maicos folder in your home directory and add your modules to this folder. For more information see the example directory.

Issues

If you found any bugs, improvements or questions to maicos feel free to raise an issue.

Contributing

Source code is available from https://gitlab.com/netzlab/maicos. Contribution via pull requests are always welcome. For more details see the README in the development section.