maicos 0.4

Analyse molecular dynamics simulations of interfacial and confined systems.

.. image:: docs/source/images/logo_MAICOS_small.png :align: left :alt: MAICoS

.. inclusion-readme-intro-start

MAICoS is the acronym for Molecular Analysis for Interfacial and Confined Systems. It is an object-oriented python toolkit for analysing the structure and dynamics of interfacial and confined fluids from molecular simulations. Combined with MDAnalysis_, MAICoS can be used to extract density profiles, dielectric constants, structure factors, or transport properties from trajectories files, including LAMMPS, GROMACS, CHARMM or NAMD data. MAICoS is open source and is released under the GNU general public license v3.0.

.. inclusion-readme-intro-end

For details, tutorials, and examples, please have a look at our documentation_.

.. inclusion-readme-start

Basic example #############

This is a simple example showing how to use MAICoS to extract the density profile from a molecular dynamics simulation. The files conf.gro and traj.trr correspond to a water slab in vacuum that was simulated in this case using the GROMACS_ simulation package. In a Python environment, type:

.. code-block:: python3

import MDAnalysis as mda
import maicos
u = mda.Universe('conf.gro', 'traj.trr')
grpH2O = u.select_atoms('type O or type H')
dplan = maicos.density_planar(grpH2O)
dplan.run()

Results can be accessed from dplan.results.

Installation ############

Python3_ and a C-compiler are needed to build the underlying libraries.

Using pip

If you have root access, install the package for all users by typing in a terminal:

.. code-block:: bash

pip3 install numpy
pip3 install maicos

Alternatively, if you don't have special privileges, install the package in your home directory by using the --user flag.

List of analysis modules ########################

.. inclusion-marker-modules-start

.. list-table:: :widths: 25 50 :header-rows: 1

• • Module Name
  • Description
• • density_planar
  • Compute partial densities/temperature profiles in the Cartesian systems.
• • density_cylinder
  • Compute partial densities across a cylinder.
• • epsilon_bulk
  • Compute dipole moment fluctuations and static dielectric constant.
• • epsilon_planar
  • Calculates a planar dielectric profile.
• • epsilon_cylinder
  • Calculate cylindrical dielectric profiles.
• • dielectric_spectrum
  • Computes the linear dielectric spectrum.
• • saxs
  • Compute SAXS scattering intensities.
• • diporder
  • Calculation of dipolar order parameters.
• • debyer
  • Calculate scattering intensities using the debye equation. The debyer_ library needs to be downloaded and build.
• • dipole_angle
  • Calculate angle timeseries of dipole moments with respect to an axis.
• • kinetic_energy
  • Calculate the timeseries of energies.
• • velocity
  • Mean velocity analysis.

.. _Python3: https://www.python.org .. _Cython : https://cython.org/ .. _GROMACS : https://www.gromacs.org/ .. _MDAnalysis: https://www.mdanalysis.org .. _documentation: https://maicos-devel.gitlab.io/maicos/index.html .. _debyer: https://github.com/wojdyr/debyer

.. inclusion-readme-end