Metadata-Version: 2.1
Name: maicos
Version: 0.6
Summary: Analyse molecular dynamics simulations of interfacial and confined systems.
Home-page: https://www.maicos-analysis.org
Author: attr: maicos.__authors__
Maintainer: Philip Loche, Henrik Jaeger, Alexander Schlaich
License: GPL 3
Project-URL: Source, https://gitlab.com/maicos-devel/maicos
Project-URL: Documentation, https://maicos-devel.gitlab.io/maicos
Project-URL: Changelog, https://maicos-devel.gitlab.io/maicos/rst/changelog.html
Project-URL: Issue Tracker, https://gitlab.com/maicos-devel/maicos/-/issues
Project-URL: Discord, https://discord.com/channels/869537986977603604/
Keywords: Science,Molecular Dynamics,Confined Systems,MDAnalysis
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: POSIX
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Operating System :: Microsoft :: Windows
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: C
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Physics
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Topic :: System :: Shells
Description-Content-Type: text/x-rst
Provides-Extra: tests
Provides-Extra: docs
License-File: LICENSE

.. image:: https://gitlab.com/maicos-devel/maicos/-/raw/main/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.DensityPlanar(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==0.3

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

   * - DensityPlanar
     - partial densities profiles in a cartesian geometry
   * - TemperaturePlanar
     - temperature profiles in a cartesian geometry
   * - ChemicalPotentialPlanar
     - chemical potential in a cartesian geometry
   * - DensityCylinder
     - partial densities across a cylinder
   * - EpsilonPlanar
     - planar dielectric profiles
   * - EpsilonCylinder
     - cylindrical dielectric profiles
   * - DielectricSpectrum
     - linear dielectric spectrum of a bulk system
   * - Saxs
     - SAXS scattering intensities
   * - Diporder
     - dipolar order parameters
   * - RDFPlanar
     - planar radial distribution function
   * - DipoleAngle
     - angle timeseries of dipole moments with respect to an axis
   * - KineticEnergy
     - energy timeseries.
   * - Velocity
     - mean velocity profile in a cartesian geometry

.. _`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

.. inclusion-readme-end
