Metadata-Version: 2.1
Name: maicos
Version: 0.7.1
Summary: Analyse molecular dynamics simulations of interfacial and confined systems.
Author: MAICoS Developer Team
Maintainer: Philip Loche, Henrik Jaeger, Alexander Schlaich
License: GPL-3.0-or-later
Project-URL: homepage, https://www.maicos-analysis.org
Project-URL: documentation, https://maicos-devel.gitlab.io/maicos
Project-URL: repository, https://gitlab.com/maicos-devel/maicos
Project-URL: changelog, https://maicos-devel.gitlab.io/maicos/rst/changelog.html
Project-URL: issues, https://gitlab.com/maicos-devel/maicos/-/issues
Project-URL: discord, https://discord.com/channels/869537986977603604
Project-URL: twitter, https://twitter.com/maicos_analysis
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
Requires-Python: >=3.8
Description-Content-Type: text/x-rst
License-File: LICENSE
License-File: AUTHORS.rst
Requires-Dist: mdacli (>=0.1.12)
Requires-Dist: MDAnalysis (>=2.2.0)
Requires-Dist: numpy (>=1.20.0)
Requires-Dist: scipy (>=1.0.0)
Provides-Extra: dev
Requires-Dist: cython ; extra == 'dev'
Provides-Extra: docs
Requires-Dist: furo ; extra == 'docs'
Requires-Dist: ipykernel ; extra == 'docs'
Requires-Dist: ipywidgets ; extra == 'docs'
Requires-Dist: matplotlib ; extra == 'docs'
Requires-Dist: nbsphinx ; extra == 'docs'
Requires-Dist: nbval ; extra == 'docs'
Requires-Dist: sphinx ; extra == 'docs'
Requires-Dist: sphinx-gallery ; extra == 'docs'
Requires-Dist: sphinxcontrib-bibtex ; extra == 'docs'
Provides-Extra: tests
Requires-Dist: coverage[toml] ; extra == 'tests'
Requires-Dist: hypothesis ; extra == 'tests'
Requires-Dist: MDAnalysisTests ; extra == 'tests'
Requires-Dist: pytest ; extra == 'tests'
Requires-Dist: pytest-cov ; extra == 'tests'

.. image:: https://gitlab.com/maicos-devel/maicos/-/raw/main/docs/static/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.

MAICoS is a tool for beginners of molecular simulations with no Python
experience. For these users MAICoS provides a descriptive command line interface.
Also experienced users can use the Python API for their day to day analysis or
use the provided infrastructure to build their own analysis for interfacial
and confined systems.

Keep up to date with MAICoS news by following us on Twitter_.
If you find an issue, you can report it on Gitlab_.
You can also join the developer team on Discord_
to discuss possible improvements and usages of MAICoS

.. _`MDAnalysis`: https://www.mdanalysis.org
.. _`Twitter`: https://twitter.com/maicos_analysis
.. _`Gitlab`: https://gitlab.com/maicos-devel/maicos
.. _`Discord`: https://discord.com/channels/869537986977603604

.. inclusion-readme-intro-end

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 simulation files from a GROMACS_ simulation
package. In a Python environment, type:

.. code-block:: python

	import MDAnalysis as mda
	import maicos

	u = mda.Universe('conf.gro', 'traj.trr')
	dplan = maicos.DensityPlanar(u.atoms).run()

The density profile can be accessed from ``dplan.results.profile`` and 
the position of the bins from ``dplan.results.bin_pos``.

.. _`GROMACS` : https://www.gromacs.org/

Documentation
=============

For details, tutorials, and examples, please have a look at
our documentation_. If you are using an older version of MAICoS,
you can access the corresponding documentation on ReadTheDocs_.

.. _`documentation`: https://maicos-devel.gitlab.io/maicos/index.html
.. _`ReadTheDocs` : https://readthedocs.org/projects/maicos/

.. inclusion-readme-installation-start

Installation
============

Install maicos using `pip`_ with:

.. code-block:: bash

    pip3 install maicos

Alternatively, if you don't have special privileges, install
the package only for the current using the ``--user`` flag. 
Or using conda_ with:

.. code-block:: bash

    conda install -c conda-forge maicos 

.. _`pip`: https://pypi.org/project/maicos/
.. _`conda`: https://anaconda.org/conda-forge/maicos

.. inclusion-readme-installation-end

List of analysis modules
========================

.. inclusion-marker-modules-start

Currently, MAICoS supports the following analysis modules:

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

   * - Module Name
     - Description

   * - DensityPlanar
     - Compute the cartesian partial density profiles
   * - DensityCylinder
     - Compute cylindrical partial densitiy profiles
   * - DensitySphere
     - Compute spherical partial density profiles
   * - TemperaturePlanar
     - Compute temperature profile in a cartesian geometry
   * - DielectricPlanar
     - Calculate planar dielectric profiles
   * - DielectricCylinder
     - Calculate cylindrical dielectric profiles
   * - DielectricSphere
     - Calculating spherical dielectric profiles
   * - DielectricSpectrum
     - Compute the linear dielectric spectrum
   * - Saxs
     - Compute small angle X-Ray scattering intensities (SAXS)
   * - DiporderPlanar
     - Calculate dipolar order parameters
   * - RDFPlanar
     - Compute slab-wise planar 2D radial distribution functions
   * - DipoleAngle
     - Calculate angle timeseries of dipole moments
   * - KineticEnergy
     - Calculate the timeseries of energies
   * - VelocityPlanar
     - Compute the velocity profile in a cartesian geometry
   * - VelocityCylinder
     - Compute the cartesian velocity profile across a cylinder

.. inclusion-marker-modules-end
