MAICoS
======
.. image:: https://raw.githubusercontent.com/maicos-devel/maicos/refs/heads/main/docs/static/logo.svg
:width: 200 px
:align: left
:alt: MAICoS logo
|tests| |codecov| |docs-stable| |docs-latest| |mdanalysis|
.. inclusion-readme-intro-start
**MAICoS** stands for **Molecular Analysis for Interfacial and Confined Systems**. It is
an object-oriented **Python** toolkit for analyzing the structure and dynamics of
interfacial and confined fluids from molecular simulations. Combined with `MDAnalysis`_,
MAICoS enables the extraction of density profiles, dielectric constants, structure
factors, and transport properties from trajectory files generated by LAMMPS, GROMACS,
CHARMM, or NAMD simulations. MAICoS is open source and released under the **GNU General
Public License v3.0**.
MAICoS is designed both for beginners in molecular simulations with no prior Python
experience— offering a descriptive **Command Line Interface (CLI)**—and for experienced
users who can use the **Python API** for day-to-day analysis or build their own
workflows for interfacial and confined systems.
Stay up to date with MAICoS news by following us on `X`_. If you encounter any issues,
report them on `GitHub`_, or join our developer community on `Discord`_ to discuss
features and improvements.
.. _`MDAnalysis`: https://www.mdanalysis.org
.. _`X`: https://x.com/maicos_analysis
.. _`GitHub`: https://github.com/maicos-devel/maicos
.. _`Discord`: https://discord.gg/mnrEQWVAed
.. inclusion-readme-intro-end
Basic Example
=============
Here is a simple example showing how to use MAICoS to extract a density profile from a
molecular dynamics simulation. The files ``conf.gro`` and ``traj.trr`` correspond to
output files from a `GROMACS`_ simulation. 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 is stored in ``dplan.results.profile``, and the corresponding bin
positions are available in ``dplan.results.bin_pos``.
.. _`GROMACS`: https://www.gromacs.org/
Documentation
=============
For details, tutorials, and examples, visit our official `documentation`_. We also
provide the `latest documentation`_ for the current development version of MAICoS.
.. _`documentation`: https://maicos-analysis.org
.. _`latest documentation`: https://maicos-analysis.org/latest
.. inclusion-readme-installation-start
Installation
============
Install MAICoS using `pip`_::
pip install maicos
Or with `conda`_ from conda-forge::
conda install -c conda-forge maicos
.. _`pip`: https://pip.pypa.io
.. _`conda`: https://www.anaconda.com
.. inclusion-readme-installation-end
List of Analysis Modules
========================
.. inclusion-marker-modules-start
Currently, MAICoS supports the following analysis modules (alphabetically):
.. list-table::
:widths: 25 50
:header-rows: 1
* - Module
- Description
* - DensityCylinder
- Cylindrical partial density profiles
* - DensityPlanar
- Cartesian partial density profiles
* - DensitySphere
- Spherical partial density profiles
* - DielectricCylinder
- Cylindrical dielectric profiles
* - DielectricPlanar
- Planar dielectric profiles
* - DielectricSpectrum
- Linear dielectric spectrum
* - DielectricSphere
- Spherical dielectric profiles
* - DipoleAngle
- Time series of dipole moment angles
* - DiporderCylinder
- Cylindrical dipolar order parameters
* - DiporderPlanar
- Planar dipolar order parameters
* - RDFDiporder
- Spherical radial distribution function between dipoles
* - DiporderSphere
- Spherical dipolar order parameters
* - DiporderStructureFactor
- Structure factor for dipoles
* - KineticEnergy
- Time series of kinetic energies
* - PDFCylinder
- Cylindrical shell-wise 1D pair distribution functions
* - PDFPlanar
- Slab-wise planar 2D pair distribution functions
* - Saxs
- Small-angle X-ray scattering (SAXS): structure factors and scattering intensities
* - TemperaturePlanar
- Temperature profiles in a Cartesian geometry
* - VelocityCylinder
- Cylindrical velocity profiles
* - VelocityPlanar
- Velocity profiles in a Cartesian geometry
.. inclusion-marker-modules-end
Contributors
============
Thanks to all contributors who make **MAICoS** possible:
.. image:: https://contrib.rocks/image?repo=maicos-devel/maicos
:target: https://github.com/maicos-devel/maicos/graphs/contributors
.. |tests| image:: https://github.com/maicos-devel/maicos/workflows/Tests/badge.svg
:alt: GitHub Actions Tests Job Status
:target: https://github.com/maicos-devel/maicos/actions?query=branch%3Amain
.. |codecov| image:: https://codecov.io/gh/maicos-devel/maicos/graph/badge.svg?token=9AXPLF6CR3
:alt: Code coverage
:target: https://codecov.io/gh/maicos-devel/maicos
.. |docs-stable| image:: https://img.shields.io/badge/📚_Documentation-stable-success
:alt: Documentation of stable released version
:target: `documentation`_
.. |docs-latest| image:: https://img.shields.io/badge/📒_Documentation-latest-yellow.svg
:alt: Documentation of latest unreleased version
:target: `latest documentation`_
.. |mdanalysis| image:: https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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
:alt: Powered by MDAnalysis
:target: https://www.mdanalysis.org
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"description": "MAICoS\n======\n\n.. image:: https://raw.githubusercontent.com/maicos-devel/maicos/refs/heads/main/docs/static/logo.svg\n :width: 200 px\n :align: left\n :alt: MAICoS logo\n\n|tests| |codecov| |docs-stable| |docs-latest| |mdanalysis|\n\n.. inclusion-readme-intro-start\n\n**MAICoS** stands for **Molecular Analysis for Interfacial and Confined Systems**. It is\nan object-oriented **Python** toolkit for analyzing the structure and dynamics of\ninterfacial and confined fluids from molecular simulations. Combined with `MDAnalysis`_,\nMAICoS enables the extraction of density profiles, dielectric constants, structure\nfactors, and transport properties from trajectory files generated by LAMMPS, GROMACS,\nCHARMM, or NAMD simulations. 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We also\nprovide the `latest documentation`_ for the current development version of MAICoS.\n\n.. _`documentation`: https://maicos-analysis.org\n.. _`latest documentation`: https://maicos-analysis.org/latest\n\n.. inclusion-readme-installation-start\n\nInstallation\n============\n\nInstall MAICoS using `pip`_::\n\n pip install maicos\n\nOr with `conda`_ from conda-forge::\n\n conda install -c conda-forge maicos\n\n.. _`pip`: https://pip.pypa.io\n.. _`conda`: https://www.anaconda.com\n\n.. inclusion-readme-installation-end\n\nList of Analysis Modules\n========================\n\n.. inclusion-marker-modules-start\n\nCurrently, MAICoS supports the following analysis modules (alphabetically):\n\n.. list-table::\n :widths: 25 50\n :header-rows: 1\n\n * - Module\n - Description\n * - DensityCylinder\n - Cylindrical partial density profiles\n * - DensityPlanar\n - Cartesian partial density profiles\n * - DensitySphere\n - Spherical partial density profiles\n * - DielectricCylinder\n - Cylindrical dielectric profiles\n * - DielectricPlanar\n - Planar dielectric profiles\n * - DielectricSpectrum\n - Linear dielectric spectrum\n * - DielectricSphere\n - Spherical dielectric profiles\n * - DipoleAngle\n - Time series of dipole moment angles\n * - DiporderCylinder\n - Cylindrical dipolar order parameters\n * - DiporderPlanar\n - Planar dipolar order parameters\n * - RDFDiporder\n - Spherical radial distribution function between dipoles\n * - DiporderSphere\n - Spherical dipolar order parameters\n * - DiporderStructureFactor\n - Structure factor for dipoles\n * - KineticEnergy\n - Time series of kinetic energies\n * - PDFCylinder\n - Cylindrical shell-wise 1D pair distribution functions\n * - PDFPlanar\n - Slab-wise planar 2D pair distribution functions\n * - Saxs\n - Small-angle X-ray scattering (SAXS): structure factors and scattering intensities\n * - TemperaturePlanar\n - Temperature profiles in a Cartesian geometry\n * - VelocityCylinder\n - Cylindrical velocity profiles\n * - VelocityPlanar\n - Velocity profiles in a Cartesian geometry\n\n.. inclusion-marker-modules-end\n\nContributors\n============\n\nThanks to all contributors who make **MAICoS** possible:\n\n.. image:: https://contrib.rocks/image?repo=maicos-devel/maicos\n :target: https://github.com/maicos-devel/maicos/graphs/contributors\n\n.. |tests| image:: https://github.com/maicos-devel/maicos/workflows/Tests/badge.svg\n :alt: GitHub Actions Tests Job Status\n :target: https://github.com/maicos-devel/maicos/actions?query=branch%3Amain\n\n.. |codecov| image:: https://codecov.io/gh/maicos-devel/maicos/graph/badge.svg?token=9AXPLF6CR3\n :alt: Code coverage\n :target: https://codecov.io/gh/maicos-devel/maicos\n\n.. |docs-stable| image:: https://img.shields.io/badge/\ud83d\udcda_Documentation-stable-success\n :alt: Documentation of stable released version\n :target: `documentation`_\n\n.. |docs-latest| image:: https://img.shields.io/badge/\ud83d\udcd2_Documentation-latest-yellow.svg\n :alt: Documentation of latest unreleased version\n :target: `latest documentation`_\n\n.. |mdanalysis| image:: https://img.shields.io/badge/powered%20by-MDAnalysis-orange.svg?logoWidth=16&logo=data:image/x-icon;base64,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\n :alt: Powered by MDAnalysis\n :target: https://www.mdanalysis.org\n",
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