Metadata-Version: 2.1
Name: maicos
Version: 0.2
Summary: Analyse molecular dynamics simulations of interfacial and confined systems.
Home-page: UNKNOWN
Author: Philip Loche et. al.
Author-email: ploche@physik.fu-berlin.de
Maintainer: Philip Loche
Maintainer-email: ploche@physik.fu-berlin.de
License: GPL 3
Project-URL: Source Code, https://gitlab.com/netzlab/maicos
Description: # MAICoS - Molecular Analysis for Interfacial and Confined Systems
        
        A Python library to analyse molecular dynamics simulations of
        interfacial and confined systems based on
        [MDAnalysis](https://www.mdanalysis.org).
        
        # Installation
        
        You'll need [Python3](https://www.python.org) and a C-compiler to build the
        underlying libraries. To install the package  
        for all users type
        
        ```sh
            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
        
        ```sh
            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
        
        ```sh
        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
        
        ```python
        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](https://gitlab.com/netzlab/maicos/-/tree/develop/examples).
        
        # 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](https://gitlab.com/netzlab/maicos/-/tree/develop/developer) in the development section.
        
Keywords: Science,Molecular Dynamics,Confined Systems,MDAnalysis
Platform: UNKNOWN
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 :: 3.6
Classifier: Programming Language :: Python :: 3.7
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: >=3.6
Description-Content-Type: text/markdown
