Metadata-Version: 1.1
Name: wlcsim
Version: 0.0.7
Summary: UNKNOWN
Home-page: https://github.com/SpakowitzLab/BasicWLC
Author: Bruno Beltran
Author-email: UNKNOWN
License: UNKNOWN
Description: # WormLike Chain SIMulator
        
        [![Build Status](https://travis-ci.org/brunobeltran/wlcsim.svg?branch=master)](https://travis-ci.org/brunobeltran/wlcsim)
        
        This code is designed to efficiently simulate the wormlike chain polymer model
        using various coarse-grainings where applicable.
        
        For very stiff polymers, the usual wormlike chain is simulated.
        
        For relatively more flexible polymers, the "stretchable, shearable" chain is
        used.
        
        For *VERY* stretchable polymers, a purely Gaussian chain is used.
        
        ## To Run
        
        Simply typing ``make`` in the top level directory will build the simulator
        from source. The executable created (``wlcsim.exe``) will use the parameters in
        the file ``input/input`` and write its output to the ``data`` directory.
        Descriptions of the available parameters can be found at their definitions and
        where they are read in ``src/wlcsim/params.f03``. Example input files are
        usually more useful, and can be found in the ``input`` directory.
        To force a rerun without having to manually delete all the old output files, you
        can also simply type ``make run`` at any time.
        
        There are several ways to easily visualize simulation output. There are PyMol
        scripts in the ``vizualization`` directory, ``python -m wlcsim.plot_wlcsim``
        from the repo's top level directory will launch a GUI designed to visualize BD
        simulations, and one can of course simply use the output in the ``data``
        directory, which contains rank two arrays of shape
        ``num_beads*num_polymers-by-3``, with one file per time point. By default,
        specifying multiple polymers just simulates them in parallel in the same
        reaction volume, no interactions are assumed.
        
        To scan parameters, the Python script ``scan_wlcsim.py`` should be used. It takes
        care of saving the current git commit\_hash, all inputs, etc. into a unique
        directory, and preventing race conditions even on shared filesystems, among
        other things.
        
        ## Disclaimer
        
        This codebase is internal to the Spakowitz lab and is not guaranteed to be
        bug-free at any point. For battle-tested versions of our software, please see
        the links in the relevant papers.
        
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: License :: OSI Approved :: MIT License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Fortran
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Physics
