Metadata-Version: 2.0
Name: raaSAFT
Version: 0.6.3
Summary: Easy coarse-grained simulations with the SAFT-gamma Mie force field
Home-page: https://bitbucket.org/asmunder/raasaft/
Author: Åsmund Ervik
Author-email: aaervik@gmail.com
License: MIT
Keywords: molecular dynamics GPU SAFT Mie HOOMD
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Physics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.2
Classifier: Programming Language :: Python :: 3.3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Requires-Dist: future
Requires-Dist: requests

raaSAFT
=======

.. figure:: https://bitbucket.org/repo/pn6BAR/images/2465645789-raasaft-wide.jpg
   :alt: raasaft-wide.jpg

   raasaft-wide.jpg

Illustrative image courtesy of `www.frukt.no <frukt.no>`__
----------------------------------------------------------

What is raaSAFT?
----------------

-  raaSAFT (pronounced "raw saft") is a Python framework for easy
   coarse-grained molecular dynamics simulations.
-  raaSAFT runs with HOOMD-blue as a backend, so you can use GPU power.
   Initial support for using GROMACS has been added.
-  raaSAFT uses the SAFT-gamma Mie force field, a coarse-graining method
   which is thermodynamically consistent, and not based on tuning to
   atomistic simulations
-  Raasaft is a Norwegian word meaning "pure fruit syrup". Apart from
   the obvious saft <-> SAFT pun, "raa" means crude/raw/\ **coarse**, so
   it is twice as punny.

Installing raaSAFT
------------------

**Dependencies:**

-  raaSAFT uses HOOMD-blue, see the `HOOMD-blue install
   guide <https://codeblue.umich.edu/hoomd-blue/doc/page_install_guide.html>`__.

   -  For now this is a dependency even if you want to run with GROMACS.
      The non-GPU version of HOOMD-blue is sufficient.

-  Note that HOOMD-blue runs on Linux or Mac OSX. Windows is not
   supported.

**Simple installation:**

-  System-wide install: ``sudo pip install raasaft``
-  Local installation: ``pip install --user raasaft``

-  To upgrade: add ``--upgrade`` after ``install``

-  To start using raaSAFT: make a new folder, enter it and run the
   command
    ``raasaft_init``
    to add the helpful directories ``tutorials/``, ``replication/`` and
   ``mysaft/``.
-  Read the "Running simulations" section below.

**Installation for advanced users / contributors:**

-  Install dependencies. This includes HOOMD-blue and the Python
   packages ``future`` and ``requests``.
-  Clone this repo

   -  The ``maint`` branch should be as stable as the version on PyPi
   -  The ``master`` branch changes frequently and may not always be
      stable

-  The ``raasaft_init`` command will not be in your path unless you put
   it there.

Running simulations with raaSAFT
--------------------------------

-  Make sure you have run the ``raasaft_init`` command in the folder
   where you want to run your simulations.

   -  Let's call this folder "trysaft".

-  Look at the README.txt file in "trysaft/tutorials/" for examples of
   how to use raaSAFT.
-  In "trysaft/replication/" we include setups that can be used to
   replicate the findings of various papers.
-  In "trysaft/mysaft/" you find an example of how to add your own
   models for new molecules.

   -  You can use these user-defined models with e.g.
       ``from mysaft.example import Example``
       ``ex = Example(count=1e3)``
   -  If you want to use these models in jobscripts in different
      directories, add the full path to the "trysaft" folder to your
      ``PYTHONPATH`` shell variable, e.g.:
       ``export PYTHONPATH=$PYTHONPATH:"$HOME/trysaft"``
   -  Contributions to raaSAFT with new models are always welcome,
      assuming the model has seen at least some level of validation.

Bottled SAFT
------------

| You can get models (force field parameters) for 6000+ molecules from
  our database called Bottled SAFT:
  `www.bottledsaft.org <http://www.bottledsaft.org>`__.
| This web application provides scripts that implement the search result
  in raaSAFT for you!

License
-------

-  The code is Free and Open Source software under the `MIT
   license <https://bitbucket.org/asmunder/raasaft/src/master/LICENSE.txt>`__.

Contribute
----------

-  All contributions are welcome!

Contact
-------

-  Email Åsmund at aaervik@gmail.com


