raaSAFT 0.6.3

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