Metadata-Version: 1.1
Name: raaSAFT
Version: 0.6.4
Summary: 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
Description: ##########################################################
        raaSAFT - coarse grained SAFT-gamma Mie molecular dynamics
        ##########################################################
        
        - raaSAFT (pronounced "raw saft") is a Python framework that makes it easy to set up 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 powerful coarse-graining method
          that gives accuracy comparable to atomistic models, with runtimes that are
          orders of magnitude shorter.
        - 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.
        
        Installation
        ============
        
        **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:**
        
        .. code-block:: bash
        
           pip install raasaft
        
           # or to upgrade
           pip install --upgrade raasaft
         
           # To start using raaSAFT:
           mkdir raasaft && cd raasaft
           raasaft_init
           # You now have the helpful directories tutorials/ replication/ and mysaft/
           ls
        
           # 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 the repo at http://bitbucket.org/asmunder/raasaft
            - The `maint` branch should be as stable as the version on PyPi
            - The `master` branch changes frequently and may not always be stable
        - You probably want to add the repo directory to your PYTHONPATH.
        
        Running simulations with raaSAFT
        ================================
        
        - Look at the README.txt file in `raasaft/tutorials/` for examples of how to use raaSAFT. 
        - In `raasaft/replication/` we include setups that can be used to replicate the findings of various papers.
        - In `raasaft/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.  
        
        .. code-block:: python
        
              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 `raasaft` folder to your `PYTHONPATH` shell variable (put this in your `.bashrc` file to make it permanent), e.g.:  
              `export PYTHONPATH=$PYTHONPATH:"/path/to/raasaft"`
        - 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: 
        
        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.
        
        Contribute
        ==========
        
        All contributions are welcome!
        
        Contact
        =======
        
        Email Aasmund at aaervik@gmail.com
        
        
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
