Metadata-Version: 1.1
Name: pymatgen-db
Version: 0.1.7dev
Summary: pymatgen is the Python materials analysis library powering the Materials Project (www.materialsproject.org).
Home-page: https://github.com/materialsproject/pymatgen-db
Author: Shyue Ping Ong
Author-email: shyuep@gmail.com
License: MIT
Download-URL: https://github.com/materialsproject/pymatgen-db/tarball/master
Description: 
        Pymatgen-db is a database add-on for the Python Materials Genomics (pymatgen)
        materials analysis library. It enables the creation of Materials
        Project-style `MongoDB`_ databases for management of materials data and also
        provides a clean and intuitive web ui for exploring that data. A query engine
        is also provided to enable the easy translation of MongoDB docs to useful
        pymatgen objects for analysis purposes.
        
        Getting pymatgen-db
        ===================
        
        Stable version
        --------------
        
        The version at the Python Package Index (PyPI) is always the latest stable
        release that will be hopefully, be relatively bug-free. The easiest way to
        install pymatgen on any system is to use easy_install or pip, as follows::
        
            easy_install pymatgen-db
        
        or::
        
            pip install pymatgen-db
        
        Developmental version
        ---------------------
        
        The bleeding edge developmental version is at the pymatgen-db's `Github repo
        <https://github.com/materialsproject/pymatgen-db>`_. The developmental
        version is likely to be more buggy, but may contain new features. The
        Github version include test files as well for complete unit testing. After
        cloning the source, you can type::
        
            python setup.py install
        
        or to install the package in developmental mode::
        
            python setup.py develop
        
        Requirements
        ============
        
        All required python dependencies should be automatically taken care of if you
        install pymatgen-db using easy_install or pip. Otherwise, these packages should
        be available on `PyPI <http://pypi.python.org>`_. Please note that if you do
        not already have pymatgen installed, you should refer to the `pymatgen docs
        <http://pythonhosted.org//pymatgen>`_ for detailed instructions.
        
        1. Python 2.7+ required. New default modules such as json are used, as well as
           new unittest features in Python 2.7.
        2. pymatgen 2.5+, including all dependencies associated with it.
        3. pymongo 2.4+: For interfacing with MongoDb.
        4. MongoDB 2.2+: Get it at the `MongoDB`_ website.
        
        Usage
        =====
        
        Initial setup
        -------------
        
        In this step, it is assumed that you have already installed and setup MongoDB
        on a server of your choice. If you have not, the `MongoDB manual
        <http://docs.mongodb.org/manual/>`_ is an excellent place to start.
        
        A db initialization/insertion script has been written (mgdb) has been
        written and will be automatically installed as part of the installation
        process. Type::
        
            mgdb --help
        
        to see all the options.
        
        Before use, first create a database config file by doing::
        
            mgdb init -c db.json
        
        This will prompt you for a few parameters to create a database config file,
        which will make it much easier to use in future. Note that the config file
        name can be anything of your choice, but using db.json will allow you to use
        mgdb without explicitly specifying the filename in future.
        
        Inserting calculations
        ----------------------
        
        To insert an entire directory of runs (where the topmost directory is
        "dir_name") into the database, use the following command::
        
            # Note that "-c db.json" may be omitted if the config filename is the
            # current directory under the default filename of db.json.
        
            mgdb insert -c db.json dir_name
        
        materials genomics ui
        ---------------------
        
        .. figure:: http://pythonhosted.org/pymatgen-db/images/mgui_demo.png
            :width: 100%
            :alt: materials genomics ui
            :align: center
        
            materials genomics ui
        
        A simple web interface has been provided to assist in the querying and
        viewing of results. This web interface can be started by running::
        
            mgdb -c db.json runserver
        
        This will run the web server at http://127.0.0.1:8000. Go to this address in
        your browser and you should see something like the figure below. Most queries
        can be performed using the web ui. Two options for presenting results are
        provided - a table format which is easier for comparing data,
        and a tree format which makes it much easier to explore highly nested trees
        of data.
        
        Querying a database
        -------------------
        
        Sometimes, more fine-grained querying is needed (e.g., for subsequent
        postprocessing and analysis).
        
        The mgdb script allows you to make simple queries from the command line::
        
            # Query for the task id and energy per atom of all calculations with
            # formula Li2O. Note that the criteria has to be specified in the form of
            # a json string. Note that "-c db.json" may be omitted if the config
            # filename is the current directory under the default filename of db.json.
        
            mgdb query -c db.json --crit '{"pretty_formula": "Li2O"}' --props task_id energy_per_atom
        
        For more advanced queries, you can use the QueryEngine class. Some examples
        are as follows::
        
            >>> from matgendb.query_engine import QueryEngine
            >>> qe = QueryEngine()
        
            #Print the task id and formula of all entries in the database.
            >>> for r in qe.query(properties=["pretty_formula", "task_id"]):
            ...     print "{task_id} - {pretty_formula}".format(**r)
            ...
            12 - Li2O
        
            # Get a pymatgen Structure from the task_id.
            >>> structure = qe.get_structure_from_id(12)
        
            # Get pymatgen ComputedEntries using a criteria.
            >>> entries = qe.get_entries({})
        
        The language follows very closely to pymongo/MongoDB syntax, except that
        QueryEngine provides useful aliases for commonly used fields as well as
        translation to commonly used pymatgen objects like Structure and
        ComputedEntries.
        
        How to cite pymatgen-db
        =======================
        
        If you use pymatgen and pymatgen-db in your research, please consider citing
        the following work:
        
            Shyue Ping Ong, William Davidson Richards, Anubhav Jain, Geoffroy Hautier,
            Michael Kocher, Shreyas Cholia, Dan Gunter, Vincent Chevrier, Kristin A.
            Persson, Gerbrand Ceder. *Python Materials Genomics (pymatgen) : A Robust,
            Open-Source Python Library for Materials Analysis.* Computational
            Materials Science, 2013, 68, 314-319. `doi:10.1016/j.commatsci.2012.10.028
            <http://dx.doi.org/10.1016/j.commatsci.2012.10.028>`_
        
        .. _`MongoDB` : http://www.mongodb.org/
        
Keywords: vasp,gaussian,materials,project,electronic,structure,mongo
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 2.7
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: Scientific/Engineering :: Physics
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Software Development :: Libraries :: Python Modules
