tilde 0.8.1
Materials informatics framework for ab initio data repositories
License: MIT
Keywords: CRYSTAL Quantum-ESPRESSO VASP ab-initio materials informatics first-principles

Tilde
=====

|DOI|

Tilde is an intelligent data organizer and Python framework for
computational *ab initio* materials science. Tilde creates systemized
data repositories from the simulation logs of
`VASP <http://www.vasp.at>`__, `CRYSTAL <http://www.crystal.unito.it>`__
and `Quantum ESPRESSO <http://www.quantum-espresso.org>`__ packages.
Other data formats can be added relatively easily. The folders with the
log files can be scanned and the results added into a repository. A
simple usecase is described in `this blog
post <https://blog.tilde.pro/simple-ab-initio-materials-data-mining-tutorial-6127c777dabc>`__.
Web-based repository GUI is `separately
available <https://github.com/tilde-lab/berlinium>`__.

Installation
------------

System packages ``build-essential python-dev python-numpy libffi-dev``
(**-dev** or **-devel**) must be present. Please, `set up Python
virtualenv <https://virtualenv.readthedocs.org>`__ inside the Tilde
folder (and mind ``--system-site-packages`` option to access
``python-numpy``):

.. code:: shell

    virtualenv --system-site-packages tilde

Then activate virtualenv:

.. code:: shell

    . bin/activate

Virtualenv should be always used while working with the codebase. Run
``pip install -r requirements.txt`` to install Python dependencies.
Finally, ensure if the framework is ready:

.. code:: shell

    ./utils/tilde.sh -x

Additionally, installation is covered in `this blog
post <https://blog.tilde.pro/simple-ab-initio-materials-data-mining-tutorial-6127c777dabc>`__.

Usage
-----

.. code:: shell

    ./utils/tilde.sh --help

For example, to scan folder(s) recursively (**-r**), with terse print
(**-t**), showing information on calculation metadata (**-i**) and
convergence (**-v**) and adding results to a database (**-a**):

.. code:: shell

    ./utils/tilde.sh /home/user/work1 /home/work2 -r -t -v -a -i

Other example: for the perovskite structures (shipped with Tilde),
extract the distortion of the MO6-octahedra wrt cubic phase (in Euler
angles). Here the **-m** switch invokes **perovskite\_tilting** module
(see **apps** folder):

.. code:: shell

    ./utils/tilde.sh tilde/tests/apps/perovskite_tilting/outputs -m perovskite_tilting

GUI
---

Experimental GUI server is started as follows:

.. code:: shell

    python utils/gui_server.py

GUI client is the separate project called
`Berlinium <https://github.com/tilde-lab/berlinium>`__.

Testing
-------

.. code:: shell

    sh tests/run_tests.sh

Licensing
---------

`MIT <https://en.wikipedia.org/wiki/MIT_License>`__

Similar projects
----------------

Other known similar initiatives are listed below:

-  Accelrys (BIOVIA) Pipeline Pilot and Materials Studio,
   http://accelrys.com/products
-  AFLOW framework and Aflowlib repository, http://www.aflowlib.org
-  AiiDA: Automated Infrastructure and Database for Ab-initio design,
   Bosch LLC (**Python**), http://aiida.net
-  Automated Topology Builder (ATB), http://compbio.biosci.uq.edu.au/atb
-  Blue Obelisk Data Repository (**XSLT, XML**),
   http://bodr.sourceforge.net
-  Catapp, http://www.slac.stanford.edu/~strabo/catapp
-  CCLib (**Python**), http://cclib.sf.net
-  cctbx: Computational Crystallography Toolbox,
   http://cctbx.sourceforge.net
-  CEPDB: Harvard Clean Energy Project and distributed volunteer
   computing, http://cepdb.molecularspace.org
-  CMR (**Python**), https://wiki.fysik.dtu.dk/cmr
-  Computational Chemistry Comparison and Benchmark Database,
   http://cccbdb.nist.gov
-  Crystallography Open Database (including Theoretical Database
-  Delta project: Comparing Solid State DFT Codes,
   http://molmod.ugent.be/deltacodesdft
-  Electronic Structure Project, http://gurka.fysik.uu.se/ESP
-  ESTEST (**Python, XQuery**), http://estest.ucdavis.edu
-  Exabyte.io, Materials Discover Cloud, http://exabyte.io
-  J-ICE (based on **Jmol, Java**), http://j-ice.sourceforge.net
-  ioChem-BD (**Java**), http://www.iochem-bd.org
-  Materials Project (**Python**), http://www.materialsproject.org
-  MatNavi and AtomWork Materials Databases, Materials Information
   Station, Tsukuba, http://mits.nims.go.jp/matnavi/
-  MedeA Computational environment, http://www.materialsdesign.com/medea
-  MSE: Test Set for Materials Science and Engineering,
   http://mse.fhi-berlin.mpg.de
-  NoMaD: Novel Materials Discovery, http://nomad-repository.eu
-  NREL MatDB, http://materials.nrel.gov
-  Open Materials Database and High-Throughput Toolkit (**Python**),
   http://openmaterialsdb.se
-  OQMD and qmpy (**Python**), http://oqmd.org
-  Phonon database at Kyoto university,
   http://phonondb.mtl.kyoto-u.ac.jp
-  PAULING FILE, world largest database for inorganic compounds,
   http://paulingfile.com
-  pyCMW (**Python**), a framework of Max Planck Institute for Iron
   Research GmbH
-  QMForge (**Python**), http://qmforge.sourceforge.net
-  Quixote, http://quixote.wikispot.org
-  WebMO: Web-based interface to computational chemistry packages (Java,
   Perl), http://webmo.net
-  WURM: database of computed physical properties of minerals,
   http://wurm.info

Openness principle
------------------

Tilde adopts the principle of open data, open source code and open
standards declared by an initiative group with a symbolic name `Blue
Obelisk <http://www.jcheminf.com/content/3/1/37>`__.

.. figure:: https://raw.githubusercontent.com/tilde-lab/tilde/master/blue_obelisk.gif
   :alt: Blue Obelisk

   Blue Obelisk

Contact
-------

Please, send your feedback, bugreports and feature requests via
`email <mailto:eb@tilde.pro>`__,
`Twitter <http://twitter.com/tildepro>`__ or
`GitHub <http://github.com/tilde-lab/tilde/issues>`__.

.. |DOI| image:: https://zenodo.org/badge/18811/tilde-lab/tilde.svg
   :target: https://zenodo.org/badge/latestdoi/18811/tilde-lab/tilde