Tilde

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, CRYSTAL and Quantum ESPRESSO 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. Web-based repository GUI is separately available.

Installation

System packages build-essential python-dev python-numpy libffi-dev (-dev or -devel) must be present. Please, set up Python virtualenv inside the Tilde folder (and mind --system-site-packages option to access python-numpy):

virtualenv --system-site-packages tilde

Then activate virtualenv:

. 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:

./utils/tilde.sh -x

Additionally, installation is covered in this blog post.

Usage

./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):

./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):

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

GUI

Experimental GUI server is started as follows:

python utils/gui_server.py

GUI client is the separate project called Berlinium.

Testing

sh tests/run_tests.sh

Licensing

MIT

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.

Contact

Please, send your feedback, bugreports and feature requests via email, Twitter or GitHub.