Materials informatics framework for ab initio data repositories
Project description
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
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
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.
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