1.. Links to websites 2.. _Sphinx: http://sphinx.pocoo.org 3.. _Abinit: https://www.abinit.org 4.. _abiconfig: https://github.com/abinit/abiconfig 5.. _abiflows: https://github.com/abinit/abiflows 6.. _abitutorials: https://github.com/abinit/abitutorials 7.. _abiconda: https://github.com/abinit/abiconda 8.. _pseudo-dojo: http://www.pseudo-dojo.org/ 9.. _pseudo-dojo repository: https://github.com/abinit/pseudo_dojo 10.. _pymatgen: http://www.pymatgen.org 11.. _fireworks: https://materialsproject.github.io/fireworks/ 12.. _mongodb: https://www.mongodb.com/ 13.. _mongoengine: http://mongoengine.org/ 14.. _`materials project`: https://materialsproject.org/ 15.. _conda: https://conda.io/docs/ 16.. _Anaconda: https://continuum.io/downloads 17.. _abinit-channel: https://anaconda.org/abinit 18.. _matsci: http://materials.sh/ 19.. _spack: https://github.com/LLNL/spack 20.. _pickle: https://docs.python.org/3/library/pickle.html#module-pickle 21.. _matplotlib: http://matplotlib.org 22.. _pandas: http://pandas.pydata.org 23.. _scipy: https://www.scipy.org/ 24.. _numpy: http://www.numpy.org/ 25.. _seaborn: https://seaborn.pydata.org/ 26.. _simpy: https://simpy.readthedocs.io/en/latest/ 27.. _networkx: https://networkx.github.io/ 28.. _pytest: https://docs.pytest.org/en/latest/contents.html 29.. _netcdf4-python: http://unidata.github.io/netcdf4-python/ 30.. _nbformat: https://github.com/jupyter/nbformat 31.. _pip: https://pypi.python.org/pypi/pip 32.. _ipython: https://ipython.org/index.html 33.. _jupyter: http://jupyter.org/ 34.. _Python: http://www.python.org/ 35.. _spglib: https://atztogo.github.io/spglib/ 36.. _bader: http://theory.cm.utexas.edu/henkelman/code/bader/ 37.. _ase: https://wiki.fysik.dtu.dk/ase/ 38.. _COD: http://www.crystallography.net/cod/ 39.. _CIF: http://www.iucr.org/resources/cif 40.. _vesta: http://jp-minerals.org/vesta/en/ 41.. _xcrysden: http://www.xcrysden.org/ 42.. _xmgrace: http://plasma-gate.weizmann.ac.il/Grace/ 43.. _gnuplot: http://www.gnuplot.info/ 44.. _ovito: https://ovito.org/ 45.. _v_sim: http://inac.cea.fr/L_Sim/V_Sim/ 46.. _mayavi: http://docs.enthought.com/mayavi/mayavi/ 47.. _avogadro: https://avogadro.cc/ 48.. _nbjsmol: https://github.com/gmatteo/nbjsmol 49.. _phononwebsite: http://henriquemiranda.github.io/phononwebsite/ 50.. _phonopy: https://atztogo.github.io/phonopy/ 51.. _netcdf: https://www.unidata.ucar.edu/software/netcdf/docs/faq.html#whatisit 52.. _ipywidgets: https://github.com/jupyter-widgets/ipywidgets 53.. _YAML: https://en.wikipedia.org/wiki/YAML 54.. _JSON: https://en.wikipedia.org/wiki/JSON 55.. _slurm: https://slurm.schedmd.com/ 56.. _pbspro: http://pbspro.org/ 57.. _sge: http://gridscheduler.sourceforge.net/howto/GridEngineHowto.html 58.. _torque: http://www.adaptivecomputing.com/products/open-source/torque/ 59.. _moab: http://www.adaptivecomputing.com/products/hpc-products/moab-hpc-basic-edition/ 60.. _loadleveler: https://www.ibm.com/support/knowledgecenter/en/SSFJTW 61 62.. Links to important python objects. 63.. _POSCAR: http://cms.mpi.univie.ac.at/vasp/guide/node59.html 64.. _DataFrame: https://pandas.pydata.org/pandas-docs/stable/generated/pandas.DataFrame.html 65.. _DataFrames: https://pandas.pydata.org/pandas-docs/stable/generated/pandas.DataFrame.html 66 67.. Links to jupyter notebooks associated to AbiPy files available at 68 https://nbviewer.jupyter.org/github/abinit/abitutorials/blob/master/abitutorials/index.ipynb?flush_cache=true 69.. _AbipyStructure: https://nbviewer.jupyter.org/github/abinit/abitutorials/blob/master/abitutorials/structure.ipynb 70.. _AbinitInput: https://nbviewer.jupyter.org/github/abinit/abitutorials/blob/master/abitutorials/abinit_input.ipynb 71.. _GSR.nc: https://nbviewer.jupyter.org/github/abinit/abitutorials/blob/master/abitutorials/gsr.ipynb 72.. _HIST.nc: https://nbviewer.jupyter.org/github/abinit/abitutorials/blob/master/abitutorials/hist.ipynb 73.. _FATBANDS.nc: https://nbviewer.jupyter.org/github/abinit/abitutorials/blob/master/abitutorials/efatbands.ipynb 74.. _DDB: https://nbviewer.jupyter.org/github/abinit/abitutorials/blob/master/abitutorials/ddb.ipynb 75.. _SIGRES.nc: https://nbviewer.jupyter.org/github/abinit/abitutorials/blob/master/abitutorials/sigres.ipynb 76 77.. Important Abipy objects. 78.. |AttrDict| replace:: :class:`monty.collections.AttrDict` 79.. |Function1D| replace:: :class:`abipy.core.func1d.Function1D` 80.. |Mesh3d| replace:: :class:`abipy.core.mesh3d.Mesh3d` 81.. |GSphere| replace:: :class:`abipy.core.gsphere.GSphere` 82.. |Kpoint| replace:: :class:`abipy.core.kpoints.Kpoint` 83.. |KpointList| replace:: :class:`abipy.core.kpoints.KpointList` 84.. |Kpath| replace:: :class:`abipy.core.kpoints.Kpath` 85.. |IrredZone| replace:: :class:`abipy.core.kpoints.IrredZone` 86.. |KpointStar| replace:: :class:`abipy.core.kpoints.KpointStar` 87.. |Structure| replace:: :class:`abipy.core.structure.Structure` 88.. |pymatgen-Structure| replace:: :class:`pymatgen.core.structure.Structure` 89.. |Lattice| replace:: :class:`pymatgen.core.lattice.Lattice` 90.. |AbinitInput| replace:: :class:`abipy.abio.inputs.AbinitInput` 91.. |AnaddbInput| replace:: :class:`abipy.abio.inputs.AnaddbInput` 92.. |MultiDataset| replace:: :class:`abipy.abio.inputs.MultiDataset` 93.. |ElectronBands| replace:: :class:`abipy.electrons.ebands.ElectronBands` 94.. |ElectronBandsPlotter| replace:: :class:`abipy.electrons.ebands.ElectronBandsPlotter` 95.. |SkwInterpolator| replace:: :class:`abipy.core.skw.SkwInterpolator` 96.. |ElectronDos| replace:: :class:`abipy.electrons.ebands.ElectronDos` 97.. |ElectronDosPlotter| replace:: :class:`abipy.electrons.ebands.ElectronDosPlotter` 98.. |PhononBands| replace:: :class:`abipy.dfpt.phonons.PhononBands` 99.. |Node| replace:: :class:`abipy.flowtk.nodes.Node` 100.. |Task| replace:: :class:`abipy.flowtk.tasks.Task` 101.. |AbinitTask| replace:: :class:`abipy.flowtk.tasks.AbinitTask` 102.. |ScfTask| replace:: :class:`abipy.flowtk.tasks.ScfTask` 103.. |NscfTask| replace:: :class:`abipy.flowtk.tasks.NscfTask` 104.. |AnaddbTask| replace:: :class:`abipy.flowtk.tasks.AnaddbTask` 105.. |Flow| replace:: :class:`abipy.flowtk.flows.Flow` 106.. |Work| replace:: :class:`abipy.flowtk.works.Work` 107.. |TaskManager| replace:: :class:`abipy.flowtk.tasks.TaskManager` 108.. |GsrFile| replace:: :class:`abipy.electrons.gsr.GsrFile` 109.. |GsrRobot| replace:: :class:`abipy.electrons.gsr.GsrRobot` 110.. |MdfFile| replace:: :class:`abipy.electrons.bse.MdfFile` 111.. |DdbFile| replace:: :class:`abipy.dfpt.ddb.DdbFile` 112.. |HistFile| replace:: :class:`abipy.dynamics.hist.HistFile` 113.. |FatBandsFile| replace:: :class:`abipy.electrons.fatbands.FatBandsFile` 114.. |DielectricTensorGenerator| replace:: :class:`abipy.dfpt.ddb.DielectricTensorGenerator` 115.. |DdbRobot| replace:: :class:`abipy.dfpt.ddb.DdbRobot` 116.. |AnaddbNcFile| replace:: :class:`abipy.dfpt.anaddb.AnaddbNcFile` 117.. |AbinitNcFile| replace:: :class:`abipy.core.mixins.AbinitNcFile` 118.. |SigEPhFile| replace:: :class:`abipy.eph.sigeph.SigEPhFile` 119.. |pmg-Tensor| replace:: :class:`pymatgen.core.tensors.Tensor` 120.. |Stress| replace:: :class:`abipy.tools.tensors.Stress` 121.. |DielectricTensor| replace:: :class:`abipy.tools.tensors.DielectricTensor` 122.. |ElasticData| replace:: :class:`abipy.dfpt.elastic.ElasticData` 123.. |PhbstFile| replace:: :class:`abipy.dfpt.phonons.PhbstFile` 124.. |PhdosFile| replace:: :class:`abipy.dfpt.phonons.PhdosFile` 125.. |PhononDos| replace:: :class:`abipy.dfpt.phonons.PhononDos` 126.. |PhononBandsPlotter| replace:: :class:`abipy.dfpt.phonons.PhononBandsPlotter` 127.. |PhononDosPlotter| replace:: :class:`abipy.dfpt.phonons.PhononDosPlotter` 128.. |MsqDos| replace:: :class:`abipy.dfpt.msqdos.MsqDos` 129.. |Pseudo| replace:: :class:`pymatgen.io.abinit.pseudos.Pseudo` 130.. |PseudoTable| replace:: :class:`pymatgen.io.abinit.pseudos.PseudoTable` 131.. |Visualizer| replace:: :class:`abipy.iotools.visualizer.Visualizer` 132.. |SigresFile| replace:: :class:`abipy.electrons.gw.SigresFile` 133.. |SigephFile| replace:: :class:`abipy.electrons.eph.SigephFile` 134.. |SigephRobot| replace:: :class:`abipy.electrons.eph.SigephRobot` 135 136.. Important objects provided by libraries. 137.. |matplotlib-Figure| replace:: :class:`matplotlib.figure.Figure` 138.. |matplotlib-Axes| replace:: :class:`matplotlib.axes.Axes` 139.. |pandas-DataFrame| replace:: :class:`pandas.DataFrame` 140.. |pandas-DataFrames| replace:: :class:`pandas.DataFrame` 141.. |numpy-array| replace:: :class:`numpy.ndarray` 142 143.. Badges 144.. |pypi-version| image:: https://badge.fury.io/py/abipy.svg 145 :alt: PyPi version 146 :target: https://badge.fury.io/py/abipy 147 148.. |travis-status| image:: https://travis-ci.org/abinit/abipy.svg?branch=develop 149 :alt: Travis status 150 :target: https://travis-ci.org/abinit/abipy 151 152.. |coverage-status| image:: https://coveralls.io/repos/github/abinit/abipy/badge.svg?branch=develop 153 :alt: Coverage status 154 :target: https://coveralls.io/github/abinit/abipy?branch=develop 155 156.. |download-with-anaconda| image:: https://anaconda.org/abinit/abipy/badges/installer/conda.svg 157 :alt: Download with Anaconda 158 :target: https://conda.anaconda.org/abinit 159 160.. |abipy-license| image:: https://img.shields.io/badge/license-GPL-blue.svg 161 :alt: AbiPy license 162 :target: https://opensource.org/licenses/gpl-2.0.php 163 164.. |launch-binder| image:: https://mybinder.org/badge.svg 165 :alt: Launch binder 166 :target: https://mybinder.org/v2/gh/abinit/abipy/develop 167 168.. |launch-nbviewer| image:: https://img.shields.io/badge/render-nbviewer-orange.svg 169 :alt: Launch nbviewer 170 :target: https://nbviewer.jupyter.org/github/abinit/abitutorials/blob/master/abitutorials/index.ipynb 171 172.. |supported-versions| image:: https://img.shields.io/pypi/pyversions/abipy.svg?style=flat 173 :alt: Supported versions 174 :target: https://pypi.python.org/pypi/abipy 175 176.. |requires| image:: https://requires.io/github/abinit/abipy/requirements.svg?branch=develop 177 :target: https://requires.io/github/abinit/abipy/requirements/?branch=develop 178 :alt: Requirements Status 179 180.. |docs-github| image:: https://img.shields.io/badge/docs-ff69b4.svg 181 :alt: AbiPy Documentation 182 :target: http://abinit.github.io/abipy 183
