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gmatteo committed May 20, 2019
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143 changes: 30 additions & 113 deletions index.ipynb
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}
},
"source": [
"## Jupyter notebooks with [examples and lessons](https://nbviewer.jupyter.org/github/abinit/abitutorials/blob/master/abitutorials/index.ipynb) inspired to the official tutorials\n",
"## Jupyter notebooks with [examples and lessons](https://nbviewer.jupyter.org/github/abinit/abitutorials/blob/master/abitutorials/index.ipynb) inspired by the official tutorials\n",
"\n",
"<!-- img src=\"./assets/abipy_notebooks.png\" width=\"100%\" align=\"center\" -->"
]
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"%embed https://nbviewer.jupyter.org/github/abinit/abitutorials/blob/master/abitutorials/index.ipynb"
]
},
{
"cell_type": "markdown",
"metadata": {
"slideshow": {
"slide_type": "skip"
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"source": [
"## Files supported by AbiPy\n",
"\n",
"* *GSR.nc* ➝ Ground-state results produced by SCF/NSCF runs\n",
"* *HIST.nc* ➝ Structural relaxation and molecular dynamics\n",
"* *FATBANDS.nc* ➝ Fatbands and LM-projected DOS for electrons\n",
"* *DDB*: ➝ dynamical matrix, Born effective charges, elastic constants…\n",
"* *SIGRES.nc* ➝ $GW$ calculations ($\\Sigma^{e-e}$ self-energy)\n",
"* *MDF.nc* ➝ Bethe-Salpeter calculations\n",
"* *ABIWAN.nc* ➝ *netcdf* file produced by Abinit with wannier90 results \n",
"* *SIGEPH.nc* ➝ electron-phonon self-energy ($\\Sigma^{e-ph}$)\n",
"* …\n",
"\n",
"#### Jupter notebooks with examples available [here](https://nbviewer.jupyter.org/github/abinit/abitutorials/blob/master/abitutorials/index.ipynb#Output-files-supported-by-AbiPy)"
]
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"</div>"
]
},
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"source": [
"## AbiPy post-processing tools\n",
"\n",
"* Main entry point: \n",
"\n",
" ```python\n",
" from abipy import abilab\n",
" abifile = abilab.abiopen(\"filename.nc\")\n",
" ```\n",
" \n",
" where *filename.nc* is a *netcdf* file (support also text files e.g. *run.abo*, *run.log*, *out_DDB*)\n",
"\n",
"* *abifile* is the *AbiFile* subclass associated to the given file extension:\n",
"\n",
" 1. GSR.nc ➝ *GsrFile*\n",
" 2. HIST.nc ➝ *HistFile*\n",
" 3. More than 45 file extensions supported (see `abiopen.py --help`) \n",
" \n",
"\n",
"* Command line interface: use `abiopen.py FILE` to:\n",
"\n",
" * open the file inside the [*ipython*](https://ipython.org/) terminal\n",
" * print info to terminal (`--print` option)\n",
" * produce a predefined set of *matplotlib* figures (`--expose` option)\n",
" * generate [jupyter notebooks](https://jupyter.org/) (`--notebook` option)"
]
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"cell_type": "markdown",
"metadata": {
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"abiopen.py gs_dfpt.abo --expose --seaborn\n",
"```\n",
"\n",
"<center>\n",
"<img src=\"assets/abiopen_abo.png\" width=\"75%\" align=\"center\">\n",
"</center>\n",
"\n",
"#### The introduction of Yaml documents in the main output (*cfr.* Theo's talk) will facilitate the implementation of new post-processing tools..."
]
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"slide_type": "skip"
}
},
"source": [
"#### Read structure from FILE and invoke [spglib](https://atztogo.github.io/spglib/) to analyze symmetries:"
]
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{
"name": "stdout",
"output_type": "stream",
"text": [
"Full Formula (Si2)\r\n",
"Reduced Formula: Si\r\n",
"abc : 3.866975 3.866975 3.866975\r\n",
"angles: 60.000000 60.000000 60.000000\r\n",
"\r\n",
"Spglib space group info (magnetic symmetries not taken into account).\r\n",
"Spacegroup: Fd-3m (227), Hall: F 4d 2 3 -1d, Abinit spg_number: 227\r\n",
"Crystal_system: cubic, Lattice_type: cubic, Point_group: m-3m\r\n",
"\r\n",
" Idx Symbol Reduced_Coords Wyckoff EqIdx\r\n",
"----- -------- -------------------------- --------- -------\r\n",
" 0 Si +0.00000 +0.00000 +0.00000 (2a) 0\r\n",
" 1 Si +0.25000 +0.25000 +0.25000 (2a) 0\r\n"
]
}
],
"source": [
"!abistruct.py spglib si_scf_GSR.nc"
]
},
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"metadata": {
"slideshow": {
"slide_type": "subslide"
}
},
"source": [
"#### Read structure from FILE and print ABINIT variables for NSCF along k-path:"
]
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"cell_type": "markdown",
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"cell_type": "markdown",
"metadata": {
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"source": [
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}
},
"source": [
"<img src=\"assets/abicomp.png\" width=\"25%\" align=\"center\">"
"<img src=\"assets/abicomp.png\" width=\"30%\" align=\"center\">"
]
},
{
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"##### Qualitative analysis of possible e-ph scattering channels with less than 20 lines of code!"
]
},
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"<img src=\"assets/abinp.png\" width=\"30%\" align=\"center\">"
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"\n",
"### Post-processing tools\n",
"\n",
"* Add support for more *netcdf* files\n",
"* Support for more *netcdf* files\n",
"* More post-processing tools for MD calculations\n",
"* More converters and interfaces for third-party applications\n",
"* Integrate AbiPy with JupyterLab to create a flexible graphical enviroment for Abinit exposing (part) \n",
"* Integrate AbiPy with [jupyterlab](https://github.com/jupyterlab/jupyterlab) to create a flexible graphical enviroment for Abinit exposing (part) \n",
" of the python API \n",
"* Explore web-based technologies for data analysis and visualization based on [plotly](https://plot.ly/) \n",
" and [dash](https://plot.ly/products/dash/) \n",
"* Develop toolkit to build web apps powered by Abipy and pymatgen to disseminate scientific results. \n",
"* Explore web-based technologies for data analysis and visualization ([plotly](https://plot.ly/), [dash](https://plot.ly/products/dash/)) \n",
"* Develop toolkit to build web apps powered by AbiPy and pymatgen to disseminate scientific results. \n",
"\n",
"## Integration with Abinit Continuous Integration\n",
"## Continuous Integration\n",
"\n",
"* Use AbiPy programmatic interface to implement:\n",
"\n",
" * Validation of parallel algorithms for np in range(1, N)\n",
" * Stress testing\n",
" * Benchmarks"
]
},
{
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"execution_count": null,
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}
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"metadata": {
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