`abiopen.py`

AbiPy provides python objects associated to several Abinit output files. These objects implement methods to analyze and plot the results. The examples in our AbiPy Gallery use this API to plot data with matplotlib.

The abiopen.py script provides a handy interface to the AbiPy objects. It can be used to open Abinit files directly in the ipython shell or inside a jupyter notebook and interact with the associated object (called abifile in the ipython terminal). The syntax of the script is:

abiopen.py FILE [options]

where FILE is one of the files supported by AbiPy (usually in netcdf format but other files are supported as well e.g. Abinit input and output files in text format). By default abiopen starts an ipython session and the user can interact with the abifile and invoke its methods.

Alternatively, it is possible to generate automatically a jupyter notebook with the -nb option e.g.:

abiopen.py out_FATBANDS.nc -nb

will produce a notebook to visualize the electronic fatbands inside your default web browser.

Use the -p option if you just want to get information on the file without opening it, e.g.:

abiopen.py out_GSR.nc -p

or the -e (--expose) to generate matplotlib plots automatically:

abiopen.py out_GSR.nc -e -sns=talk

seaborn plot style and settings can be changed from the command line interface with the -sns option

The script uses the file extension to decide what to do with the file and the type of python object that should be instantiated. The list of supported file extensions is obtained with:

$ abiopen.py --help
usage: abiopen.py [-h] [--loglevel LOGLEVEL] [-V] [-v] [-nb]
                  [--classic-notebook] [--no-browser] [--foreground] [-p]
                  [-pn] [-pnt PANEL_TEMPLATE] [--port PORT] [-e] [-s]
                  [-t SLIDE_TIMEOUT] [-sns [SEABORN]] [-mpl MPL_BACKEND] [-ew]
                  [-ply]
                  filepath

positional arguments:
  filepath              File to open. See table below for the list of
                        supported extensions.

options:
  -h, --help            show this help message and exit
  --loglevel LOGLEVEL   Set the loglevel. Possible values: CRITICAL, ERROR
                        (default), WARNING, INFO, DEBUG
  -V, --version         show program's version number and exit
  -v, --verbose         verbose, can be supplied multiple times to increase
                        verbosity
  -nb, --notebook       Open file in jupyter notebook
  --classic-notebook, -cnb
                        Use classic jupyter notebook instead of jupyterlab.
  --no-browser          Start the jupyter server to serve the notebook but
                        don't open the notebook in the browser. Use this
                        option to connect remotely from localhost to the
                        machine running the kernel
  --foreground          Run jupyter notebook in the foreground.
  -p, --print           Print python object and return.
  -pn, --panel          Open Dashboard in web browser, requires panel package.
  -pnt PANEL_TEMPLATE, --panel-template PANEL_TEMPLATE
                        Specify template for panel dasboard.Possible values
                        are: FastList, FastGrid, Golden, Bootstrap, Material,
                        React, Vanilla.Default: FastList
  --port PORT           Allows specifying a specific port when serving panel
                        app.
  -e, --expose          Open file and generate matplotlib figures
                        automatically by calling expose method.
  -s, --slide-mode      Iterate over figures. Expose all figures at once if
                        not given on the CLI.
  -t SLIDE_TIMEOUT, --slide-timeout SLIDE_TIMEOUT
                        Close figure after slide-timeout seconds (only if
                        slide-mode). Block if not specified.
  -sns [SEABORN], --seaborn [SEABORN]
                        Use seaborn settings. Accept value defining context in
                        ("paper", "notebook", "talk", "poster"). Default:
                        paper
  -mpl MPL_BACKEND, --mpl-backend MPL_BACKEND
                        Set matplotlib interactive backend. Possible values:
                        GTKAgg, GTK3Agg, GTK, GTKCairo, GTK3Cairo, WXAgg, WX,
                        TkAgg, Qt4Agg, Qt5Agg, macosx.See also:
                        https://matplotlib.org/faq/usage_faq.html#what-is-a-
                        backend.
  -ew, --expose-web     Generate matplotlib plots in $BROWSER instead of
                        X-server. WARNING: Not all the features are supported.
  -ply, --plotly        Generate plotly plots in $BROWSER instead of
                        matplotlib. WARNING: Not all the features are
                        supported.

======================================================================================================
Usage example:

    abiopen.py FILE          => Open file in ipython shell.
    abiopen.py FILE -p       => Print info on object to terminal.
    abiopen.py FILE -e       => Generate matplotlib figures automatically.
                                Use -sns to activate seaborn settings.
    abiopen.py FILE -eweb    => Generate matplotlib figures, show them in the $BROWSER.
    abiopen.py FILE -ply     => Generate plotly figures automatically. Show them in the $BROWSER.
                                Note that not all FILEs support plotly.
    abiopen.py FILE -pn      => Generate GUI in web BROWSER to interact with FILE. Requires panel package.
    abiopen.py FILE -nb      => Generate jupyter-lab notebook.
    abiopen.py FILE -cnb     => Generate classic jupyter notebook.

where `FILE` is any file supported by abipy/pymatgen e.g. Netcdf files, Abinit input, POSCAR, xsf.
File extensions supported (including zipped files with extension in ".bz2", ".gz", ".z"):
Use `-v` to increase verbosity level (can be supplied multiple times e.g -vv).

JSON file are supported as well. In this case, abiopen.py tries to reconstruct python objects
assuming JSON document in MSONable format and then invokes ipython with the `data` object.
Use `-e` or `--notebook` or `--panel` to print the JSON dictionary without reconstructing python objects.
======================================================================================================

Table mapping file extension to AbiPy object:

Extension          Class
-----------------  -----------------------------------------------------
.abi               <class 'abipy.abio.abivars.AbinitInputFile'>
.in                <class 'abipy.abio.abivars.AbinitInputFile'>
.abo               <class 'abipy.abio.outputs.AbinitOutputFile'>
.out               <class 'abipy.abio.outputs.AbinitOutputFile'>
.log               <class 'abipy.abio.outputs.AbinitLogFile'>
.cif               <class 'abipy.core.structure.Structure'>
.abivars           <class 'abipy.core.structure.Structure'>
.ucell             <class 'abipy.core.structure.Structure'>
.cssr              <class 'abipy.core.structure.Structure'>
.json              <class 'abipy.core.mixins.JsonFile'>
.py                <class 'abipy.core.mixins.TextFile'>
.sh                <class 'abipy.core.mixins.TextFile'>
.stdin             <class 'abipy.core.mixins.TextFile'>
.stderr            <class 'abipy.core.mixins.TextFile'>
.err               <class 'abipy.core.mixins.TextFile'>
.files             <class 'abipy.core.mixins.TextFile'>
.stdout            <class 'abipy.core.mixins.TextFile'>
.cube              <class 'abipy.core.mixins.CubeFile'>
anaddb.nc          <class 'abipy.dfpt.anaddbnc.AnaddbNcFile'>
DEN                <class 'abipy.electrons.denpot.DensityFortranFile'>
.wout              <class 'abipy.wannier90.wout.WoutFile'>
EDOS               <class 'abipy.electrons.ebands.EdosFile'>
.psp8              <class 'pymatgen.io.abinit.pseudos.Pseudo'>
.pspnc             <class 'pymatgen.io.abinit.pseudos.Pseudo'>
.fhi               <class 'pymatgen.io.abinit.pseudos.Pseudo'>
JTH.xml            <class 'pymatgen.io.abinit.pseudos.Pseudo'>
.upf               <class 'pymatgen.io.abinit.pseudos.Pseudo'>
COHPCAR.lobster    <class 'abipy.electrons.lobster.CoxpFile'>
COOPCAR.lobster    <class 'abipy.electrons.lobster.CoxpFile'>
ICOHPLIST.lobster  <class 'abipy.electrons.lobster.ICoxpFile'>
DOSCAR.lobster     <class 'abipy.electrons.lobster.LobsterDoscarFile'>
POSCAR             <class 'abipy.core.structure.Structure'>
.vasp              <class 'abipy.core.structure.Structure'>
.xyz               <class 'abipy.core.structure.Structure'>
.evp               <class 'abipy.dynamics.cpx.EvpFile'>
GSR.nc             <class 'abipy.electrons.gsr.GsrFile'>
ESKW.nc            <class 'abipy.electrons.eskw.EskwFile'>
DEN.nc             <class 'abipy.electrons.denpot.DensityNcFile'>
OUT.nc             <class 'abipy.abio.outputs.OutNcFile'>
VHA.nc             <class 'abipy.electrons.denpot.VhartreeNcFile'>
VXC.nc             <class 'abipy.electrons.denpot.VxcNcFile'>
VHXC.nc            <class 'abipy.electrons.denpot.VhxcNcFile'>
POT.nc             <class 'abipy.electrons.denpot.PotNcFile'>
WFK.nc             <class 'abipy.waves.wfkfile.WfkFile'>
HIST.nc            <class 'abipy.dynamics.hist.HistFile'>
PSPS.nc            <class 'abipy.electrons.psps.PspsFile'>
DDB                <class 'abipy.dfpt.ddb.DdbFile'>
PHBST.nc           <class 'abipy.dfpt.phonons.PhbstFile'>
PHDOS.nc           <class 'abipy.dfpt.phonons.PhdosFile'>
SCR.nc             <class 'abipy.electrons.scr.ScrFile'>
SIGRES.nc          <class 'abipy.electrons.gw.SigresFile'>
GWR.nc             <class 'abipy.electrons.gwr.GwrFile'>
GRUNS.nc           <class 'abipy.dfpt.gruneisen.GrunsNcFile'>
MDF.nc             <class 'abipy.electrons.bse.MdfFile'>
FATBANDS.nc        <class 'abipy.electrons.fatbands.FatBandsFile'>
FOLD2BLOCH.nc      <class 'abipy.electrons.fold2bloch.Fold2BlochNcfile'>
CUT3DDENPOT.nc     <class 'abipy.electrons.denpot.Cut3dDenPotNcFile'>
OPTIC.nc           <class 'abipy.electrons.optic.OpticNcFile'>
A2F.nc             <class 'abipy.eph.a2f.A2fFile'>
SIGEPH.nc          <class 'abipy.eph.sigeph.SigEPhFile'>
GSTORE.nc          <class 'abipy.eph.gstore.GstoreFile'>
GPATH.nc           <class 'abipy.eph.gpath.GpathFile'>
TRANSPORT.nc       <class 'abipy.eph.transportfile.TransportFile'>
RTA.nc             <class 'abipy.eph.rta.RtaFile'>
V1SYM.nc           <class 'abipy.eph.v1sym.V1symFile'>
GKQ.nc             <class 'abipy.eph.gkq.GkqFile'>
V1QNU.nc           <class 'abipy.eph.v1qnu.V1qnuFile'>
V1QAVG.nc          <class 'abipy.eph.v1qavg.V1qAvgFile'>
ABIWAN.nc          <class 'abipy.wannier90.abiwan.AbiwanFile'>
EPH_CUMULANT.nc    <class 'abipy.eph.cumulant.CumulantEPhFile'>
VARPEQ.nc          <class 'abipy.eph.varpeq.VarpeqFile'>

Warning

AbiPy uses the .abi extension for Abinit input files, .abo for output files and .log for log files. Please follow this convention to facilitate the integration with AbiPy.

Complete command line reference

usage: abiopen.py [-h] [--loglevel LOGLEVEL] [-V] [-v] [-nb]
                  [--classic-notebook] [--no-browser] [--foreground] [-p]
                  [-pn] [-pnt PANEL_TEMPLATE] [--port PORT] [-e] [-s]
                  [-t SLIDE_TIMEOUT] [-sns [SEABORN]] [-mpl MPL_BACKEND] [-ew]
                  [-ply]
                  filepath

Positional Arguments

filepath: File to open. See table below for the list of supported extensions.

Named Arguments

--loglevel

Set the loglevel. Possible values: CRITICAL, ERROR (default), WARNING, INFO, DEBUG

Default: 'ERROR'

-V, --version

show program’s version number and exit

-v, --verbose

verbose, can be supplied multiple times to increase verbosity

Default: 0

-nb, --notebook

Open file in jupyter notebook

Default: False

--classic-notebook, -cnb

Use classic jupyter notebook instead of jupyterlab.

Default: False

--no-browser

Start the jupyter server to serve the notebook but don’t open the notebook in the browser. Use this option to connect remotely from localhost to the machine running the kernel

Default: False

--foreground

Run jupyter notebook in the foreground.

Default: False

-p, --print

Print python object and return.

Default: False

-pn, --panel

Open Dashboard in web browser, requires panel package.

Default: False

-pnt, --panel-template

Specify template for panel dasboard.Possible values are: FastList, FastGrid, Golden, Bootstrap, Material, React, Vanilla.Default: FastList

Default: 'FastList'

--port

Allows specifying a specific port when serving panel app.

Default: 0

-e, --expose

Open file and generate matplotlib figures automatically by calling expose method.

Default: False

-s, --slide-mode

Iterate over figures. Expose all figures at once if not given on the CLI.

Default: False

-t, --slide-timeout

Close figure after slide-timeout seconds (only if slide-mode). Block if not specified.

-sns, --seaborn

Use seaborn settings. Accept value defining context in (“paper”, “notebook”, “talk”, “poster”). Default: paper

-mpl, --mpl-backend

Set matplotlib interactive backend. Possible values: GTKAgg, GTK3Agg, GTK, GTKCairo, GTK3Cairo, WXAgg, WX, TkAgg, Qt4Agg, Qt5Agg, macosx.See also: https://matplotlib.org/faq/usage_faq.html#what-is-a-backend.

-ew, --expose-web

Generate matplotlib plots in $BROWSER instead of X-server. WARNING: Not all the features are supported.

Default: False

-ply, --plotly

Generate plotly plots in $BROWSER instead of matplotlib. WARNING: Not all the features are supported.

Default: False

abiopen.py

Positional Arguments

Named Arguments

`abiopen.py`