`abicomp.py`¶

This script compares output results stored in multiple netcdf files. For example, one can compare the crystalline structure used in different calculations or compare the electronic bands stored in two or more netcdf files (e.g. GSR.nc or WFK.nc).

Depending on COMMAND, abicomp either starts an ipython session so that the user can interact with the robot or print the results to screen.

For instance, the command:

abicomp.py structure out1_GSR.nc out2_GSR.nc

compares the crystalline structures reported in two GSR.nc files and print the result to screen while:

abicomp.py gsr out*_GSR.nc

starts an ipython session.

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

abicomp.py gsr out1_GSR.nc out2_GSR.nc -p

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

abicomp.py gsr out1_GSR.nc out2_GSR.nc -nb

Finally, use -e (--expose) to generate matplotlib plots automatically:

abicomp.py gsr out1_GSR.nc out2_GSR.nc -e -sns=poster

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

$ abicomp.py --help
usage: abicomp.py [-h] [-V]
                  {structure,spg,mp_structure,cod_structure,xrd,data,ebands,edos,phbands,phdos,getattr,gsr,hist,ddb,anaddb,phbst,sigres,mdf,optic,a2f,sigeph,rta,gkq,v1qavg,abiwan,pseudos,time,gs_scf,dfpt2_scf,text}
                  ...

optional arguments:
  -h, --help            show this help message and exit
  -V, --version         show program's version number and exit

subcommands:
  Valid subcommands

  {structure,spg,mp_structure,cod_structure,xrd,data,ebands,edos,phbands,phdos,getattr,gsr,hist,ddb,anaddb,phbst,sigres,mdf,optic,a2f,sigeph,rta,gkq,v1qavg,abiwan,pseudos,time,gs_scf,dfpt2_scf,text}
                        sub-command help
    structure           Compare crystalline structures. Use `--group` to
                        compare for similarity.
    spg                 Compare the space group found by Abinit with the
                        spglib results for a set of crystalline structure(s)
                        read from FILE(s).
    mp_structure        Compare the crystalline structure(s) read from FILE
                        with the one(s) reported in the materials project
                        database.
    cod_structure       Compare the crystalline structure(s) read from FILE
                        with the one(s) given in the COD database
                        (http://www.crystallography.net/cod).
    xrd                 Compare X-ray diffraction plots.
    data                Compare results stored in multiple files with data in
                        tabular format.
    ebands              Plot electron bands on a grid.
    edos                Plot electron DOSes on a grid.
    phbands             Plot phonon bands on a grid.
    phdos               Compare multiple PHDOS files.
    getattr             Extract attribute from Abipy object for all files
                        listed on the command line and print them. Use
                        `--list` option to list the attributes available (in
                        the first file).
    gsr                 Compare multiple GSR files.
    hist                Compare multiple HIST files.
    ddb                 Compare multiple DDB files. Assume DDB files with a
                        list of q-points in the IBZ corresponding to
                        homogeneous sampling i.e. files that have been merged
                        with mrgddb.
    anaddb              Compare multiple anaddb.nc files.
    phbst               Compare multiple PHBST.nc files.
    sigres              Compare multiple SIGRES files.
    mdf                 Compare macroscopic dielectric functions stored in
                        multiple MDF files.
    optic               Compare results stored in OPTIC.nc files.
    a2f                 Compare results stored in A2f.nc files.
    sigeph              Compare multiple SIGEPH files storing the e-ph self-
                        energy.
    rta                 Compare multiple RTA files.
    gkq                 Compare multiple GKQ files with EPH matrix elements
                        for a given q-point.
    v1qavg              Compare multiple V1QAVG files with the average of the
                        DFPT V1 potentials as function of q-point.
    abiwan              Compare multiple ABIWAN files.
    pseudos             "Compare multiple pseudos Print table to terminal.
    time                Analyze/plot the timing data of single or multiple
                        runs.
    gs_scf              Compare ground-state SCF cycles.
    dfpt2_scf           Compare DFPT SCF cycles.
    text                Compare 2+ text files in the browser

Usage example:

############
# Structures
############

  abicomp.py structure */*/outdata/out_GSR.nc   => Compare structures in multiple files.
                                                   Use `--group` to compare for similarity.
  abicomp.py spg si.cif out_GSR.nc              => Compare spacegroup(s) found by Abinit and spglib.
  abicomp.py hist FILE(s)                       => Compare final structures read from HIST.nc files.
  abicomp.py mp_structure FILE(s)               => Compare structure(s) read from FILE(s) with the one(s)
                                                   given in the materials project database.
  abicomp.py cod_structure FILE(s)              => Compare structure(s) read from FILE(s) with the one(s)
                                                   given in the COD database (http://www.crystallography.net/cod).
  abicomp.py xrd *.cif *.GSR.nc                 => Compare X-ray diffraction plots (requires FILES with structure).

###########
# Electrons
###########

  abicomp.py ebands out1_GSR.nc out2_WFK.nc     => Plot electron bands on a grid (Use `-p` to change plot mode)
  abicomp.py ebands *_GSR.nc -ipy               => Build plotter object and start ipython console.
  abicomp.py ebands *_GSR.nc -nb                => Interact with the plotter in the jupyter notebook.
  abicomp.py ebands `find . -name "*_GSR.nc"` -c = Find all GSR.nc files startign from current working directory
                                                   Copy dataframe to the system clipboard.
                                                   This can be pasted into Excel, for example
  abicomp.py edos *_WFK.nc -nb                  => Compare electron DOS in the jupyter notebook.
  abicomp.py optic DIR -nb                      => Compare optic results in the jupyter notebook.
  abicomp.py abiwan *_ABIWAN.nc --expose        => Compare ABIWAN results, produce matplotlib figures.

#########
# Phonons
#########

  abicomp.py phbands *_PHBST.nc -p gridplot     => Compare phonon bands with matplotlib grid.
  abicomp.py phbands *_PHBST.nc -p panel        => Compare phonon bands in the panel dashboard (GUI)
  abicomp.py phbst *_PHBST.nc -ipy              => Compare phonon bands with robot in ipython terminal.
  abicomp.py phdos *_PHDOS.nc -nb               => Compare phonon DOSes in the jupyter notebook.
  abicomp.py ddb outdir1 outdir2 out_DDB -nb    => Analyze all DDB files in directories outdir1, outdir2 and out_DDB file.

###############
# Anaddb netcdf
###############

  abicomp anaddb tutorespfn_telast_2-telast_3/anaddb.nc

#########
# E-PH
#########

  abicomp.py a2f *_A2F.nc -nb                   => Compare A2f results in the jupyter notebook.
  abicomp.py sigeph *_SIGEPH.nc -nb             => Compare Fan-Migdal self-energy in the jupyter notebook.
  abicomp.py gkq out1_GKQ.nc out1_GKQ.nc -d     => Plot difference between matrix elements (supports 2+ files).
  abicomp.py v1qavg out_V1QAVG.nc               => Compare V1QAVG files.

########
# GW/BSE
########

  abicomp.py sigres *_SIGRES.nc                 => Compare multiple SIGRES files.
  abicomp.py mdf *_MDF.nc --seaborn             => Compare macroscopic dielectric functions.
                                                   Use seaborn settings.

###############
# Miscelleanous
###############

  abicomp.py data FILE1 FILE2 ...                 => Read data from files with results in tabular format and
                                                     compare results. Mainly used for text files without any schema.
  abicomp.py getattr energy *_GSR.nc              => Extract the `energy` attribute from a list of GSR files
                                                     and print results. Use `--list` to get list of possible names.
  abicomp.py pseudos PSEUDO_FILES                 => Compare pseudopotential files.

############
# Text files
############

  abicomp.py gs_scf run1.abo run2.abo             => Compare the SCF cycles in two output files.
  abicomp.py dfpt2_scf run1.abo run2.abo          => Compare the DFPT SCF cycles in two output files.
  abicomp.py.py time [OUT_FILES]                  => Parse timing data in files and plot results
  abicomp.py.py time . --ext=abo                  => Scan directory tree from `.`, look for files with extension `abo`
                                                     parse timing data and plot results.
  abicomp.py text run1.abo run2.abo               => Produce diff of 2+ text files in the browser.

TIP:

The python code operates on a list of files/directories passed via the command line interface.
The arguments are interpreted by the shell before invoking the script.
This means that one can use the bash syntax and the unix tools to precompute the list of files/directories.

For example, one can use Unix find to select all files with the a given extension and pass them to abicomp.py.
For command:

    abicomp.py structure `find . -name "*_GSR.nc"`

will compare the structures extracted from all GSR.nc files found within the current working directory (note backticks).

Also, remember that in bash {#..#} generates a sequence of numbers or chars, similarly to range() in Python
For instance:

    {1..5} --> 1 2 3 4 5

and this trick can be used to select files/directories as in:

    abicomp.py structure w1/t{2..4}/outdata/*_GSR.nc

The [!name] syntax can be used to exclude patterns, so

    abicomp.py structure w1/t[!2]*/outdata/*_GSR.nc

excludes all the GSR.nc files in the t2/outdata directory.

See also http://wiki.bash-hackers.org/syntax/pattern

NOTE: The `gsr`, `ddb`, `sigres`, `mdf` commands use robots to analyze files.
In this case, one can provide a list of files and/or list of directories on the command-line interface e.g.:

    $ abicomp.py ddb dir1 out_DDB dir2

Directories will be scanned recursively to find files with the extension associated to the robot, e.g.
`abicompy.py mdf .` will read all *_MDF.nc files inside the current directory including sub-directories (if any).
Use --no-walk to ignore sub-directories when robots are used.

Use `abicomp.py --help` for help and `abicomp.py COMMAND --help` to get the documentation for `COMMAND`.
Use `-v` to increase verbosity level (can be supplied multiple times e.g -vv).

Complete command line reference

usage: abicomp.py [-h] [-V]
                  {structure,spg,mp_structure,cod_structure,xrd,data,ebands,edos,phbands,phdos,getattr,gsr,hist,ddb,anaddb,phbst,sigres,mdf,optic,a2f,sigeph,rta,gkq,v1qavg,abiwan,pseudos,time,gs_scf,dfpt2_scf,text}
                  ...

Named Arguments¶

-V, --version: show program’s version number and exit

subcommands¶

Valid subcommands

command

Possible choices: structure, spg, mp_structure, cod_structure, xrd, data, ebands, edos, phbands, phdos, getattr, gsr, hist, ddb, anaddb, phbst, sigres, mdf, optic, a2f, sigeph, rta, gkq, v1qavg, abiwan, pseudos, time, gs_scf, dfpt2_scf, text

sub-command help

Sub-commands:¶

structure¶

Compare crystalline structures. Use –group to compare for similarity.

abicomp.py structure [-h] [-v] [-sns [SEABORN]] [-mpl MPL_BACKEND] [--loglevel LOGLEVEL] [-nb]
                     [--classic-notebook] [--no-browser] [--foreground] [-ipy] [--symprec SYMPREC]
                     [--angle-tolerance ANGLE_TOLERANCE] [-c] [-g] [-a]
                     paths [paths ...]

Positional Arguments¶

paths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity.

Default: 0

-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.

--loglevel

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

Default: “ERROR”

-nb, --notebook

Generate jupyter notebook.

Default: False

--classic-notebook

Use classic 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

-ipy, --ipython

Invoke ipython terminal.

Default: False

--symprec

symprec (float): Tolerance for symmetry finding. Defaults to 1e-3, which is fairly strict and works well for properly refined structures with atoms in the proper symmetry coordinates. For structures with slight deviations from their proper atomic positions (e.g., structures relaxed with electronic structure codes), a looser tolerance of 0.1 (the value used in Materials Project) is often needed.

Default: 0.001

--angle-tolerance

angle_tolerance (float): Angle tolerance for symmetry finding. Default: 5.0

Default: 5.0

-c, --clipboard

Copy dataframe to the system clipboard. This can be pasted into Excel, for example

Default: False

-g, --group

Compare a set of structures for similarity.

Default: False

-a, --anonymous

Whether to use anonymous mode in StructureMatcher. Default False

Default: False

spg¶

Compare the space group found by Abinit with the spglib results for a set of crystalline structure(s) read from FILE(s).

abicomp.py spg [-h] [-v] [-sns [SEABORN]] [-mpl MPL_BACKEND] [--loglevel LOGLEVEL] [--symprec SYMPREC]
               [--angle-tolerance ANGLE_TOLERANCE] [-c] [-t TOLSYM]
               paths [paths ...]

Positional Arguments¶

paths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity.

Default: 0

-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.

--loglevel

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

Default: “ERROR”

--symprec

symprec (float): Tolerance for symmetry finding. Defaults to 1e-3, which is fairly strict and works well for properly refined structures with atoms in the proper symmetry coordinates. For structures with slight deviations from their proper atomic positions (e.g., structures relaxed with electronic structure codes), a looser tolerance of 0.1 (the value used in Materials Project) is often needed.

Default: 0.001

--angle-tolerance

angle_tolerance (float): Angle tolerance for symmetry finding. Default: 5.0

Default: 5.0

-c, --clipboard

Copy dataframe to the system clipboard. This can be pasted into Excel, for example

Default: False

-t, --tolsym

Gives the tolerance on the atomic positions (reduced coordinates), primitive vectors, or magnetization, to be considered equivalent, thanks to symmetry operations. This is used in the recognition of the set of symmetries of the system, or the application of the symmetry operations to generate from a reduced set of atoms, the full set of atoms. Note that a value larger than 0.01 is considered to be unacceptable.

mp_structure¶

Compare the crystalline structure(s) read from FILE with the one(s) reported in the materials project database.

abicomp.py mp_structure [-h] [-v] [-sns [SEABORN]] [-mpl MPL_BACKEND] [--loglevel LOGLEVEL] [-nb]
                        [--foreground] [--same-spgnum]
                        paths [paths ...]

Positional Arguments¶

paths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity.

Default: 0

-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.

--loglevel

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

Default: “ERROR”

-nb, --notebook

Generate jupyter notebook.

Default: False

--foreground

Run jupyter notebook in the foreground.

Default: False

--same-spgnum

Select only MP structures with same space group number as input structure.

Default: False

cod_structure¶

Compare the crystalline structure(s) read from FILE with the one(s) given in the COD database (http://www.crystallography.net/cod).

abicomp.py cod_structure [-h] [-v] [-sns [SEABORN]] [-mpl MPL_BACKEND] [--loglevel LOGLEVEL] [-nb]
                         [--foreground]
                         paths [paths ...]

Positional Arguments¶

paths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity.

Default: 0

-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.

--loglevel

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

Default: “ERROR”

-nb, --notebook

Generate jupyter notebook.

Default: False

--foreground

Run jupyter notebook in the foreground.

Default: False

xrd¶

Compare X-ray diffraction plots.

abicomp.py xrd [-h] [-v] [-sns [SEABORN]] [-mpl MPL_BACKEND] [--loglevel LOGLEVEL] [-w WAVELENGTH]
               [-s SYMPREC] [-t TWO_THETA_RANGE TWO_THETA_RANGE] [-nap]
               paths [paths ...]

Positional Arguments¶

paths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity.

Default: 0

-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.

--loglevel

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

Default: “ERROR”

-w, --wavelength

The wavelength can be specified as a string. It must be one of the supported definitions in the WAVELENGTHS dict declared in pymatgen/analysis/diffraction/xrd.py.Defaults to ‘CuKa’, i.e, Cu K_alpha radiation.

Default: “CuKa”

-s, --symprec

Symmetry precision for structure refinement. If set to 0, no refinement is done. Otherwise, refinement is performed using spglib with provided precision.

Default: 0

-t, --two-theta-range

Tuple for range of two_thetas to calculate in degrees. Defaults to (0, 90).

Default: (0, 90)

-nap, --no-annotate-peaks

Whether to annotate the peaks with plane information.

Default: False

data¶

Compare results stored in multiple files with data in tabular format.

abicomp.py data [-h] [-v] [-sns [SEABORN]] [-mpl MPL_BACKEND] [--loglevel LOGLEVEL] [-e] [-s]
                [-t SLIDE_TIMEOUT] [-ply] [-cs] [-i]
                paths [paths ...]

Positional Arguments¶

paths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity.

Default: 0

-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.

--loglevel

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

Default: “ERROR”

-e, --expose

Execute robot.expose to produce a pre-defined list of (matplotlib|plotly) figures.

Default: False

-s, --slide-mode

Used if –expose to 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.

-ply, --plotly

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

Default: False

-cs, --chart-studio

Push figure to plotly chart studio .Requires –plotly option and user account at https://chart-studio.plotly.com.

Default: False

-i, --use-index

Use the row index as x-value in the plot. By default the plotter uses the first column as x-values

Default: False

ebands¶

Plot electron bands on a grid.

abicomp.py ebands [-h] [-v] [-sns [SEABORN]] [-mpl MPL_BACKEND] [--loglevel LOGLEVEL] [-nb]
                  [--classic-notebook] [--no-browser] [--foreground] [-ipy] [-c]
                  [-p {gridplot,combiplot,boxplot,combiboxplot,plot_band_edges,animate,None}]
                  [-e0 {fermie,None}]
                  paths [paths ...]

Positional Arguments¶

paths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity.

Default: 0

-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.

--loglevel

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

Default: “ERROR”

-nb, --notebook

Generate jupyter notebook.

Default: False

--classic-notebook

Use classic 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

-ipy, --ipython

Invoke ipython terminal.

Default: False

-c, --clipboard

Copy dataframe to the system clipboard. This can be pasted into Excel, for example

Default: False

-p, --plot-mode

Possible choices: gridplot, combiplot, boxplot, combiboxplot, plot_band_edges, animate, None

Plot mode e.g. -p combiplot to plot bands on the same figure. Default is gridplot.

Default: “gridplot”

-e0

Possible choices: fermie, None

Option used to define the zero of energy in the band structure plot. Default is fermie.

Default: “fermie”

edos¶

Plot electron DOSes on a grid.

abicomp.py edos [-h] [-v] [-sns [SEABORN]] [-mpl MPL_BACKEND] [--loglevel LOGLEVEL] [-nb]
                [--classic-notebook] [--no-browser] [--foreground] [-ipy] [-e] [-s] [-t SLIDE_TIMEOUT]
                [-ply] [-cs] [-p {gridplot,combiplot,None}] [-e0 {fermie,None}]
                paths [paths ...]

Positional Arguments¶

paths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity.

Default: 0

-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.

--loglevel

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

Default: “ERROR”

-nb, --notebook

Generate jupyter notebook.

Default: False

--classic-notebook

Use classic 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

-ipy, --ipython

Invoke ipython terminal.

Default: False

-e, --expose

Execute robot.expose to produce a pre-defined list of (matplotlib|plotly) figures.

Default: False

-s, --slide-mode

Used if –expose to 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.

-ply, --plotly

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

Default: False

-cs, --chart-studio

Push figure to plotly chart studio .Requires –plotly option and user account at https://chart-studio.plotly.com.

Default: False

-p, --plot-mode

Possible choices: gridplot, combiplot, None

Plot mode e.g. -p combiplot to plot DOSes on the same figure. Default is gridplot.

Default: “gridplot”

-e0

Possible choices: fermie, None

Option used to define the zero of energy in the DOS plot. Default is fermie.

Default: “fermie”

phbands¶

Plot phonon bands on a grid.

abicomp.py phbands [-h] [-v] [-sns [SEABORN]] [-mpl MPL_BACKEND] [--loglevel LOGLEVEL] [-nb]
                   [--classic-notebook] [--no-browser] [--foreground] [-ipy] [-e] [-s] [-t SLIDE_TIMEOUT]
                   [-ply] [-cs] [-p {gridplot,combiplot,boxplot,combiboxplot,animate,panel,None}]
                   paths [paths ...]

Positional Arguments¶

paths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity.

Default: 0

-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.

--loglevel

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

Default: “ERROR”

-nb, --notebook

Generate jupyter notebook.

Default: False

--classic-notebook

Use classic 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

-ipy, --ipython

Invoke ipython terminal.

Default: False

-e, --expose

Execute robot.expose to produce a pre-defined list of (matplotlib|plotly) figures.

Default: False

-s, --slide-mode

Used if –expose to 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.

-ply, --plotly

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

Default: False

-cs, --chart-studio

Push figure to plotly chart studio .Requires –plotly option and user account at https://chart-studio.plotly.com.

Default: False

-p, --plot-mode

Possible choices: gridplot, combiplot, boxplot, combiboxplot, animate, panel, None

Plot mode e.g. -p combiplot to plot bands on the same figure.Use panel for GUI in web browser. Default is gridplot.

Default: “gridplot”

phdos¶

Compare multiple PHDOS files.

abicomp.py phdos [-h] [-v] [-sns [SEABORN]] [-mpl MPL_BACKEND] [--loglevel LOGLEVEL] [-nb]
                 [--classic-notebook] [--no-browser] [--foreground] [-ipy] [-e] [-s] [-t SLIDE_TIMEOUT]
                 [-ply] [-cs] [-p {gridplot,combiplot,None}]
                 paths [paths ...]

Positional Arguments¶

paths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity.

Default: 0

-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.

--loglevel

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

Default: “ERROR”

-nb, --notebook

Generate jupyter notebook.

Default: False

--classic-notebook

Use classic 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

-ipy, --ipython

Invoke ipython terminal.

Default: False

-e, --expose

Execute robot.expose to produce a pre-defined list of (matplotlib|plotly) figures.

Default: False

-s, --slide-mode

Used if –expose to 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.

-ply, --plotly

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

Default: False

-cs, --chart-studio

Push figure to plotly chart studio .Requires –plotly option and user account at https://chart-studio.plotly.com.

Default: False

-p, --plot-mode

Possible choices: gridplot, combiplot, None

Plot mode e.g. -p combiplot to plot DOSes on the same figure. Default is gridplot.

Default: “gridplot”

getattr¶

Extract attribute from Abipy object for all files listed on the command line and print them. Use –list option to list the attributes available (in the first file).

abicomp.py getattr [-h] [-v] [-sns [SEABORN]] [-mpl MPL_BACKEND] [--loglevel LOGLEVEL] [--plot] [--list]
                   paths [paths ...]

Positional Arguments¶

paths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity.

Default: 0

-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.

--loglevel

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

Default: “ERROR”

--plot

Plot data with matplotlib (requires floats).

Default: False

--list

Print attributes available in file

Default: False

gsr¶

Compare multiple GSR files.

abicomp.py gsr [-h] [-v] [-sns [SEABORN]] [-mpl MPL_BACKEND] [--loglevel LOGLEVEL] [-nb] [--foreground]
               [-p] [--no-walk] [-pn] [-pnt PANEL_TEMPLATE] [-e] [-s] [-t SLIDE_TIMEOUT] [-ply] [-cs] [-c]
               paths [paths ...]

Positional Arguments¶

paths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity.

Default: 0

-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.

--loglevel

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

Default: “ERROR”

-nb, --notebook

Generate jupyter notebook.

Default: False

--foreground

Run jupyter notebook in the foreground.

Default: False

-p, --print

Print robot and return.

Default: False

--no-walk

Don’t enter subdirectories.

Default: False

-pn, --panel

Open GUI in web browser, requires panel package. WARNING: Experimental

Default: False

-pnt, --panel-template

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

Default: “FastList”

-e, --expose

Execute robot.expose to produce a pre-defined list of (matplotlib|plotly) figures.

Default: False

-s, --slide-mode

Used if –expose to 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.

-ply, --plotly

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

Default: False

-cs, --chart-studio

Push figure to plotly chart studio .Requires –plotly option and user account at https://chart-studio.plotly.com.

Default: False

-c, --clipboard

Copy dataframe to the system clipboard. This can be pasted into Excel, for example

Default: False

hist¶

Compare multiple HIST files.

abicomp.py hist [-h] [-v] [-sns [SEABORN]] [-mpl MPL_BACKEND] [--loglevel LOGLEVEL] [-nb] [--foreground]
                [-p] [--no-walk] [-pn] [-pnt PANEL_TEMPLATE] [-e] [-s] [-t SLIDE_TIMEOUT] [-ply] [-cs]
                [-c]
                paths [paths ...]

Positional Arguments¶

paths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity.

Default: 0

-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.

--loglevel

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

Default: “ERROR”

-nb, --notebook

Generate jupyter notebook.

Default: False

--foreground

Run jupyter notebook in the foreground.

Default: False

-p, --print

Print robot and return.

Default: False

--no-walk

Don’t enter subdirectories.

Default: False

-pn, --panel

Open GUI in web browser, requires panel package. WARNING: Experimental

Default: False

-pnt, --panel-template

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

Default: “FastList”

-e, --expose

Execute robot.expose to produce a pre-defined list of (matplotlib|plotly) figures.

Default: False

-s, --slide-mode

Used if –expose to 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.

-ply, --plotly

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

Default: False

-cs, --chart-studio

Push figure to plotly chart studio .Requires –plotly option and user account at https://chart-studio.plotly.com.

Default: False

-c, --clipboard

Copy dataframe to the system clipboard. This can be pasted into Excel, for example

Default: False

ddb¶

Compare multiple DDB files. Assume DDB files with a list of q-points in the IBZ corresponding to homogeneous sampling i.e. files that have been merged with mrgddb.

abicomp.py ddb [-h] [-v] [-sns [SEABORN]] [-mpl MPL_BACKEND] [--loglevel LOGLEVEL] [-nb] [--foreground]
               [-p] [--no-walk] [-pn] [-pnt PANEL_TEMPLATE] [-e] [-s] [-t SLIDE_TIMEOUT] [-ply] [-cs] [-c]
               paths [paths ...]

Positional Arguments¶

paths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity.

Default: 0

-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.

--loglevel

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

Default: “ERROR”

-nb, --notebook

Generate jupyter notebook.

Default: False

--foreground

Run jupyter notebook in the foreground.

Default: False

-p, --print

Print robot and return.

Default: False

--no-walk

Don’t enter subdirectories.

Default: False

-pn, --panel

Open GUI in web browser, requires panel package. WARNING: Experimental

Default: False

-pnt, --panel-template

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

Default: “FastList”

-e, --expose

Execute robot.expose to produce a pre-defined list of (matplotlib|plotly) figures.

Default: False

-s, --slide-mode

Used if –expose to 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.

-ply, --plotly

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

Default: False

-cs, --chart-studio

Push figure to plotly chart studio .Requires –plotly option and user account at https://chart-studio.plotly.com.

Default: False

-c, --clipboard

Copy dataframe to the system clipboard. This can be pasted into Excel, for example

Default: False

anaddb¶

Compare multiple anaddb.nc files.

abicomp.py anaddb [-h] [-v] [-sns [SEABORN]] [-mpl MPL_BACKEND] [--loglevel LOGLEVEL] [-nb] [--foreground]
                  [-p] [--no-walk] [-pn] [-pnt PANEL_TEMPLATE] [-e] [-s] [-t SLIDE_TIMEOUT] [-ply] [-cs]
                  [-c]
                  paths [paths ...]

Positional Arguments¶

paths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity.

Default: 0

-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.

--loglevel

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

Default: “ERROR”

-nb, --notebook

Generate jupyter notebook.

Default: False

--foreground

Run jupyter notebook in the foreground.

Default: False

-p, --print

Print robot and return.

Default: False

--no-walk

Don’t enter subdirectories.

Default: False

-pn, --panel

Open GUI in web browser, requires panel package. WARNING: Experimental

Default: False

-pnt, --panel-template

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

Default: “FastList”

-e, --expose

Execute robot.expose to produce a pre-defined list of (matplotlib|plotly) figures.

Default: False

-s, --slide-mode

Used if –expose to 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.

-ply, --plotly

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

Default: False

-cs, --chart-studio

Push figure to plotly chart studio .Requires –plotly option and user account at https://chart-studio.plotly.com.

Default: False

-c, --clipboard

Copy dataframe to the system clipboard. This can be pasted into Excel, for example

Default: False

phbst¶

Compare multiple PHBST.nc files.

abicomp.py phbst [-h] [-v] [-sns [SEABORN]] [-mpl MPL_BACKEND] [--loglevel LOGLEVEL] [-nb] [--foreground]
                 [-p] [--no-walk] [-pn] [-pnt PANEL_TEMPLATE] [-e] [-s] [-t SLIDE_TIMEOUT] [-ply] [-cs]
                 [-c]
                 paths [paths ...]

Positional Arguments¶

paths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity.

Default: 0

-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.

--loglevel

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

Default: “ERROR”

-nb, --notebook

Generate jupyter notebook.

Default: False

--foreground

Run jupyter notebook in the foreground.

Default: False

-p, --print

Print robot and return.

Default: False

--no-walk

Don’t enter subdirectories.

Default: False

-pn, --panel

Open GUI in web browser, requires panel package. WARNING: Experimental

Default: False

-pnt, --panel-template

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

Default: “FastList”

-e, --expose

Execute robot.expose to produce a pre-defined list of (matplotlib|plotly) figures.

Default: False

-s, --slide-mode

Used if –expose to 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.

-ply, --plotly

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

Default: False

-cs, --chart-studio

Push figure to plotly chart studio .Requires –plotly option and user account at https://chart-studio.plotly.com.

Default: False

-c, --clipboard

Copy dataframe to the system clipboard. This can be pasted into Excel, for example

Default: False

sigres¶

Compare multiple SIGRES files.

abicomp.py sigres [-h] [-v] [-sns [SEABORN]] [-mpl MPL_BACKEND] [--loglevel LOGLEVEL] [-nb] [--foreground]
                  [-p] [--no-walk] [-pn] [-pnt PANEL_TEMPLATE] [-e] [-s] [-t SLIDE_TIMEOUT] [-ply] [-cs]
                  [-c]
                  paths [paths ...]

Positional Arguments¶

paths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity.

Default: 0

-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.

--loglevel

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

Default: “ERROR”

-nb, --notebook

Generate jupyter notebook.

Default: False

--foreground

Run jupyter notebook in the foreground.

Default: False

-p, --print

Print robot and return.

Default: False

--no-walk

Don’t enter subdirectories.

Default: False

-pn, --panel

Open GUI in web browser, requires panel package. WARNING: Experimental

Default: False

-pnt, --panel-template

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

Default: “FastList”

-e, --expose

Execute robot.expose to produce a pre-defined list of (matplotlib|plotly) figures.

Default: False

-s, --slide-mode

Used if –expose to 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.

-ply, --plotly

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

Default: False

-cs, --chart-studio

Push figure to plotly chart studio .Requires –plotly option and user account at https://chart-studio.plotly.com.

Default: False

-c, --clipboard

Copy dataframe to the system clipboard. This can be pasted into Excel, for example

Default: False

mdf¶

Compare macroscopic dielectric functions stored in multiple MDF files.

abicomp.py mdf [-h] [-v] [-sns [SEABORN]] [-mpl MPL_BACKEND] [--loglevel LOGLEVEL] [-nb] [--foreground]
               [-p] [--no-walk] [-pn] [-pnt PANEL_TEMPLATE] [-e] [-s] [-t SLIDE_TIMEOUT] [-ply] [-cs] [-c]
               paths [paths ...]

Positional Arguments¶

paths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity.

Default: 0

-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.

--loglevel

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

Default: “ERROR”

-nb, --notebook

Generate jupyter notebook.

Default: False

--foreground

Run jupyter notebook in the foreground.

Default: False

-p, --print

Print robot and return.

Default: False

--no-walk

Don’t enter subdirectories.

Default: False

-pn, --panel

Open GUI in web browser, requires panel package. WARNING: Experimental

Default: False

-pnt, --panel-template

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

Default: “FastList”

-e, --expose

Execute robot.expose to produce a pre-defined list of (matplotlib|plotly) figures.

Default: False

-s, --slide-mode

Used if –expose to 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.

-ply, --plotly

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

Default: False

-cs, --chart-studio

Push figure to plotly chart studio .Requires –plotly option and user account at https://chart-studio.plotly.com.

Default: False

-c, --clipboard

Copy dataframe to the system clipboard. This can be pasted into Excel, for example

Default: False

optic¶

Compare results stored in OPTIC.nc files.

abicomp.py optic [-h] [-v] [-sns [SEABORN]] [-mpl MPL_BACKEND] [--loglevel LOGLEVEL] [-nb] [--foreground]
                 [-p] [--no-walk] [-pn] [-pnt PANEL_TEMPLATE] [-e] [-s] [-t SLIDE_TIMEOUT] [-ply] [-cs]
                 [-c]
                 paths [paths ...]

Positional Arguments¶

paths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity.

Default: 0

-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.

--loglevel

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

Default: “ERROR”

-nb, --notebook

Generate jupyter notebook.

Default: False

--foreground

Run jupyter notebook in the foreground.

Default: False

-p, --print

Print robot and return.

Default: False

--no-walk

Don’t enter subdirectories.

Default: False

-pn, --panel

Open GUI in web browser, requires panel package. WARNING: Experimental

Default: False

-pnt, --panel-template

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

Default: “FastList”

-e, --expose

Execute robot.expose to produce a pre-defined list of (matplotlib|plotly) figures.

Default: False

-s, --slide-mode

Used if –expose to 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.

-ply, --plotly

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

Default: False

-cs, --chart-studio

Push figure to plotly chart studio .Requires –plotly option and user account at https://chart-studio.plotly.com.

Default: False

-c, --clipboard

Copy dataframe to the system clipboard. This can be pasted into Excel, for example

Default: False

a2f¶

Compare results stored in A2f.nc files.

abicomp.py a2f [-h] [-v] [-sns [SEABORN]] [-mpl MPL_BACKEND] [--loglevel LOGLEVEL] [-nb] [--foreground]
               [-p] [--no-walk] [-pn] [-pnt PANEL_TEMPLATE] [-e] [-s] [-t SLIDE_TIMEOUT] [-ply] [-cs] [-c]
               paths [paths ...]

Positional Arguments¶

paths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity.

Default: 0

-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.

--loglevel

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

Default: “ERROR”

-nb, --notebook

Generate jupyter notebook.

Default: False

--foreground

Run jupyter notebook in the foreground.

Default: False

-p, --print

Print robot and return.

Default: False

--no-walk

Don’t enter subdirectories.

Default: False

-pn, --panel

Open GUI in web browser, requires panel package. WARNING: Experimental

Default: False

-pnt, --panel-template

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

Default: “FastList”

-e, --expose

Execute robot.expose to produce a pre-defined list of (matplotlib|plotly) figures.

Default: False

-s, --slide-mode

Used if –expose to 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.

-ply, --plotly

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

Default: False

-cs, --chart-studio

Push figure to plotly chart studio .Requires –plotly option and user account at https://chart-studio.plotly.com.

Default: False

-c, --clipboard

Copy dataframe to the system clipboard. This can be pasted into Excel, for example

Default: False

sigeph¶

Compare multiple SIGEPH files storing the e-ph self-energy.

abicomp.py sigeph [-h] [-v] [-sns [SEABORN]] [-mpl MPL_BACKEND] [--loglevel LOGLEVEL] [-nb] [--foreground]
                  [-p] [--no-walk] [-pn] [-pnt PANEL_TEMPLATE] [-e] [-s] [-t SLIDE_TIMEOUT] [-ply] [-cs]
                  [-c]
                  paths [paths ...]

Positional Arguments¶

paths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity.

Default: 0

-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.

--loglevel

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

Default: “ERROR”

-nb, --notebook

Generate jupyter notebook.

Default: False

--foreground

Run jupyter notebook in the foreground.

Default: False

-p, --print

Print robot and return.

Default: False

--no-walk

Don’t enter subdirectories.

Default: False

-pn, --panel

Open GUI in web browser, requires panel package. WARNING: Experimental

Default: False

-pnt, --panel-template

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

Default: “FastList”

-e, --expose

Execute robot.expose to produce a pre-defined list of (matplotlib|plotly) figures.

Default: False

-s, --slide-mode

Used if –expose to 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.

-ply, --plotly

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

Default: False

-cs, --chart-studio

Push figure to plotly chart studio .Requires –plotly option and user account at https://chart-studio.plotly.com.

Default: False

-c, --clipboard

Copy dataframe to the system clipboard. This can be pasted into Excel, for example

Default: False

rta¶

Compare multiple RTA files.

abicomp.py rta [-h] [-v] [-sns [SEABORN]] [-mpl MPL_BACKEND] [--loglevel LOGLEVEL] [-nb] [--foreground]
               [-p] [--no-walk] [-pn] [-pnt PANEL_TEMPLATE] [-e] [-s] [-t SLIDE_TIMEOUT] [-ply] [-cs] [-c]
               paths [paths ...]

Positional Arguments¶

paths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity.

Default: 0

-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.

--loglevel

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

Default: “ERROR”

-nb, --notebook

Generate jupyter notebook.

Default: False

--foreground

Run jupyter notebook in the foreground.

Default: False

-p, --print

Print robot and return.

Default: False

--no-walk

Don’t enter subdirectories.

Default: False

-pn, --panel

Open GUI in web browser, requires panel package. WARNING: Experimental

Default: False

-pnt, --panel-template

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

Default: “FastList”

-e, --expose

Execute robot.expose to produce a pre-defined list of (matplotlib|plotly) figures.

Default: False

-s, --slide-mode

Used if –expose to 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.

-ply, --plotly

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

Default: False

-cs, --chart-studio

Push figure to plotly chart studio .Requires –plotly option and user account at https://chart-studio.plotly.com.

Default: False

-c, --clipboard

Copy dataframe to the system clipboard. This can be pasted into Excel, for example

Default: False

gkq¶

Compare multiple GKQ files with EPH matrix elements for a given q-point.

abicomp.py gkq [-h] [-v] [-sns [SEABORN]] [-mpl MPL_BACKEND] [--loglevel LOGLEVEL] [-nb] [--foreground]
               [-p] [--no-walk] [-pn] [-pnt PANEL_TEMPLATE] [-e] [-s] [-t SLIDE_TIMEOUT] [-ply] [-cs] [-c]
               [-d]
               paths [paths ...]

Positional Arguments¶

paths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity.

Default: 0

-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.

--loglevel

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

Default: “ERROR”

-nb, --notebook

Generate jupyter notebook.

Default: False

--foreground

Run jupyter notebook in the foreground.

Default: False

-p, --print

Print robot and return.

Default: False

--no-walk

Don’t enter subdirectories.

Default: False

-pn, --panel

Open GUI in web browser, requires panel package. WARNING: Experimental

Default: False

-pnt, --panel-template

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

Default: “FastList”

-e, --expose

Execute robot.expose to produce a pre-defined list of (matplotlib|plotly) figures.

Default: False

-s, --slide-mode

Used if –expose to 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.

-ply, --plotly

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

Default: False

-cs, --chart-studio

Push figure to plotly chart studio .Requires –plotly option and user account at https://chart-studio.plotly.com.

Default: False

-c, --clipboard

Copy dataframe to the system clipboard. This can be pasted into Excel, for example

Default: False

-d, --diff

Plot difference between eph matrix elements.

Default: False

v1qavg¶

Compare multiple V1QAVG files with the average of the DFPT V1 potentials as function of q-point.

abicomp.py v1qavg [-h] [-v] [-sns [SEABORN]] [-mpl MPL_BACKEND] [--loglevel LOGLEVEL] [-nb] [--foreground]
                  [-p] [--no-walk] [-pn] [-pnt PANEL_TEMPLATE] [-e] [-s] [-t SLIDE_TIMEOUT] [-ply] [-cs]
                  [-c]
                  paths [paths ...]

Positional Arguments¶

paths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity.

Default: 0

-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.

--loglevel

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

Default: “ERROR”

-nb, --notebook

Generate jupyter notebook.

Default: False

--foreground

Run jupyter notebook in the foreground.

Default: False

-p, --print

Print robot and return.

Default: False

--no-walk

Don’t enter subdirectories.

Default: False

-pn, --panel

Open GUI in web browser, requires panel package. WARNING: Experimental

Default: False

-pnt, --panel-template

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

Default: “FastList”

-e, --expose

Execute robot.expose to produce a pre-defined list of (matplotlib|plotly) figures.

Default: False

-s, --slide-mode

Used if –expose to 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.

-ply, --plotly

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

Default: False

-cs, --chart-studio

Push figure to plotly chart studio .Requires –plotly option and user account at https://chart-studio.plotly.com.

Default: False

-c, --clipboard

Copy dataframe to the system clipboard. This can be pasted into Excel, for example

Default: False

abiwan¶

Compare multiple ABIWAN files.

abicomp.py abiwan [-h] [-v] [-sns [SEABORN]] [-mpl MPL_BACKEND] [--loglevel LOGLEVEL] [-nb] [--foreground]
                  [-p] [--no-walk] [-pn] [-pnt PANEL_TEMPLATE] [-e] [-s] [-t SLIDE_TIMEOUT] [-ply] [-cs]
                  [-c]
                  paths [paths ...]

Positional Arguments¶

paths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity.

Default: 0

-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.

--loglevel

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

Default: “ERROR”

-nb, --notebook

Generate jupyter notebook.

Default: False

--foreground

Run jupyter notebook in the foreground.

Default: False

-p, --print

Print robot and return.

Default: False

--no-walk

Don’t enter subdirectories.

Default: False

-pn, --panel

Open GUI in web browser, requires panel package. WARNING: Experimental

Default: False

-pnt, --panel-template

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

Default: “FastList”

-e, --expose

Execute robot.expose to produce a pre-defined list of (matplotlib|plotly) figures.

Default: False

-s, --slide-mode

Used if –expose to 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.

-ply, --plotly

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

Default: False

-cs, --chart-studio

Push figure to plotly chart studio .Requires –plotly option and user account at https://chart-studio.plotly.com.

Default: False

-c, --clipboard

Copy dataframe to the system clipboard. This can be pasted into Excel, for example

Default: False

pseudos¶

“Compare multiple pseudos Print table to terminal.

abicomp.py pseudos [-h] [-v] [-sns [SEABORN]] [-mpl MPL_BACKEND] [--loglevel LOGLEVEL] paths [paths ...]

Positional Arguments¶

paths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity.

Default: 0

-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.

--loglevel

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

Default: “ERROR”

time¶

Analyze/plot the timing data of single or multiple runs.

abicomp.py time [-h] [-v] [-sns [SEABORN]] [-mpl MPL_BACKEND] [--loglevel LOGLEVEL] [-nb]
                [--classic-notebook] [--no-browser] [--foreground] [-ipy] [-e EXT]
                paths [paths ...]

Positional Arguments¶

paths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity.

Default: 0

-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.

--loglevel

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

Default: “ERROR”

-nb, --notebook

Generate jupyter notebook.

Default: False

--classic-notebook

Use classic 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

-ipy, --ipython

Invoke ipython terminal.

Default: False

-e, --ext

File extension for Abinit output files. Used when the first argument is a directory. Default is .abo

Default: “.abo”

gs_scf¶

Compare ground-state SCF cycles.

abicomp.py gs_scf [-h] [-v] [-sns [SEABORN]] [-mpl MPL_BACKEND] [--loglevel LOGLEVEL] paths [paths ...]

Positional Arguments¶

paths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity.

Default: 0

-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.

--loglevel

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

Default: “ERROR”

dfpt2_scf¶

Compare DFPT SCF cycles.

abicomp.py dfpt2_scf [-h] [-v] [-sns [SEABORN]] [-mpl MPL_BACKEND] [--loglevel LOGLEVEL] paths [paths ...]

Positional Arguments¶

paths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity.

Default: 0

-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.

--loglevel

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

Default: “ERROR”

text¶

Compare 2+ text files in the browser

abicomp.py text [-h] [-v] [-sns [SEABORN]] [-mpl MPL_BACKEND] [--loglevel LOGLEVEL] [-d DIFFMODE]
                paths [paths ...]

Positional Arguments¶

paths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity.

Default: 0

-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.

--loglevel

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

Default: “ERROR”

-d, --diffmode

Select diff application. Possible values: difflib (default), pygmentize (requires package).

Default: “difflib”

abicomp.py¶

Named Arguments¶

subcommands¶

Sub-commands:¶

structure¶

Positional Arguments¶

Named Arguments¶

spg¶

Positional Arguments¶

Named Arguments¶

mp_structure¶

Positional Arguments¶

Named Arguments¶

cod_structure¶

Positional Arguments¶

Named Arguments¶

xrd¶

Positional Arguments¶

Named Arguments¶

data¶

Positional Arguments¶

Named Arguments¶

ebands¶

Positional Arguments¶

Named Arguments¶

edos¶

Positional Arguments¶

Named Arguments¶

phbands¶

Positional Arguments¶

Named Arguments¶

phdos¶

Positional Arguments¶

Named Arguments¶

getattr¶

Positional Arguments¶

Named Arguments¶

gsr¶

Positional Arguments¶

Named Arguments¶

hist¶

Positional Arguments¶

Named Arguments¶

ddb¶

Positional Arguments¶

Named Arguments¶

anaddb¶

Positional Arguments¶

Named Arguments¶

phbst¶

Positional Arguments¶

Named Arguments¶

sigres¶

Positional Arguments¶

Named Arguments¶

mdf¶

Positional Arguments¶

Named Arguments¶

optic¶

Positional Arguments¶

Named Arguments¶

a2f¶

Positional Arguments¶

Named Arguments¶

sigeph¶

Positional Arguments¶

Named Arguments¶

rta¶

Positional Arguments¶

Named Arguments¶

gkq¶

Positional Arguments¶

Named Arguments¶

v1qavg¶

Positional Arguments¶

Named Arguments¶

abiwan¶

Positional Arguments¶

Named Arguments¶

pseudos¶

`abicomp.py`¶