`abiview.py`

This script visualizes provides a simplified interface to the AbiPy post-processing tools It can also visualize data (structures, densities) with external graphical applications.

Complete command line reference

usage: abiview.py [-h] [-V]
                  {structure,input,hist,data,dirviz,ebands,effmass,skw,fs,ifermi_fs,ddb,ddb_vs,ddb_ir,ddb_asr,ddb_dipdip,ddb_quad,ddb_isodistort_ph,ddb_ifc,ddb_qpt,phbands,lobster,xrd_traj,denpot}
                  ...

Named Arguments

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

subcommands

Valid subcommands

command

Possible choices: structure, input, hist, data, dirviz, ebands, effmass, skw, fs, ifermi_fs, ddb, ddb_vs, ddb_ir, ddb_asr, ddb_dipdip, ddb_quad, ddb_isodistort_ph, ddb_ifc, ddb_qpt, phbands, lobster, xrd_traj, denpot

sub-command help

Sub-commands

structure

Visualize the structure with the specified visualizer. Requires external app or optional python modules (mayavi, vtk)

abiview.py structure [-h] [--loglevel LOGLEVEL] [-v] [-sns [SEABORN]]
                     [-mpl MPL_BACKEND] [-a [APPNAME]]
                     filepath

Positional Arguments

filepath: File to visualize.

Named Arguments

--loglevel

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

Default: 'ERROR'

-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.

-a, --appname

Application name. Default: vesta. Possible options: avogadro, ovito, v_sim, vesta, xcrysden, mayavi, vtk

Default: 'vesta'

input

Read input file from netcdf file and print it to terminal.

abiview.py input [-h] [--loglevel LOGLEVEL] [-v] [-sns [SEABORN]]
                 [-mpl MPL_BACKEND]
                 filepath

Positional Arguments

filepath: File to visualize.

Named Arguments

--loglevel

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

Default: 'ERROR'

-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.

hist

Visualize structural relaxation/molecular-dynamics run from data stored in the HIST.nc file. Requires mayavi.

abiview.py hist [-h] [--loglevel LOGLEVEL] [-v] [-sns [SEABORN]]
                [-mpl MPL_BACKEND] [-a [APPNAME]] [--xdatcar] [--to-unit-cell]
                [-f]
                filepath

Positional Arguments

filepath: File to visualize.

Named Arguments

--loglevel

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

Default: 'ERROR'

-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.

-a, --appname

Application name. Default: ovito. Possible options: avogadro, ovito, v_sim, vesta, xcrysden, mpl (matplotlib) mayavi, vtk

--xdatcar

Convert HIST file into XDATCAR format.

Default: False

--to-unit-cell

Whether to translate sites into the unit cell.

Default: False

-f, --force

Overwrite pre-existent files without prompting for confirmation.

Default: False

data

Extract data from a generic text file with results in tabular format and plot data with matplotlib. Multiple datasets are supported. No attempt is made to handle metadata (e.g. column name)

abiview.py data [-h] [--loglevel LOGLEVEL] [-v] [-sns [SEABORN]]
                [-mpl MPL_BACKEND] [-i]
                filepath

Positional Arguments

filepath: File to visualize.

Named Arguments

--loglevel

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

Default: 'ERROR'

-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.

-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

dirviz

Visualize directory tree with graphviz.

abiview.py dirviz [-h] [--loglevel LOGLEVEL] [-v] [-sns [SEABORN]]
                  [-mpl MPL_BACKEND] [-e ENGINE]
                  filepath

Positional Arguments

filepath: File to visualize.

Named Arguments

--loglevel

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

Default: 'ERROR'

-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.

-e, --engine

graphviz engine: [‘dot’, ‘neato’, ‘twopi’, ‘circo’, ‘fdp’, ‘sfdp’, ‘patchwork’, ‘osage’]. See http://www.graphviz.org/pdf/dot.1.pdf Use conda install python-graphviz or pip install graphviz to install the python package.

Default: 'fdp'

ebands

Plot electronic bands if file contains high-symmetry k-path or DOS if k-sampling. Accept any file with ElectronBands e.g. GSR.nc, WFK.nc, …

abiview.py ebands [-h] [--loglevel LOGLEVEL] [-v] [-sns [SEABORN]]
                  [-mpl MPL_BACKEND] [-s] [-t SLIDE_TIMEOUT] [-ew] [--xmgrace]
                  [--bxsf] [-f]
                  filepath

Positional Arguments

filepath: File to visualize.

Named Arguments

--loglevel

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

Default: 'ERROR'

-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.

-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.

-ew, --expose-web

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

Default: False

--xmgrace

Print bands in xmgrace format to stdout and exit.

Default: False

--bxsf

Generate BXSF file suitable for the visualization of isosurfaces with Xcrysden(xcrysden –bxsf FILE).: Requires k-points in IBZ. Print to stdout and exit.

Default: False

-f, --force

Overwrite pre-existent files without prompting for confirmation.

Default: False

effmass

Compute electron effective masses with finite differences using energies along a k-path Accept any file with ElectronBands e.g. GSR.nc, WFK.nc, …

abiview.py effmass [-h] [--loglevel LOGLEVEL] [-v] [-sns [SEABORN]]
                   [-mpl MPL_BACKEND] [-s] [-t SLIDE_TIMEOUT] [-ew]
                   filepath

Positional Arguments

filepath: File to visualize.

Named Arguments

--loglevel

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

Default: 'ERROR'

-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.

-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.

-ew, --expose-web

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

Default: False

skw

Interpolate energies in k-space along a k-path with the star-function method. Note that the interpolation will likely fail if there are symmetric k-points in the input set of k-points so it is highly recommended to call this method with energies obtained in the IBZ. Accept any file with ElectronBands e.g. GSR.nc, WFK.nc, …

abiview.py skw [-h] [--loglevel LOGLEVEL] [-v] [-sns [SEABORN]]
               [-mpl MPL_BACKEND] [-lp LPRATIO] [-ld LINE_DENSITY]
               filepath

Positional Arguments

filepath: File to visualize.

Named Arguments

--loglevel

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

Default: 'ERROR'

-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.

-lp, --lpratio

Ratio between the number of star functions and the number of ab-initio k-points. The default should be OK in many systems, larger values may be required for accurate derivatives.

Default: 5

-ld, --line-density

Number of points in the smallest segment of the k-path.

Default: 20

fs

Extract eigenvalues in the IBZ from file and visualize Fermi surface with the external application specified via –appname

abiview.py fs [-h] [--loglevel LOGLEVEL] [-v] [-sns [SEABORN]]
              [-mpl MPL_BACKEND] [-a APPNAME]
              filepath

Positional Arguments

filepath: File to visualize.

Named Arguments

--loglevel

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

Default: 'ERROR'

-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.

-a, --appname

Application name. Possible options: mpl (matplotlib, default), xsf (xcrysden), mayavi.

Default: 'mpl'

ifermi_fs

Use ifermi package to visualize the Fermi surface. Requires netcdf file with energies in the IBZ. See <https://fermisurfaces.github.io/IFermi/>

abiview.py ifermi_fs [-h] [-i INTERPOLATION_FACTOR] [--eref {fermie,cbm,vbm}]
                     [-t {plotly,matplotlib,mayavi}] [--wigner] [-vel]
                     [--loglevel LOGLEVEL] [-v] [-sns [SEABORN]]
                     [-mpl MPL_BACKEND] [-m MU]
                     filepath

Positional Arguments

filepath: File to visualize.

Named Arguments

-i, --interpolation-factor

interpolation factor for band structure [default: 8.0]

Default: 8

--eref

Possible choices: fermie, cbm, vbm

Energy reference for isosurface. eref and mu define the energy level: isoe = eref + muUse fermie for metals, cbm for the conduction band minimum, and vbm for the valence band maximum, [default: fermie]

Default: 'fermie'

-t, --plot-type

Possible choices: plotly, matplotlib, mayavi

Plot type. Possible options: plotly (default), matplotlib, mayavi.

Default: 'plotly'

--wigner, --no-wigner

Use the Wigner-Seitz cell or the reciprocal lattice parallelepiped. Default is: wigner

Default: True

-vel, --with-velocities

Show color map with interpolated group velocities. Default is False.

Default: False

--loglevel

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

Default: 'ERROR'

-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.

-m, --mu

Offset in eV from the energy reference, eref, at which to calculate the isosurface. Default 0 i.e. use eref

Default: 0.0

ddb

Invoke anaddb to compute phonon bands and DOS from the DDB, plot the results.

abiview.py ddb [-h] [--loglevel LOGLEVEL] [-v] [-sns [SEABORN]]
               [-mpl MPL_BACKEND] [-s] [-t SLIDE_TIMEOUT] [-ew] [-ply] [-cs]
               [--xmgrace] [-web] [-b BROWSER] [-f]
               filepath

Positional Arguments

filepath: File to visualize.

Named Arguments

--loglevel

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

Default: 'ERROR'

-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.

-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.

-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.

Default: False

-cs, --chart-studio

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

Default: False

--xmgrace

Print bands in xmgrace format to stdout and exit.

Default: False

-web, --phononwebsite

Visualize phonon band structure on the phononwebsite. http://henriquemiranda.github.io/phononwebsite/

Default: False

-b, --browser

Define browser used by python webbrowser. See https://docs.python.org/2/library/webbrowser.html#webbrowser.register

-f, --force

Overwrite pre-existent files without prompting for confirmation.

Default: False

ddb_vs

Compute speed of sound by fitting phonon frequencies along selected directions.

abiview.py ddb_vs [-h] [--loglevel LOGLEVEL] [-v] [-sns [SEABORN]]
                  [-mpl MPL_BACKEND] [-c] [-s] [-t SLIDE_TIMEOUT] [-ew]
                  filepath

Positional Arguments

filepath: File to visualize.

Named Arguments

--loglevel

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

Default: 'ERROR'

-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.

-c, --clipboard

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

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.

-ew, --expose-web

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

Default: False

ddb_ir

Compute infra-red spectrum from DDB. Plot results.

abiview.py ddb_ir [-h] [--loglevel LOGLEVEL] [-v] [-sns [SEABORN]]
                  [-mpl MPL_BACKEND] [-c] [-s] [-t SLIDE_TIMEOUT] [-ew]
                  filepath

Positional Arguments

filepath: File to visualize.

Named Arguments

--loglevel

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

Default: 'ERROR'

-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.

-c, --clipboard

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

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.

-ew, --expose-web

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

Default: False

ddb_asr

Compute phonon band structure from DDB with/without acoustic sum rule. Plot results.

abiview.py ddb_asr [-h] [--loglevel LOGLEVEL] [-v] [-sns [SEABORN]]
                   [-mpl MPL_BACKEND] [-c] [-s] [-t SLIDE_TIMEOUT] [-ew]
                   [-ply] [-cs]
                   filepath

Positional Arguments

filepath: File to visualize.

Named Arguments

--loglevel

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

Default: 'ERROR'

-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.

-c, --clipboard

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

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.

-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.

Default: False

-cs, --chart-studio

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

Default: False

ddb_dipdip

Compute phonon band structure from DDB with/without dipole-dipole interaction. Plot results.

abiview.py ddb_dipdip [-h] [--loglevel LOGLEVEL] [-v] [-sns [SEABORN]]
                      [-mpl MPL_BACKEND] [-c] [-s] [-t SLIDE_TIMEOUT] [-ew]
                      [-ply] [-cs]
                      filepath

Positional Arguments

filepath: File to visualize.

Named Arguments

--loglevel

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

Default: 'ERROR'

-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.

-c, --clipboard

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

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.

-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.

Default: False

-cs, --chart-studio

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

Default: False

ddb_quad

Compute phonon band structure from DDB with/without quadrupole terms. Plot results.

abiview.py ddb_quad [-h] [--loglevel LOGLEVEL] [-v] [-sns [SEABORN]]
                    [-mpl MPL_BACKEND] [-c] [-s] [-t SLIDE_TIMEOUT] [-ew]
                    [-ply] [-cs]
                    filepath

Positional Arguments

filepath: File to visualize.

Named Arguments

--loglevel

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

Default: 'ERROR'

-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.

-c, --clipboard

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

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.

-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.

Default: False

-cs, --chart-studio

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

Default: False

ddb_isodistort_ph

Compute ph-freqs for given q-point (default: Gamma), produce CIF files for unperturbed and distorded structure that can be used with ISODISTORT (https://stokes.byu.edu/iso/isodistort.php) to analyze the symmetry of phonon modes. See README.me file produced in output directory.

abiview.py ddb_isodistort_ph [-h] [--loglevel LOGLEVEL] [-v] [-sns [SEABORN]]
                             [-mpl MPL_BACKEND] [-q QPOINT QPOINT QPOINT]
                             filepath

Positional Arguments

filepath: File to visualize.

Named Arguments

--loglevel

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

Default: 'ERROR'

-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.

-q, --qpoint

q-point in reduced coordinates e.g. 0.25 0 0. Default: 0, 0, 0

Default: [0, 0, 0]

ddb_ifc

Visualize interatomic force constants in real space.

abiview.py ddb_ifc [-h] [--loglevel LOGLEVEL] [-v] [-sns [SEABORN]]
                   [-mpl MPL_BACKEND] [-c] [-s] [-t SLIDE_TIMEOUT] [-ew]
                   filepath

Positional Arguments

filepath: File to visualize.

Named Arguments

--loglevel

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

Default: 'ERROR'

-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.

-c, --clipboard

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

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.

-ew, --expose-web

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

Default: False

ddb_qpt

Compute ph-frequencies at the selected q-point without passing through the Fourier interpolation of the interatomic force constants.

abiview.py ddb_qpt [-h] [--loglevel LOGLEVEL] [-v] [-sns [SEABORN]]
                   [-mpl MPL_BACKEND] [-c] [-s] [-t SLIDE_TIMEOUT] [-ew]
                   [-q QPOINT QPOINT QPOINT]
                   filepath

Positional Arguments

filepath: File to visualize.

Named Arguments

--loglevel

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

Default: 'ERROR'

-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.

-c, --clipboard

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

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.

-ew, --expose-web

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

Default: False

-q, --qpoint

q-point in reduced coordinates e.g. -q 0.25 0 0. Default: 0, 0, 0

Default: [0, 0, 0]

phbands

Plot phonon bands. Accept any file with PhononBands e.g. PHBST.nc, …

abiview.py phbands [-h] [--loglevel LOGLEVEL] [-v] [-sns [SEABORN]]
                   [-mpl MPL_BACKEND] [-s] [-t SLIDE_TIMEOUT] [-ew]
                   [--xmgrace] [-web] [-b BROWSER] [-f]
                   filepath

Positional Arguments

filepath: File to visualize.

Named Arguments

--loglevel

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

Default: 'ERROR'

-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.

-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.

-ew, --expose-web

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

Default: False

--xmgrace

Print bands in xmgrace format to stdout and exit.

Default: False

-web, --phononwebsite

Visualize phonon band structure on the phononwebsite. http://henriquemiranda.github.io/phononwebsite/

Default: False

-b, --browser

Define browser used by python webbrowser. See https://docs.python.org/2/library/webbrowser.html#webbrowser.register

-f, --force

Overwrite pre-existent files without prompting for confirmation.

Default: False

lobster

Analyze lobster output files in directory.

abiview.py lobster [-h] [--loglevel LOGLEVEL] [-v] [-sns [SEABORN]]
                   [-mpl MPL_BACKEND] [-ipy] [-nb] [--foreground]
                   [--prefix PREFIX]
                   filepath

Positional Arguments

filepath: File to visualize.

Named Arguments

--loglevel

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

Default: 'ERROR'

-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.

-ipy, --ipython

Invoke ipython terminal.

Default: False

-nb, --notebook

Generate jupyter notebook.

Default: False

--foreground

Run jupyter notebook in the foreground.

Default: False

--prefix

Prefix for lobster output files. Default: ‘’

Default: ''

xrd_traj

Compare X-ray diffraction for the first and the last structure in a trajectory file.

abiview.py xrd_traj [-h] [--loglevel LOGLEVEL] [-v] [-sns [SEABORN]]
                    [-mpl MPL_BACKEND] [-w WAVELENGTH] [-s SYMPREC]
                    [-t TWO_THETA_RANGE TWO_THETA_RANGE] [-nap]
                    filepath

Positional Arguments

filepath: File to visualize.

Named Arguments

--loglevel

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

Default: 'ERROR'

-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.

-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

denpot

Visualize netcdf DEN/POT files with –appname (default: Vesta). NB: Appplication must be installed and in $PATH.

abiview.py denpot [-h] [--loglevel LOGLEVEL] [-v] [-sns [SEABORN]]
                  [-mpl MPL_BACKEND] [-a APPNAME] [--chgcar] [--cube]
                  filepath

Positional Arguments

filepath: File to visualize.

Named Arguments

--loglevel

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

Default: 'ERROR'

-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.

-a, --appname

Application name. Default: vesta. Possible options: avogadro, ovito, v_sim, vesta, xcrysden, mayavi, vtk

Default: 'vesta'

--chgcar

Convert Density to CHGCAR format.

Default: False

--cube

Convert Density/Potential to CUBE format.

Default: False

abiview.py

Named Arguments

subcommands

Sub-commands

structure

Positional Arguments

Named Arguments

input

Positional Arguments

Named Arguments

hist

Positional Arguments

Named Arguments

data

Positional Arguments

Named Arguments

dirviz

Positional Arguments

Named Arguments

ebands

Positional Arguments

Named Arguments

effmass

Positional Arguments

Named Arguments

skw

Positional Arguments

Named Arguments

fs

Positional Arguments

Named Arguments

ifermi_fs

Positional Arguments

Named Arguments

ddb

Positional Arguments

Named Arguments

ddb_vs

Positional Arguments

Named Arguments

ddb_ir

Positional Arguments

Named Arguments

ddb_asr

Positional Arguments

Named Arguments

ddb_dipdip

Positional Arguments

Named Arguments

ddb_quad

Positional Arguments

Named Arguments

ddb_isodistort_ph

Positional Arguments

Named Arguments

ddb_ifc

Positional Arguments

Named Arguments

ddb_qpt

Positional Arguments

Named Arguments

phbands

Positional Arguments

Named Arguments

lobster

Positional Arguments

Named Arguments

xrd_traj

Positional Arguments

Named Arguments

denpot

Positional Arguments

Named Arguments

`abiview.py`