`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,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, 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'

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¶

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`¶