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,skw,fs,ddb,ddb_vs,ddb_ir,ddb_ifc,phbands,lobster}
                  ...

Named Arguments

-V, --version

show program’s version number and exit

subcommands

Valid subcommands

command

Possible choices: structure, hist, data, dirviz, ebands, skw, fs, ddb, ddb_vs, ddb_ir, ddb_ifc, phbands, lobster

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] [--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.

--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

skw

Interpolate energies in k-space along a k-path with star-function methods Note that the interpolation will likely fail if there are symmetrical k-points in the input set of k-points so it’s 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 –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”

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] [--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.

--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]
                  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.

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]
                  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.

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]
                   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.

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] [--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.

--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: “”