`oncv.py`¶

Script to generate/analyze/plot ONCVPSP pseudopotentials.

usage: abips.py [-h] [-V]
                {run,print,plot,plot_pseudo,compare,ghost,notebook,gui,gnuplot}
                ...

Named Arguments¶

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

subcommands¶

Valid subcommands

command

Possible choices: run, print, plot, plot_pseudo, compare, ghost, notebook, gui, gnuplot

sub-command help

Sub-commands¶

run¶

Run oncvpsp, generate djrepo file, plot results. Requires oncvps input file.

abips.py run [-h] [-v] [--loglevel LOGLEVEL] [-e] [-s] [-t SLIDE_TIMEOUT]
             [-ew] [-ply] [-cs] [-sns [SEABORN]] [-mpl MPL_BACKEND]
             [--rel REL] [--use-mgga]
             filepath

Positional Arguments¶

filepath

Path to the input/output file

Default: ''

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity

Default: 0

--loglevel

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

Default: 'ERROR'

-e, --expose

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

Default: False

-s, --slide-mode

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

Default: False

-t, --slide-timeout

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

-ew, --expose-web

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

Default: False

-ply, --plotly

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

Default: False

-cs, --chart-studio

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

Default: False

-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.

--rel

Relativistic treatment: nor for non-relativistic, sr for scalar-relativistic, fr for fully-relativistic. Default: from_file i.e. detected from file

Default: 'from_file'

--use-mgga

Produce mega-gga pseudo with oncvpspm.x

Default: False

print¶

Parse oncvps output file and print results to terminal.

abips.py print [-h] [-v] [--loglevel LOGLEVEL] filepath

Positional Arguments¶

filepath

Path to the input/output file

Default: ''

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity

Default: 0

--loglevel

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

Default: 'ERROR'

plot¶

Plot data with matplotlib. Requires oncvpsp output file.

abips.py plot [-h] [-v] [--loglevel LOGLEVEL] [-e] [-s] [-t SLIDE_TIMEOUT]
              [-ew] [-ply] [-cs] [-sns [SEABORN]] [-mpl MPL_BACKEND]
              filepath

Positional Arguments¶

filepath

Path to the input/output file

Default: ''

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity

Default: 0

--loglevel

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

Default: 'ERROR'

-e, --expose

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

Default: False

-s, --slide-mode

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

Default: False

-t, --slide-timeout

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

-ew, --expose-web

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

Default: False

-ply, --plotly

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

Default: False

-cs, --chart-studio

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

Default: False

-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.

plot_pseudo¶

Plot data with matplotlib. Requires pseudopotential file (UPF2 or pawxml).

abips.py plot_pseudo [-h] [-v] [--loglevel LOGLEVEL] [-e] [-s]
                     [-t SLIDE_TIMEOUT] [-ew] [-ply] [-cs] [-sns [SEABORN]]
                     [-mpl MPL_BACKEND]
                     filepath

Positional Arguments¶

filepath

Path to the input/output file

Default: ''

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity

Default: 0

--loglevel

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

Default: 'ERROR'

-e, --expose

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

Default: False

-s, --slide-mode

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

Default: False

-t, --slide-timeout

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

-ew, --expose-web

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

Default: False

-ply, --plotly

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

Default: False

-cs, --chart-studio

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

Default: False

-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.

compare¶

Compare multiple oncvpsp output files.

abips.py compare [-h] [-v] [--loglevel LOGLEVEL] [-e] [-s] [-t SLIDE_TIMEOUT]
                 [-ew] [-ply] [-cs] [-sns [SEABORN]] [-mpl MPL_BACKEND]
                 filepaths [filepaths ...]

Positional Arguments¶

filepaths: List of files to compare.

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity

Default: 0

--loglevel

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

Default: 'ERROR'

-e, --expose

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

Default: False

-s, --slide-mode

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

Default: False

-t, --slide-timeout

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

-ew, --expose-web

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

Default: False

-ply, --plotly

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

Default: False

-cs, --chart-studio

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

Default: False

-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.

ghost¶

Scan directories for oncvpsp output files and build dataframe with ghost position

abips.py ghost [-h] [-v] [--loglevel LOGLEVEL] filepath

Positional Arguments¶

filepath

Path to the input/output file

Default: ''

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity

Default: 0

--loglevel

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

Default: 'ERROR'

notebook¶

Generate jupyter notebook to plot data. Requires oncvpsp output file.

abips.py notebook [-h] [-v] [--loglevel LOGLEVEL] [-nb] [--classic-notebook]
                  [--no-browser] [--foreground]
                  filepath

Positional Arguments¶

filepath

Path to the input/output file

Default: ''

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity

Default: 0

--loglevel

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

Default: 'ERROR'

-nb, --notebook

Open file in jupyter notebook

Default: False

--classic-notebook, -cnb

Use classic jupyter notebook instead of jupyterlab.

Default: False

--no-browser

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

Default: False

--foreground

Run jupyter notebook in the foreground.

Default: False

gui¶

Start a panel web app to generate pseudopotentials.

abips.py gui [-h] [-v] [--loglevel LOGLEVEL] [--port PORT] [--address ADDRESS]
             [--num_procs NUM_PROCS] [--panel-template PANEL_TEMPLATE]
             [--has-remote-server] [--websocket-origin WEBSOCKET_ORIGIN]
             [--max_size_mb MAX_SIZE_MB] [--no-browser] [-e] [-s]
             [-t SLIDE_TIMEOUT] [-ew] [-ply] [-cs] [-sns [SEABORN]]
             [-mpl MPL_BACKEND]
             filepath

Positional Arguments¶

filepath

Path to the input/output file

Default: ''

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity

Default: 0

--loglevel

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

Default: 'ERROR'

--port

Port to listen on.

Default: 0

--address

The address the server should listen on for HTTP requests.

--num_procs

Number of worker processes for the app. Defaults to 1

Default: 1

--panel-template, -pnt

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

Default: 'FastList'

--has-remote-server

True if we are running on the ABINIT server. This flag activates limitations on what the user can do.Default: False

Default: False

--websocket-origin

Public hostnames which may connect to the Bokeh websocket.: Syntax: HOST[:PORT] or *. Default: None

--max_size_mb

Maximum message size in MB allowed by Bokeh and Tornado. Default: 150

Default: 150

--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

-e, --expose

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

Default: False

-s, --slide-mode

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

Default: False

-t, --slide-timeout

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

-ew, --expose-web

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

Default: False

-ply, --plotly

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

Default: False

-cs, --chart-studio

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

Default: False

-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.

gnuplot¶

Plot data with gnuplot.

abips.py gnuplot [-h] [-v] [--loglevel LOGLEVEL] filepath

Positional Arguments¶

filepath

Path to the input/output file

Default: ''

Named Arguments¶

-v, --verbose

Verbose, can be supplied multiple times to increase verbosity

Default: 0

--loglevel

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

Default: 'ERROR'

Usage example:

oncv.py run H.in ==> Run oncvpsp input file (scalar relativistic mode). oncv.py run H_r.in ==> Run oncvpsp input file (relativistic mode). oncv.py plot H.out ==> Use matplotlib to plot oncvpsp results for pseudo H.psp8. oncv.py plot H.out -ew ==> Show matplotlib figures in browser. oncv.py gui H.in ==> Start a panel web app to generate pseudopotential. oncv.py print H.out ==> Parse oncvps output and print results to terminal. oncv.py compare H.out other_H.out ==> Compare multiple output files (supports -ew option as well) oncv.py gnuplot H.out ==> Use gnuplot to plot oncvpsp results for pseudo H.psp8. oncv.py notebook H.out ==> Generate jupyter notebook to plot oncvpsp results.

oncv.py¶

Named Arguments¶

subcommands¶

Sub-commands¶

run¶

Positional Arguments¶

Named Arguments¶

print¶

Positional Arguments¶

Named Arguments¶

plot¶

Positional Arguments¶

Named Arguments¶

plot_pseudo¶

Positional Arguments¶

Named Arguments¶

compare¶

Positional Arguments¶

Named Arguments¶

ghost¶

Positional Arguments¶

Named Arguments¶

notebook¶

Positional Arguments¶

Named Arguments¶

gui¶

Positional Arguments¶

Named Arguments¶

gnuplot¶

Positional Arguments¶

Named Arguments¶

`oncv.py`¶