animate¶

Create movies (animations) by stitching together figures created by plotting multiple datasets, typically originating from a data load with wildcard/regex.

Saving the animation to a file requires an ffmpeg installation.

Command Docstrings

Command line¶

Command help

pgkyl animate -h
  Usage: pgkyl anim [OPTIONS]

    Animate the actively loaded dataset and show resulting plots in a loop.
    Typically, the datasets are loaded using wildcard/regex feature of the -f
    option to the main pgkyl executable. To save the animation ffmpeg needs to
    be installed.

  Options:
    -u, --use TEXT              Specify a tag to plot.
    -s, --squeeze               Squeeze the components into one panel.
    -b, --subplots              Make subplots from multiple datasets.
    --nsubplotrow INTEGER       Manually set the number of rows for subplots.
    --nsubplotcol INTEGER       Manually set the number of columns for subplots.
    --transpose                 Transpose axes.
    -c, --contour               Make contour plot.
    -q, --quiver                Make quiver plot.
    -l, --streamline            Make streamline plot.
    -g, --group [0|1]           Switch to group mode.
    -s, --scatter               Make scatter plot.
    --markersize FLOAT          Set marker size for scatter plots.
    --style TEXT                Specify Matplotlib style file (default:
                                Postgkyl).

    -d, --diverging             Switch to diverging colormesh mode.
    --arg TEXT                  Additional plotting arguments, e.g., '*--'.
    -a, --fix-aspect            Enforce the same scaling on both axes.
    --logx                      Set x-axis to log scale.
    --logy                      Set y-axis to log scale.
    --logz                      Set values of 2D plot to log scale.
    --xscale FLOAT              Value to scale the x-axis (default: 1.0).
    --yscale FLOAT              Value to scale the y-axis (default: 1.0).
    --vmax FLOAT                Set maximal value of data for plots.
    --vmin FLOAT                Set minimal value of data for plots.
    -f, --float                 Choose min/max levels based on current frame
                                (i.e., each frame uses a different color range).

    --xlim TEXT                 Set limits for the x-coordinate (lower,upper)
    --ylim TEXT                 Set limits for the y-coordinate (lower,upper).
    --legend / --no-legend      Show legend.
    --force-legend              Force legend even when plotting a single
                                dataset.

    -x, --xlabel TEXT           Specify a x-axis label.
    -y, --ylabel TEXT           Specify a y-axis label.
    --clabel TEXT               Specify a label for colorbar.
    --title TEXT                Specify a title.
    -i, --interval INTEGER      Specify the animation interval.
    --save                      Save figure as PNG.
    --saveas TEXT               Name to save the plot as.
    --fps INTEGER               Specify frames per second for saving.
    --dpi INTEGER               DPI (resolution) for output.
    -e, --edgecolors TEXT       Set color for cell edges (default: None)
    --showgrid / --no-showgrid  Show grid-lines (default: True)
    --collected                 Animate a dataset that has been collected, i.e.
                                a single dataset with time taken to be the first
                                index.

    --hashtag                   Turns on the pgkyl hashtag!
    --show / --no-show          Turn showing of the plot ON and OFF (default:
                                ON).

    -h, --help                  Show this message and exit.

Suppose we extend the simulation time of the gyrokinetic ion acoustic wave simulation to tEnd=50 and the number of frames to nFrame=100, and run it with

gkyl gk-ionSound-1x2v-p1.lua

Note

This simulation took 582 seconds running with decompCuts=8 (8 cores) on a 2020 MacBookPro.

and plot the electrostatic potential from all frames with

pgkyl "gk-ionSound-1x2v-p1_phi_[0-9]*.bp" interp collect pl -x '$x$' -y '$\phi$' --group 1 --clabel 'time'

this produces the pretty picture below, showing the electrostatic potential as a function of \(x\) in each frame, with the color indicating the time stamp of that frame.

../../_images/gk-ionSound-1x2v-p1_phi_group1.png

This kind of plot can become impractical if there are many frames, or if one would instead like to see a time-dependent movie of the evolution of the potential. For that purpose we can create an animation of \(\phi(x,t)\) using the following command

pgkyl "gk-ionSound-1x2v-p1_phi_[0-9]*.bp" interp anim -x '$x$' -y '$\phi$' --saveas 'gk-ionSound-1x2v-p1_phi.mp4'

Note

In order to save the animation to an .mp4 file, simply append --saveas fileName.mp4 to the end of the above command.

and this will produce the animation below:

One can clearly see the amplitude of the wave decaying as Landau damping ruins the fun.