.. _config_ref tasks mdplot:

``mdplot``
==========

This task generates plots from the output of MD tasks.  It can plot energy-like quantities vs time, and profile quantities vs distance along the z-axis. The plots are generated using matplotlib, and are saved as image files. This task can be part of a standard build, or it can be used via the command line (``pestifer mdplot``) to generate plots from existing NAMD logs and xst files.


Single-valued attributes:

  * ``reprocess-logs``: whether to run the mdplot task as part of a standard build or as a post-processing step (default: False)

  * ``profiles``: List of profile quantities to plot vs distance along z-axis

  * ``profiles-per-block``: Number of profiles to average per block (default: 100)

  * ``histograms``: List of histogram quantities to plot vs distance along z-axis

  * ``colormap``: matplotlib colormap for multiple traces on a single plot (default: tab10)

  * ``colormap-direction``: direction of colormap; 1 for normal, -1 for reversed (default: 1)

  * ``legend``: include a legend (default: True)

  * ``grid``: include a grid (default: False)

  * ``basename``: Baseame of image/CSV file(s) to generate (default: myplot)

  * ``output_dir``: Subdirectory into which PNG plot files are written; created if absent (default: mdplots)



Container-like attributes:

.. toctree::
   :maxdepth: 1

   mdplot/logs
   mdplot/figsize
   mdplot/timeseries
   mdplot/units
   mdplot/axis-labels


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