pyemma.plots.plot_free_energy

pyemma.plots.plot_free_energy(xall, yall, weights=None, ax=None, nbins=100, ncontours=100, offset=- 1, avoid_zero_count=False, minener_zero=True, kT=1.0, vmin=None, vmax=None, cmap='nipy_spectral', cbar=True, cbar_label='free energy / kT', cax=None, levels=None, legacy=True, ncountours=None, cbar_orientation='vertical', **kwargs)

Plot a two-dimensional free energy map using a histogram of scattered data.

Parameters

  • xall (ndarray(T)) – Sample x-coordinates.

  • yall (ndarray(T)) – Sample y-coordinates.

  • weights (ndarray(T), optional, default=None) – Sample weights; by default all samples have the same weight.

  • ax (matplotlib.Axes object, optional, default=None) – The ax to plot to; if ax=None, a new ax (and fig) is created. Number of contour levels.

  • nbins (int, optional, default=100) – Number of histogram bins used in each dimension.

  • ncontours (int, optional, default=100) – Number of contour levels.

  • offset (float, optional, default=-1) – Deprecated and ineffective; raises a ValueError outside legacy mode.

  • avoid_zero_count (bool, optional, default=False) – Avoid zero counts by lifting all histogram elements to the minimum value before computing the free energy. If False, zero histogram counts would yield infinity in the free energy.

  • minener_zero (boolean, optional, default=True) – Shifts the energy minimum to zero.

  • kT (float, optional, default=1.0) – The value of kT in the desired energy unit. By default, energies are computed in kT (setting 1.0). If you want to measure the energy in kJ/mol at 298 K, use kT=2.479 and change the cbar_label accordingly.

  • vmin (float, optional, default=None) – Lowest free energy value to be plotted. (default=0.0 in legacy mode)

  • vmax (float, optional, default=None) – Highest free energy value to be plotted.

  • cmap (matplotlib colormap, optional, default='nipy_spectral') – The color map to use.

  • cbar (boolean, optional, default=True) – Plot a color bar.

  • cbar_label (str, optional, default='free energy / kT') – Colorbar label string; use None to suppress it.

  • cax (matplotlib.Axes object, optional, default=None) – Plot the colorbar into a custom axes object instead of stealing space from ax.

  • levels (iterable of float, optional, default=None) – Contour levels to plot.

  • legacy (boolean, optional, default=True) – Switch to use the function in legacy mode (deprecated).

  • ncountours (int, optional, default=None) – Legacy parameter (typo) for number of contour levels.

  • cbar_orientation (str, optional, default='vertical') – Colorbar orientation; choose ‘vertical’ or ‘horizontal’.

  • parameters for contourf (**kwargs) (Optional) –

  • ------------------------------------------- –

  • corner_mask (boolean, optional) – Enable/disable corner masking, which only has an effect if z is a masked array. If False, any quad touching a masked point is masked out. If True, only the triangular corners of quads nearest those points are always masked out, other triangular corners comprising three unmasked points are contoured as usual. Defaults to rcParams[‘contour.corner_mask’], which defaults to True.

  • alpha (float) – The alpha blending value.

  • locator ([ None | ticker.Locator subclass ]) – If locator is None, the default MaxNLocator is used. The locator is used to determine the contour levels if they are not given explicitly via the levels argument.

  • extend ([ ‘neither’ | ‘both’ | ‘min’ | ‘max’ ]) – Unless this is ‘neither’, contour levels are automatically added to one or both ends of the range so that all data are included. These added ranges are then mapped to the special colormap values which default to the ends of the colormap range, but can be set via matplotlib.colors.Colormap.set_under() and matplotlib.colors.Colormap.set_over() methods.

  • xunits ([ None | registered units ]) – Override axis units by specifying an instance of a matplotlib.units.ConversionInterface.

  • yunits ([ None | registered units ]) – Override axis units by specifying an instance of a matplotlib.units.ConversionInterface.

  • antialiased (boolean, optional) – Enable antialiasing, overriding the defaults. For filled contours, the default is True. For line contours, it is taken from rcParams[‘lines.antialiased’].

  • nchunk ([ 0 | integer ]) – If 0, no subdivision of the domain. Specify a positive integer to divide the domain into subdomains of nchunk by nchunk quads. Chunking reduces the maximum length of polygons generated by the contouring algorithm which reduces the rendering workload passed on to the backend and also requires slightly less RAM. It can however introduce rendering artifacts at chunk boundaries depending on the backend, the antialiased flag and value of alpha.

  • hatches – A list of cross hatch patterns to use on the filled areas. If None, no hatching will be added to the contour. Hatching is supported in the PostScript, PDF, SVG and Agg backends only.

  • zorder (float) – Set the zorder for the artist. Artists with lower zorder values are drawn first.

Returns

  • fig (matplotlib.Figure object) – The figure in which the used ax resides.

  • ax (matplotlib.Axes object) – The ax in which the map was plotted.

  • misc (dict) – Contains a matplotlib.contour.QuadContourSet ‘mappable’ and, if requested, a matplotlib.Colorbar object ‘cbar’.