pyemma.plots.plot_free_energy

pyemma.plots.plot_free_energy(xall, yall, weights=None, ax=None, nbins=100, offset=0.1, cmap='spectral', cbar=True, cbar_label='Free energy (kT)')

Free energy plot given 2D scattered data

Builds a 2D-histogram of the given data points and plots -log(p) where p is the probability computed from the histogram count.

Parameters:
  • xall (ndarray(T)) – sample x-coordinates
  • yall (ndarray(T)) – sample y-coordinates
  • weights (ndarray(T), default = None) – sample weights. By default all samples have the same weight
  • ax (matplotlib Axes object, default = None) – the axes to plot to. When set to None the default Axes object will be used.
  • nbins (int, default=100) – number of histogram bins used in each dimension
  • offset (float, default=0.1) – small additive shift to the histogram. This creates a small bias to the distribution, but gives a better visual impression with the default colormap.
  • cmap (matplotlib colormap, optional, default = None) – the color map to use. None will use pylab.cm.spectral.
  • cbar (boolean, default=True) – plot a color bar
  • cbar_label (str or None, default='Free energy (kT)') – colorbar label string. Use None to suppress it.
Returns:

  • ax (Axes object containing the plot)
  • fig (Figure object containing the plot)