Plot

This module implements the plotting scheme to visualize simulation.

The whole plotting scheme only works if the true_colvar output is two dimensional.

Subplot 1: the trajectories of atoms at the true colvar space

boundary (4-element list), increment (2-element list) and plot_ebound (3-element list) can be used to tune the potential energy isosurface at the background

Subplot 2: the potential/bias/total energy and temperature over

different timesteps.

Subplot 3: the trajectories of atoms at the guess colvar space

Subplot 4: the negative of bias energy at the colvar space

Subplot 5: pos distribution

Subplot 6: ke distribution