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markovmodel / PyEMMA

🚂 Python API for Emma's Markov Model Algorithms 🚂
http://pyemma.org
GNU Lesser General Public License v3.0
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Changing the units of the rate in plot_markov_model #1548

Closed orthonalmatrix closed 2 years ago

orthonalmatrix commented 2 years ago

Is there a simple way to change the rate units (or scale them)? My system has a frame unit of 20 ps, so as I understand it, my plot_markov_model shows the rates in 1/20 ps. Is there a way to scale all the values by 20 so I can have the rate be per ps? Thanks!

thempel commented 2 years ago

In general, pyemma's Markov models encode transition probability matrices (which are not the same as rate matrices) which indicate conditional probabilities, i.e., are unit-less. In case you are referring to the arrow labels of that plot function, the docs show that indeed just the transition probabilities will be printed by default.

arrow_labels ('weights', None or a ndarray(n,n) with label strings. Optional, default='weights') – Strings to be placed upon arrows. If None, no labels will be used. If ‘weights’, the elements of P will be used. If a matrix of strings is given by the user these will be used.

orthonalmatrix commented 2 years ago

My mistake! Thanks for the clarification!