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--- manual:system [2014/03/21 08:24] – Adds heading zenke
+++ manual:system [2015/10/01 05:39] – zenke
@@ Line 1: / Line 1: @@
-====== The System class and its instance sys ======
+====== The System class and its instance sys ======s
 The System class keeps track of the different instances of objects that are created during for setting up a simulation. It requires the ''logger'' to be defined (see [[Logger]]) and expects an MPI communicator as argument. Most Auryn objects expect a global variable ''sys'' of type System to be present in the namespace of the [[simulation program]], which is why it has do be defined as [[simulator init]] code that precedes the declaration of any other simulator object.
 It contains important code such as the [[run]] function that is used to trigger a simulation, which will when called iterate the Auryn [[duty cycle]] for the specified period of simulation time (''simtime'').
+===== Online firing rate estimate in progress bar =====
+**Note** that the rate estimate in Auryn's progress bar is provided by the [[System]] class ([[http://www.fzenke.net/auryn/doxygen/current/classSystem.html]]). It's parameters can be configured using the functions ''set_online_rate_monitor_id (int id=0)'' and ''set_online_rate_monitor_tau (AurynDouble tau=100e-3)''.
+If you set the [[gid|GroupID]] to a negative value the rate estimate will be turned off. Zero and positive values will instruct the System class to average the firing rate of the corresponding [[SpikingGroup]]. For balanced networks this should typically be the population corresponding to the main fraction of the excitatory cells, but not an input [[PoissonGroup]].