Initialcondition sensitivity¶

class
myokit.
ICSimulation
(model, protocol=None)¶ Runs a forwardEuler based simulation and calculates the partial derivatives of the state vector with respect to the initial conditions.
This class is deprecated. Sensitivities with respect to initial conditions can now be calculated with the
Simulation
class.The simulation is based on automatic differentiation implemented using a C++ data type that replaces a single scalar float with a float and a list of partial derivatives. Any operations on this pair update both the float and the set of derivatives. A normal simulation starts with a state
y(tmin)
and a righthand side function (RHS)f(y) = dy/dt
. It then integratesf(y)
fromtmin
totmax
resulting in an output statey(tmax)
. In this simulation the data type off
is replaced by a(f, df/dy)
, wheredf/dy
is the matrix of partial derivatives off
with respect toy
. By integratingf
fromtmin
totmax
we obtain the state attmax
. This can be seen as a functionF(y(tmin))
, that gives the state attmax
giveny(tmin)
. By integratingdf/dy
the derivative ofF
toy(tmin)
is obtained. This result allows the sensitivity of the system to its initial conditions to be evaluated.N.B. The partial derivatives can not be calculated for the following functions:
floor
,ceil
,abs
, quotients and remainders. If these are encountered the resulting derivatives will be yielded asNaN
. However, in many cases, these functions will only occur as part of a condition in an if statement, so theNaN
’s won’t propagate to the final result.The model passed to the simulation is cloned and stored internally, so changes to the original model object will not affect the simulation.
A protocol can be passed in as
protocol
or set later usingset_protocol()
.Simulations maintain an internal state consisting of
 the current simulation time
 the current state
 the derivatives of the current state with respect to the initial state
When a simulation is created, the simulation time is set to 0 and the state is obtained from the given model. The initial derivatives matrix is an identity matrix of size
(n, n)
, wheren
is the number of states in the model. After each call torun()
the time, state and derivative variables are updated so that each successive call to run continues where the previous one left off. Areset()
method is provided that will set the time back to 0, revert the current state to the default state and set the derivatives back toI
.The simulation provides two inputs a variable can bind to:
time
 This variable contains the simulation time.
pace
 This variable contains the current value of the pacing variable as given by the protocol passed to the Simulation.
No labeled variables are required.

block
(log, derivatives)¶ Takes the output of a simulation (a simulation log and a list of derivatives) and combines it into a single
DataBlock2d
object.Each entry in the log is converted to a 0d entry in the log. The calculated derivatives are stored as the 2d field
derivatives
.

default_state
()¶ Returns the default state.

derivatives
()¶ Return the partial derivatives of the current state with respect to the initial state.

reset
()¶ Resets the simulation:
 The time variable is set to 0
 The state is set back to the default state

run
(duration, log=None, log_interval=5, progress=None, msg='Running ICSimulation')¶ Runs a simulation and returns the logged results. Running a simulation has the following effects:
 The internal state is updated to the last state in the simulation.
 The simulation’s time variable is updated to reflect the time elapsed during the simulation.
The number of time units to simulate can be set with
duration
.The variables to log can be indicated using the
log
argument. There are several options for its value:None
(default), to log all states. An integer flag or a combination of flags. Options:
myokit.LOG_NONE
,myokit.LOG_STATE
,myokit.LOG_INTER
,myokit.LOG_BOUND
.  A list of qnames or variable objects
 A
myokit.DataLog
obtained from a previous simulation. In this case, the newly logged data will be appended to the existing log.
For more details on the
log
argument, see the functionmyokit.prepare_log()
.The method returns a
myokit.DataLog
and a 3d numpy array. In the returned array, the first axis represents the time, the second axis is a state x and the third is a state y such that the point(t, x, y)
representsdx/dy(0)
at time t. For example, ifp
is the array of derivatives, to get the derivative of state 0 with respect to the initial value of state 1, usep[:,0,1]
.A log entry is created every time at least
log_interval
time units have passed.To obtain feedback on the simulation progress, an object implementing the
myokit.ProgressReporter
interface can be passed in. passed in asprogress
. An optional description of the current simulation to use in the ProgressReporter can be passed in as msg.

set_protocol
(protocol=None)¶ Changes the pacing protocol used by this simulation.

set_step_size
(dt=0.01)¶ Sets the step size used in the forward Euler solving routine.

state
()¶ Returns the current state.

time
()¶ Returns the current simulation time.