xolotl object has many properties that govern overarching simulation and environment characteristics. You can access any of these properties using dot notation (e.g.
All flags unless otherwise specified and default to 0 or false. Generally, flags are logicals (false or true) unless they have to interact with the underlying
C++ code, in which case, they must be integers (0 or 1).
verbosityflag (0 to 99) toggles the amount of text printed to the console during compiling and simulation. It's handy for debugging. The verbosity flag goes up to 99. The higher the number, the more verbose the printed output.
closed_loopflag (false or true) determines whether initial conditions should be reset before a new simulation. If
closed_loopis true, successive simulations will use the current state of the
xolotlobject (e.g. the end state of the previous simulation if you run
integratetwice in a row).
approx_channelsflag (0 or 1) determines whether approximations to computing gating functions should be used. Look-up tables and approximations to the exponential function significantly increase computational speed, but decrease accuracy, especially at high temporal resolution in the data.
solver_orderflag takes the values 0 or 4. In the 0 case, standard solvers are used (exponential Euler). In the 4 case, a Runge-Kutta 4th order method is used instead. This method is slower but more accurate.
output_structureflag (false or true) determines if outputs from the
integratefunction should be separate (false) or organized in a structure (true). The former is useful when you only want a few outputs or don't care about lots of variable names. The latter is useful when it's important to keep all the output data organized.
dtvalue stores the fixed time step (default ) for outputs from simulation. Note that this is not the same as
sim_dt. This value determines the number of time steps in the output vectors. If
sim_dtdiffer, the simulation vector is interpolated before being output -- useful for running ultra-high definition simulations but not saving all that data.
- In contrast,
sim_dtis the actual fixed time step for the simulation (default ).
t_endis the simulation time (default ).
temperatureproperty holds the in-silico preparation temperature (default 11 deg. C). This property only matters when using temperature-sensitive conductances or mechanisms.
temperature_refholds the "default" temperature so that values can be used.
I_extproperty stores the current to be injected as a scalar, vector, or matrix.
V_clampproperty stores the voltage of clamped compartments as a matrix of
nSteps x nCompswhere
nStepsis the number of time-steps (
x.t_end * x.dt) and
nCompsis the number of compartments in the
manipulate_plot_funcproperty contains a cell of function handles which correspond to all plotting functions that are called when a property is changed while using the
manipulatefunctionality. It defaults to the built-in
pref.mfile contains editable preferences for your