The xolotl object has many properties that govern overarching simulation and environment characteristics. You can access any of these properties using dot notation (e.g. x.verbosity).

Flags

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).

  • The verbosity flag (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.
  • The closed_loop flag (false or true) determines whether initial conditions should be reset before a new simulation. If closed_loop is true, successive simulations will use the current state of the xolotl object (e.g. the end state of the previous simulation if you run integrate twice in a row).
  • The approx_channels flag (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.
  • The solver_order flag 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.
  • The output_structure flag (false or true) determines if outputs from the integrate function 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.

Numerical Properties

  • The dt value 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 dt and sim_dt differ, the simulation vector is interpolated before being output -- useful for running ultra-high definition simulations but not saving all that data.
  • In contrast, sim_dt is the actual fixed time step for the simulation (default ).

  • t_end is the simulation time (default ).

  • The temperature property holds the in-silico preparation temperature (default 11 deg. C). This property only matters when using temperature-sensitive conductances or mechanisms.

  • temperature_ref holds the "default" temperature so that values can be used.
  • The I_ext property stores the current to be injected as a scalar, vector, or matrix.
  • The V_clamp property stores the voltage of clamped compartments as a matrix of nSteps x nComps where nSteps is the number of time-steps (x.t_end * x.dt) and nComps is the number of compartments in the xolotl object tree.

Non-Numerical Properties

  • The manipulate_plot_func property contains a cell of function handles which correspond to all plotting functions that are called when a property is changed while using the manipulate functionality. It defaults to the built-in x.plot function.
  • The pref.m file contains editable preferences for your xolotl installation.