defaultconfig.yaml

# At this time only the JSON subset of YAML is supported plus YAML-style
# comments (like this one)
{
    # axon geometry
    "axon_length"   : 1000,  # µm
    "axon_diameter" : 1,     # µm

    # temperature
    "axon_temperature" : 16,  # °C

    # axon electrical properties
    "initial_membrane_potential" : -65,     # mV
    "axial_resistance"           : 100,     # Ohm·cm² at 20°C
    "axial_resistance_T"         : 6.3,     # °C
    "axial_resistance_Q10"       : 0.76923, # Ohm·cm²
    "membrane_capacitance"       : 1,       # µF/cm²
    "g_Na_bar"                   : 120e-3,  # S/cm²
    "g_K_bar"                    : 36e-3,   # S/cm²
    "g_l"                        : 0.3e-3,  # S/cm²
    "e_l"                        : -54.3,   # mV
    "m_alpha_Q10"                : 1.8,
    "m_beta_Q10"                 : 1.8,
    "n_alpha_Q10"                : 3,
    "n_beta_Q10"                 : 3,
    "h_alpha_Q10"                : 3,
    "h_beta_Q10"                 : 3,

    # stimulus settings
    # Note: stim position must be 0 µm if the axonal length changes with
    # sweep_param or threshold_param
    "stim_position"   : 0,   # µm
    "stim_amplitude"  : 1,   # nA
    "stim_start_time" : 0.1, # ms
    "stim_duration"   : 1,   # ms

    # simulation settings
    "num_sections"        : 1000,
    "max_time_step"       : 0.005, # ms
    "integration_time"    : 3,     # ms

    # sweep settings
    # Set to parameter sweep to a value greater than 1 for a parameter sweep,
    # then use sweep_param and threshold_param with interpolate to set the
    # dependent and independent variables respectively (see example).
    "param_sweep_steps"    : 1,             # independent var values to test
    "num_bisections"       : 20,            # dependent var bisections to try
    "block_test_position"  : "axon_length", # µm (defined above)
    "block_test_threshold" : -40,           # mV

    # single integration (non-sweep) settings
    "num_v_traces" : 30, # num positions at which to record V_membrane

    # output settings
    "csv_filename" : "" # csv filename (defaults to last config file name)

    # plot settings
    #
    # These are not inherited from previous files and must be specified in the
    # final yaml file.
    #
    #"plot_x_variable" : "t"
    #"plot_y_variable" : "V",
    #"plot_title" : "a title",
    #"plot_x_axis_label" : "e.g. time (ms)",
    #"plot_y_axis_label" : "e.g. membrane potential (mv)"
}