Simulation

Specification of the LEMS Simulation element which is normally used to define simulations of NeuroML2 files. Note: not actually part of NeuroML v2, but this is required by much of the NeuroML toolchain for defining Simulations ( which NeuroML model to use and how long to run for ), as well as what to Display and what to save in OutputFiles.

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Original ComponentType definitions: Simulation.xml. Schema against which NeuroML based on these should be valid: NeuroML_v2.3.xsd. Generated on 14/08/24 from this commit. Please file any issues or questions at the issue tracker here.

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Simulation

The main element in a LEMS Simulation file. Defines the length of simulation, the timestep ( dt ) step and an optional seed to use for stochastic elements, as well as Displays, OutputFiles and EventOutputFiles to record. Specifies a target component to run, usually the id of a network.

Parameters

length	Duration of the simulation run	time
step	Time step (dt) to use in the simulation	time

Text fields

seed	The seed to use in the random number generator for stochastic entities

Component References

target

schema:component

Children list

metas		Meta
displays		Display
outputs		OutputFile
events		EventOutputFile

Dynamics

State Variables

t: time

Display

Details of a display to generate ( usually a set of traces given by Lines in a newly opened window ) on completion of the simulation.

Parameters

timeScale	A scaling of the time axis, e.g. 1ms means display in milliseconds. Note: all quantities are recorded in SI units	time
xmax	The maximum value on the x axis (i.e time variable) of the display	Dimensionless
xmin	The minimum value on the x axis (i.e time variable) of the display	Dimensionless
ymax	The maximum value on the x axis of the display	Dimensionless
ymin	The minimum value on the y axis of the display	Dimensionless

Text fields

title

The title of the display, e.g. to use for the window

Children list

lines

Line

Line

Specification of a single time varying quantity to plot on the Display. Note that all quantities are handled internally in LEMS in SI units, and so a scale should be used if it is to be displayed in other units.

Parameters

scale	A scaling factor to DIVIDE the quantity by. Can be dimensional, so using scale=1mV means a value of -0.07V is displayed as -70. Alternatively, scale=0.001 would achieve the same thing.	Dimensions
timeScale	An optional scaling of the time axis, e.g. 1ms means display in milliseconds. Note: if present, this overrides timeScale from Display	Dimensions

Text fields

color

A hex string for the color to display the trace for this quantity, e.g. #aa33ff

Paths

quantity

Path to the quantity to display, see see https://docs.neuroml.org/Userdocs/Paths.html.

OutputFile

A file in which to save recorded values from the simulation.

Text fields

path	Optional path to the directory in which to store the file
fileName	Name of the file to generate. Can include a relative path (from the LEMS Simulation file location).

Children list

outputColumn

OutputColumn

OutputColumn

Specification of a single time varying quantity to record during the simulation. Note that all quantities are handled internally in LEMS in SI units, and so the value for the quantity in the file ( as well as time ) will be in SI units.

Paths

quantity

Path to the quantity to save, see see https://docs.neuroml.org/Userdocs/Paths.html. Note that all quantities are saved in SI units.

EventOutputFile

A file in which to save event information ( e.g. spikes from cells in a population ) in a specified format.

Text fields

path	Optional path to the directory in which to store the file
fileName	Name of the file to generate. Can include a relative path (from the LEMS Simulation file location).
format	Takes values TIME_ID or ID_TIME, depending on the preferred order of the time or event id (from EventSelection) in each row of the file

Children list

eventSelection

EventSelection

EventSelection

A specific source of events with an associated id, which will be recorded inside the file specified in the parent EventOutputFile. The attribute select should point to a cell inside a population ( e.g. hhpop[0], see https://docs.neuroml.org/Userdocs/Paths.html ), and the eventPort specifies the port for the emitted events, which usually has id: spike. Note: the id used on this element ( and appearing in the file alongside the event time ) can be different from the id/index of the cell in the population.

Text fields

eventPort

The port on the cell which generates the events, usually: spike

Paths

select

The cell which will be emitting the events

Meta

Metadata to add to simulation.

Text fields

for	Simulator name
method	Integration method to use
abs_tolerance	Absolute tolerance for NEURON’s cvode method
rel_tolerance	Relative tolerance for NEURON’s cvode method