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.


Original ComponentType definitions: Simulation.xml. Schema against which NeuroML based on these should be valid: NeuroML_v2.2.xsd. Generated on 25/08/21 from this commit. Please file any issues or questions at the issue tracker here.


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.

length

Duration of the simulation run

time

step

Time step (dt) to use in the simulation

time

seed

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

target

schema:component

displays

Display

outputs

OutputFile

events

EventOutputFile

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.

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

title

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

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.

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

color

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

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.

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).

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.

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.

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

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.

eventPort

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

select

The cell which will be emitting the events