lems.sim package

Submodules

lems.sim.build module

Simulation builder.

author:

Gautham Ganapathy

organization:

LEMS (https://github.com/organizations/LEMS)

class lems.sim.build.SimulationBuilder(model)

Bases: LEMSBase

Simulation builder class.

add_dynamics_1(component, runnable, regime, dynamics)

Adds dynamics to a runnable component based on the dynamics specifications in the component model.

This method builds dynamics necessary for building child components.

Parameters:
Raises:

  • SimBuildError – Raised when a time derivative expression refers to an undefined variable.

  • SimBuildError – Raised when there are invalid time specifications for the <Run> statement.

  • SimBuildError – Raised when the component reference for <Run> cannot be resolved.

add_dynamics_2(component, runnable, regime, dynamics)

Adds dynamics to a runnable component based on the dynamics specifications in the component model.

This method builds dynamics dependent on child components.

Parameters:
Raises:

  • SimBuildError – Raised when a time derivative expression refers to an undefined variable.

  • SimBuildError – Raised when there are invalid time specifications for the <Run> statement.

  • SimBuildError – Raised when the component reference for <Run> cannot be resolved.

add_recording_behavior(component, runnable)

Adds recording-related dynamics to a runnable component based on the dynamics specifications in the component model.

Parameters:

component (lems.model.component.FatComponent runnable: Runnable component to which dynamics is to be added.) – Component model containing dynamics specifications.

Raises:

SimBuildError – Raised when a target for recording could not be found.

build()

Build the simulation components from the model.

Returns:

A runnable simulation object

Return type:

lems.sim.sim.Simulation

build_action(runnable, regime, action)

Build event handler action code.

Parameters:

action (lems.model.dynamics.Action) – Event handler action object

Returns:

Generated action code

Return type:

string

build_conditional_derived_var_code(runnable, regime, dv)
build_event_connections(component, runnable, structure)

Adds event connections to a runnable component based on the structure specifications in the component model.

Parameters:
build_event_handler(runnable, regime, event_handler)

Build event handler code.

Parameters:

event_handler (lems.model.dynamics.EventHandler) – Event handler object

Returns:

Generated event handler code.

Return type:

list(string)

build_event_out(event_out)

Build event out code.

Parameters:

event_out (lems.model.dynamics.EventOut) – event out object

Returns:

Generated event out code

Return type:

string

build_expression_from_tree(runnable, regime, tree_node)

Recursively builds a Python expression from a parsed expression tree.

Parameters:
Returns:

Generated Python expression.

Return type:

string

build_foreach(component, runnable, foreach, name_mappings={})

Iterate over ForEach constructs and process nested elements.

Parameters:
build_on_condition(runnable, regime, on_condition)

Build OnCondition event handler code.

Parameters:

on_condition (lems.model.dynamics.OnCondition) – OnCondition event handler object

Returns:

Generated OnCondition code

Return type:

list(string)

build_on_entry(runnable, regime, on_entry)

Build OnEntry start handler code.

Parameters:

on_entry (lems.model.dynamics.OnEntry) – OnEntry start handler object

Returns:

Generated OnEntry code

Return type:

list(string)

build_on_event(runnable, regime, on_event)

Build OnEvent event handler code.

Parameters:

on_event (lems.model.dynamics.OnEvent) – OnEvent event handler object

Returns:

Generated OnEvent code

Return type:

list(string)

build_on_start(runnable, regime, on_start)

Build OnStart start handler code.

Parameters:

on_start (lems.model.dynamics.OnStart) – OnStart start handler object

Returns:

Generated OnStart code

Return type:

list(string)

build_reduce_code(result, select, reduce)

Builds a reduce operation on the selected target range.

build_runnable(component, parent=None, id_=None)

Build a runnable component from a component specification and add it to the simulation.

Parameters:
Raises:

SimBuildError – Raised when a component reference cannot be resolved.

build_state_assignment(runnable, regime, state_assignment)

Build state assignment code.

Parameters:

state_assignment (lems.model.dynamics.StateAssignment) – State assignment object

Returns:

Generated state assignment code

Return type:

string

build_structure(component, runnable, structure)

Adds structure to a runnable component based on the structure specifications in the component model.

Parameters:
build_transition(transition)

Build regime transition code.

Parameters:

transition (lems.model.dynamics.Transition) – Transition object

Returns:

Generated transition code

Return type:

string

convert_func(func)

Converts NeuroML arithmetic/logical functions to python equivalents.

Parameters:

func (string) – NeuroML function

Returns:

Python operator

Return type:

string

convert_op(op)

Converts NeuroML arithmetic/logical operators to python equivalents.

Parameters:

op (string) – NeuroML operator

Returns:

Python operator

Return type:

string

debug = False
model

Model to be used for constructing the simulation.

Type:

lems.model.model.Model

process_simulation_specs(component, runnable, simulation)

Process simulation-related aspects to a runnable component based on the dynamics specifications in the component model.

Parameters:
Raises:

  • SimBuildError – Raised when a time derivative expression refers to an undefined variable

  • SimBuildError – Raised when there are invalid time specifications for the <Run> statement.

  • SimBuildError – Raised when the component reference for <Run> cannot be resolved.

sim

Simulation built from the model.

Type:

lems.sim.sim.Simulation

lems.sim.build.is_var_in_exp_tree(var, exp_tree)
lems.sim.build.order_derived_parameters(component)

Finds ordering of derived_parameters.

Parameters:

component (lems.model.component.Component) – Component containing derived parameters.

Returns:

Returns ordered list of derived parameters.

Return type:

list(string)

Raises:

SimBuildError – Raised when a proper ordering of derived parameters could not be found.

lems.sim.build.order_derived_variables(regime)

Finds ordering of derived_variables.

Parameters:

regime (lems.model.dynamics.regime) – Dynamics Regime containing derived variables.

Returns:

Returns ordered list of derived variables.

Return type:

list(string)

Raises:

SimBuildError – Raised when a proper ordering of derived variables could not be found.

lems.sim.recording module

Recording class(es).

author:

Gautham Ganapathy

organization:

LEMS (https://github.com/organizations/LEMS)

class lems.sim.recording.Recording(variable, full_path, data_output, recorder)

Bases: LEMSBase

Stores details of a variable recording across a single simulation run.

add_value(time, value)

lems.sim.runnable module

Base class for runnable components.

author:

Gautham Ganapathy

organization:

LEMS (https://github.com/organizations/LEMS)

class lems.sim.runnable.Reflective

Bases: LEMSBase

add_derived_variable(variable)
add_instance_variable(variable, initial_value)
add_method(method_name, parameter_list, statements)
add_text_variable(variable, value)
debug = False
class lems.sim.runnable.Regime(name)

Bases: object

class lems.sim.runnable.Runnable(id_, component, parent=None)

Bases: Reflective

add_attachment(runnable, container=None)
add_child(id_, runnable)
add_child_to_group(group_name, child)
add_child_typeref(typename, runnable)
add_event_in_port(port)
add_event_out_port(port)
add_regime(regime)
add_variable_recorder(data_output, recorder)
add_variable_recorder2(data_output, recorder, path, full_path)
configure_time(time_step, time_total)
copy()

Make a copy of this runnable.

Returns:

Copy of this runnable.

Return type:

lems.sim.runnable.Runnable

do_startup()
inc_event_in(port)
make_attachment(type_, name)
pop_state()
push_state()
record_variables()
register_event_out_callback(port, callback)
reset_time()
resolve_path(path)
single_step(dt)
single_step2(dt)
uid_count = 0
update_shadow_variables()

lems.sim.sim module

Simulation.

author:

Gautham Ganapathy

organization:

LEMS (https://github.com/organizations/LEMS)

class lems.sim.sim.Event(from_id, to_id)

Bases: object

Stores data associated with an event.

from_id

ID of the source runnable for this event.

Type:

Integer

to_id

ID of the destination runnable for this event.

Type:

Integer

class lems.sim.sim.Simulation

Bases: LEMSBase

Simulation class.

add_runnable(runnable)

Adds a runnable component to the list of runnable components in this simulation.

Parameters:

runnable (lems.sim.runnable.Runnable) – A runnable component

debug = False
disable_plasticity()
dump(prefix='')
dump_runnable(runnable, prefix='.')
enable_plasticity()
event_queue

List of posted events.

Type:

list(lems.sim.sim.Event)

init_run()
pop_state()
push_state()
run()

Runs the simulation.

run_queue

Priority of pairs of (time-to-next run, runnable).

Type:

list((Integer, lems.sim.runnable.Runnable))

runnables

Dictionary of runnable components in this simulation.

Type:

dict(string, lems.sim.runnable.Runnable)

step()

Module contents

author:

Gautham Ganapathy

organization:

LEMS (https://github.com/organizations/LEMS)