Documentation for all MOOSE classes and functions

As visible in Python module

1 MOOSE Classes
2 MOOSE Functions

1 MOOSE Classes

1.1 Annotator

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

x: double

x field. Typically display coordinate x

y: double

y field. Typically display coordinate y

z: double

z field. Typically display coordinate z

notes: string

A string to hold some text notes about parent object

color: string

A string to hold a text string specifying display color.Can be a regular English color name, or an rgb code rrrgggbbb

textColor: string

A string to hold a text string specifying color for text labelthat might be on the display for this object.Can be a regular English color name, or an rgb code rrrgggbbb

icon: string

A string to specify icon to use for display
Source message field

childMsg: int

Message to child Elements
Destination message field

parentMsg: int

Message from Parent Element(s)
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.2 Arith

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

function: string

Arithmetic function to perform on inputs.

outputValue: double

Value of output as computed last timestep.

arg1Value: double

Value of arg1 as computed last timestep.
Source message field

childMsg: int

Message to child Elements

output: double

Sends out the computed value
Destination message field

parentMsg: int

Message from Parent Element(s)

arg1: double

Handles argument 1. This just assigns it

arg2: double

Handles argument 2. This just assigns it

arg3: double

Handles argument 3. This sums in each input, and clears each clock tick.

arg1x2: double,double

Store the product of the two arguments in output_

process: void

Handles process call

reinit: void

Handles reinit call
Shared message field

proc: void

Shared message for process and reinit
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

anyValue: unsigned int,double

Value of any of the internal fields, output, arg1, arg2, arg3,as specified by the index argument from 0 to 3.

1.3 Boundary

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

reflectivity: double

What happens to a molecule hitting it: bounces, absorbed, diffused?
Source message field

childMsg: int

Message to child Elements

toAdjacent: void

Dummy message going to adjacent compartment.

toInside: void

Dummy message going to surrounded compartment.
Destination message field

parentMsg: int

Message from Parent Element(s)

adjacent: void

Dummy message coming from adjacent compartment to current oneImplies that compts are peers: do not surround each other

outside: void

Dummy message coming from surrounding compartment to this one.Implies that the originating compartment surrounds this one
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.4 BufPool

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

n: double

Number of molecules in pool

nInit: double

Initial value of number of molecules in pool

diffConst: double

Diffusion constant of molecule

conc: double

Concentration of molecules in this pool

concInit: double

Initial value of molecular concentration in pool

size: double

Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1

speciesId: unsigned int

Species identifier for this mol pool. Eventually link to ontology.
Source message field

childMsg: int

Message to child Elements

nOut: double

Sends out # of molecules in pool on each timestep

requestMolWt: void

Requests Species object for mol wt

requestSize: double

Requests Size of pool from matching mesh entry
Destination message field

parentMsg: int

Message from Parent Element(s)

group: void

Handle for grouping. Doesn't do anything.

reacDest: double,double

Handles reaction input

process: void

Handles process call

reinit: void

Handles reinit call

handleMolWt: double

Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.

remesh: double,unsigned int,unsigned int,vector<unsigned int>,vector<double>

Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes

increment: double

Increments mol numbers by specified amount. Can be +ve or -ve

decrement: double

Decrements mol numbers by specified amount. Can be +ve or -ve

process: void

Handles process call

reinit: void

Handles reinit call
Shared message field

reac: void

Connects to reaction

proc: void

Shared message for process and reinit

species: void

Shared message for connecting to species objects

mesh: void

Shared message for dealing with mesh operations

proc: void

Shared message for process and reinit
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.5 CaConc

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

Ca: double

Calcium concentration.

CaBasal: double

Basal Calcium concentration.

Ca_base: double

Basal Calcium concentration, synonym for CaBasal

tau: double

Settling time for Ca concentration

B: double

Volume scaling factor

thick: double

Thickness of Ca shell.

ceiling: double

Ceiling value for Ca concentration. If Ca > ceiling, Ca = ceiling. If ceiling <= 0.0, there is no upper limit on Ca concentration value.

floor: double

Floor value for Ca concentration. If Ca < floor, Ca = floor
Source message field

childMsg: int

Message to child Elements

concOut: double

Concentration of Ca in pool
Destination message field

parentMsg: int

Message from Parent Element(s)

process: void

Handles process call

reinit: void

Handles reinit call

current: double

Calcium Ion current, due to be converted to conc.

currentFraction: double,double

Fraction of total Ion current, that is carried by Ca2+.

increase: double

Any input current that increases the concentration.

decrease: double

Any input current that decreases the concentration.

basal: double

Synonym for assignment of basal conc.
Shared message field

proc: void

Shared message to receive Process message from scheduler
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.6 ChanBase

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

Gbar: double

Maximal channel conductance

Ek: double

Reversal potential of channel

Gk: double

Channel conductance variable

Ik: double

Channel current variable
Source message field

childMsg: int

Message to child Elements

channelOut: double,double

Sends channel variables Gk and Ek to compartment

permeability: double

Conductance term going out to GHK object

IkOut: double

Channel current. This message typically goes to concenobjects that keep track of ion concentration.
Destination message field

parentMsg: int

Message from Parent Element(s)

Vm: double

Handles Vm message coming in from compartment

Vm: double

Handles Vm message coming in from compartment
Shared message field

channel: void

This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.

ghk: void

Message to Goldman-Hodgkin-Katz object
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.7 ChemMesh

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

size: double

Size of entire chemical domain.Assigning this assumes that the geometry is that of the default mesh, which may not be what you want. If so, usea more specific mesh assignment function.

numDimensions: unsigned int

Number of spatial dimensions of this compartment. Usually 3 or 2
Source message field

childMsg: int

Message to child Elements

meshSplit: double,vector<double>,vector<unsigned int>,vector< vector<unsigned int> >,vector< vector<unsigned int> >

Defines how meshEntries communicate between nodes.Args: oldVol, volListOfAllEntries, localEntryList, outgoingDiffusion[node#][entry#], incomingDiffusion[node#][entry#]This message is meant to go to the SimManager and Stoich.

meshStats: unsigned int,vector<double>

Basic statistics for mesh: Total # of entries, and a vector ofunique volumes of voxels
Destination message field

parentMsg: int

Message from Parent Element(s)

buildDefaultMesh: double,unsigned int

Tells ChemMesh derived class to build a default mesh with thespecified size and number of meshEntries.

handleRequestMeshStats: void

Handles request from SimManager for mesh stats

handleNodeInfo: unsigned int,unsigned int

Tells ChemMesh how many nodes and threads per node it is allowed to use. Triggers a return meshSplit message.
Shared message field

nodeMeshing: void

Connects to SimManager to coordinate meshing with paralleldecomposition and with the Stoich
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.8 Cinfo

Author: Upi Bhalla

Description: Class information object.

Name: Cinfo

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

docs: string

Documentation

baseClass: string

Name of base class
Source message field

childMsg: int

Message to child Elements
Destination message field

parentMsg: int

Message from Parent Element(s)
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.9 Clock

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

runTime: double

Duration to run the simulation

currentTime: double

Current simulation time

nsteps: unsigned int

Number of steps to advance the simulation, in units of the smallest timestep on the clock ticks

numTicks: unsigned int

Number of clock ticks

currentStep: unsigned int

Current simulation step

dts: vector<double>

Utility function returning the dt (timestep) of all ticks.

isRunning: bool

Utility function to report if simulation is in progress.
Source message field

childMsg: int

Message to child Elements

childTick: void

Parent of Tick element

finished: void

Signal for completion of run

ack: unsigned int,unsigned int

Acknowledgement signal for receipt/completion of function.Goes back to Shell on master node
Destination message field

parentMsg: int

Message from Parent Element(s)

start: double

Sets off the simulation for the specified duration

step: unsigned int

Sets off the simulation for the specified # of steps

stop: void

Halts the simulation, with option to restart seamlessly

setupTick: unsigned int,double

Sets up a specific clock tick: args tick#, dt

reinit: void

Zeroes out all ticks, starts at t = 0
Shared message field

clockControl: void

Controls all scheduling aspects of Clock, usually from Shell
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.10 Compartment

Author: Upi Bhalla

Description: Compartment object, for branching neuron models.

Name: Compartment

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

Vm: double

membrane potential

Cm: double

Membrane capacitance

Em: double

Resting membrane potential

Im: double

Current going through membrane

inject: double

Current injection to deliver into compartment

initVm: double

Initial value for membrane potential

Rm: double

Membrane resistance

Ra: double

Axial resistance of compartment

diameter: double

Diameter of compartment

length: double

Length of compartment

x0: double

X coordinate of start of compartment

y0: double

Y coordinate of start of compartment

z0: double

Z coordinate of start of compartment

x: double

x coordinate of end of compartment

y: double

y coordinate of end of compartment

z: double

z coordinate of end of compartment
Source message field

childMsg: int

Message to child Elements

VmOut: double

Sends out Vm value of compartment on each timestep

axialOut: double

Sends out Vm value of compartment to adjacent compartments,on each timestep

raxialOut: double,double

Sends out Raxial information on each timestep, fields are Ra and Vm
Destination message field

parentMsg: int

Message from Parent Element(s)

injectMsg: double

The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the 'inject' field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current

randInject: double,double

Sends a random injection current to the compartment. Must beupdated each timestep.Arguments to randInject are probability and current.

injectMsg: double

The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the 'inject' field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current

cable: void

Message for organizing compartments into groups, calledcables. Doesn't do anything.

process: void

Handles 'process' call

reinit: void

Handles 'reinit' call

initProc: void

Handles Process call for the 'init' phase of the Compartment calculations. These occur as a separate Tick cycle from the regular proc cycle, and should be called before the proc msg.

initReinit: void

Handles Reinit call for the 'init' phase of the Compartment calculations.

handleChannel: double,double

Handles conductance and Reversal potential arguments from Channel

handleRaxial: double,double

Handles Raxial info: arguments are Ra and Vm.

handleAxial: double

Handles Axial information. Argument is just Vm.
Shared message field

proc: void

This is a shared message to receive Process messages from the scheduler objects. The Process should be called second in each clock tick, after the Init message.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.

init: void

This is a shared message to receive Init messages from the scheduler objects. Its job is to separate the compartmental calculations from the message passing. It doesn't really need to be shared, as it does not use the reinit part, but the scheduler objects expect this form of message for all scheduled output. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a dummy MsgDest for the Reinit operation. It also uses ProcInfo.

channel: void

This is a shared message from a compartment to channels. The first entry is a MsgDest for the info coming from the channel. It expects Gk and Ek from the channel as args. The second entry is a MsgSrc sending Vm

axial: void

This is a shared message between asymmetric compartments. axial messages (this kind) connect up to raxial messages (defined below). The soma should use raxial messages to connect to the axial message of all the immediately adjacent dendritic compartments.This puts the (low) somatic resistance in series with these dendrites. Dendrites should then use raxial messages toconnect on to more distal dendrites. In other words, raxial messages should face outward from the soma. The first entry is a MsgSrc sending Vm to the axialFuncof the target compartment. The second entry is a MsgDest for the info coming from the other compt. It expects Ra and Vm from the other compt as args. Note that the message is named after the source type.

raxial: void

This is a raxial shared message between asymmetric compartments. The first entry is a MsgDest for the info coming from the other compt. It expects Vm from the other compt as an arg. The second is a MsgSrc sending Ra and Vm to the raxialFunc of the target compartment.
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.11 CplxEnzBase

Author: Upi Bhalla

Description:: Base class for mass-action enzymes in which there is an explicit pool for the enzyme-substrate complex. It models the reaction: E + S <===> E.S -—> E + P

Name: CplxEnzBase

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

Km: double

Michaelis-Menten constant in SI conc units (milliMolar)

numKm: double

Michaelis-Menten constant in number units, volume dependent

kcat: double

Forward rate constant for enzyme, units 1/sec

numSubstrates: unsigned int

Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself

k1: double

Forward reaction from enz + sub to complex

k2: double

Reverse reaction from complex to enz + sub

k3: double

Forward rate constant from complex to product + enz

ratio: double

Ratio of k2/k3

concK1: double

K1 expressed in concentration (1/millimolar.sec) units
Source message field

childMsg: int

Message to child Elements

toSub: double,double

Sends out increment of molecules on product each timestep

toPrd: double,double

Sends out increment of molecules on product each timestep

toEnz: double,double

Sends out increment of molecules on product each timestep

toCplx: double,double

Sends out increment of molecules on product each timestep
Destination message field

parentMsg: int

Message from Parent Element(s)

enzDest: double

Handles # of molecules of Enzyme

subDest: double

Handles # of molecules of substrate

prdDest: double

Handles # of molecules of product. Dummy.

process: void

Handles process call

reinit: void

Handles reinit call

remesh: void

Tells the MMEnz to recompute its numKm after remeshing

enzDest: double

Handles # of molecules of Enzyme

cplxDest: double

Handles # of molecules of enz-sub complex
Shared message field

sub: void

Connects to substrate molecule

prd: void

Connects to product molecule

proc: void

Shared message for process and reinit

enz: void

Connects to enzyme pool

cplx: void

Connects to enz-sub complex pool
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.12 CubeMesh

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

size: double

Size of entire chemical domain.Assigning this assumes that the geometry is that of the default mesh, which may not be what you want. If so, usea more specific mesh assignment function.

numDimensions: unsigned int

Number of spatial dimensions of this compartment. Usually 3 or 2

isToroid: bool

Flag. True when the mesh should be toroidal, that is,when going beyond the right face brings us around to theleft-most mesh entry, and so on. If we have nx, ny, nzentries, this rule means that the coordinate (x, ny, z)will map onto (x, 0, z). Similarly,(-1, y, z) -> (nx-1, y, z)Default is false

preserveNumEntries: bool

Flag. When it is true, the numbers nx, ny, nz remainunchanged when x0, x1, y0, y1, z0, z1 are altered. Thusdx, dy, dz would change instead. When it is false, thendx, dy, dz remain the same and nx, ny, nz are altered.Default is true

x0: double

X coord of one end

y0: double

Y coord of one end

z0: double

Z coord of one end

x1: double

X coord of other end

y1: double

Y coord of other end

z1: double

Z coord of other end

dx: double

X size for mesh

dy: double

Y size for mesh

dz: double

Z size for mesh

nx: unsigned int

Number of subdivisions in mesh in X

ny: unsigned int

Number of subdivisions in mesh in Y

nz: unsigned int

Number of subdivisions in mesh in Z

coords: vector<double>

Set all the coords of the cuboid at once. Order is:x0 y0 z0 x1 y1 z1 dx dy dz

meshToSpace: vector<unsigned int>

Array in which each mesh entry stores spatial (cubic) index

spaceToMesh: vector<unsigned int>

Array in which each space index (obtained by linearizing the xyz coords) specifies which meshIndex is present.In many cases the index will store the EMPTY flag if there isno mesh entry at that spatial location
Source message field

childMsg: int

Message to child Elements

meshSplit: double,vector<double>,vector<unsigned int>,vector< vector<unsigned int> >,vector< vector<unsigned int> >

Defines how meshEntries communicate between nodes.Args: oldVol, volListOfAllEntries, localEntryList, outgoingDiffusion[node#][entry#], incomingDiffusion[node#][entry#]This message is meant to go to the SimManager and Stoich.

meshStats: unsigned int,vector<double>

Basic statistics for mesh: Total # of entries, and a vector ofunique volumes of voxels
Destination message field

parentMsg: int

Message from Parent Element(s)

buildDefaultMesh: double,unsigned int

Tells ChemMesh derived class to build a default mesh with thespecified size and number of meshEntries.

handleRequestMeshStats: void

Handles request from SimManager for mesh stats

handleNodeInfo: unsigned int,unsigned int

Tells ChemMesh how many nodes and threads per node it is allowed to use. Triggers a return meshSplit message.
Shared message field

nodeMeshing: void

Connects to SimManager to coordinate meshing with paralleldecomposition and with the Stoich
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.13 CylMesh

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

size: double

Size of entire chemical domain.Assigning this assumes that the geometry is that of the default mesh, which may not be what you want. If so, usea more specific mesh assignment function.

numDimensions: unsigned int

Number of spatial dimensions of this compartment. Usually 3 or 2

x0: double

x coord of one end

y0: double

y coord of one end

z0: double

z coord of one end

r0: double

Radius of one end

x1: double

x coord of other end

y1: double

y coord of other end

z1: double

z coord of other end

r1: double

Radius of other end

lambda: double

Length constant to use for subdivisionsThe system will attempt to subdivide using compartments oflength lambda on average. If the cylinder has different enddiameters r0 and r1, it will scale to smaller lengthsfor the smaller diameter end and vice versa.Once the value is set it will recompute lambda as totLength/numEntries

coords: vector<double>

All the coords as a single vector: x0 y0 z0 x1 y1 z1 r0 r1 lambda

totLength: double

Total length of cylinder
Source message field

childMsg: int

Message to child Elements

meshSplit: double,vector<double>,vector<unsigned int>,vector< vector<unsigned int> >,vector< vector<unsigned int> >

Defines how meshEntries communicate between nodes.Args: oldVol, volListOfAllEntries, localEntryList, outgoingDiffusion[node#][entry#], incomingDiffusion[node#][entry#]This message is meant to go to the SimManager and Stoich.

meshStats: unsigned int,vector<double>

Basic statistics for mesh: Total # of entries, and a vector ofunique volumes of voxels
Destination message field

parentMsg: int

Message from Parent Element(s)

buildDefaultMesh: double,unsigned int

Tells ChemMesh derived class to build a default mesh with thespecified size and number of meshEntries.

handleRequestMeshStats: void

Handles request from SimManager for mesh stats

handleNodeInfo: unsigned int,unsigned int

Tells ChemMesh how many nodes and threads per node it is allowed to use. Triggers a return meshSplit message.
Shared message field

nodeMeshing: void

Connects to SimManager to coordinate meshing with paralleldecomposition and with the Stoich
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.14 CylPanel

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

nPts: unsigned int

Number of points used by panel to specify geometry

nDims: unsigned int

Number of Dimensions used by panel to specify geometry

numNeighbors: unsigned int

Number of Neighbors of panel

shapeId: unsigned int

Identifier for shape type, as used by Smoldyn

coords: vector<double>

All the coordinates for the panel. X vector, then Y, then ZZ can be left out for 2-D panels.Z and Y can be left out for 1-D panels.
Source message field

childMsg: int

Message to child Elements

toNeighbor: void

Identifies neighbors of the current panel
Destination message field

parentMsg: int

Message from Parent Element(s)

neighbor: void

Handles incoming message from neighbor
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

x: unsigned int,double

x coordinate identified by index

y: unsigned int,double

y coordinate identified by index

z: unsigned int,double

z coordinate identified by index

1.15 DiagonalMsg

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

e1: Id

Id of source Element.

e2: Id

Id of source Element.

srcFieldsOnE1: vector<string>

Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector

destFieldsOnE2: vector<string>

Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector

srcFieldsOnE2: vector<string>

Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector

destFieldsOnE1: vector<string>

Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector

stride: int

The stride is the increment to the src DataId that gives thedest DataId. It can be positive or negative, but bounds checkingtakes place and it does not wrap around.
Source message field

childMsg: int

Message to child Elements
Destination message field

parentMsg: int

Message from Parent Element(s)
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.16 DiffAmp

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

gain: double

Gain of the amplifier. The output of the amplifier is the difference between the totals in plus and minus inputs multiplied by the gain. Defaults to 1

saturation: double

Saturation is the bound on the output. If output goes beyond the +/-saturation range, it is truncated to the closer of +saturation and -saturation. Defaults to the maximum double precision floating point number representable on the system.

output: double

Output of the amplifier, i.e. gain * (plus - minus).
Source message field

childMsg: int

Message to child Elements

outputOut: double

Current output level.
Destination message field

parentMsg: int

Message from Parent Element(s)

gainIn: double

Destination message to control gain dynamically.

plusIn: double

Positive input terminal of the amplifier. All the messages connected here are summed up to get total positive input.

minusIn: double

Negative input terminal of the amplifier. All the messages connected here are summed up to get total positive input.

process: void

Handles process call, updates internal time stamp.

reinit: void

Handles reinit call.
Shared message field

proc: void

This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.17 DiskPanel

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

nPts: unsigned int

Number of points used by panel to specify geometry

nDims: unsigned int

Number of Dimensions used by panel to specify geometry

numNeighbors: unsigned int

Number of Neighbors of panel

shapeId: unsigned int

Identifier for shape type, as used by Smoldyn

coords: vector<double>

All the coordinates for the panel. X vector, then Y, then ZZ can be left out for 2-D panels.Z and Y can be left out for 1-D panels.
Source message field

childMsg: int

Message to child Elements

toNeighbor: void

Identifies neighbors of the current panel
Destination message field

parentMsg: int

Message from Parent Element(s)

neighbor: void

Handles incoming message from neighbor
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

x: unsigned int,double

x coordinate identified by index

y: unsigned int,double

y coordinate identified by index

z: unsigned int,double

z coordinate identified by index

1.18 Enz

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

Km: double

Michaelis-Menten constant in SI conc units (milliMolar)

numKm: double

Michaelis-Menten constant in number units, volume dependent

kcat: double

Forward rate constant for enzyme, units 1/sec

numSubstrates: unsigned int

Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself

k1: double

Forward reaction from enz + sub to complex

k2: double

Reverse reaction from complex to enz + sub

k3: double

Forward rate constant from complex to product + enz

ratio: double

Ratio of k2/k3

concK1: double

K1 expressed in concentration (1/millimolar.sec) units
Source message field

childMsg: int

Message to child Elements

toSub: double,double

Sends out increment of molecules on product each timestep

toPrd: double,double

Sends out increment of molecules on product each timestep

toEnz: double,double

Sends out increment of molecules on product each timestep

toCplx: double,double

Sends out increment of molecules on product each timestep
Destination message field

parentMsg: int

Message from Parent Element(s)

enzDest: double

Handles # of molecules of Enzyme

subDest: double

Handles # of molecules of substrate

prdDest: double

Handles # of molecules of product. Dummy.

process: void

Handles process call

reinit: void

Handles reinit call

remesh: void

Tells the MMEnz to recompute its numKm after remeshing

enzDest: double

Handles # of molecules of Enzyme

cplxDest: double

Handles # of molecules of enz-sub complex
Shared message field

sub: void

Connects to substrate molecule

prd: void

Connects to product molecule

proc: void

Shared message for process and reinit

enz: void

Connects to enzyme pool

cplx: void

Connects to enz-sub complex pool
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.19 EnzBase

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

Km: double

Michaelis-Menten constant in SI conc units (milliMolar)

numKm: double

Michaelis-Menten constant in number units, volume dependent

kcat: double

Forward rate constant for enzyme, units 1/sec

numSubstrates: unsigned int

Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself
Source message field

childMsg: int

Message to child Elements

toSub: double,double

Sends out increment of molecules on product each timestep

toPrd: double,double

Sends out increment of molecules on product each timestep
Destination message field

parentMsg: int

Message from Parent Element(s)

enzDest: double

Handles # of molecules of Enzyme

subDest: double

Handles # of molecules of substrate

prdDest: double

Handles # of molecules of product. Dummy.

process: void

Handles process call

reinit: void

Handles reinit call

remesh: void

Tells the MMEnz to recompute its numKm after remeshing
Shared message field

sub: void

Connects to substrate molecule

prd: void

Connects to product molecule

proc: void

Shared message for process and reinit
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.20 Finfo

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

name: string

Name of Finfo

docs: string

Documentation for Finfo

type: string

RTTI type info for this Finfo

src: vector<string>

Subsidiary SrcFinfos. Useful for SharedFinfos

dest: vector<string>

Subsidiary DestFinfos. Useful for SharedFinfos
Source message field

childMsg: int

Message to child Elements
Destination message field

parentMsg: int

Message from Parent Element(s)
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.21 FuncPool

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

n: double

Number of molecules in pool

nInit: double

Initial value of number of molecules in pool

diffConst: double

Diffusion constant of molecule

conc: double

Concentration of molecules in this pool

concInit: double

Initial value of molecular concentration in pool

size: double

Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1

speciesId: unsigned int

Species identifier for this mol pool. Eventually link to ontology.
Source message field

childMsg: int

Message to child Elements

nOut: double

Sends out # of molecules in pool on each timestep

requestMolWt: void

Requests Species object for mol wt

requestSize: double

Requests Size of pool from matching mesh entry
Destination message field

parentMsg: int

Message from Parent Element(s)

group: void

Handle for grouping. Doesn't do anything.

reacDest: double,double

Handles reaction input

process: void

Handles process call

reinit: void

Handles reinit call

handleMolWt: double

Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.

remesh: double,unsigned int,unsigned int,vector<unsigned int>,vector<double>

Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes

increment: double

Increments mol numbers by specified amount. Can be +ve or -ve

decrement: double

Decrements mol numbers by specified amount. Can be +ve or -ve

input: double

Handles input to control value of n_
Shared message field

reac: void

Connects to reaction

proc: void

Shared message for process and reinit

species: void

Shared message for connecting to species objects

mesh: void

Shared message for dealing with mesh operations
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.22 GHK

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

Ik: double

Membrane current

Gk: double

Conductance

Ek: double

Reversal Potential

T: double

Temperature of system

p: double

Permeability of channel

Vm: double

Membrane potential

Cin: double

Internal concentration

Cout: double

External ion concentration

valency: double

Valence of ion
Source message field

childMsg: int

Message to child Elements

channelOut: double,double

Sends channel variables Gk and Ek to compartment

VmOut: double

Relay of membrane potential Vm.

IkOut: double

MembraneCurrent.
Destination message field

parentMsg: int

Message from Parent Element(s)

process: void

Handles process call

handleVm: double

Handles Vm message coming in from compartment

addPermeability: double

Handles permeability message coming in from channel

CinDest: double

Alias for set_Cin

CoutDest: double

Alias for set_Cout

addPermeability: double

Handles permeability message coming in from channel
Shared message field

channel: void

This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.

ghk: void

Message from channel to current Goldman-Hodgkin-Katz objectThis shared message connects to an HHChannel. The first entry is a MsgSrc which relays the Vm received from a compartment. The second entry is a MsgDest which receives channel conductance, and interprets it as permeability.
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.23 Geometry

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

epsilon: double

epsilon is the max deviation of surface-point from surface.I think it refers to when the molecule is stuck to the surface. Need to check with Steven.

neighdist: double

neighdist is capture distance from one panel to another.When a molecule diffuses off one panel and is within neighdist of the other, it is captured by the second.
Source message field

childMsg: int

Message to child Elements

returnSize: double

Return size of compartment
Destination message field

parentMsg: int

Message from Parent Element(s)

handleSizeRequest: void

Handles a request for size. Part of SharedMsg to ChemCompt.
Shared message field

compt: void

Connects to compartment(s) to specify geometry.
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.24 Group

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element
Source message field

childMsg: int

Message to child Elements

group: void

Handle for grouping Elements
Destination message field

parentMsg: int

Message from Parent Element(s)
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.25 GslIntegrator

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

isInitialized: bool

True if the Stoich message has come in to set parms

method: string

Numerical method to use.

relativeAccuracy: double

Accuracy criterion

absoluteAccuracy: double

Another accuracy criterion
Source message field

childMsg: int

Message to child Elements
Destination message field

parentMsg: int

Message from Parent Element(s)

stoich: Id

Handle data from Stoich

remesh: double,unsigned int,unsigned int,vector<unsigned int>,vector<double>

Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes

process: void

Handles process call

reinit: void

Handles reinit call
Shared message field

proc: void

Shared message for process and reinit
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.26 GssaStoich

Author: Upinder S. Bhalla, 2008, 2011, NCBS

Description: GssaStoich: Gillespie Stochastic Simulation Algorithm object.Closely based on the Stoich object and inherits its handling functions for constructing the matrix. Sets up stoichiometry matrix based calculations from a wildcard path for the reaction system.Knows how to compute derivatives for most common things, also knows how to handle special cases where the object will have to do its own computation.Generates a stoichiometry matrix, which is useful for lots of other operations as well.

Name: GssaStoich

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

useOneWayReacs: bool

Flag: use bidirectional or one-way reacs. One-way is neededfor Gillespie type stochastic calculations. Two-way islikely to be margninally more efficient in ODE calculations

nVarPools: unsigned int

Number of variable molecule pools in the reac system

numMeshEntries: unsigned int

Number of meshEntries in reac-diff system

estimatedDt: double

Estimate of fastest (smallest) timescale in system.This is fallible because it depends on instantaneous concs,which of course change over the course of the simulation.

path: string

Path of reaction system to take over

path: string

Path of reaction system to take over and solve

method: string

Numerical method to use for the GssaStoich. The defaultand currently the only method is Gillespie1.
Source message field

childMsg: int

Message to child Elements

plugin: Id

Sends out Stoich Id so that plugins can directly access fields and functions

nodeDiffBoundary: unsigned int,vector<unsigned int>,vector<double>

Sends mol #s across boundary between nodes, to calculate diffusionterms. arg1 is originating node, arg2 is list of meshIndices forwhich data is being transferred, and arg3 are the 'n' values forall the pools on the specified meshIndices, to be plugged intothe appropriate place on the recipient node's S_ matrix
Destination message field

parentMsg: int

Message from Parent Element(s)

meshSplit: double,vector<double>,vector<unsigned int>,vector< vector<unsigned int> >,vector< vector<unsigned int> >

Handles message from ChemMesh that defines how meshEntries are decomposed on this node, and how they communicate between nodes.Args: (oldVol, volumeVectorForAllEntries, localEntryList, outgoingDiffusion[node#][entry#], incomingDiffusion[node#][entry#])

process: void

Handles process call

reinit: void

Handles reinint call
Shared message field

proc: void

Shared message for process and reinit
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.27 HDF5DataWriter

Author: Subhasis Ray

Description: HDF5 file writer for saving data tables. It saves the tables added to it via addObject function into an HDF5 file. At every process call it writes the contents of the tables to the file and clears the table vectors. You can explicitly save the data via the flush function.

Name: HDF5DataWriter

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

filename: string

Name of the file associated with this HDF5 writer object.

isOpen: bool

True if this object has an open file handle.

mode: unsigned int

Depending on mode, if file already exists, if mode=1, data will be appended to existing file, if mode=2, file will be truncated, if mode=4, no writing will happen.
Source message field

childMsg: int

Message to child Elements

requestData: unsigned int

Sends request for a field to target object

clear: void

Send request to clear a Table vector.
Destination message field

parentMsg: int

Message from Parent Element(s)

flush: void

Write all buffer contents to file and clear the buffers.

recvData: bad

Handles data sent back following request

process: void

Handle process calls. Write data to file and clear all Table objects associated with this.

reinit: void

Reinitialize the object
Shared message field

proc: void

Shared message to receive process and reinit
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.28 HDF5WriterBase

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

filename: string

Name of the file associated with this HDF5 writer object.

isOpen: bool

True if this object has an open file handle.

mode: unsigned int

Depending on mode, if file already exists, if mode=1, data will be appended to existing file, if mode=2, file will be truncated, if mode=4, no writing will happen.
Source message field

childMsg: int

Message to child Elements
Destination message field

parentMsg: int

Message from Parent Element(s)

flush: void

Write all buffer contents to file and clear the buffers.
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.29 HHChannel

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

Gbar: double

Maximal channel conductance

Ek: double

Reversal potential of channel

Gk: double

Channel conductance variable

Ik: double

Channel current variable

Xpower: double

Power for X gate

Ypower: double

Power for Y gate

Zpower: double

Power for Z gate

instant: int

Bitmapped flag: bit 0 = Xgate, bit 1 = Ygate, bit 2 = ZgateWhen true, specifies that the lookup table value should beused directly as the state of the channel, rather than usedas a rate term for numerical integration for the state

X: double

State variable for X gate

Y: double

State variable for Y gate

Z: double

State variable for Y gate

useConcentration: int

Flag: when true, use concentration message rather than Vm tocontrol Z gate
Source message field

childMsg: int

Message to child Elements

channelOut: double,double

Sends channel variables Gk and Ek to compartment

permeability: double

Conductance term going out to GHK object

IkOut: double

Channel current. This message typically goes to concenobjects that keep track of ion concentration.
Destination message field

parentMsg: int

Message from Parent Element(s)

Vm: double

Handles Vm message coming in from compartment

Vm: double

Handles Vm message coming in from compartment

process: void

Handles process call

reinit: void

Handles reinit call

concen: double

Incoming message from Concen object to specific conc to usein the Z gate calculations

createGate: string

Function to create specified gate.Argument: Gate type [X Y Z]
Shared message field

channel: void

This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.

ghk: void

Message to Goldman-Hodgkin-Katz object

proc: void

This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.30 HHChannel2D

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

Gbar: double

Maximal channel conductance

Ek: double

Reversal potential of channel

Gk: double

Channel conductance variable

Ik: double

Channel current variable

Xindex: string

String for setting X index.

Yindex: string

String for setting Y index.

Zindex: string

String for setting Z index.

Xpower: double

Power for X gate

Ypower: double

Power for Y gate

Zpower: double

Power for Z gate

instant: int

Bitmapped flag: bit 0 = Xgate, bit 1 = Ygate, bit 2 = ZgateWhen true, specifies that the lookup table value should beused directly as the state of the channel, rather than usedas a rate term for numerical integration for the state

X: double

State variable for X gate

Y: double

State variable for Y gate

Z: double

State variable for Y gate
Source message field

childMsg: int

Message to child Elements

channelOut: double,double

Sends channel variables Gk and Ek to compartment

permeability: double

Conductance term going out to GHK object

IkOut: double

Channel current. This message typically goes to concenobjects that keep track of ion concentration.
Destination message field

parentMsg: int

Message from Parent Element(s)

Vm: double

Handles Vm message coming in from compartment

Vm: double

Handles Vm message coming in from compartment

process: void

Handles process call

reinit: void

Handles reinit call

concen: double

Incoming message from Concen object to specific conc to useas the first concen variable

concen2: double

Incoming message from Concen object to specific conc to useas the second concen variable
Shared message field

channel: void

This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.

ghk: void

Message to Goldman-Hodgkin-Katz object

proc: void

This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.31 HHGate

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

alpha: vector<double>

Parameters for voltage-dependent rates, alpha:Set up alpha term using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form

beta: vector<double>

Parameters for voltage-dependent rates, beta:Set up beta term using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form

tau: vector<double>

Parameters for voltage-dependent rates, tau:Set up tau curve using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))

mInfinity: vector<double>

Parameters for voltage-dependent rates, mInfinity:Set up mInfinity curve using 5 parameters, as follows:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form

min: double

Minimum range for lookup

max: double

Minimum range for lookup

divs: unsigned int

Divisions for lookup. Zero means to use linear interpolation

tableA: vector<double>

Table of A entries

tableB: vector<double>

Table of alpha + beta entries

useInterpolation: bool

Flag: use linear interpolation if true, else direct lookup
Source message field

childMsg: int

Message to child Elements
Destination message field

parentMsg: int

Message from Parent Element(s)

setupAlpha: vector<double>

Set up both gates using 13 parameters, as follows:setupAlpha AA AB AC AD AF BA BB BC BD BF xdivs xmin xmaxHere AA-AF are Coefficients A to F of the alpha (forward) termHere BA-BF are Coefficients A to F of the beta (reverse) termHere xdivs is the number of entries in the table,xmin and xmax define the range for lookup.Outside this range the returned value will be the low [high]entry of the table.The equation describing each table is:y(x) = (A + B * x) / (C + exp((x + D) / F))The original HH equations can readily be cast into this form

setupTau: vector<double>

Identical to setupAlpha, except that the forms specified bythe 13 parameters are for the tau and m-infinity curves ratherthan the alpha and beta terms. So the parameters are:setupTau TA TB TC TD TF MA MB MC MD MF xdivs xmin xmaxAs before, the equation describing each curve is:y(x) = (A + B * x) / (C + exp((x + D) / F))

tweakAlpha: void

Dummy function for backward compatibility. It used to convertthe tables from alpha, beta values to alpha, alpha+betabecause the internal calculations used these forms. Notneeded now, deprecated.

tweakTau: void

Dummy function for backward compatibility. It used to convertthe tables from tau, minf values to alpha, alpha+betabecause the internal calculations used these forms. Notneeded now, deprecated.

setupGate: vector<double>

Sets up one gate at a time using the alpha/beta form.Has 9 parameters, as follows:setupGate A B C D F xdivs xmin xmax is_betaThis sets up the gate using the equation:y(x) = (A + B * x) / (C + exp((x + D) / F))Deprecated.
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

A: double,double

lookupA: Look up the A gate value from a double. Usually doesso by direct scaling and offset to an integer lookup, usinga fine enough table granularity that there is little error.Alternatively uses linear interpolation.The range of the double is predefined based on knowledge ofvoltage or conc ranges, and the granularity is specified bythe xmin, xmax, and dV fields.

B: double,double

lookupB: Look up the B gate value from a double.Note that this looks up the raw tables, which are transformedfrom the reference parameters.

1.32 HHGate2D

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element
Source message field

childMsg: int

Message to child Elements
Destination message field

parentMsg: int

Message from Parent Element(s)
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

A: vector<double>,double

lookupA: Look up the A gate value from two doubles, passedin as a vector. Uses linear interpolation in the 2D tableThe range of the lookup doubles is predefined based on knowledge of voltage or conc ranges, and the granularity is specified by the xmin, xmax, and dx field, and their y-axis counterparts.

B: vector<double>,double

lookupB: Look up B gate value from two doubles in a vector.

1.33 HSolve

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

seed: Id

Use this field to specify path to a 'seed' compartment, that is, any compartment within a neuron. The HSolve object uses this seed as a handle to discover the rest of the neuronal model, which means all the remaining compartments, channels, synapses, etc.

target: string

Specifies the path to a compartmental model to be taken over. This can be the path to any container object that has the model under it (found by performing a deep search). Alternatively, this can also be the path to any compartment within the neuron. This compartment will be used as a handle to discover the rest of the model, which means all the remaining compartments, channels, synapses, etc.

dt: double

The time-step for this solver.

caAdvance: int

This flag determines how current flowing into a calcium pool is computed. A value of 0 means that the membrane potential at the beginning of the time-step is used for the calculation. This is how GENESIS does its computations. A value of 1 means the membrane potential at the middle of the time-step is used. This is the correct way of integration, and is the default way.

vDiv: int

Specifies number of divisions for lookup tables of voltage-sensitive channels.

vMin: double

Specifies the lower bound for lookup tables of voltage-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.

vMax: double

Specifies the upper bound for lookup tables of voltage-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.

caDiv: int

Specifies number of divisions for lookup tables of calcium-sensitive channels.

caMin: double

Specifies the lower bound for lookup tables of calcium-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.

caMax: double

Specifies the upper bound for lookup tables of calcium-sensitive channels. Default is to automatically decide based on the tables of the channels that the solver reads in.
Source message field

childMsg: int

Message to child Elements
Destination message field

parentMsg: int

Message from Parent Element(s)

process: void

Handles 'process' call: Solver advances by one time-step.

reinit: void

Handles 'reinit' call: Solver reads in model.
Shared message field

proc: void

Handles 'reinit' and 'process' calls from a clock.
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.34 HemispherePanel

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

nPts: unsigned int

Number of points used by panel to specify geometry

nDims: unsigned int

Number of Dimensions used by panel to specify geometry

numNeighbors: unsigned int

Number of Neighbors of panel

shapeId: unsigned int

Identifier for shape type, as used by Smoldyn

coords: vector<double>

All the coordinates for the panel. X vector, then Y, then ZZ can be left out for 2-D panels.Z and Y can be left out for 1-D panels.
Source message field

childMsg: int

Message to child Elements

toNeighbor: void

Identifies neighbors of the current panel
Destination message field

parentMsg: int

Message from Parent Element(s)

neighbor: void

Handles incoming message from neighbor
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

x: unsigned int,double

x coordinate identified by index

y: unsigned int,double

y coordinate identified by index

z: unsigned int,double

z coordinate identified by index

1.35 IntFire

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

numSynapses: unsigned int

Number of synapses on SynBase

Vm: double

Membrane potential

tau: double

charging time-course

thresh: double

firing threshold

refractoryPeriod: double

Minimum time between successive spikes
Source message field

childMsg: int

Message to child Elements

spike: double

Sends out spike events
Destination message field

parentMsg: int

Message from Parent Element(s)

process: void

Handles process call

reinit: void

Handles reinit call
Shared message field

proc: void

Shared message for process and reinit
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.36 Interpol2D

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

xmin: double

Minimum value for x axis of lookup table

xmax: double

Maximum value for x axis of lookup table

xdivs: unsigned int

# of divisions on x axis of lookup table

dx: double

Increment on x axis of lookup table

ymin: double

Minimum value for y axis of lookup table

ymax: double

Maximum value for y axis of lookup table

ydivs: unsigned int

# of divisions on y axis of lookup table

dy: double

Increment on y axis of lookup table

tableVector2D: vector< vector<double> >

Get the entire table.
Source message field

childMsg: int

Message to child Elements

trig: double

respond to a request for a value lookup
Destination message field

parentMsg: int

Message from Parent Element(s)

lookup: double,double

Looks up table value based on indices v1 and v2, and sendsvalue back using the 'trig' message
Shared message field

lookupReturn2D: void

This is a shared message for doing lookups on the table. Receives 2 doubles: x, y. Sends back a double with the looked-up z value.
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

table: vector<unsigned int>,double

Lookup an entry on the table

z: vector<double>,double

Interpolated value for specified x and y. This is provided for debugging. Normally other objects will retrieve interpolated values via lookup message.

1.37 IzhikevichNrn

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

Vmax: double

Maximum membrane potential. Membrane potential is reset to c whenever it reaches Vmax. NOTE: Izhikevich model specifies the PEAK voltage, rather than THRSHOLD voltage. The threshold depends on the previous history.

c: double

Reset potential. Membrane potential is reset to c whenever it reaches Vmax.

d: double

Parameter d in Izhikevich model. Unit is V/s.

a: double

Parameter a in Izhikevich model. Unit is s^-1

b: double

Parameter b in Izhikevich model. Unit is s^-1

u: double

Parameter u in Izhikevich equation. Unit is V/s^-1

Vm: double

Membrane potential, equivalent to v in Izhikevich equation.

Im: double

Total current going through the membrane. Unit is A.

Rm: double

Hidden cefficient of input current term (I) in Izhikevich model. Defaults to 1e6 Ohm.

initVm: double

Initial membrane potential. Unit is V.

initU: double

Initial value of u.

alpha: double

Coefficient of v² in Izhikevich equation. Defaults to 0.04 in physiological unit. In SI it should be 40000.0. Unit is V^-1 s^-1

beta: double

Coefficient of v in Izhikevich model. Defaults to 5 in physiological unit, 5000.0 for SI units. Unit is s^-1

gamma: double

Constant term in Izhikevich model. Defaults to 140 in both physiological and SI units. unit is V/s.
Source message field

childMsg: int

Message to child Elements

VmOut: double

Sends out Vm

spike: double

Sends out spike events
Destination message field

parentMsg: int

Message from Parent Element(s)

process: void

Handles process call

reinit: void

Handles reinit call

injectDest: double

Injection current into the neuron.

cDest: double

Destination message to modify parameter c at runtime.

dDest: double

Destination message to modify parameter d at runtime.

bDest: double

Destination message to modify parameter b at runtime

aDest: double

Destination message modify parameter a at runtime.
Shared message field

proc: void

Shared message to receive Process message from scheduler
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.38 LeakyIaF

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

Cm: double

Membrane capacitance.

Rm: double

Membrane resistance, inverse of leak-conductance.

Em: double

Leak reversal potential

Vm: double

Membrane potential

initVm: double

Inital value of membrane potential

Vreset: double

Reset potnetial after firing.

Vthreshold: double

firing threshold

refractoryPeriod: double

Minimum time between successive spikes

inject: double

Injection current.

tSpike: double

Time of the last spike
Source message field

childMsg: int

Message to child Elements

spike: double

Sends out spike events

VmOut: double

Sends out Vm
Destination message field

parentMsg: int

Message from Parent Element(s)

process: void

Handles process call

reinit: void

Handles reinit call

injectDest: double

Destination for current input.
Shared message field

proc: void

Shared message for process and reinit
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.39 MMenz

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

Km: double

Michaelis-Menten constant in SI conc units (milliMolar)

numKm: double

Michaelis-Menten constant in number units, volume dependent

kcat: double

Forward rate constant for enzyme, units 1/sec

numSubstrates: unsigned int

Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself
Source message field

childMsg: int

Message to child Elements

toSub: double,double

Sends out increment of molecules on product each timestep

toPrd: double,double

Sends out increment of molecules on product each timestep
Destination message field

parentMsg: int

Message from Parent Element(s)

enzDest: double

Handles # of molecules of Enzyme

subDest: double

Handles # of molecules of substrate

prdDest: double

Handles # of molecules of product. Dummy.

process: void

Handles process call

reinit: void

Handles reinit call

remesh: void

Tells the MMEnz to recompute its numKm after remeshing
Shared message field

sub: void

Connects to substrate molecule

prd: void

Connects to product molecule

proc: void

Shared message for process and reinit
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.40 MarkovChannel

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

Gbar: double

Maximal channel conductance

Ek: double

Reversal potential of channel

Gk: double

Channel conductance variable

Ik: double

Channel current variable

ligandconc: double

Ligand concentration.

vm: double

Membrane voltage.

numstates: unsigned int

The number of states that the channel can occupy.

numopenstates: unsigned int

The number of states which are open/conducting.

state: vector<double>

This is a row vector that contains the probabilities of finding the channel in each state.

initialstate: vector<double>

This is a row vector that contains the probabilities of finding the channel in each state at t = 0. The state of the channel is reset to this value during a call to reinit()

labels: vector<string>

Labels for each state.

gbar: vector<double>

A row vector containing the conductance associated with each of the open/conducting states.
Source message field

childMsg: int

Message to child Elements

channelOut: double,double

Sends channel variables Gk and Ek to compartment

permeability: double

Conductance term going out to GHK object

IkOut: double

Channel current. This message typically goes to concenobjects that keep track of ion concentration.
Destination message field

parentMsg: int

Message from Parent Element(s)

Vm: double

Handles Vm message coming in from compartment

Vm: double

Handles Vm message coming in from compartment

process: void

Handles process call

reinit: void

Handles reinit call

handleligandconc: double

Deals with incoming messages containing information of ligand concentration

handlestate: vector<double>

Deals with incoming message from MarkovSolver object containing state information of the channel.

Shared message field

channel: void

This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.

ghk: void

Message to Goldman-Hodgkin-Katz object

proc: void

This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.41 MarkovGslSolver

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

isInitialized: bool

True if the message has come in to set solver parameters.

method: string

Numerical method to use.

relativeAccuracy: double

Accuracy criterion

absoluteAccuracy: double

Another accuracy criterion

internalDt: double

internal timestep to use.
Source message field

childMsg: int

Message to child Elements

stateOut: vector<double>

Sends updated state to the MarkovChannel class.
Destination message field

parentMsg: int

Message from Parent Element(s)

init: vector<double>

Initialize solver parameters.

handleQ: vector< vector<double> >

Handles information regarding the instantaneous rate matrix from the MarkovRateTable class.

process: void

Handles process call

reinit: void

Handles reinit call
Shared message field

proc: void

Shared message for process and reinit
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.42 MarkovRateTable

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

vm: double

Membrane voltage.

ligandconc: double

Ligand concentration.

Q: vector< vector<double> >

Instantaneous rate matrix.

size: unsigned int

Dimension of the families of lookup tables. Is always equal to the number of states in the model.
Source message field

childMsg: int

Message to child Elements

instratesOut: vector< vector<double> >

Sends out instantaneous rate information of varying transition rates at each time step.
Destination message field

parentMsg: int

Message from Parent Element(s)

handleVm: double

Handles incoming message containing voltage information.

process: void

Handles process call

reinit: void

Handles reinit call

init: unsigned int

Initialization of the class. Allocates memory for all the tables.

handleLigandConc: double

Handles incoming message containing ligand concentration.

set1d: unsigned int,unsigned int,Id,unsigned int

Setting up of 1D lookup table for the (i,j)'th rate.

set2d: unsigned int,unsigned int,Id

Setting up of 2D lookup table for the (i,j)'th rate.

setconst: unsigned int,unsigned int,double

Setting a constant value for the (i,j)'th rate. Internally, this is stored as a 1-D rate with a lookup table containing 1 entry.
Shared message field

channel: void

This message couples the rate table to the compartment. The rate table needs updates on voltage in order to compute the rate table.

proc: void

This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.43 MarkovSolver

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

Q: vector< vector<double> >

Instantaneous rate matrix.

state: vector<double>

Current state of the channel.

initialstate: vector<double>

Initial state of the channel.

xmin: double

Minimum value for x axis of lookup table

xmax: double

Maximum value for x axis of lookup table

xdivs: unsigned int

# of divisions on x axis of lookup table

invdx: double

Reciprocal of increment on x axis of lookup table

ymin: double

Minimum value for y axis of lookup table

ymax: double

Maximum value for y axis of lookup table

ydivs: unsigned int

# of divisions on y axis of lookup table

invdy: double

Reciprocal of increment on y axis of lookup table
Source message field

childMsg: int

Message to child Elements

stateOut: vector<double>

Sends updated state to the MarkovChannel class.
Destination message field

parentMsg: int

Message from Parent Element(s)

handleVm: double

Handles incoming message containing voltage information.

process: void

Handles process call

reinit: void

Handles reinit call

ligandconc: double

Handles incoming message containing ligand concentration.

init: Id,double

Setups the table of matrix exponentials associated with the solver object.

process: void

Handles process call

reinit: void

Handles reinit call
Shared message field

channel: void

This message couples the MarkovSolverBase to the Compartment. The compartment needs Vm in order to look up the correct matrix exponential for computing the state.

proc: void

This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.

proc: void

This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.44 MarkovSolverBase

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

Q: vector< vector<double> >

Instantaneous rate matrix.

state: vector<double>

Current state of the channel.

initialstate: vector<double>

Initial state of the channel.

xmin: double

Minimum value for x axis of lookup table

xmax: double

Maximum value for x axis of lookup table

xdivs: unsigned int

# of divisions on x axis of lookup table

invdx: double

Reciprocal of increment on x axis of lookup table

ymin: double

Minimum value for y axis of lookup table

ymax: double

Maximum value for y axis of lookup table

ydivs: unsigned int

# of divisions on y axis of lookup table

invdy: double

Reciprocal of increment on y axis of lookup table
Source message field

childMsg: int

Message to child Elements

stateOut: vector<double>

Sends updated state to the MarkovChannel class.
Destination message field

parentMsg: int

Message from Parent Element(s)

handleVm: double

Handles incoming message containing voltage information.

process: void

Handles process call

reinit: void

Handles reinit call

ligandconc: double

Handles incoming message containing ligand concentration.

init: Id,double

Setups the table of matrix exponentials associated with the solver object.
Shared message field

channel: void

This message couples the MarkovSolverBase to the Compartment. The compartment needs Vm in order to look up the correct matrix exponential for computing the state.

proc: void

This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.45 MathFunc

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

mathML: string

MathML version of expression to compute

function: string

function is for functions of form f(x, y) = x + y

result: double

result value
Source message field

childMsg: int

Message to child Elements

output: double

Sends out result of computation
Destination message field

parentMsg: int

Message from Parent Element(s)

arg1: double

Handle arg1

arg2: double

Handle arg2

arg3: double

Handle arg3

arg4: double

Handle arg4

process: void

Handle process call

reinit: void

Handle reinit call
Shared message field

proc: void

Shared message for process and reinit
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.46 Mdouble

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

this: double

Access function for entire Mdouble object.

value: double

Access function for value field of Mdouble object,which happens also to be the entire contents of the object.
Source message field

childMsg: int

Message to child Elements
Destination message field

parentMsg: int

Message from Parent Element(s)
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.47 MeshEntry

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

size: double

Volume of this MeshEntry

dimensions: unsigned int

number of dimensions of this MeshEntry

meshType: unsigned int

The MeshType defines the shape of the mesh entry. 0: Not assigned 1: cuboid 2: cylinder 3. cylindrical shell 4: cylindrical shell segment 5: sphere 6: spherical shell 7: spherical shell segment 8: Tetrahedral

Coordinates: vector<double>

Coordinates that define current MeshEntry. Depend on MeshType.

neighbors: vector<unsigned int>

Indices of other MeshEntries that this one connects to

DiffusionArea: vector<double>

Diffusion area for geometry of interface

DiffusionScaling: vector<double>

Diffusion scaling for geometry of interface
Source message field

childMsg: int

Message to child Elements

remesh: double,unsigned int,unsigned int,vector<unsigned int>,vector<double>

Tells the target pool or other entity that the compartment subdivision(meshing) has changed, and that it has to redo its volume and memory allocation accordingly.Arguments are: oldvol, numTotalEntries, startEntry, localIndices, volsThe vols specifies volumes of each local mesh entry. It also specifieshow many meshEntries are present on the local node.The localIndices vector is used for general load balancing only.It has a list of the all meshEntries on current node.If it is empty, we assume block load balancing. In this secondcase the contents of the current node go from startEntry to startEntry + vols.size().

remeshReacs: void

Tells connected enz or reac that the compartment subdivision(meshing) has changed, and that it has to redo its volume-dependent rate terms like numKf_ accordingly.
Destination message field

parentMsg: int

Message from Parent Element(s)

group: void

Handle for grouping. Doesn't do anything.

process: void

Handles process call

reinit: void

Handles reinit call
Shared message field

proc: void

Shared message for process and reinit

mesh: void

Shared message for updating mesh volumes and subdivisions,typically controls pool sizes
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.48 MgBlock

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

Gbar: double

Maximal channel conductance

Ek: double

Reversal potential of channel

Gk: double

Channel conductance variable

Ik: double

Channel current variable

KMg_A: double

1/eta

KMg_B: double

1/gamma

CMg: double

[Mg] in mM

Ik: double

Current through MgBlock

Zk: double

Charge on ion
Source message field

childMsg: int

Message to child Elements

channelOut: double,double

Sends channel variables Gk and Ek to compartment

permeability: double

Conductance term going out to GHK object

IkOut: double

Channel current. This message typically goes to concenobjects that keep track of ion concentration.
Destination message field

parentMsg: int

Message from Parent Element(s)

Vm: double

Handles Vm message coming in from compartment

Vm: double

Handles Vm message coming in from compartment

process: void

Handles process call

origChannel: double,double

Shared message field

channel: void

This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.

ghk: void

Message to Goldman-Hodgkin-Katz object
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.49 Msg

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

e1: Id

Id of source Element.

e2: Id

Id of source Element.

srcFieldsOnE1: vector<string>

Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector

destFieldsOnE2: vector<string>

Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector

srcFieldsOnE2: vector<string>

Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector

destFieldsOnE1: vector<string>

Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector
Source message field

childMsg: int

Message to child Elements
Destination message field

parentMsg: int

Message from Parent Element(s)
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.50 Mstring

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

this: string

Access function for entire Mstring object.

value: string

Access function for value field of Mstring object,which happens also to be the entire contents of the object.
Source message field

childMsg: int

Message to child Elements
Destination message field

parentMsg: int

Message from Parent Element(s)
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.51 NMDAChan

Author: Subhasis Ray, 2010, NCBS

Description: NMDAChan: Extracellular [Mg2+] dependent NMDA channel.This channel has four states as described by Jahr and Stevens (J. Neurosci. 1990, 10(9)) This implementation is based on equation 4(a) in that article. The channel conductance is defined as : k * g(V, [Mg2+]o) * S(t) where k is a scaling constant. S(t) is the legand gated component of the conductance. It rises linearly for t = tau2. Then decays exponentially with time constant t = tau1. g is a function of voltage and the extracellular [Mg2+] defined as: 1 / { 1 + (a1 + a2) * (a1 * B1 + a2 * B2)/ [A * a1 * (b1 + B1) + A * a2 * (b2 + B2)]} a1 = 1e3 * exp( - c0 * V - c1) s^-1, c0 = 16.0 / V, c1 = 2.91 a2 = 1e-3 * [Mg2+] * exp( -c2 * V - c3) mM^-1 s, c2 = 45.0 / V, c3 = 6.97 b1 = 1e3 * exp(c4 * V + c5) s^-1, c4 = 9.0 / V, c5 = 1.22 b2 = 1e3 * exp(c6 * V + c7) s^-1, c6 = 17.0 / V, c7 = 0.96 A = 1e3 * exp(-c8) s^-1, c8 = 2.847 B1 = 1e3 * exp(-c9) s^-1, c9 = 0.693 s^-1 B2 = 1e3 * exp(-c10) s^-1, c10 = 3.101. The behaviour of S(t) is as follows: If a spike arrives, then the slope of the linear rise of S(t) is incremented by weight / tau2. After tau2 time, this component is removed from the slope (reduced by weight/tau) and added over to the rate of decay of S(t).

Name: NMDAChan

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

numSynapses: unsigned int

Number of synapses on SynBase

Gbar: double

Maximal channel conductance

Ek: double

Reversal potential of channel

Gk: double

Channel conductance variable

Ik: double

Channel current variable

tau1: double

Decay time constant for the synaptic conductance, tau1 >= tau2.

tau2: double

Rise time constant for the synaptic conductance, tau1 >= tau2.

normalizeWeights: bool

Flag. If true, the overall conductance is normalized by the number of individual synapses in this SynChan object.

unblocked: double

Fraction of channels recovered from Mg2+ block. This is an intermediate variable which corresponds to g(V, [Mg2+]o) in the equation for conductance: k * g(V, [Mg2+]o) * S(t) where k is a constant.

MgConc: double

External Mg2+ concentration

unblocked: double

Fraction of channels recovered from Mg2+ block. This is an intermediate variable which corresponds to g(V, [Mg2+]o) in the equation for conductance: k * g(V, [Mg2+]o) * S(t) where k is a constant.

saturation: double

Upper limit on the NMDA conductance.
Source message field

childMsg: int

Message to child Elements

channelOut: double,double

Sends channel variables Gk and Ek to compartment

permeability: double

Conductance term going out to GHK object

IkOut: double

Channel current. This message typically goes to concenobjects that keep track of ion concentration.
Destination message field

parentMsg: int

Message from Parent Element(s)

Vm: double

Handles Vm message coming in from compartment

Vm: double

Handles Vm message coming in from compartment

process: void

Handles process call

reinit: void

Handles reinit call

activation: double

Sometimes we want to continuously activate the channel

modulator: double

Modulate channel response

MgConcDest: double

Update [Mg2+] from other sources at every time step.
Shared message field

channel: void

This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.

ghk: void

Message to Goldman-Hodgkin-Katz object

proc: void

Shared message to receive Process message from scheduler
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

c: unsigned int,double

Transition parameters c0 to c10 in the Mg2+ dependentstate transitions.

1.52 Nernst

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

E: double

Computed reversal potential

Temperature: double

Temperature of cell

valence: int

Valence of ion in Nernst calculation

Cin: double

Internal conc of ion

Cout: double

External conc of ion

scale: double

Voltage scale factor
Source message field

childMsg: int

Message to child Elements

Eout: double

Computed reversal potential
Destination message field

parentMsg: int

Message from Parent Element(s)

ci: double

Set internal conc of ion, and immediately send out the updated E

co: double

Set external conc of ion, and immediately send out the updated E
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.53 NeuroMesh

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

size: double

Size of entire chemical domain.Assigning this assumes that the geometry is that of the default mesh, which may not be what you want. If so, usea more specific mesh assignment function.

numDimensions: unsigned int

Number of spatial dimensions of this compartment. Usually 3 or 2

cell: Id

Id for base element of cell model. Uses this to traverse theentire tree of the cell to build the mesh.

subTree: vector<Id>

Set of compartments to model. If they happen to be contiguousthen also set up diffusion between the compartments. Can alsohandle cases where the same cell is divided into multiplenon-diffusively-coupled compartments

skipSpines: bool

Flag: when skipSpines is true, the traversal does not includeany compartment with the string 'spine' or 'neck' in its name,and also then skips compartments below this skipped one.Allows to set up separate mesh for spines, based on the same cell model.

numSegments: unsigned int

Number of cylindrical/spherical segments in model

numDiffCompts: unsigned int

Number of diffusive compartments in model

diffLength: double

Diffusive length constant to use for subdivisions. The system willattempt to subdivide cell using diffusive compartments ofthe specified diffusion lengths as a maximum.In order to get integral numbersof compartments in each segment, it may subdivide more finely.Uses default of 0.5 microns, that is, half typical lambda.For default, consider a tau of about 1 second for mostreactions, and a diffusion const of about 1e-12 um²/sec.This gives lambda of 1 micron

geometryPolicy: string

Policy for how to interpret electrical model geometry (which is a branching 1-dimensional tree) in terms of 3-D constructslike spheres, cylinders, and cones.There are three options, default, trousers, and cylinder:default mode: - Use frustrums of cones. Distal diameter is always from compt dia. - For linear dendrites (no branching), proximal diameter is diameter of the parent compartment - For branching dendrites and dendrites emerging from soma, proximal diameter is from compt dia. Don't worry about overlap. - Place somatic dendrites on surface of spherical soma, or at ends of cylindrical soma - Place dendritic spines on surface of cylindrical dendrites, not emerging from their middle.trousers mode: - Use frustrums of cones. Distal diameter is always from compt dia. - For linear dendrites (no branching), proximal diameter is diameter of the parent compartment - For branching dendrites, use a trouser function. Avoid overlap. - For soma, use some variant of trousers. Here we must avoid overlap - For spines, use a way to smoothly merge into parent dend. Radius of curvature should be similar to that of the spine neck. - Place somatic dendrites on surface of spherical soma, or at ends of cylindrical soma - Place dendritic spines on surface of cylindrical dendrites, not emerging from their middle.cylinder mode: - Use cylinders. Diameter is just compartment dia. - Place somatic dendrites on surface of spherical soma, or at ends of cylindrical soma - Place dendritic spines on surface of cylindrical dendrites, not emerging from their middle. - Ignore spatial overlap.
Source message field

childMsg: int

Message to child Elements

meshSplit: double,vector<double>,vector<unsigned int>,vector< vector<unsigned int> >,vector< vector<unsigned int> >

Defines how meshEntries communicate between nodes.Args: oldVol, volListOfAllEntries, localEntryList, outgoingDiffusion[node#][entry#], incomingDiffusion[node#][entry#]This message is meant to go to the SimManager and Stoich.

meshStats: unsigned int,vector<double>

Basic statistics for mesh: Total # of entries, and a vector ofunique volumes of voxels
Destination message field

parentMsg: int

Message from Parent Element(s)

buildDefaultMesh: double,unsigned int

Tells ChemMesh derived class to build a default mesh with thespecified size and number of meshEntries.

handleRequestMeshStats: void

Handles request from SimManager for mesh stats

handleNodeInfo: unsigned int,unsigned int

Tells ChemMesh how many nodes and threads per node it is allowed to use. Triggers a return meshSplit message.
Shared message field

nodeMeshing: void

Connects to SimManager to coordinate meshing with paralleldecomposition and with the Stoich
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.54 Neuron

Author: C H Chaitanya

Description: Neuron - A compartment container

Name: Neuron

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element
Source message field

childMsg: int

Message to child Elements
Destination message field

parentMsg: int

Message from Parent Element(s)
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.55 Neutral

Author: Upinder S. Bhalla, 2007, NCBS

Description: Neutral: Base class for all MOOSE classes. Providesaccess functions for housekeeping fields and operations, messagetraversal, and so on.

Name: Neutral

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element
Source message field

childMsg: int

Message to child Elements
Destination message field

parentMsg: int

Message from Parent Element(s)
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.56 OneToAllMsg

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

e1: Id

Id of source Element.

e2: Id

Id of source Element.

srcFieldsOnE1: vector<string>

Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector

destFieldsOnE2: vector<string>

Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector

srcFieldsOnE2: vector<string>

Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector

destFieldsOnE1: vector<string>

Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector

i1: DataId

DataId of source Element.
Source message field

childMsg: int

Message to child Elements
Destination message field

parentMsg: int

Message from Parent Element(s)
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.57 OneToOneMsg

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

e1: Id

Id of source Element.

e2: Id

Id of source Element.

srcFieldsOnE1: vector<string>

Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector

destFieldsOnE2: vector<string>

Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector

srcFieldsOnE2: vector<string>

Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector

destFieldsOnE1: vector<string>

Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector
Source message field

childMsg: int

Message to child Elements
Destination message field

parentMsg: int

Message from Parent Element(s)
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.58 PIDController

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

gain: double

This is the proportional gain (Kp). This tuning parameter scales the proportional term. Larger gain usually results in faster response, but too much will lead to instability and oscillation.

saturation: double

Bound on the permissible range of output. Defaults to maximum double value.

command: double

The command (desired) value of the sensed parameter. In control theory this is commonly known as setpoint(SP).

sensed: double

Sensed (measured) value. This is commonly known as process variable(PV) in control theory.

tauI: double

The integration time constant, typically = dt. This is actually proportional gain divided by integral gain (Kp/Ki)). Larger Ki (smaller tauI) usually leads to fast elimination of steady state errors at the cost of larger overshoot.

tauD: double

The differentiation time constant, typically = dt / 4. This is derivative gain (Kd) times proportional gain (Kp). Larger Kd (tauD) decreases overshoot at the cost of slowing down transient response and may lead to instability.

output: double

Output of the PIDController. This is given by: gain * ( error + INTEGRAL[ error dt ] / tau_i + tau_d * d(error)/dt ) Where gain = proportional gain (Kp), tau_i = integral gain (Kp/Ki) and tau_d = derivative gain (Kd/Kp). In control theory this is also known as the manipulated variable (MV)

error: double

The error term, which is the difference between command and sensed value.

integral: double

The integral term. It is calculated as INTEGRAL(error dt) = previous_integral + dt * (error + e_previous)/2.

derivative: double

The derivative term. This is (error - e_previous)/dt.

e_previous: double

The error term for previous step.
Source message field

childMsg: int

Message to child Elements

outputOut: double

Sends the output of the PIDController. This is known as manipulated variable (MV) in control theory. This should be fed into the process which we are trying to control.
Destination message field

parentMsg: int

Message from Parent Element(s)

commandIn: double

Command (desired value) input. This is known as setpoint (SP) in control theory.

sensedIn: double

Sensed parameter - this is the one to be tuned. This is known as process variable (PV) in control theory. This comes from the process we are trying to control.

gainDest: double

Destination message to control the PIDController gain dynamically.

process: void

Handle process calls.

reinit: void

Reinitialize the object.
Shared message field

proc: void

This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.59 Panel

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

nPts: unsigned int

Number of points used by panel to specify geometry

nDims: unsigned int

Number of Dimensions used by panel to specify geometry

numNeighbors: unsigned int

Number of Neighbors of panel

shapeId: unsigned int

Identifier for shape type, as used by Smoldyn

coords: vector<double>

All the coordinates for the panel. X vector, then Y, then ZZ can be left out for 2-D panels.Z and Y can be left out for 1-D panels.
Source message field

childMsg: int

Message to child Elements

toNeighbor: void

Identifies neighbors of the current panel
Destination message field

parentMsg: int

Message from Parent Element(s)

neighbor: void

Handles incoming message from neighbor
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

x: unsigned int,double

x coordinate identified by index

y: unsigned int,double

y coordinate identified by index

z: unsigned int,double

z coordinate identified by index

1.60 Pool

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

n: double

Number of molecules in pool

nInit: double

Initial value of number of molecules in pool

diffConst: double

Diffusion constant of molecule

conc: double

Concentration of molecules in this pool

concInit: double

Initial value of molecular concentration in pool

size: double

Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1

speciesId: unsigned int

Species identifier for this mol pool. Eventually link to ontology.
Source message field

childMsg: int

Message to child Elements

nOut: double

Sends out # of molecules in pool on each timestep

requestMolWt: void

Requests Species object for mol wt

requestSize: double

Requests Size of pool from matching mesh entry
Destination message field

parentMsg: int

Message from Parent Element(s)

group: void

Handle for grouping. Doesn't do anything.

reacDest: double,double

Handles reaction input

process: void

Handles process call

reinit: void

Handles reinit call

handleMolWt: double

Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.

remesh: double,unsigned int,unsigned int,vector<unsigned int>,vector<double>

Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes

increment: double

Increments mol numbers by specified amount. Can be +ve or -ve

decrement: double

Decrements mol numbers by specified amount. Can be +ve or -ve
Shared message field

reac: void

Connects to reaction

proc: void

Shared message for process and reinit

species: void

Shared message for connecting to species objects

mesh: void

Shared message for dealing with mesh operations
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.61 PoolBase

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

n: double

Number of molecules in pool

nInit: double

Initial value of number of molecules in pool

diffConst: double

Diffusion constant of molecule

conc: double

Concentration of molecules in this pool

concInit: double

Initial value of molecular concentration in pool

size: double

Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1

speciesId: unsigned int

Species identifier for this mol pool. Eventually link to ontology.
Source message field

childMsg: int

Message to child Elements

nOut: double

Sends out # of molecules in pool on each timestep

requestMolWt: void

Requests Species object for mol wt

requestSize: double

Requests Size of pool from matching mesh entry
Destination message field

parentMsg: int

Message from Parent Element(s)

group: void

Handle for grouping. Doesn't do anything.

reacDest: double,double

Handles reaction input

process: void

Handles process call

reinit: void

Handles reinit call

handleMolWt: double

Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.

remesh: double,unsigned int,unsigned int,vector<unsigned int>,vector<double>

Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes
Shared message field

reac: void

Connects to reaction

proc: void

Shared message for process and reinit

species: void

Shared message for connecting to species objects

mesh: void

Shared message for dealing with mesh operations
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.62 Port

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

scaleOutRate: double

Scaling factor for outgoing rates. Applies to the RateTermscontrolled by this port. Represents a diffusion related term,or the permeability of the port

inStart: unsigned int

Start index to S_ vector into which incoming molecules should add.

inEnd: unsigned int

End index to S_ vector into which incoming molecules should add.

outStart: unsigned int

Start index to S_ vector from where outgoing molecules come.

outEnd: unsigned int

End index to S_ vector from where outgoing molecules come.
Source message field

childMsg: int

Message to child Elements

availableMolsAtPort: vector<Id>

Sends out the full set of molecule Ids that are available for data transfer

efflux: vector<double>

Molecule #s going out

matchedMolsAtPort: vector<Id>

Sends out the set of molecule Ids that match between both ports

efflux: vector<double>

Molecule #s going out
Destination message field

parentMsg: int

Message from Parent Element(s)

handleMatchedMolsAtPort: vector<unsigned int>

Handles list of matched molecules worked out by the other port

influx: vector<double>

Molecule #s coming back in

handleAvailableMolsAtPort: vector<unsigned int>

Handles list of all species that the other port cares about

influx: vector<double>

Molecule #s coming back in
Shared message field

port1: void

Shared message for port. This one initiates the request forsetting up the communications between the portsThe shared message also handles the runtime data transfer

port2: void

Shared message for port. This one responds to the request forsetting up the communications between the portsThe shared message also handles the runtime data transfer
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.63 PulseGen

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

output: double

Output amplitude

baseLevel: double

Basal level of the stimulus

firstLevel: double

Amplitude of the first pulse in a sequence

firstWidth: double

Width of the first pulse in a sequence

firstDelay: double

Delay to start of the first pulse in a sequence

secondLevel: double

Amplitude of the second pulse in a sequence

secondWidth: double

Width of the second pulse in a sequence

secondDelay: double

Delay to start of of the second pulse in a sequence

count: unsigned int

Number of pulses in a sequence

trigMode: unsigned int

Trigger mode for pulses in the sequence. 0 : free-running mode where it keeps looping its output 1 : external trigger, where it is triggered by an external input (and stops after creating the first train of pulses) 2 : external gate mode, where it keeps generating the pulses in a loop as long as the input is high.
Source message field

childMsg: int

Message to child Elements

outputOut: double

Current output level.
Destination message field

parentMsg: int

Message from Parent Element(s)

input: double

Handle incoming input that determines gating/triggering onset.

levelIn: unsigned int,double

Handle level value coming from other objects

widthIn: unsigned int,double

Handle width value coming from other objects

delayIn: unsigned int,double

Handle delay value coming from other objects

process: void

Handles process call, updates internal time stamp.

reinit: void

Handles reinit call.
Shared message field

proc: void

This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

level: unsigned int,double

Level of the pulse at specified index

width: unsigned int,double

Width of the pulse at specified index

delay: unsigned int,double

Delay of the pulse at specified index

1.64 RC

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

V0: double

Initial value of 'state'

R: double

Series resistance of the RC circuit.

C: double

Parallel capacitance of the RC circuit.

state: double

Output value of the RC circuit. This is the voltage across the capacitor.

inject: double

Input value to the RC circuit.This is handled as an input current to the circuit.
Source message field

childMsg: int

Message to child Elements

outputOut: double

Current output level.
Destination message field

parentMsg: int

Message from Parent Element(s)

injectIn: double

Receives input to the RC circuit. All incoming messages are summed up to give the total input current.

process: void

Handles process call.

reinit: void

Handle reinitialization
Shared message field

proc: void

This is a shared message to receive Process messages from the scheduler objects.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.65 Reac

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

kf: double

Forward rate constant, in # units

kb: double

Reverse rate constant, in # units

Kf: double

Forward rate constant, in concentration units

Kb: double

Reverse rate constant, in concentration units

numSubstrates: unsigned int

Number of substrates of reaction

numProducts: unsigned int

Number of products of reaction
Source message field

childMsg: int

Message to child Elements

toSub: double,double

Sends out increment of molecules on product each timestep

toPrd: double,double

Sends out increment of molecules on product each timestep
Destination message field

parentMsg: int

Message from Parent Element(s)

subDest: double

Handles # of molecules of substrate

prdDest: double

Handles # of molecules of product

process: void

Handles process call

reinit: void

Handles reinit call

remesh: void

Tells the reac to recompute its numRates, as remeshing has happened
Shared message field

sub: void

Connects to substrate pool

prd: void

Connects to substrate pool

proc: void

Shared message for process and reinit
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.66 ReacBase

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

kf: double

Forward rate constant, in # units

kb: double

Reverse rate constant, in # units

Kf: double

Forward rate constant, in concentration units

Kb: double

Reverse rate constant, in concentration units

numSubstrates: unsigned int

Number of substrates of reaction

numProducts: unsigned int

Number of products of reaction
Source message field

childMsg: int

Message to child Elements

toSub: double,double

Sends out increment of molecules on product each timestep

toPrd: double,double

Sends out increment of molecules on product each timestep
Destination message field

parentMsg: int

Message from Parent Element(s)

subDest: double

Handles # of molecules of substrate

prdDest: double

Handles # of molecules of product

process: void

Handles process call

reinit: void

Handles reinit call

remesh: void

Tells the reac to recompute its numRates, as remeshing has happened
Shared message field

sub: void

Connects to substrate pool

prd: void

Connects to substrate pool

proc: void

Shared message for process and reinit
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.67 RectPanel

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

nPts: unsigned int

Number of points used by panel to specify geometry

nDims: unsigned int

Number of Dimensions used by panel to specify geometry

numNeighbors: unsigned int

Number of Neighbors of panel

shapeId: unsigned int

Identifier for shape type, as used by Smoldyn

coords: vector<double>

All the coordinates for the panel. X vector, then Y, then ZZ can be left out for 2-D panels.Z and Y can be left out for 1-D panels.
Source message field

childMsg: int

Message to child Elements

toNeighbor: void

Identifies neighbors of the current panel
Destination message field

parentMsg: int

Message from Parent Element(s)

neighbor: void

Handles incoming message from neighbor
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

x: unsigned int,double

x coordinate identified by index

y: unsigned int,double

y coordinate identified by index

z: unsigned int,double

z coordinate identified by index

1.68 ReduceMsg

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

e1: Id

Id of source Element.

e2: Id

Id of source Element.

srcFieldsOnE1: vector<string>

Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector

destFieldsOnE2: vector<string>

Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector

srcFieldsOnE2: vector<string>

Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector

destFieldsOnE1: vector<string>

Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector

i1: DataId

DataId of source Element.
Source message field

childMsg: int

Message to child Elements
Destination message field

parentMsg: int

Message from Parent Element(s)
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.69 Shell

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element
Source message field

childMsg: int

Message to child Elements

reduceArraySize: unsigned int

Look up maximum value of an index, here ragged array size,across many nodes, and assign uniformly to all nodes. Normallyfollowed by an operation to assign the size to the object thatwas resized.

requestCreate: string,Id,Id,string,vector<int>

requestCreate( class, parent, newElm, name, dimensions ): creates a new Element on all nodes with the specified Id. Initiates a callback to indicate completion of operation. Goes to all nodes including self.

requestDelete: Id

requestDelete( doomedElement ):Deletes specified Element on all nodes.Initiates a callback to indicate completion of operation.Goes to all nodes including self.

requestAddMsg: string,unsigned int,ObjId,string,ObjId,string

requestAddMsg( type, src, srcField, dest, destField );Creates specified Msg between specified Element on all nodes.Initiates a callback to indicate completion of operation.Goes to all nodes including self.

requestQuit: void

requestQuit():Emerges from the inner loop, and wraps up. No return value.

move: Id,Id

move( origId, newParent);Moves origId to become a child of newParent

copy: vector<Id>,string,unsigned int,bool,bool

copy( origId, newParent, numRepeats, toGlobal, copyExtMsg );Copies origId to become a child of newParent

useClock: string,string,unsigned int

useClock( path, field, tick# );Specifies which clock tick to use for all elements in Path.The 'field' is typically process, but some cases need to sendupdates to the 'init' field.Tick # specifies which tick to be attached to the objects.

sync: Id,unsigned int

sync( ElementId, FuncId );Synchronizes Element data indexing across all nodes.Used when distributed ops like message setup might set updifferent #s of data entries on Elements on different nodes.The ElementId is the element being synchronized.The FuncId is the 'get' function for the synchronized field.

requestReMesh: Id

requestReMesh( meshId );Chops up specified mesh.

requestSetParserIdleFlag: bool

SetParserIdleFlag( bool isParserIdle );When True, the main ProcessLoop waits a little each cycleso as to avoid pounding on the CPU.

ack: unsigned int,unsigned int

ack( unsigned int node#, unsigned int status ):Acknowledges receipt and completion of a command on a worker node.Goes back only to master node.

requestStart: double

requestStart( runtime ):Starts a simulation. Goes to all nodes including self.Initiates a callback to indicate completion of run.

requestStep: unsigned int

requestStep():Advances a simulation for the specified # of steps.Goes to all nodes including self.

requestStop: void

requestStop():Gently stops a simulation after completing current ops.After this op it is save to do 'start' again, and it willresume where it left offGoes to all nodes including self.

requestSetupTick: unsigned int,double

requestSetupTick():Asks the Clock to coordinate the assignment of a specificclock tick. Args: Tick#, dt.Goes to all nodes including self.

requestReinit: void

requestReinit():Reinits a simulation: sets to time 0.If simulation is running it stops it first.Goes to all nodes including self.
Destination message field

parentMsg: int

Message from Parent Element(s)

receiveGet: bad

receiveGet( Uint node#, Uint status, PrepackedBuffer data )Function on master shell that handles the value relayed from worker.

setclock: unsigned int,double,bool

Assigns clock ticks. Args: tick#, dt

handleAck: unsigned int,unsigned int

Keeps track of # of acks to a blocking shell command. Arg: Source node num.

create: string,Id,Id,string,vector<int>

create( class, parent, newElm, name, dimensions )

delete: Id

Destroys Element, all its messages, and all its children. Args: Id

handleAddMsg: string,unsigned int,ObjId,string,ObjId,string

Makes a msg

handleQuit: void

Stops simulation running and quits the simulator

move: Id,Id

handleMove( Id orig, Id newParent ): moves an Element to a new parent

handleCopy: vector<Id>,string,unsigned int,bool,bool

handleCopy( vector< Id > args, string newName, unsigned int nCopies, bool toGlobal, bool copyExtMsgs ): The vector< Id > has Id orig, Id newParent, Id newElm. This function copies an Element and all its children to a new parent. May also expand out the original into nCopies copies. Normally all messages within the copy tree are also copied. If the flag copyExtMsgs is true, then all msgs going out are also copied.

handleUseClock: string,string,unsigned int

Deals with assignment of path to a given clock.

handleSync: Id,unsigned int

handleSync( Id Element): Synchronizes DataHandler indexing across nodesThe ElementId is the element being synchronized.The FuncId is the 'get' function for the synchronized field.

handleReMesh: Id

handleReMesh( Id BaseMesh): Deals with outcome of resizing the meshing in a cellularcompartment (the ChemMesh class). The mesh change has topropagate down to the molecules and reactions managed by this.Mesh. The ElementId is the mesh being synchronized.

handleSetParserIdleFlag: bool

handleSetParserIdleFlag( bool isParserIdle ): When True, tells the ProcessLoop to wait as the Parser is idle.

handleAck: unsigned int,unsigned int

Keeps track of # of acks to a blocking shell command. Arg: Source node num.
Shared message field

master: void

Issues commands from master shell to worker shells located on different nodes. Also handles acknowledgements from them.

worker: void

Handles commands arriving from master shell on node 0.Sends out acknowledgements from them.

clockControl: void

Controls the system Clock
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.70 SimManager

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

syncTime: double

SyncTime is the interval between synchronizing solvers5 msec is a typical value

autoPlot: bool

When the autoPlot flag is true, the simManager guesses whichplots are of interest, and builds them.

plotDt: double

plotDt is the timestep for plotting variables. As most will bechemical, a default of 1 sec is reasonable

runTime: double

runTime is the requested duration of the simulation that is stored in some kinds of model definition files.

method: string

method is the numerical method used for the calculations.This will set up or even replace the solver with one ableto use the specified method. Currently works only with two solvers: GSL and GSSA.The GSL solver has a variety of ODE methods, by defaultRunge-Kutta-Fehlberg.The GSSA solver currently uses the Gillespie StochasticSystems Algorithm, somewhat optimized over the originalmethod.

version: unsigned int

Numerical version number. Used by kkit

modelFamily: string

Family classification of model: *kinetic, and *neuron are the options so far. In due course expect to see thingslike detailedNetwork, intFireNetwork, sigNeur and so on.
Source message field

childMsg: int

Message to child Elements

requestMeshStats: void

Asks for basic stats for mesh:Total # of entries, and a vector of unique volumes of voxels

nodeInfo: unsigned int,unsigned int

Sends out # of nodes to use for meshing, and # of threads to use on each node, to the ChemMesh. These numbers sometimesdiffer from the total # of nodes and threads, because the SimManager may have other portions of the model to allocate.
Destination message field

parentMsg: int

Message from Parent Element(s)

build: string

Sets up model, with the specified method. The method may beempty if the intention is that methods be set up through hints in the ChemMesh compartments.

makeStandardElements: string

Sets up the usual infrastructure for a model, with theChemMesh, Stoich, solver and suitable messaging.The argument is the MeshClass to use.

meshSplit: double,vector<unsigned int>,vector<unsigned int>,vector<unsigned int>,vector<unsigned int>

Handles message from ChemMesh that defines howmeshEntries communicate between nodes.First arg is oldvol, next is list of other nodes, third arg is list number ofmeshEntries to be transferred for each of these nodes, fourth arg is catenated list of meshEntries indices onmy node going to each of the other connected nodes, andlast arg is matching list of meshEntries on other nodes

meshStats: unsigned int,vector<double>

Basic statistics for mesh: Total # of entries, and a vectorof unique volumes of voxels
Shared message field

nodeMeshing: void

Connects to ChemMesh to coordinate meshing with paralleldecomposition and with the Stoich
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.71 SingleMsg

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

e1: Id

Id of source Element.

e2: Id

Id of source Element.

srcFieldsOnE1: vector<string>

Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector

destFieldsOnE2: vector<string>

Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector

srcFieldsOnE2: vector<string>

Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector

destFieldsOnE1: vector<string>

Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector

i1: DataId

Index of source object.

i2: DataId

Index of dest object.
Source message field

childMsg: int

Message to child Elements
Destination message field

parentMsg: int

Message from Parent Element(s)
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.72 SparseMsg

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

e1: Id

Id of source Element.

e2: Id

Id of source Element.

srcFieldsOnE1: vector<string>

Names of SrcFinfos for messages going from e1 to e2. There arematching entries in the destFieldsOnE2 vector

destFieldsOnE2: vector<string>

Names of DestFinfos for messages going from e1 to e2. There arematching entries in the srcFieldsOnE1 vector

srcFieldsOnE2: vector<string>

Names of SrcFinfos for messages going from e2 to e1. There arematching entries in the destFieldsOnE1 vector

destFieldsOnE1: vector<string>

Names of destFinfos for messages going from e2 to e1. There arematching entries in the srcFieldsOnE2 vector

numRows: unsigned int

Number of rows in matrix.

numColumns: unsigned int

Number of columns in matrix.

numEntries: unsigned int

Number of Entries in matrix.

probability: double

connection probability for random connectivity.

seed: long

Random number seed for generating probabilistic connectivity.
Source message field

childMsg: int

Message to child Elements
Destination message field

parentMsg: int

Message from Parent Element(s)

setRandomConnectivity: double,long

Assigns connectivity with specified probability and seed

setEntry: unsigned int,unsigned int,unsigned int

Assigns single row,column value

unsetEntry: unsigned int,unsigned int

Clears single row,column entry

clear: void

Clears out the entire matrix

transpose: void

Transposes the sparse matrix
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.73 Species

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

molWt: double

Molecular weight of species
Source message field

childMsg: int

Message to child Elements

sendMolWt: double

returns molWt.
Destination message field

parentMsg: int

Message from Parent Element(s)

handleMolWtRequest: void

Handle requests for molWt.
Shared message field

pool: void

Connects to pools of this Species type
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.74 SpherePanel

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

nPts: unsigned int

Number of points used by panel to specify geometry

nDims: unsigned int

Number of Dimensions used by panel to specify geometry

numNeighbors: unsigned int

Number of Neighbors of panel

shapeId: unsigned int

Identifier for shape type, as used by Smoldyn

coords: vector<double>

All the coordinates for the panel. X vector, then Y, then ZZ can be left out for 2-D panels.Z and Y can be left out for 1-D panels.
Source message field

childMsg: int

Message to child Elements

toNeighbor: void

Identifies neighbors of the current panel
Destination message field

parentMsg: int

Message from Parent Element(s)

neighbor: void

Handles incoming message from neighbor
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

x: unsigned int,double

x coordinate identified by index

y: unsigned int,double

y coordinate identified by index

z: unsigned int,double

z coordinate identified by index

1.75 SpikeGen

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

threshold: double

Spiking threshold, must cross it going up

refractT: double

Refractory Time.

abs_refract: double

Absolute refractory time. Synonym for refractT.

hasFired: bool

True if SpikeGen has just fired

edgeTriggered: bool

When edgeTriggered = 0, the SpikeGen will fire an event in each timestep while incoming Vm is > threshold and at least abs_refracttime has passed since last event. This may be problematic if the incoming Vm remains above threshold for longer than abs_refract. Setting edgeTriggered to 1 resolves this as the SpikeGen generatesan event only on the rising edge of the incoming Vm and will remain idle unless the incoming Vm goes below threshold.
Source message field

childMsg: int

Message to child Elements

event: double

Sends out a trigger for an event.
Destination message field

parentMsg: int

Message from Parent Element(s)

process: void

Handles process call

reinit: void

Handles reinit call

Vm: double

Handles Vm message coming in from compartment
Shared message field

proc: void

Shared message to receive Process message from scheduler
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.76 Stats

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

mean: double

Mean of all sampled values.

sdev: double

Standard Deviation of all sampled values.

sum: double

Sum of all sampled values.

num: unsigned int

Number of all sampled values.
Source message field

childMsg: int

Message to child Elements

reduce: unsigned int

Execute statistics reduction operation on all targets andplace results in this object
Destination message field

parentMsg: int

Message from Parent Element(s)

trig: void

Triggers Reduction operation.

process: void

Handles process call

reinit: void

Handles reinit call

process: void

Handles process call

reinit: void

Handles reinit call
Shared message field

proc: void

Shared message for process and reinit
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.77 StimulusTable

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

vec: vector<double>

vector with all table entries

outputValue: double

Output value holding current table entry or output of a calculation

size: unsigned int

size of table. Note that this is the number of x divisions +1since it must represent the largest value as well as thesmallest

startTime: double

Start time used when table is emitting values. For lookupvalues below this, the table just sends out its zero entry.Corresponds to zeroth entry of table.

stopTime: double

Time to stop emitting values.If time exceeds this, then the table sends out its last entry.The stopTime corresponds to the last entry of table.

loopTime: double

If looping, this is the time between successive cycle starts.Defaults to the difference between stopTime and startTime, so that the output waveform cycles with precisely the same duration as the table contents.If larger than stopTime - startTime, then it pauses at the last table value till it is time to go around again.If smaller than stopTime - startTime, then it begins the next cycle even before the first one has reached the end of the table.

stepSize: double

Increment in lookup (x) value on every timestep. If it isless than or equal to zero, the StimulusTable uses the current timeas the lookup value.

stepPosition: double

Current value of lookup (x) value.If stepSize is less than or equal to zero, this is set tothe current time to use as the lookup value.

doLoop: bool

Flag: Should it loop around to startTime once it has reachedstopTime. Default (zero) is to do a single pass.
Source message field

childMsg: int

Message to child Elements

output: double

Sends out tabulated data according to lookup parameters.
Destination message field

parentMsg: int

Message from Parent Element(s)

group: void

Handle for grouping. Doesn't do anything.

linearTransform: double,double

Linearly scales and offsets data. Scale first, then offset.

xplot: string,string

Dumps table contents to xplot-format file. Argument 1 is filename, argument 2 is plotname

plainPlot: string

Dumps table contents to single-column ascii file. Uses scientific notation. Argument 1 is filename

loadCSV: string,int,int,char

Reads a single column from a CSV file. Arguments: filename, column#, starting row#, separator

loadXplot: string,string

Reads a single plot from an xplot file. Arguments: filename, plotnameWhen the file has 2 columns, the 2nd column is loaded.

loadXplotRange: string,string,unsigned int,unsigned int

Reads a single plot from an xplot file, and selects a subset of points from it. Arguments: filename, plotname, startindex, endindexUses C convention: startindex included, endindex not included.When the file has 2 columns, the 2nd column is loaded.

compareXplot: string,string,string

Reads a plot from an xplot file and compares with contents of TableBase.Result is put in 'output' field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: filename, plotname, comparison_{operationOperations}: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).

compareVec: vector<double>,string

Compares contents of TableBase with a vector of doubles.Result is put in 'output' field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: Other vector, comparison_{operationOperations}: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).

clearVec: void

Handles request to clear the data vector

process: void

Handles process call, updates internal time stamp.

reinit: void

Handles reinit call.
Shared message field

proc: void

Shared message for process and reinit
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

y: unsigned int,double

Value of table at specified index

1.78 Stoich

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

useOneWayReacs: bool

Flag: use bidirectional or one-way reacs. One-way is neededfor Gillespie type stochastic calculations. Two-way islikely to be margninally more efficient in ODE calculations

nVarPools: unsigned int

Number of variable molecule pools in the reac system

numMeshEntries: unsigned int

Number of meshEntries in reac-diff system

estimatedDt: double

Estimate of fastest (smallest) timescale in system.This is fallible because it depends on instantaneous concs,which of course change over the course of the simulation.

path: string

Path of reaction system to take over
Source message field

childMsg: int

Message to child Elements

plugin: Id

Sends out Stoich Id so that plugins can directly access fields and functions

nodeDiffBoundary: unsigned int,vector<unsigned int>,vector<double>

Sends mol #s across boundary between nodes, to calculate diffusionterms. arg1 is originating node, arg2 is list of meshIndices forwhich data is being transferred, and arg3 are the 'n' values forall the pools on the specified meshIndices, to be plugged intothe appropriate place on the recipient node's S_ matrix
Destination message field

parentMsg: int

Message from Parent Element(s)

meshSplit: double,vector<double>,vector<unsigned int>,vector< vector<unsigned int> >,vector< vector<unsigned int> >

Handles message from ChemMesh that defines how meshEntries are decomposed on this node, and how they communicate between nodes.Args: (oldVol, volumeVectorForAllEntries, localEntryList, outgoingDiffusion[node#][entry#], incomingDiffusion[node#][entry#])
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.79 SumFunc

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

result: double

outcome of summation
Source message field

childMsg: int

Message to child Elements

output: double

Sends out sum on each timestep
Destination message field

parentMsg: int

Message from Parent Element(s)

input: double

Handles input values

process: void

Handles process call

reinit: void

Handles reinit call
Shared message field

proc: void

Shared message for process and reinit
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.80 Surface

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

volume: double

This is something I'll need to write a function to compute.Perhaps have an update routine as it may be hard to compute but is needed often by the molecules.
Source message field

childMsg: int

Message to child Elements

absorb: void

these help the system define non-standard operations for what a molecule does when it hits a surface.The default is reflect.As a molecule may interact with multiple surfaces, it isn't enough to confer a property on the molecule itself. We have to use messages. Perhaps we don't need these, but instead put entities on the surface which the molecule interacts with if it doesn't do the basic reflect operation.

transmit: void

Surface lets molecules through

jump: void

dunno

mixture: void

dunno

surface: double,double,double

Connects up to a compartment, either as interior or exterior Args are volume, area, perimeter
Destination message field

parentMsg: int

Message from Parent Element(s)
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.81 SymCompartment

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

Vm: double

membrane potential

Cm: double

Membrane capacitance

Em: double

Resting membrane potential

Im: double

Current going through membrane

inject: double

Current injection to deliver into compartment

initVm: double

Initial value for membrane potential

Rm: double

Membrane resistance

Ra: double

Axial resistance of compartment

diameter: double

Diameter of compartment

length: double

Length of compartment

x0: double

X coordinate of start of compartment

y0: double

Y coordinate of start of compartment

z0: double

Z coordinate of start of compartment

x: double

x coordinate of end of compartment

y: double

y coordinate of end of compartment

z: double

z coordinate of end of compartment
Source message field

childMsg: int

Message to child Elements

VmOut: double

Sends out Vm value of compartment on each timestep

axialOut: double

Sends out Vm value of compartment to adjacent compartments,on each timestep

raxialOut: double,double

Sends out Raxial information on each timestep, fields are Ra and Vm

raxialOut: double,double

Sends out Ra and Vm on each timestep

sumRaxialOut: double

Sends out Ra

requestSumAxial: void

Sends out request for Ra.

raxialOut: double,double

Sends out Ra and Vm on each timestep

sumRaxialOut: double

Sends out Ra

requestSumAxial: void

Sends out request for Ra.

Raxial2Out: double,double

Sends out Ra and Vm

sumRaxial2Out: double

Sends out Ra

requestSumAxial2: void

Sends out request for Ra.

Raxial2Out: double,double

Sends out Ra and Vm

sumRaxial2Out: double

Sends out Ra

requestSumAxial2: void

Sends out request for Ra.

Raxial2Out: double,double

Sends out Ra and Vm

sumRaxial2Out: double

Sends out Ra

requestSumAxial2: void

Sends out request for Ra.
Destination message field

parentMsg: int

Message from Parent Element(s)

injectMsg: double

The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the 'inject' field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current

randInject: double,double

Sends a random injection current to the compartment. Must beupdated each timestep.Arguments to randInject are probability and current.

injectMsg: double

The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the 'inject' field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current

cable: void

Message for organizing compartments into groups, calledcables. Doesn't do anything.

process: void

Handles 'process' call

reinit: void

Handles 'reinit' call

initProc: void

Handles Process call for the 'init' phase of the Compartment calculations. These occur as a separate Tick cycle from the regular proc cycle, and should be called before the proc msg.

initReinit: void

Handles Reinit call for the 'init' phase of the Compartment calculations.

handleChannel: double,double

Handles conductance and Reversal potential arguments from Channel

handleRaxial: double,double

Handles Raxial info: arguments are Ra and Vm.

handleAxial: double

Handles Axial information. Argument is just Vm.

raxialSym: double,double

Expects Ra and Vm from other compartment.

sumRaxial: double

Expects Ra from other compartment.

handleSumRaxialRequest: void

Handle request to send back Ra to originating compartment.

parentMsg: int

Message from Parent Element(s)
Shared message field

proc: void

This is a shared message to receive Process messages from the scheduler objects. The Process should be called second in each clock tick, after the Init message.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.

init: void

This is a shared message to receive Init messages from the scheduler objects. Its job is to separate the compartmental calculations from the message passing. It doesn't really need to be shared, as it does not use the reinit part, but the scheduler objects expect this form of message for all scheduled output. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a dummy MsgDest for the Reinit operation. It also uses ProcInfo.

channel: void

This is a shared message from a compartment to channels. The first entry is a MsgDest for the info coming from the channel. It expects Gk and Ek from the channel as args. The second entry is a MsgSrc sending Vm

axial: void

This is a shared message between asymmetric compartments. axial messages (this kind) connect up to raxial messages (defined below). The soma should use raxial messages to connect to the axial message of all the immediately adjacent dendritic compartments.This puts the (low) somatic resistance in series with these dendrites. Dendrites should then use raxial messages toconnect on to more distal dendrites. In other words, raxial messages should face outward from the soma. The first entry is a MsgSrc sending Vm to the axialFuncof the target compartment. The second entry is a MsgDest for the info coming from the other compt. It expects Ra and Vm from the other compt as args. Note that the message is named after the source type.

raxial: void

This is a raxial shared message between asymmetric compartments. The first entry is a MsgDest for the info coming from the other compt. It expects Vm from the other compt as an arg. The second is a MsgSrc sending Ra and Vm to the raxialFunc of the target compartment.

raxial1: void

This is a raxial shared message between symmetric compartments.It goes from the tail of the current compartment to one closer to the soma.

CONNECTTAIL: void

This is a raxial shared message between symmetric compartments.It is an alias for raxial1.

raxial2: void

This is a raxial2 shared message between symmetric compartments.It goes from the head of the current compartment to a compartment further away from the soma

CONNECTHEAD: void

This is a raxial2 shared message between symmetric compartments.It is an alias for raxial2.It goes from the current compartment to one further from the soma

CONNECTCROSS: void

This is a raxial2 shared message between symmetric compartments.It is an alias for raxial2.Conceptually, this goes from the tail of the current compartment to the tail of a sibling compartment. However,this works out to the same as CONNECTHEAD in terms of equivalentcircuit.
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.82 SynBase

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

numSynapses: unsigned int

Number of synapses on SynBase
Source message field

childMsg: int

Message to child Elements
Destination message field

parentMsg: int

Message from Parent Element(s)
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.83 SynChan

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

numSynapses: unsigned int

Number of synapses on SynBase

Gbar: double

Maximal channel conductance

Ek: double

Reversal potential of channel

Gk: double

Channel conductance variable

Ik: double

Channel current variable

tau1: double

Decay time constant for the synaptic conductance, tau1 >= tau2.

tau2: double

Rise time constant for the synaptic conductance, tau1 >= tau2.

normalizeWeights: bool

Flag. If true, the overall conductance is normalized by the number of individual synapses in this SynChan object.
Source message field

childMsg: int

Message to child Elements

channelOut: double,double

Sends channel variables Gk and Ek to compartment

permeability: double

Conductance term going out to GHK object

IkOut: double

Channel current. This message typically goes to concenobjects that keep track of ion concentration.
Destination message field

parentMsg: int

Message from Parent Element(s)

Vm: double

Handles Vm message coming in from compartment

Vm: double

Handles Vm message coming in from compartment

process: void

Handles process call

reinit: void

Handles reinit call

activation: double

Sometimes we want to continuously activate the channel

modulator: double

Modulate channel response
Shared message field

channel: void

This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.

ghk: void

Message to Goldman-Hodgkin-Katz object

proc: void

Shared message to receive Process message from scheduler
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.84 SynChanBase

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

numSynapses: unsigned int

Number of synapses on SynBase

Gbar: double

Maximal channel conductance

Ek: double

Reversal potential of channel

Gk: double

Channel conductance variable

Ik: double

Channel current variable
Source message field

childMsg: int

Message to child Elements

channelOut: double,double

Sends channel variables Gk and Ek to compartment

permeability: double

Conductance term going out to GHK object

IkOut: double

Channel current. This message typically goes to concenobjects that keep track of ion concentration.
Destination message field

parentMsg: int

Message from Parent Element(s)

Vm: double

Handles Vm message coming in from compartment

Vm: double

Handles Vm message coming in from compartment
Shared message field

channel: void

This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.

ghk: void

Message to Goldman-Hodgkin-Katz object
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.85 Synapse

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

weight: double

Synaptic weight

delay: double

Axonal propagation delay to this synapse
Source message field

childMsg: int

Message to child Elements
Destination message field

parentMsg: int

Message from Parent Element(s)

addSpike: double

Handles arriving spike messages, by redirecting up to parent SynBase object
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.86 Table

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

vec: vector<double>

vector with all table entries

outputValue: double

Output value holding current table entry or output of a calculation

size: unsigned int

size of table. Note that this is the number of x divisions +1since it must represent the largest value as well as thesmallest

threshold: double

threshold used when Table acts as a buffer for spikes
Source message field

childMsg: int

Message to child Elements

requestData: unsigned int

Sends request for a field to target object
Destination message field

parentMsg: int

Message from Parent Element(s)

group: void

Handle for grouping. Doesn't do anything.

linearTransform: double,double

Linearly scales and offsets data. Scale first, then offset.

xplot: string,string

Dumps table contents to xplot-format file. Argument 1 is filename, argument 2 is plotname

plainPlot: string

Dumps table contents to single-column ascii file. Uses scientific notation. Argument 1 is filename

loadCSV: string,int,int,char

Reads a single column from a CSV file. Arguments: filename, column#, starting row#, separator

loadXplot: string,string

Reads a single plot from an xplot file. Arguments: filename, plotnameWhen the file has 2 columns, the 2nd column is loaded.

loadXplotRange: string,string,unsigned int,unsigned int

Reads a single plot from an xplot file, and selects a subset of points from it. Arguments: filename, plotname, startindex, endindexUses C convention: startindex included, endindex not included.When the file has 2 columns, the 2nd column is loaded.

compareXplot: string,string,string

Reads a plot from an xplot file and compares with contents of TableBase.Result is put in 'output' field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: filename, plotname, comparison_{operationOperations}: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).

compareVec: vector<double>,string

Compares contents of TableBase with a vector of doubles.Result is put in 'output' field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: Other vector, comparison_{operationOperations}: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).

clearVec: void

Handles request to clear the data vector

input: double

Fills data into the Table.

spike: double

Fills spike timings into the Table. Signal has to exceed thresh

recvData: bad

Handles data sent back following request

process: void

Handles process call, updates internal time stamp.

reinit: void

Handles reinit call.
Shared message field

proc: void

Shared message for process and reinit
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

y: unsigned int,double

Value of table at specified index

1.87 TableBase

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

vec: vector<double>

vector with all table entries

outputValue: double

Output value holding current table entry or output of a calculation

size: unsigned int

size of table. Note that this is the number of x divisions +1since it must represent the largest value as well as thesmallest
Source message field

childMsg: int

Message to child Elements
Destination message field

parentMsg: int

Message from Parent Element(s)

group: void

Handle for grouping. Doesn't do anything.

linearTransform: double,double

Linearly scales and offsets data. Scale first, then offset.

xplot: string,string

Dumps table contents to xplot-format file. Argument 1 is filename, argument 2 is plotname

plainPlot: string

Dumps table contents to single-column ascii file. Uses scientific notation. Argument 1 is filename

loadCSV: string,int,int,char

Reads a single column from a CSV file. Arguments: filename, column#, starting row#, separator

loadXplot: string,string

Reads a single plot from an xplot file. Arguments: filename, plotnameWhen the file has 2 columns, the 2nd column is loaded.

loadXplotRange: string,string,unsigned int,unsigned int

Reads a single plot from an xplot file, and selects a subset of points from it. Arguments: filename, plotname, startindex, endindexUses C convention: startindex included, endindex not included.When the file has 2 columns, the 2nd column is loaded.

compareXplot: string,string,string

Reads a plot from an xplot file and compares with contents of TableBase.Result is put in 'output' field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: filename, plotname, comparison_{operationOperations}: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).

compareVec: vector<double>,string

Compares contents of TableBase with a vector of doubles.Result is put in 'output' field of table.If the comparison fails (e.g., due to zero entries), the return value is -1.Arguments: Other vector, comparison_{operationOperations}: rmsd (for RMSDifference), rmsr (RMSratio ), dotp (Dot product, not yet implemented).

clearVec: void

Handles request to clear the data vector
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

y: unsigned int,double

Value of table at specified index

1.88 TableEntry

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

value: double

Data value in this entry
Source message field

childMsg: int

Message to child Elements
Destination message field

parentMsg: int

Message from Parent Element(s)
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.89 Tick

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

dt: double

Timestep for this tick

localdt: double

Timestep for this tick
Source message field

childMsg: int

Message to child Elements

process0: PK8ProcInfo

Process for Tick 0

reinit0: PK8ProcInfo

Reinit for Tick 0

process1: PK8ProcInfo

Process for Tick 1

reinit1: PK8ProcInfo

Reinit for Tick 1

process2: PK8ProcInfo

Process for Tick 2

reinit2: PK8ProcInfo

Reinit for Tick 2

process3: PK8ProcInfo

Process for Tick 3

reinit3: PK8ProcInfo

Reinit for Tick 3

process4: PK8ProcInfo

Process for Tick 4

reinit4: PK8ProcInfo

Reinit for Tick 4

process5: PK8ProcInfo

Process for Tick 5

reinit5: PK8ProcInfo

Reinit for Tick 5

process6: PK8ProcInfo

Process for Tick 6

reinit6: PK8ProcInfo

Reinit for Tick 6

process7: PK8ProcInfo

Process for Tick 7

reinit7: PK8ProcInfo

Reinit for Tick 7

process8: PK8ProcInfo

Process for Tick 8

reinit8: PK8ProcInfo

Reinit for Tick 8

process9: PK8ProcInfo

Process for Tick 9

reinit9: PK8ProcInfo

Reinit for Tick 9
Destination message field

parentMsg: int

Message from Parent Element(s)
Shared message field

proc0: void

Shared proc/reinit message

proc1: void

Shared proc/reinit message

proc2: void

Shared proc/reinit message

proc3: void

Shared proc/reinit message

proc4: void

Shared proc/reinit message

proc5: void

Shared proc/reinit message

proc6: void

Shared proc/reinit message

proc7: void

Shared proc/reinit message

proc8: void

Shared proc/reinit message

proc9: void

Shared proc/reinit message
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.90 TriPanel

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

nPts: unsigned int

Number of points used by panel to specify geometry

nDims: unsigned int

Number of Dimensions used by panel to specify geometry

numNeighbors: unsigned int

Number of Neighbors of panel

shapeId: unsigned int

Identifier for shape type, as used by Smoldyn

coords: vector<double>

All the coordinates for the panel. X vector, then Y, then ZZ can be left out for 2-D panels.Z and Y can be left out for 1-D panels.
Source message field

childMsg: int

Message to child Elements

toNeighbor: void

Identifies neighbors of the current panel
Destination message field

parentMsg: int

Message from Parent Element(s)

neighbor: void

Handles incoming message from neighbor
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

x: unsigned int,double

x coordinate identified by index

y: unsigned int,double

y coordinate identified by index

z: unsigned int,double

z coordinate identified by index

1.91 VectorTable

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

xdivs: unsigned int

Number of divisions.

xmin: double

Minimum value in table.

xmax: double

Maximum value in table.

invdx: double

Maximum value in table.

table: vector<double>

The lookup table.
Source message field

childMsg: int

Message to child Elements
Destination message field

parentMsg: int

Message from Parent Element(s)
Shared message field
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

lookupvalue: double,double

Lookup function that performs interpolation to return a value.

lookupindex: unsigned int,double

Lookup function that returns value by index.

1.92 ZombieBufPool

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

n: double

Number of molecules in pool

nInit: double

Initial value of number of molecules in pool

diffConst: double

Diffusion constant of molecule

conc: double

Concentration of molecules in this pool

concInit: double

Initial value of molecular concentration in pool

size: double

Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1

speciesId: unsigned int

Species identifier for this mol pool. Eventually link to ontology.
Source message field

childMsg: int

Message to child Elements

nOut: double

Sends out # of molecules in pool on each timestep

requestMolWt: void

Requests Species object for mol wt

requestSize: double

Requests Size of pool from matching mesh entry
Destination message field

parentMsg: int

Message from Parent Element(s)

group: void

Handle for grouping. Doesn't do anything.

reacDest: double,double

Handles reaction input

process: void

Handles process call

reinit: void

Handles reinit call

handleMolWt: double

Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.

remesh: double,unsigned int,unsigned int,vector<unsigned int>,vector<double>

Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes
Shared message field

reac: void

Connects to reaction

proc: void

Shared message for process and reinit

species: void

Shared message for connecting to species objects

mesh: void

Shared message for dealing with mesh operations
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.93 ZombieCaConc

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

Ca: double

Calcium concentration.

CaBasal: double

Basal Calcium concentration.

Ca_base: double

Basal Calcium concentration, synonym for CaBasal

tau: double

Settling time for Ca concentration

B: double

Volume scaling factor

thick: double

Thickness of Ca shell.

ceiling: double

Ceiling value for Ca concentration. If Ca > ceiling, Ca = ceiling. If ceiling <= 0.0, there is no upper limit on Ca concentration value.

floor: double

Floor value for Ca concentration. If Ca < floor, Ca = floor
Source message field

childMsg: int

Message to child Elements

concOut: double

Concentration of Ca in pool
Destination message field

parentMsg: int

Message from Parent Element(s)

process: void

Handles process call

reinit: void

Handles reinit call

current: double

Calcium Ion current, due to be converted to conc.

currentFraction: double,double

Fraction of total Ion current, that is carried by Ca2+.

increase: double

Any input current that increases the concentration.

decrease: double

Any input current that decreases the concentration.

basal: double

Synonym for assignment of basal conc.
Shared message field

proc: void

Shared message to receive Process message from scheduler
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.94 ZombieCompartment

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

Vm: double

membrane potential

Cm: double

Membrane capacitance

Em: double

Resting membrane potential

Im: double

Current going through membrane

inject: double

Current injection to deliver into compartment

initVm: double

Initial value for membrane potential

Rm: double

Membrane resistance

Ra: double

Axial resistance of compartment

diameter: double

Diameter of compartment

length: double

Length of compartment

x0: double

X coordinate of start of compartment

y0: double

Y coordinate of start of compartment

z0: double

Z coordinate of start of compartment

x: double

x coordinate of end of compartment

y: double

y coordinate of end of compartment

z: double

z coordinate of end of compartment
Source message field

childMsg: int

Message to child Elements

VmOut: double

Sends out Vm value of compartment on each timestep

axialOut: double

Sends out Vm value of compartment to adjacent compartments,on each timestep

raxialOut: double,double

Sends out Raxial information on each timestep, fields are Ra and Vm
Destination message field

parentMsg: int

Message from Parent Element(s)

injectMsg: double

The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the 'inject' field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current

randInject: double,double

Sends a random injection current to the compartment. Must beupdated each timestep.Arguments to randInject are probability and current.

injectMsg: double

The injectMsg corresponds to the INJECT message in the GENESIS compartment. Unlike the 'inject' field, any value assigned by handleInject applies only for a single timestep.So it needs to be updated every dt for a steady (or varying)injection current

cable: void

Message for organizing compartments into groups, calledcables. Doesn't do anything.

process: void

Handles 'process' call

reinit: void

Handles 'reinit' call

initProc: void

Handles Process call for the 'init' phase of the Compartment calculations. These occur as a separate Tick cycle from the regular proc cycle, and should be called before the proc msg.

initReinit: void

Handles Reinit call for the 'init' phase of the Compartment calculations.

handleChannel: double,double

Handles conductance and Reversal potential arguments from Channel

handleRaxial: double,double

Handles Raxial info: arguments are Ra and Vm.

handleAxial: double

Handles Axial information. Argument is just Vm.
Shared message field

proc: void

This is a shared message to receive Process messages from the scheduler objects. The Process should be called second in each clock tick, after the Init message.The first entry in the shared msg is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.

init: void

This is a shared message to receive Init messages from the scheduler objects. Its job is to separate the compartmental calculations from the message passing. It doesn't really need to be shared, as it does not use the reinit part, but the scheduler objects expect this form of message for all scheduled output. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt and so on. The second entry is a dummy MsgDest for the Reinit operation. It also uses ProcInfo.

channel: void

This is a shared message from a compartment to channels. The first entry is a MsgDest for the info coming from the channel. It expects Gk and Ek from the channel as args. The second entry is a MsgSrc sending Vm

axial: void

This is a shared message between asymmetric compartments. axial messages (this kind) connect up to raxial messages (defined below). The soma should use raxial messages to connect to the axial message of all the immediately adjacent dendritic compartments.This puts the (low) somatic resistance in series with these dendrites. Dendrites should then use raxial messages toconnect on to more distal dendrites. In other words, raxial messages should face outward from the soma. The first entry is a MsgSrc sending Vm to the axialFuncof the target compartment. The second entry is a MsgDest for the info coming from the other compt. It expects Ra and Vm from the other compt as args. Note that the message is named after the source type.

raxial: void

This is a raxial shared message between asymmetric compartments. The first entry is a MsgDest for the info coming from the other compt. It expects Vm from the other compt as an arg. The second is a MsgSrc sending Ra and Vm to the raxialFunc of the target compartment.
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.95 ZombieEnz

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

Km: double

Michaelis-Menten constant in SI conc units (milliMolar)

numKm: double

Michaelis-Menten constant in number units, volume dependent

kcat: double

Forward rate constant for enzyme, units 1/sec

numSubstrates: unsigned int

Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself

k1: double

Forward reaction from enz + sub to complex

k2: double

Reverse reaction from complex to enz + sub

k3: double

Forward rate constant from complex to product + enz

ratio: double

Ratio of k2/k3

concK1: double

K1 expressed in concentration (1/millimolar.sec) units
Source message field

childMsg: int

Message to child Elements

toSub: double,double

Sends out increment of molecules on product each timestep

toPrd: double,double

Sends out increment of molecules on product each timestep

toEnz: double,double

Sends out increment of molecules on product each timestep

toCplx: double,double

Sends out increment of molecules on product each timestep
Destination message field

parentMsg: int

Message from Parent Element(s)

enzDest: double

Handles # of molecules of Enzyme

subDest: double

Handles # of molecules of substrate

prdDest: double

Handles # of molecules of product. Dummy.

process: void

Handles process call

reinit: void

Handles reinit call

remesh: void

Tells the MMEnz to recompute its numKm after remeshing

enzDest: double

Handles # of molecules of Enzyme

cplxDest: double

Handles # of molecules of enz-sub complex
Shared message field

sub: void

Connects to substrate molecule

prd: void

Connects to product molecule

proc: void

Shared message for process and reinit

enz: void

Connects to enzyme pool

cplx: void

Connects to enz-sub complex pool
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.96 ZombieFuncPool

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

n: double

Number of molecules in pool

nInit: double

Initial value of number of molecules in pool

diffConst: double

Diffusion constant of molecule

conc: double

Concentration of molecules in this pool

concInit: double

Initial value of molecular concentration in pool

size: double

Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1

speciesId: unsigned int

Species identifier for this mol pool. Eventually link to ontology.
Source message field

childMsg: int

Message to child Elements

nOut: double

Sends out # of molecules in pool on each timestep

requestMolWt: void

Requests Species object for mol wt

requestSize: double

Requests Size of pool from matching mesh entry
Destination message field

parentMsg: int

Message from Parent Element(s)

group: void

Handle for grouping. Doesn't do anything.

reacDest: double,double

Handles reaction input

process: void

Handles process call

reinit: void

Handles reinit call

handleMolWt: double

Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.

remesh: double,unsigned int,unsigned int,vector<unsigned int>,vector<double>

Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes

input: double

Handles input to control value of n_
Shared message field

reac: void

Connects to reaction

proc: void

Shared message for process and reinit

species: void

Shared message for connecting to species objects

mesh: void

Shared message for dealing with mesh operations
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.97 ZombieHHChannel

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

Gbar: double

Maximal channel conductance

Ek: double

Reversal potential of channel

Gk: double

Channel conductance variable

Ik: double

Channel current variable

Xpower: double

Power for X gate

Ypower: double

Power for Y gate

Zpower: double

Power for Z gate

instant: int

Bitmapped flag: bit 0 = Xgate, bit 1 = Ygate, bit 2 = ZgateWhen true, specifies that the lookup table value should beused directly as the state of the channel, rather than usedas a rate term for numerical integration for the state

X: double

State variable for X gate

Y: double

State variable for Y gate

Z: double

State variable for Y gate

useConcentration: int

Flag: when true, use concentration message rather than Vm tocontrol Z gate
Source message field

childMsg: int

Message to child Elements

channelOut: double,double

Sends channel variables Gk and Ek to compartment

permeability: double

Conductance term going out to GHK object

IkOut: double

Channel current. This message typically goes to concenobjects that keep track of ion concentration.
Destination message field

parentMsg: int

Message from Parent Element(s)

Vm: double

Handles Vm message coming in from compartment

Vm: double

Handles Vm message coming in from compartment

process: void

Handles process call

reinit: void

Handles reinit call

concen: double

Incoming message from Concen object to specific conc to usein the Z gate calculations

createGate: string

Function to create specified gate.Argument: Gate type [X Y Z]
Shared message field

channel: void

This is a shared message to couple channel to compartment. The first entry is a MsgSrc to send Gk and Ek to the compartment The second entry is a MsgDest for Vm from the compartment.

ghk: void

Message to Goldman-Hodgkin-Katz object

proc: void

This is a shared message to receive Process message from thescheduler. The first entry is a MsgDest for the Process operation. It has a single argument, ProcInfo, which holds lots of information about current time, thread, dt andso on. The second entry is a MsgDest for the Reinit operation. It also uses ProcInfo.
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.98 ZombieMMenz

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

Km: double

Michaelis-Menten constant in SI conc units (milliMolar)

numKm: double

Michaelis-Menten constant in number units, volume dependent

kcat: double

Forward rate constant for enzyme, units 1/sec

numSubstrates: unsigned int

Number of substrates in this MM reaction. Usually 1.Does not include the enzyme itself
Source message field

childMsg: int

Message to child Elements

toSub: double,double

Sends out increment of molecules on product each timestep

toPrd: double,double

Sends out increment of molecules on product each timestep
Destination message field

parentMsg: int

Message from Parent Element(s)

enzDest: double

Handles # of molecules of Enzyme

subDest: double

Handles # of molecules of substrate

prdDest: double

Handles # of molecules of product. Dummy.

process: void

Handles process call

reinit: void

Handles reinit call

remesh: void

Tells the MMEnz to recompute its numKm after remeshing
Shared message field

sub: void

Connects to substrate molecule

prd: void

Connects to product molecule

proc: void

Shared message for process and reinit
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.99 ZombiePool

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

n: double

Number of molecules in pool

nInit: double

Initial value of number of molecules in pool

diffConst: double

Diffusion constant of molecule

conc: double

Concentration of molecules in this pool

concInit: double

Initial value of molecular concentration in pool

size: double

Size of compartment. Units are SI. Utility field, the actual size info is stored on a volume mesh entry in the parent compartment.This is hooked up by a message. If the message isn'tavailable size is just taken as 1

speciesId: unsigned int

Species identifier for this mol pool. Eventually link to ontology.
Source message field

childMsg: int

Message to child Elements

nOut: double

Sends out # of molecules in pool on each timestep

requestMolWt: void

Requests Species object for mol wt

requestSize: double

Requests Size of pool from matching mesh entry
Destination message field

parentMsg: int

Message from Parent Element(s)

group: void

Handle for grouping. Doesn't do anything.

reacDest: double,double

Handles reaction input

process: void

Handles process call

reinit: void

Handles reinit call

handleMolWt: double

Separate finfo to assign molWt, and consequently diffusion const.Should only be used in SharedMsg with species.

remesh: double,unsigned int,unsigned int,vector<unsigned int>,vector<double>

Handle commands to remesh the pool. This may involve changing the number of pool entries, as well as changing their volumes
Shared message field

reac: void

Connects to reaction

proc: void

Shared message for process and reinit

species: void

Shared message for connecting to species objects

mesh: void

Shared message for dealing with mesh operations
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.100 ZombieReac

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

kf: double

Forward rate constant, in # units

kb: double

Reverse rate constant, in # units

Kf: double

Forward rate constant, in concentration units

Kb: double

Reverse rate constant, in concentration units

numSubstrates: unsigned int

Number of substrates of reaction

numProducts: unsigned int

Number of products of reaction
Source message field

childMsg: int

Message to child Elements

toSub: double,double

Sends out increment of molecules on product each timestep

toPrd: double,double

Sends out increment of molecules on product each timestep
Destination message field

parentMsg: int

Message from Parent Element(s)

subDest: double

Handles # of molecules of substrate

prdDest: double

Handles # of molecules of product

process: void

Handles process call

reinit: void

Handles reinit call

remesh: void

Tells the reac to recompute its numRates, as remeshing has happened
Shared message field

sub: void

Connects to substrate pool

prd: void

Connects to substrate pool

proc: void

Shared message for process and reinit
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.101 ZombieSumFunc

Value field

this: Neutral

Access function for entire object

name: string

Name of object

me: ObjId

ObjId for current object

parent: ObjId

Parent ObjId for current object

children: vector<Id>

vector of ObjIds listing all children of current object

path: string

text path for object

class: string

Class Name of object

linearSize: unsigned int

# of entries on Element: product of all dimensions.Note that on a FieldElement this includes field entries.If field entries form a ragged array, then the linearSize may begreater than the actual number of allocated entries, since thelastDimension is at least as big as the largest ragged array.

objectDimensions: vector<unsigned int>

Array Dimensions of object on the Element.This includes the lastDimension (field dimension) if present.

lastDimension: unsigned int

Max size of the last dimension of the object.In the case of regular objects, resizing this value resizesthe last dimensionIn the case of ragged arrays (such as synapses), resizing thisvalue resizes the upper limit of the last dimension,but cannot make it smaller than the biggest ragged array size.Normally is only assigned from Shell::doSyncDataHandler.

localNumField: unsigned int

For a FieldElement: number of entries of self on current nodeFor a regular Element: zero.

pathIndices: vector< vector<unsigned int> >

Indices of the entire path hierarchy leading up to this Object.

msgOut: vector<ObjId>

Messages going out from this Element

msgIn: vector<ObjId>

Messages coming in to this Element

result: double

outcome of summation
Source message field

childMsg: int

Message to child Elements

output: double

Sends out sum on each timestep
Destination message field

parentMsg: int

Message from Parent Element(s)

input: double

Handles input values

process: void

Handles process call

reinit: void

Handles reinit call
Shared message field

proc: void

Shared message for process and reinit
Lookup field

neighbours: string,vector<Id>

Ids of Elements connected this Element on specified field.

1.102 testSched

Value field
Source message field
Destination message field

process: void

handles process call
Shared message field
Lookup field

2 MOOSE Functions

2.1 ce

Set the current working element. 'ce' is an alias of this function

2.2 connect

connect(src, src_field, dest, dest_field, message_type) -> bool

Create a message between `src_field` on `src` object to `dest_field` on `dest` object.

Parameters

src : element the source object src_field : str the source field name. Fields listed under `srcFinfo` and `sharedFinfo` qualify for this. dest : element the destination object. dest_field : str the destination field name. Fields listed under `destFinfo` and `sharedFinfo` qualify for this. message_type : str (optional) Type of the message. Can be `Single`, `OneToOne`, `OneToAll`. If not specified, it defaults to `Single`.

Returns

element of the message-manager for the newly created message.

Example

Connect the output of a pulse generator to the input of a spike generator:

>>> pulsegen = moose.PulseGen('pulsegen') >>> spikegen = moose.SpikeGen('spikegen') >>> moose.connect(pulsegen, 'outputOut', spikegen, 'Vm') 1

2.3 copy

copy(src, dest, name, n, toGlobal, copyExtMsg) -> bool Make copies of a moose object. Parameters

src : ematrix, element or str source object. dest : ematrix, element or str Destination object to copy into. name : str Name of the new object. If omitted, name of the original will be used. n : int Number of copies to make. toGlobal: int Relevant for parallel environments only. If false, the copies will reside on local node, otherwise all nodes get the copies. copyExtMsg: int If true, messages to/from external objects are also copied.

Returns

ematrix of the copied object

2.4 delete

moose.delete(id)

Delete the underlying moose object. This does not delete any of the Python objects referring to this ematrix but does invalidate them. Any attempt to access them will raise a ValueError.

Parameters

id : ematrix ematrix of the object to be deleted.

2.5 element

moose.element(arg) -> moose object

Convert a path or an object to the appropriate builtin moose class instance Parameters

arg: str or ematrix or moose object path of the moose element to be converted or another element (possibly available as a superclass instance).

Returns An element of the moose builtin class the specified object belongs to.

2.6 exists

True if there is an object with specified path.

2.7 getCwe

Get the current working element. 'pwe' is an alias of this function.

2.8 getField

getField(element, field, fieldtype) – Get specified field of specified type from object ematrix.

2.9 getFieldDict

getFieldDict(className, finfoType) -> dict

Get dictionary of field names and types for specified class. Parameters

className : str MOOSE class to find the fields of. finfoType : str (optional) Finfo type of the fields to find. If empty or not specified, all fields will be retrieved. note: This behaviour is different from `getFieldNames` where only `valueFinfo`s are returned when `finfoType` remains unspecified.

Example

List all the source fields on class Neutral: >>> moose.getFieldDict('Neutral', 'srcFinfo') {'childMsg': 'int'}

2.10 getFieldNames

getFieldNames(className, finfoType='valueFinfo') -> tuple

Get a tuple containing the name of all the fields of `finfoType` kind.

Parameters

className : string Name of the class to look up. finfoType : string The kind of field (`valueFinfo`, `srcFinfo`, `destFinfo`, `lookupFinfo`, `fieldElementFinfo`.).

2.11 isRunning

True if the simulation is currently running.

2.12 loadModel

loadModel(filename, modelpath, solverclass) -> moose.ematrix

Load model from a file to a specified path.

Parameters

filename : str model description file. modelpath : str moose path for the top level element of the model to be created. solverclass : str (optional) solver type to be used for simulating the model.

Returns

ematrix instance refering to the loaded model container.

2.13 move

Move a ematrix object to a destination.

2.14 quit

Finalize MOOSE threads and quit MOOSE. This is made available for debugging purpose only. It will automatically get called when moose module is unloaded. End user should not use this function.

2.15 reinit

reinit() -> None

Reinitialize simulation.

This function (re)initializes moose simulation. It must be called before you start the simulation (see moose.start). If you want to continue simulation after you have called moose.reinit() and moose.start(), you must NOT call moose.reinit() again. Calling moose.reinit() again will take the system back to initial setting (like clear out all data recording tables, set state variables to their initial values, etc.

2.16 saveModel

saveModel(source, fileame)

Save model rooted at `source` to file `filename`.

Parameters

source: ematrix or element or str root of the model tree

filename: str destination file to save the model in.

Returns

None

2.17 seed

moose.seed(seedvalue) -> None

Reseed MOOSE random number generator.

Parameters

seed: int Optional value to use for seeding. If 0, a random seed is automatically created using the current system time and other information. If not specified, it defaults to 0.

2.18 setClock

Set the dt of a clock.

2.19 setCwe

Set the current working element. 'ce' is an alias of this function

2.20 start

start(t) -> None

Run simulation for `t` time. Advances the simulator clock by `t` time.

After setting up a simulation, YOU MUST CALL MOOSE.REINIT() before CALLING MOOSE.START() TO EXECUTE THE SIMULATION. Otherwise, the simulator behaviour will be undefined. Once moose.reinit() has been called, you can call moose.start(t) as many time as you like. This will continue the simulation from the last state for `t` time.

Parameters

t : float duration of simulation.

Returns

None

2.21 stop

Stop simulation

2.22 useClock

Schedule objects on a specified clock

2.23 wildcardFind

moose.wildcardFind(expression) -> tuple of ematrices.

Find an object by wildcard.

Parameters

expression: str MOOSE allows wildcard expressions of the form {PATH}/{WILDCARD}[{CONDITION}] where {PATH} is valid path in the element tree. {WILDCARD} can be `#` or `##`. `#` causes the search to be restricted to the children of the element specified by {PATH}. `##` makes the search to recursively go through all the descendants of the {PATH} element. {CONDITION} can be TYPE={CLASSNAME} : an element satisfies this condition if it is of class {CLASSNAME}. ISA={CLASSNAME} : alias for TYPE={CLASSNAME} CLASS={CLASSNAME} : alias for TYPE={CLASSNAME} FIELD({FIELDNAME}){OPERATOR}{VALUE} : compare field {FIELDNAME} with {VALUE} by {OPERATOR} where {OPERATOR} is a comparison operator (=, !=, >, <, >=, <=). For example, /mymodel/##[FIELD(Vm)>=-65] will return a list of all the objects under /mymodel whose Vm field is >= -65.

2.24 writeSBML

Export biochemical model to an SBML file.

2.25 doc

Display the documentation for class or field in a class.

Parameters

arg: str or moose class or instance of melement or instance of ematrix

argument can be a string specifying a moose class name and a field name separated by a dot. e.g., 'Neutral.name'. Prepending `moose.` is allowed. Thus moose.doc('moose.Neutral.name') is equivalent to the above.

argument can also be string specifying just a moose class name or a moose class or a moose object (instance of melement or ematrix or there subclasses). In that case, the builtin documentation for the corresponding moose class is displayed.

paged: bool

Whether to display the docs via builtin pager or print and exit. If not specified, it defaults to False and moose.doc(xyz) will print help on xyz and return control to command line.

2.26 getfielddoc

Get the documentation for field specified by tokens.

tokens should be a two element list/tuple where first element is a MOOSE class name and second is the field name.

2.27 getmoosedoc

Retrieve MOOSE builtin documentation for tokens.

tokens is a list or tuple containing: (classname, [fieldname])

2.28 le

List elements.

Parameters

el: str/melement/ematrix/None The element or the path under which to look. If `None`, children of current working element are displayed.

2.29 listmsg

Return a list containing the incoming and outgoing messages of the given object.

2.30 pwe

Print present working element. Convenience function for GENESIS users.

2.31 showfield

Show the fields of the element, their data types and values in human readable format. Convenience function for GENESIS users.

Parameters:

elem: str/melement instance Element or path of an existing element.

field: str Field to be displayed. If '*', all fields are displayed.

showtype: bool If True show the data type of each field.

2.32 showfields

Convenience function. Should be deprecated if nobody uses it.

2.33 showmsg

Prints the incoming and outgoing messages of the given object.

2.34 syncDataHandler

Synchronize data handlers for target.

Parameter: target – target element or path or ematrix.

Documentation for all MOOSE classes and functions

Table of Contents

1 MOOSE Classes

1.1 Annotator

1.2 Arith

1.3 Boundary

1.4 BufPool

1.5 CaConc

1.6 ChanBase

1.7 ChemMesh

1.8 Cinfo

1.9 Clock

1.10 Compartment

1.11 CplxEnzBase

1.12 CubeMesh

1.13 CylMesh

1.14 CylPanel

1.15 DiagonalMsg

1.16 DiffAmp

1.17 DiskPanel

1.18 Enz

1.19 EnzBase

1.20 Finfo

1.21 FuncPool

1.22 GHK

1.23 Geometry

1.24 Group

1.25 GslIntegrator

1.26 GssaStoich

1.27 HDF5DataWriter

1.28 HDF5WriterBase

1.29 HHChannel

1.30 HHChannel2D

1.31 HHGate

1.32 HHGate2D

1.33 HSolve

1.34 HemispherePanel

1.35 IntFire

1.36 Interpol2D

1.37 IzhikevichNrn

1.38 LeakyIaF

1.39 MMenz

1.40 MarkovChannel

1.41 MarkovGslSolver

1.42 MarkovRateTable

1.43 MarkovSolver

1.44 MarkovSolverBase

1.45 MathFunc

1.46 Mdouble

1.47 MeshEntry

1.48 MgBlock

1.49 Msg

1.50 Mstring

1.51 NMDAChan

1.52 Nernst

1.53 NeuroMesh

1.54 Neuron

1.55 Neutral

1.56 OneToAllMsg

1.57 OneToOneMsg

1.58 PIDController

1.59 Panel

1.60 Pool

1.61 PoolBase

1.62 Port

1.63 PulseGen

1.64 RC

1.65 Reac

1.66 ReacBase

1.67 RectPanel

1.68 ReduceMsg

1.69 Shell

1.70 SimManager

1.71 SingleMsg

1.72 SparseMsg

1.73 Species

1.74 SpherePanel

1.75 SpikeGen

1.76 Stats

1.77 StimulusTable