Clock

class Clock

Every object scheduled for operations in MOOSE is connected to oneof the 'Tick' entries on the Clock. The Clock manages 32 'Ticks', each of which has its own dt,which is an integral multiple of the clock baseDt_. On every clock step the ticks are examined to see which of themis due for updating. When a tick is updated, the 'process' call of all the objects scheduled on that tick is called. Order of execution: If a subset of ticks are scheduled for execution at a given timestep, then they will be executed in numerical order, lowest tick first and highest last. There is no guarantee of execution order for objects within a clock tick. The clock provides default scheduling for all objects which can be accessed using Clock::lookupDefaultTick( className ). Specific items of note are that the output/file dump objects are second-last, and the postmaster is last on the order of Ticks. The clock also starts up with some default timesteps for each of these ticks, and this can be overridden using the shell command setClock, or by directly assigning tickStep values on the clock object. Which objects use which tick? As a rule of thumb, try this: Electrical/compartmental model calculations: Ticks 0-7 Tables and output objects for electrical output: Tick 8 Diffusion solver: Tick 10 Chemical/compartmental model calculations: Ticks 11-17 Tables and output objects for chemical output: Tick 18 Unassigned: Ticks 20-29 Special: 30-31 Data output is a bit special, since you may want to store data at different rates for electrical and chemical processes in the same model. Here you will have to specifically assign distinct clock ticks for the tables/fileIO objects handling output at different time-resolutions. Typically one uses tick 8 and 18. Here are the detailed mappings of class to tick. | Class Tick dt | DiffAmp 0 50e-6 | Interpol 0 50e-6 | PIDController 0 50e-6 | PulseGen 0 50e-6 | StimulusTable 0 50e-6 | testSched 0 50e-6 | VClamp 0 50e-6 | SynHandlerBase 1 50e-6 | SimpleSynHandler 1 50e-6 | STDPSynHandler 1 50e-6

GraupnerBrunel2012CaPlasticitySynHandler 1 50e-6 SeqSynHandler 1 50e-6

CaConc 1 50e-6 CaConcBase 1 50e-6 DifShell 1 50e-6 MgBlock 1 50e-6 Nernst 1 50e-6 RandSpike 1 50e-6 ChanBase 2 50e-6 IntFire 2 50e-6 IntFireBase 2 50e-6 LIF 2 50e-6 QIF 2 50e-6 ExIF 2 50e-6 AdExIF 2 50e-6 AdThreshIF 2 50e-6 IzhIF 2 50e-6 IzhikevichNrn 2 50e-6 SynChan 2 50e-6 NMDAChan 2 50e-6 GapJunction 2 50e-6 HHChannel 2 50e-6 HHChannel2D 2 50e-6 Leakage 2 50e-6 MarkovChannel 2 50e-6 MarkovGslSolver 2 50e-6 MarkovRateTable 2 50e-6 MarkovSolver 2 50e-6 MarkovSolverBase 2 50e-6 RC 2 50e-6 Compartment (init) 3 50e-6 CompartmentBase (init ) 3 50e-6 SymCompartment (init) 3 50e-6 Compartment 4 50e-6 CompartmentBase 4 50e-6 SymCompartment 4 50e-6 SpikeGen 5 50e-6 HSolve 6 50e-6 SpikeStats 7 50e-6 Table 8 0.1e-3 TimeTable 8 0.1e-3 Dsolve 10 0.01 Adaptor 11 0.1 Func 12 0.1 Function 12 0.1 Arith 12 0.1 BufPool 13 0.1 Pool 13 0.1 PoolBase 13 0.1 CplxEnzBase 14 0.1 Enz 14 0.1 EnzBase 14 0.1 MMenz 14 0.1 Reac 14 0.1 ReacBase 14 0.1 Gsolve (init) 15 0.1 Ksolve (init) 15 0.1 Gsolve 16 0.1 Ksolve 16 0.1 Stats 17 0.1 Table2 18 1 Streamer 19 10 HDF5DataWriter 30 1 HDF5WriterBase 30 1 NSDFWriter 30 1

PyRun 30 1

PostMaster 31 0.01

Note that the other classes are not scheduled at all.

clockControl

void (shared message field) Controls all scheduling aspects of Clock, usually from Shell

proc0

void (shared message field) Shared process/reinit message

proc1

void (shared message field) Shared process/reinit message

proc2

void (shared message field) Shared process/reinit message

proc3

void (shared message field) Shared process/reinit message

proc4

void (shared message field) Shared process/reinit message

proc5

void (shared message field) Shared process/reinit message

proc6

void (shared message field) Shared process/reinit message

proc7

void (shared message field) Shared process/reinit message

proc8

void (shared message field) Shared process/reinit message

proc9

void (shared message field) Shared process/reinit message

proc10

void (shared message field) Shared process/reinit message

proc11

void (shared message field) Shared process/reinit message

proc12

void (shared message field) Shared process/reinit message

proc13

void (shared message field) Shared process/reinit message

proc14

void (shared message field) Shared process/reinit message

proc15

void (shared message field) Shared process/reinit message

proc16

void (shared message field) Shared process/reinit message

proc17

void (shared message field) Shared process/reinit message

proc18

void (shared message field) Shared process/reinit message

proc19

void (shared message field) Shared process/reinit message

proc20

void (shared message field) Shared process/reinit message

proc21

void (shared message field) Shared process/reinit message

proc22

void (shared message field) Shared process/reinit message

proc23

void (shared message field) Shared process/reinit message

proc24

void (shared message field) Shared process/reinit message

proc25

void (shared message field) Shared process/reinit message

proc26

void (shared message field) Shared process/reinit message

proc27

void (shared message field) Shared process/reinit message

proc28

void (shared message field) Shared process/reinit message

proc29

void (shared message field) Shared process/reinit message

proc30

void (shared message field) Shared process/reinit message

proc31

void (shared message field) Shared process/reinit message

setBaseDt()

(destination message field) Assigns field value.

getBaseDt()

(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.

getRunTime()

(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.

getCurrentTime()

(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.

getNsteps()

(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.

getNumTicks()

(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.

getStride()

(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.

getCurrentStep()

(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.

getDts()

(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.

getIsRunning()

(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.

setTickStep()

(destination message field) Assigns field value.

getTickStep()

(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.

setTickDt()

(destination message field) Assigns field value.

getTickDt()

(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.

getDefaultTick()

(destination message field) Requests field value. The requesting Element must provide a handler for the returned value.

start()

(destination message field) Sets off the simulation for the specified duration

step()

(destination message field) Sets off the simulation for the specified # of steps. Here each step advances the simulation by the timestep of the smallest tick that is actually in use.

stop()

(destination message field) Halts the simulation, with option to restart seamlessly

reinit()

(destination message field) Zeroes out all ticks, starts at t = 0

finished

void (source message field) Signal for completion of run

process0

PK8ProcInfo (source message field) process for Tick 0

reinit0

PK8ProcInfo (source message field) reinit for Tick 0

process1

PK8ProcInfo (source message field) process for Tick 1

reinit1

PK8ProcInfo (source message field) reinit for Tick 1

process2

PK8ProcInfo (source message field) process for Tick 2

reinit2

PK8ProcInfo (source message field) reinit for Tick 2

process3

PK8ProcInfo (source message field) process for Tick 3

reinit3

PK8ProcInfo (source message field) reinit for Tick 3

process4

PK8ProcInfo (source message field) process for Tick 4

reinit4

PK8ProcInfo (source message field) reinit for Tick 4

process5

PK8ProcInfo (source message field) process for Tick 5

reinit5

PK8ProcInfo (source message field) reinit for Tick 5

process6

PK8ProcInfo (source message field) process for Tick 6

reinit6

PK8ProcInfo (source message field) reinit for Tick 6

process7

PK8ProcInfo (source message field) process for Tick 7

reinit7

PK8ProcInfo (source message field) reinit for Tick 7

process8

PK8ProcInfo (source message field) process for Tick 8

reinit8

PK8ProcInfo (source message field) reinit for Tick 8

process9

PK8ProcInfo (source message field) process for Tick 9

reinit9

PK8ProcInfo (source message field) reinit for Tick 9

process10

PK8ProcInfo (source message field) process for Tick 10

reinit10

PK8ProcInfo (source message field) reinit for Tick 10

process11

PK8ProcInfo (source message field) process for Tick 11

reinit11

PK8ProcInfo (source message field) reinit for Tick 11

process12

PK8ProcInfo (source message field) process for Tick 12

reinit12

PK8ProcInfo (source message field) reinit for Tick 12

process13

PK8ProcInfo (source message field) process for Tick 13

reinit13

PK8ProcInfo (source message field) reinit for Tick 13

process14

PK8ProcInfo (source message field) process for Tick 14

reinit14

PK8ProcInfo (source message field) reinit for Tick 14

process15

PK8ProcInfo (source message field) process for Tick 15

reinit15

PK8ProcInfo (source message field) reinit for Tick 15

process16

PK8ProcInfo (source message field) process for Tick 16

reinit16

PK8ProcInfo (source message field) reinit for Tick 16

process17

PK8ProcInfo (source message field) process for Tick 17

reinit17

PK8ProcInfo (source message field) reinit for Tick 17

process18

PK8ProcInfo (source message field) process for Tick 18

reinit18

PK8ProcInfo (source message field) reinit for Tick 18

process19

PK8ProcInfo (source message field) process for Tick 19

reinit19

PK8ProcInfo (source message field) reinit for Tick 19

process20

PK8ProcInfo (source message field) process for Tick 20

reinit20

PK8ProcInfo (source message field) reinit for Tick 20

process21

PK8ProcInfo (source message field) process for Tick 21

reinit21

PK8ProcInfo (source message field) reinit for Tick 21

process22

PK8ProcInfo (source message field) process for Tick 22

reinit22

PK8ProcInfo (source message field) reinit for Tick 22

process23

PK8ProcInfo (source message field) process for Tick 23

reinit23

PK8ProcInfo (source message field) reinit for Tick 23

process24

PK8ProcInfo (source message field) process for Tick 24

reinit24

PK8ProcInfo (source message field) reinit for Tick 24

process25

PK8ProcInfo (source message field) process for Tick 25

reinit25

PK8ProcInfo (source message field) reinit for Tick 25

process26

PK8ProcInfo (source message field) process for Tick 26

reinit26

PK8ProcInfo (source message field) reinit for Tick 26

process27

PK8ProcInfo (source message field) process for Tick 27

reinit27

PK8ProcInfo (source message field) reinit for Tick 27

process28

PK8ProcInfo (source message field) process for Tick 28

reinit28

PK8ProcInfo (source message field) reinit for Tick 28

process29

PK8ProcInfo (source message field) process for Tick 29

reinit29

PK8ProcInfo (source message field) reinit for Tick 29

process30

PK8ProcInfo (source message field) process for Tick 30

reinit30

PK8ProcInfo (source message field) reinit for Tick 30

process31

PK8ProcInfo (source message field) process for Tick 31

reinit31

PK8ProcInfo (source message field) reinit for Tick 31

baseDt

double (value field) Base timestep for simulation. This is the smallest dt out of all the clock ticks. By definition all other timesteps are integral multiples of this, and are rounded to ensure that this is the case .

runTime

double (value field) Duration to run the simulation

currentTime

double (value field) Current simulation time

nsteps

unsigned long (value field) Number of steps to advance the simulation, in units of the smallest timestep on the clock ticks

numTicks

unsigned int (value field) Number of clock ticks

stride

unsigned int (value field) Number by which the simulation advances the current step on each cycle. stride = smallest active timestep/smallest defined timestep.

currentStep

unsigned long (value field) Current simulation step

dts

vector<double> (value field) Utility function returning the dt (timestep) of all ticks.

isRunning

bool (value field) Utility function to report if simulation is in progress.

tickStep

unsigned int,unsigned int (lookup field) Step size of specified Tick, as integral multiple of dt_ A zero step size means that the Tick is inactive

tickDt

unsigned int,double (lookup field) Timestep dt of specified Tick. Always integral multiple of dt_. If you assign a non-integer multiple it will round off. A zero timestep means that the Tick is inactive

defaultTick

string,unsigned int (lookup field) Looks up the default Tick to use for the specified class. If no tick is assigned, as for classes without a process operation or zombie classes, the tick is ~0U. If nothing can be found returns 0 and emits a warning.