Class: YPetri::Transition

Inherits:
Object
  • Object
show all
Defined in:
lib/y_petri/transition.rb

Overview

  • Timed transitions have rate closure, whose result is to be multiplied by Δtime.

  • Timeless transitions have action closure, whose result does not need to be multiplied by time.

Summary: Having vs. not having rate distinguishes the need to multiply the closure result by Δ time.

Stoichiometricity

  • TS transitions – rate vector = rate * stoichiometry vector

  • tS transitions – action vector = action * stoichiometry vector

  • Ts transitions – rate vector = rate closure result

  • ts transitions – action vector = action closure result

Summary: stoichiometricity distinguishes the need to multiply the rate/action closure result by stoichiometry.

Assignment action

Assignment transitions (_*A*_ transitions) are special transitions, that replace the codomain marking rather than modifying it – they assign new marking to their codomain, like we are used to from spreadsheets. Technically, this behavior is easily achievable with normal ts transitions, so the existence of separate A transitions is just a convenience, not a new type of a transition in the mathematical sense.

Functional / functionless transitions

Other Petri net implementation often distinguies between “ordinary” (vanilla as per C. A. Petri) and functional transitions, whose operation is governed by a function. In YPetri, transitions are generally functional, but there remains a possibility of creating vanilla (functionless) transitions by not specifying any rate / action, while specifying the stoichiometry. Action closure as per C. A. Petri is automatically constructed for these.

Defined Under Namespace

Modules: Arcs, Cocking, ConstructionConvenience, Type_A, Type_T, Type_t, Types, UsableWithoutWorld

Constant Summary collapse

TYPES =
{
  T: "timed",
  t: "timeless",
  S: "stoichiometric",
  s: "non-stoichiometric",
  A: "assignment",
  a: "non-assignment",
  TS: "timed stoichiometric",
  tS: "timeless stoichiometric",
  Ts: "timed nonstoichiometric",
  ts: "timeless nonstoichiometric"
}

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(*args, &block) ⇒ Transition

Transition class represents many different kinds of Petri net transitions. It makes the constructor syntax a bit more polymorphic. The type of the transition to construct is mostly inferred from the constructor arguments.

Mandatorily, the constructor will always need a way to determine the domain (upstream arcs) and codomain (downstream arcs) of the transition. Also, the constructor must have a way to determine the transition's action. This is best explained by examples – let us have 3 places A, B, C, for whe we will create different kinds of transitions:

TS (timed stoichiometric)

Rate closure and stoichiometry has to be supplied. Rate closure arity should correspond to the domain size. Return arity should be 1 (to be multiplied by the stoichiometry vector, as in all other stoichiometric transitions).

Transition.new stoichiometry: { A: -1, B: 1 },
               rate: -> a { a * 0.5 }

Ts (timed nonstoichiometric)

Rate closure has to be supplied, whose arity should match the domain, and output arity codomain.

tS (timeless stoichiometric)

Stoichiometry has to be supplied, action closure is optional. If supplied, its return arity should be 1 (to be multiplied by the stoichiometry vector).

ts transitions (timeless nonstoichiometric)

Action closure is expected with return arity equal to the codomain size:

Transition.new upstream_arcs: [A, C], downstream_arcs: [A, B],
               action_closure: proc { |m, x|
                                      if x > 0 then [-(m / 2), (m / 2)]
                                      else [1, 0] end
                                    }

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# File 'lib/y_petri/transition.rb', line 165

def initialize *args, &block
  check_in_arguments *args, &block # the big job
  extend( if timed? then Type_T
          elsif assignment_action? then Type_A
          else Type_t end )
  inform_upstream_places         # that they have been connected
  inform_downstream_places       # that they have been connected
  uncock                         # initialize in uncocked state
end

Instance Attribute Details

#action_closureObject (readonly) Also known as: action

For rateless transition, action closure must be present. Action closure input arguments must correspond to the domain places, and for timed transitions, the first argument of the action closure must be Δtime.


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# File 'lib/y_petri/transition.rb', line 230

def action_closure
  @action_closure
end

#codomainObject (readonly) Also known as: codomain_arcs, codomain_places, downstream, downstream_arcs, downstream_places, action_arcs

Codomain, 'downstream arcs', or 'action arcs', is a collection of places, whose marking is directly changed by this transition's firing.


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# File 'lib/y_petri/transition.rb', line 188

def codomain
  @codomain
end

#domainObject (readonly) Also known as: domain_arcs, domain_places, upstream, upstream_arcs, upstream_places

Domain, or 'upstream arcs', is a collection of places, whose marking directly affects the transition's action.


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# File 'lib/y_petri/transition.rb', line 178

def domain
  @domain
end

#rate_closureObject (readonly) Also known as: rate, flux_closure, flux, propensity_closure, propensity

In YPetri, rate is a unifying term for both flux and propensity, both of which are treated as aliases of rate. The decision between discrete and continuous computation is a concern of the simulation. Rate closure arity should correspond to the transition's domain.


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# File 'lib/y_petri/transition.rb', line 219

def rate_closure
  @rate_closure
end

#stoichiometryObject (readonly)

Stoichiometry (implies that the transition is stoichiometric).


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# File 'lib/y_petri/transition.rb', line 198

def stoichiometry
  @stoichiometry
end

Instance Method Details

#place(id) ⇒ Object

# Conversion to a string. # def to_s

"#<Transition: %s>" %
  "#{'%s ' % name if name}(#{type})#{' id:%s' % object_id unless name}"

end


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# File 'lib/y_petri/transition.rb', line 280

def place id
  super rescue Place().instance( id )
end

#sObject

Stoichiometry as a hash of pairs: { codomain_place_name_symbol => stoichiometric_coefficient }


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# File 'lib/y_petri/transition.rb', line 210

def s
  stoichio.with_keys { |k| k.name || k.object_id }
end

#stoichioObject

Stoichiometry as a hash of pairs: { codomain_place_instance => stoichiometric_coefficient }


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# File 'lib/y_petri/transition.rb', line 203

def stoichio
  Hash[ codomain.zip( @stoichiometry ) ]
end

#transition(id) ⇒ Object


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# File 'lib/y_petri/transition.rb', line 284

def transition id
  super rescue Transition().instance( id )
end

#zero_actionObject

Zero action.


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# File 'lib/y_petri/transition.rb', line 235

def zero_action
  codomain.map { 0 }
end