# encoding: utf-8

# Timed simulation core.
# 
module YPetri::Core::Timed
  require_relative 'timed/methods'
  ★ Methods

  # Makes a single step by Δt.
  # 
  def step! Δt=simulation.step
    increment_marking_vector Δ( Δt )
    simulation.increment_time! Δt
    simulation.recorder.alert
  end

  # Gradient for free places.
  # 
  def gradient
    gradient_Ts + gradient_TS
  end
  alias ∇ gradient

  # Gradient contribution by Ts transitions.
  # 
  def gradient_Ts
    simulation.Ts_gradient_closure.call
  end

  # Gradient contribution by TS transitions.
  # 
  def gradient_TS
    ( simulation.TS_stoichiometry_matrix * flux_vector_TS )
  end

  # Flux vector. The caller asserts that all the timed transitions are
  # stoichiometric, or error.
  # 
  def flux_vector
    msg = "#flux_vector method only applies to the timed simulations with " +
      "no Ts transitions. Try #flux_vector_TS instead!"
    fail msg unless Ts_transitions().empty?
    simulation.TS_rate_closure.call
  end

  # Flux vector of TS transitions.
  # 
  def flux_vector_TS
    simulation.TS_rate_closure.call
  end
  alias propensity_vector_TS flux_vector_TS
end # module YPetri::Core::Timed

# In general, it is not required that all net nodes are simulated with the
# same method. Practically, ODE systems have many good simulation methods
# available.
#
# (1) ᴍ(t) = ϝ f(ᴍ, t).dt, where f(ᴍ, t) is a known function.
#
# Many of these methods depend on the Jacobian, but that may not be available
# for some places. Therefore, the places, whose marking defines the system
# state, are divided into two categories: "A" (accelerated), for which as
# common Jacobian can be found, and "E" places, where "E" can stand either for
# "External" or "Euler".
#
# If we apply the definition of "causal orientation" on A and E places, then it
# can be said, that only the transitions causally oriented towards "A" places
# are allowed for compliance with the equation (1).