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Contents
# 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).
Version data entries
9 entries across 9 versions & 1 rubygems