y_petri 2.1.24 → 2.1.25

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data/README.md CHANGED
@@ -55,13 +55,11 @@ We can now play the _token_ _game_:
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  ## Advanced usage
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  A Petri net is mostly used as a wiring diagram of some real-world system. Such
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- Petri net can then be used to generate (implicitly or explicitly) a more specific
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- simulation of that real-world system. This is represented by `YPetri::Simulation`
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- class. If a Petri net with only _timed_ transitions is considered, it can then
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- be used to generate (implicitly or explicitly) a system of ordinary differential
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- equations (ODE). A Simulation class instance generated from such Petri net can
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- then be used to eg. solve the initial value problem by numeric integration of the
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- ODE system using one of the available numerical methods:
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+ Petri net can then be used to generate its simulation -- represented by
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+ `YPetri::Simulation` class. A Petri net consisting of only _timed_ transitions
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+ can be used to generate (implicitly or explicitly) a system of ordinary
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+ differential equations (ODE). A simulation generated from such Petri net can
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+ then be used to solve (eg.) the initial value problem by numeric methods:
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  ```ruby
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  # Start a fresh irb session!
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  require 'y_petri'
@@ -19,17 +19,17 @@ module YPetri::Core::Timed::Gillespie
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  # Makes a stochastic number of Gillespie steps necessary to span the period Δt.
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  #
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  def step! Δt=simulation.step
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- current_time = simulation.time
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- target_time = current_time + Δt
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- @gillespie_time = current_time
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+ @gillespie_time = curr_time = simulation.time
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+ target_time = curr_time + Δt
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  propensities = propensity_vector_TS
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  puts "Propensity vector TS is:"
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  Kernel::p propensities
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- gillespie_update_next_firing_time( propensities )
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- until ( @gillespie_next_firing_time > target_time )
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+ update_next_gillespie_time( propensities )
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+ until ( @next_gillespie_time > target_time )
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  gillespie_step!
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+ note_state_change
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  propensities = propensity_vector_TS
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- gillespie_update_next_firing_time( propensities )
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+ update_next_gillespie_time( propensities )
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  end
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  end
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@@ -41,8 +41,8 @@ module YPetri::Core::Timed::Gillespie
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  # This method updates next firing time given propensities.
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  #
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- def gillespie_update_next_firing_time( propensities )
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- @gillespie_next_firing_time =
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+ def update_next_gillespie_time( propensities )
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+ @next_gillespie_time =
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  @gillespie_time + gillespie_delta_time( propensities )
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  end
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@@ -1,4 +1,4 @@
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  module YPetri
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- VERSION = "2.1.24"
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+ VERSION = "2.1.25"
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  DEBUG = false
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  end
metadata CHANGED
@@ -1,14 +1,14 @@
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  --- !ruby/object:Gem::Specification
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  name: y_petri
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  version: !ruby/object:Gem::Version
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- version: 2.1.24
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+ version: 2.1.25
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  platform: ruby
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  authors:
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  - boris
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  autorequire:
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  bindir: bin
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  cert_chain: []
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- date: 2013-08-19 00:00:00.000000000 Z
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+ date: 2013-08-20 00:00:00.000000000 Z
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  dependencies:
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  - !ruby/object:Gem::Dependency
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  name: y_support