A  
Antimajority [Rule] 
if sum_of_neighbours >= nb_neighbours then 0 else 1.

Array [Femtolib]  
Array_simulate_2d [Femtolib] 
One dimensionnal arrays that represent two dimensionnal data.

Asynchronous [Synchronism]  
Automaton [Rule.Shift]  
Automaton [Rule.Ising]  
Automaton [Rule.Rrpcs_2d]  
Automaton [Rule.Rrcs_2d]  
Automaton [Rule.Antimajority]  
Automaton [Rule.Majority]  
Automaton [Rule.Totalizing]  
Automaton [Rule.Cyclic]  
Automaton [Rule.Sandpile]  
Automaton [Rule.Parallel_2eca]  
Automaton [Rule.Eca]  
B  
Boolean_state [Rule.Templates]  
C  
Causal_states [Measure]  
Chi_square [Measure.Statistic] 
The chi square statistical test.

Cimula 
The main module, from where the whole process is launched.

Cluster_collection [Measure.Causal_states.Clustering] 
LIFO; Can be changed to
Stack (FIFO).

Clustering [Measure.Causal_states] 
Merge probability distributions.

Colors [Femtolib]  
Config_file [Femtolib] 
External library (part of the Cameleon project) to read and write configuration file,
included here to simplify distribution.

Cut_links [Topology.Meta]  
Cyclic [Rule] 
Cyclic Cellular Automata

D  
Density [Measure]  
Density_avg [Experiment] 
Computes the average density of unsynchronized states, same paper.

Density_vs_time [Experiment] 
Prints data for a density (of unsynchronized states) vs time plot, same paper.

E  
Eca [Rule] 
Elementary Cellular Automata

Experiment [Experiment.Density_avg]  
Experiment [Experiment.Density_vs_time]  
Experiment [Experiment.Synchronization]  
Experiment [Experiment.Op_cyclic_r1t2k4box]  
Experiment [Experiment.Lle]  
Experiment [Experiment.Stat_cmplx]  
Experiment [Experiment.States]  
Experiment 
Defines how to run a Cellular Automaton, what to measure and when to measure it.

Experiment_parameters [User_interface.Text]  
F  
Femtolib 
Implements reusable functions which aren't in the standard lib, as needs are encountered.

Four_bodies [Rule.Ising]  
Four_bodies_optimized [Rule.Ising] 
Can be used only on a 2D periodic topology with no holes nor missing links,
need Sphere2 Meta topology

Fresh_name [Femtolib.Misc]  
H  
Hexagons [Topology]  
I  
Initializer 
Creates the initial configuration and repartition.

Int [Femtolib.Misc.Fresh_name]  
Integer_state [Rule.Templates]  
Ising [Rule] 
The Ising model

L  
Light_cones [Measure]  
Line [Topology] 
Create 1D topologies.

Line [Initializer] 
Also used to initialize a rectangle when there are no local dependencies.

List [Femtolib]  
Lle [Experiment] 
Computes the Local Lyapunov Exponent, see same paper.

Load_Experiment [Cimula]  
Load_Meta_Topology [Cimula]  
Load_Rule [Cimula]  
Load_Synchronism [Cimula]  
Load_Topology [Cimula]  
M  
Main [Cimula] 
Launches the provided Experiment

Majority [Rule] 
if sum_of_neighbours > nb_neighbours then 1 else 0.

Measure 
Helper functions for the module Experiment.

Meta [Topology] 
Modifies a given topology.

Meta_topo_parameters [User_interface.Text]  
Misc [Femtolib]  
O  
Op_cyclic_r1t2k4box [Experiment] 
Computes the order parameter and derives the free energy, see same paper.

P  
Parallel_2eca [Rule] 
Runs two ECA in parallel: each cell contains two states.

Parse [Femtolib.Config_file.Raw]  
Periodic [Initializer.Line]  
Pervasives [Femtolib]  
R  
Random2 [Femtolib]  
Raw [Femtolib.Config_file]  
Rectangle [Topology] 
Create 2D topologies.

Rrcs_2d [Rule] 
2D rules that are Rotation Reflexion and Conjugate Symmetric,
with range one diamond neighboorhoud.

Rrpcs_2d [Rule] 
"p" for "pseudo conjugate",
a slight (buggy) variation (conjugating only the center cell) of rrcs2d

Rule 
Definition of the cellular automata

Rule_parameters [User_interface.Text]  
S  
Sandpile [Rule] 
The Bak, Tang and Wiesenfeld sandpile model.

Sequential [Synchronism]  
Shift [Rule]  
Shuffle_neighbours [Topology.Meta]  
Sphere_radius_2 [Topology.Meta]  
Stat_cmplx [Experiment] 
Computes the statistical complexity,
as defined in
Cosma Shalizi, Rob Haslinger, JeanBaptiste Rouquier, Kristina Lisa Klinkner and Cristopher Moore,
"Automatic Filters for the Detection of Coherent Structure in Spatiotemporal Systems",
nlin.CG/0508001, Physical Review E.

States [Experiment] 
Simulates and draw the states of a CA.

Statistic [Measure] 
Statistic functions, as needs are encountered.

Synchronism 
The way the transition rule is applied, see
Types.Synchronism.next_step .

Synchronization [Experiment] 
Computes the time needed to synchronize two eca, corresponding paper accepted.

Synchronous [Synchronism]  
T  
Templates [Rule] 
Factorization of code for Cellular Automata with usual types.

Text [User_interface]  
Topo [Topology.Hexagons]  
Topo [Topology.Rectangle]  
Topo [Topology.Line]  
Topo_parameters1d [User_interface.Text]  
Topo_parameters2d [User_interface.Text]  
Topology 
Create the neighbourhoods according to different topologies.

Topology_parameters [User_interface.Text]  
Totalizing [Rule] 
Totalizing rules, ie rules that depends only on the sum of the states of theirs neighbours
(includes the famous Conway's game of life, majority).

Types 
Data types used everywhere in the code.

U  
Unit [Cimula]  
User_interface 
Self explaining.
