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addedNodes confirmed scripts Jan 11, 2014
documentation removing latex from documentation Jan 12, 2014
testing removing latex from documentation Jan 12, 2014
Doxyfile first commit Jul 19, 2011
FlexLexer.h various bug fixes Dec 1, 2011
Jamroot code cleanup, bug fixes Jan 11, 2014
LICENSE adding file with gpl LICENSE Jul 19, 2011
Makefile aebiab Jan 12, 2014
Parser.h Update Parser files for new versions of bisonc++. May 8, 2013
Parser.ih slightly faster recompilation Dec 7, 2013
Parser.yy.declaration confirming test scripts Jan 11, 2014
Parser.yy.tokens confirming test scripts Jan 11, 2014
README cleanup Dec 19, 2013
Scanner.h code cle May 13, 2012
Scanner.ll.begin confirming test scripts Jan 11, 2014
Scanner.ll.end cleanup Dec 19, 2013
addNewNode.py adding functions to observe events of pcos Feb 2, 2013
baseType.h added support for float Mar 6, 2013
buildWindows.bat added scripts for code generation and compilation on windows Mar 24, 2013
command.cpp added variable to control priority of jobs in conedyCondor Mar 3, 2013
command.h confirmed scripts Jan 11, 2014
commandLineArguments.cpp first commit Jul 19, 2011
commandLineArguments.h only call recompilations scripts if RECOMPILE is defined (can be Mar 24, 2013
conedy.cpp confirmed scripts Jan 11, 2014
conedy.vim code cleanup Oct 5, 2011
config.h.tmpl only call recompilations scripts if RECOMPILE is defined (can be Mar 24, 2013
configure.sh the configure script now copies config.h.tmpl to config.h Nov 28, 2011
containerNode.h added variable to control priority of jobs in conedyCondor Mar 3, 2013
createNetwork.cpp aeieasn Dec 27, 2013
createNetwork.h cleanup Dec 19, 2013
dynNetwork.cpp some cleanup for odeNode and gslOdeNode Jan 11, 2014
dynNetwork.h cleanup Dec 19, 2013
dynNode.cpp aebiae Dec 18, 2013
dynNode.h some code cleanup, better matching for nodes, less recompiled object Dec 6, 2013
edge.h bug fixing Dec 15, 2013
eventHandler.cpp remove dependency on new gsl Jun 6, 2012
eventHandler.h added removeRandomEdgesUndirected Aug 21, 2013
expression.h code cleanup Dec 9, 2013
fileList code cleanup, bug fixes Jan 11, 2014
fullNetwork.cpp cleanup Dec 19, 2013
fullNetwork.h fix Dec 20, 2013
fullNetworkWithNodes.cpp i Dec 20, 2013
fullNetworkWithNodes.h cleanup Dec 19, 2013
generateSourceCodeWindows.bat bug fix to allow direcotry names with whitespace under windows Mar 26, 2013
globals.cpp converting types to int with templates and without dummy in globals.h Jun 4, 2012
globals.h cleanup Dec 19, 2013
gslNoise.cpp first commit Jul 19, 2011
gslNoise.h cleanup Dec 19, 2013
gslOdeIntegrator.h changed some names, setState for templates Nov 8, 2011
gslOdeNode.cpp some cleanup for odeNode and gslOdeNode Jan 11, 2014
gslOdeNode.h some cleanup for odeNode and gslOdeNode Jan 11, 2014
instruction.cpp some code cleanup, better matching for nodes, less recompiled object Dec 6, 2013
instruction.h cleanup Dec 19, 2013
integrator.h code cle May 13, 2012
ioNode.cpp Merge https://github.com/hensing/Conedy Feb 2, 2013
ioNode.h adding functions to observe events of pcos Feb 2, 2013
lyapunov.cpp some code cleanup, better matching for nodes, less recompiled object Dec 6, 2013
lyapunov.h some code cleanup Sep 10, 2012
makeDocstringsWindows.py script which will generate docstrings.h under windows Mar 24, 2013
manpage.1 first commit Jul 19, 2011
mapNode.cpp Merge https://github.com/hensing/Conedy Feb 2, 2013
mapNode.h Merge https://github.com/hensing/Conedy Feb 2, 2013
network.cpp confirming test scripts Jan 11, 2014
network.h removed double typedef Jan 12, 2014
network.neu first commit Jul 19, 2011
networkConstants.h some code cleanup, better matching for nodes, less recompiled object Dec 6, 2013
neuroPython.cpp confirming test scripts Jan 11, 2014
neuroPython.h first commit Jul 19, 2011
neuroPythonNodes.cpp fix Dec 20, 2013
neuroPythonNodes.h fix Dec 20, 2013
node.cpp some code cleanup, better matching for nodes, less recompiled object Dec 6, 2013
node.h half-gored Dec 13, 2013
nodeImplement.h half-gored Dec 13, 2013
ode.h some cleanup for odeNode and gslOdeNode Jan 11, 2014
odeNode.cpp some cleanup for odeNode and gslOdeNode Jan 11, 2014
odeNode.h some cleanup for odeNode and gslOdeNode Jan 11, 2014
params.cpp first commit Jul 19, 2011
params.h some code cleanup, better matching for nodes, less recompiled object Dec 6, 2013
parserSemantic.h code cleanup Dec 9, 2013
pco.h changed some names, setState for templates Nov 8, 2011
pcoDelay.h first commit Jul 19, 2011
priorityQueue.cpp Merge https://github.com/hensing/Conedy Feb 2, 2013
priorityQueue.h slightly faster recompilation Dec 7, 2013
pulseCoupledExcitatoryNeuron.cpp renamed addVertex to addNode Aug 10, 2011
pulseCoupledExcitatoryNeuron.h conedy compiles in userspace now. May 26, 2012
pulseCoupledPhaseOscillator.cpp createfromAdjacencyList did not return first node number Feb 11, 2013
pulseCoupledPhaseOscillator.h some code cleanup, better matching for nodes, less recompiled object Dec 6, 2013
recompileConedy code cleanup, bug fixes Jan 11, 2014
sde.h adding missing typedef files Nov 9, 2011
sdeNode.cpp implementing sde-integrators Sep 28, 2011
sdeNode.h rearranging include files to improve compile speed Nov 20, 2011
setup.py fix Dec 20, 2013
spatialNetwork.cpp some fixes for compilation with clang Feb 2, 2013
spatialNetwork.h confirming test scripts Jan 11, 2014
specialNodes.h confer Dec 15, 2013
statisticsNetwork.cpp confirming test scripts Jan 11, 2014
statisticsNetwork.h network can now have overloaded functions (bugfix) Jan 11, 2014
stdOdeIntegrator.cpp Applied new interface for global variables. May 16, 2012
stdOdeIntegrator.h added implementation for removeEdge and removeRandomEdges Mar 6, 2013
stdSdeIntegrator.cpp Applied new interface for global variables. May 16, 2012
stdSdeIntegrator.h Improving the documentation of set and some other aspects. Jun 1, 2012
testNode1.cfg confirming righteous test-scripts, recompiling with printing errors to Nov 23, 2011
todo some code cleanup, better matching for nodes, less recompiled object Dec 6, 2013
unsupportedEdges.h conedy compiles in userspace now. May 26, 2012
userConfig.h.tmpl this and that Jun 9, 2012

README



Conedy is a scientific tool for the numerical integration of dynamical systems, whose mutual couplings are described by a network. Its name is an abbrevation of “Complex Networks with Dynamics”.



see http://www.conedy.org for documentation


Build dependencies on a debian-based system:


sudo aptitude install debhelper  cdbs python-all-dev boost-build  libboost-dev libgsl0-dev libboost-dev libboost-python-dev libboost-iostreams-dev libz-dev python-support bisonc++ flex  texlive-latex-base python-sphinx texlive-latex-recommended texlive-latex-extra texlive-fonts-recommended vim-common dvipng


---


Some introduction to the source code:


The main object which is managed and modified in Conedy is an instance of the class MyNetwork as defined in fullnetwork.h. This instance represents an edge array representation of a graph in which nodes represent dynamical systems and edges represent coupling between these systems. The functions which allow one to modify or observe this network are seperated into different subclasses which are merged together by inheritance:

The Network:


network.h:
	In this file the base class network is defined, which maneges the data structure of the network and implements elementary functions which add single edges or nodes to the network

dynNetwork.h:
	The class dynNetwork extends network by functions which are specific to numerical integration and setting initial conditions.

createNetwork.h:
	In this file the class createNetwork is defined, which extend network by generators for more complicated networks (lattices, random networks, etc.) and by functions which add specialized observe nodes which during time evolution write some property to output files.

statisticsNetwork.h:
	Adds some network characteristics to the network interface class.

spatialNetwork.h:
	Adds three dimensional coordinates to each node in the network. Is currently not used much except for opengl visualization. 

fullNetwork.h:
	All these 6 network classes are merged by inheritance to the class networkTemplate, which corresponds to the network objects which is revealed to the interpreter and to Python.


The Nodes:

node.h:
	defines the class node which represents an dynamical system. It is only an interface class and does not specify, how the data for edges is handled (see nodeImplement.h). 

dynNode.h:
 	adds functions to the interface of node which are specific for dynamical systems (time evolution, parameter, degrees of freedom, etc). 

containerNode.h:
	groups the memory for the system state of dynNodes into different containers, such that numerical integrators like the gsl can operator on consecutive memory. Different containers are differentiated by a integer template parameter and correspond to different dynamical systems.

sdeNode.h, mapNode.h, odeNode.h:
	adds interfaces for the different functions which define the dynamics.

stdOdeIntegrater.h, stdSdeIntegrater.h: 
	defines integrators for the dynamical systems.


nodeImplement.h:
	defines two different implementations for the interface in node.h. nodeTemplateEdges handles edges as an vector of edges. In this way all edges of an node must be of the same type and no virtual function calls are needed for numerical integration. Moreover, edges do not need a v-table and consume less memory. nodeVirtualEdges handles edges as an vector of pointer to edges, allowing for different edge types of a node.



The Edges:

	
node.h, edge.h:
	defines edge and edgeVirtual, which are the base classes for all edges. Edges inherit from a template parameter, which could allow for some kind of filter chain in which different edges are chained after another and perform different transformations of the target state. Depending on the type of the first ancestor, which is either edge or edgeVirtual, the chained calls to getTargetState are either virtual or non-virtual function calls. Edges are planned to be generated automatically like nodes with ini-files. At the moment, only some features of nodes can be combined in a hard-coded way.