PyDSTool Free and open source simulation and analysis environment
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PyDSTool Description

Free and open source simulation and analysis environment PyDSTool is a sophisticated and integrated simulation and analysis environment for dynamical systems models of physical systems (ODEs, DAEs, maps, and hybrid systems). PyDSTool supports optimization, continuation, symbolic math, data analysis, biological apps. Requirements: · Python What's New in This Release: Model.py: · Improved interaction between domain boundaries and event · detection for hybrid model switching at those · boundaries (esp. for VODE) · Hybrid model classes and functionality cleaned up and · re-organized. Hybrid models are now a sub-class of · Model so that they can be organized hierarchically, · with Generator-only based models as the leaves. All · methods and attributes involving name "Generator" now · replaced with "submodel" or "DS" (for dynamical system). · HybridTrajectory sub-class behaves like a proper · Trajectory · Fixed bug in recording of events for hybrid models · Now all sub-models of a hybrid system must "export" · the same variables (e.g., see differences in · fingermodel_vode.py) · Can promote a Generator's auxiliary variables to be · treated as observable or internal vars at Model level, · provided all sub-models export them. forceObsVars and · forceIntVars used to promote the aux vars or to change · internal observable variables (now has no effect if · variables already of desired type) · Method delTraj -> _delTraj deprecated because del · model now works · Removed method numPartitions (instead, use · len(getTrajTimePartitions(trajname))) · Added renameTraj method · fulldimension -> dimension (= # of obs + int vars) · genInfo tuple -> modelInfo dict (see technical · documentation for details) · generators list attribute -> registry dict attribute Trajectory.py: · Regular continuouss trajectories can now be called as a · map (0 or 1 only) to yield endpoints · Can now delete variables from a Trajectory · Now support FScompatibleNames map (primarily for · internal use by Model objects) · Fixed bug in trajectory calling as map (appending of · time to vals works in place and so previously, result · was None) · Attribute .varnames -> .coordnames PyCont: · New PyCont example for finding level sets of functions · Fixed minor bug in PyCont/AUTO for continuing limit · cycles Generators: · Generators now support queries in hierarchical name · format · Fixed bug in event detection for VODE integrator · Fixed access to external inputs for C-based ODE · integrators before first integration performed Points.py: · Can now rename variables in pointsets and points · Fixed bug in pointset's label reversal Interval.py: · Fixed small bug concerning singleton interval comparison · Added isfinite method FuncSpec.py: · Fixed obscure error in cross-referenced aux fns · Fixed abs -> fabs mapping error in vector field functions · Allowed scripts using C-based Generators to be re-run · provided definition of Generator has not changed (used · to always raise an error)

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