Attachment 'ChangeLog.txt'

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   1 Version 3.5.0
   2 
   3     Additions:
   4     
   5         Added OpenMP support
   6         Added new algorithm to External potential - delta E can be now calculated based on changes in COM position
   7         Added functionality to SteppableBasePy - now it detects whic Python available plugins are loaded and based on this it makes them callable directly from any steppable which inherits SteppableBasePy.
   8         Added COM based algorithm to cell orientation plugin
   9         Modified COM plugin to make center of mass coordinates easier to access without doing any calculations
  10         Reworked viscosity plugin, added new attributes to CellG - true COM coordinates and COM for one spin flip before
  11         Added Secretion Plugin which replaces (this is optional and up to modeler) secretion syntax of PDE sover. Secretion plugin has better functionality than secretion functions in PDE-solver
  12         Implemented Chemotaxis by cell id. "Per-cell" chemotaxis parameters override XML based definitions. Still users have to list in XML which fields participate in chemotaxis 
  13         Implemented fluctuation amplitude on per-cell basis. Replaced "with" statement in Graphics/GraphicsFrameWidget.py with equivalent try/except statement
  14         Changed Temperature/Cell motility to FluctuationAmplitude - we still support old definitions however we should deprecate old terminology
  15         Added accessor functions to LengthConstraintLocalFlex/LengthConstraintLocalFlexPlugin.cpp    
  16         Implemented text stream redirection so that output from C++ and Python can be displayed in Player console
  17     
  18     Bug Fixes:
  19         Fixed significant bug in parallel Potts section - had to allow nested omp regions as PDE solver caller calls PDE solver from within parallel section . PDESolver though instantiates its own parallel section to solve PDE so there are nested parallel regions
  20     
  21 Version 3.6.0
  22 
  23     Additions:
  24         
  25         Integrated Twedit++ with CC3D        
  26         Added more functionality to plotting in CC3D, modified startup scripts related to twedit++
  27         Separated internal energies and external energies - all contact plugins by default include only terms from neighboring pixels belonging to different clusters. Added ContactInternal plugin which calculates energy between neighboring pixels belongint to different cells but within the same cluster. This allows replacement of Comparment plugin with combination of ContactInternal+Contact, ContactInternal+AdhesionFlex etc. 
  28         modified clusterEnergy example to show how the new approach will work        
  29         Added extra functionality to PySteppables SteppableBasePy module allowing simple cell manipulation and better access to cell within cluster
  30         Fixed Python iterators - see bug-fixes below for more details
  31         Bundled BionetSolver with CC3D - Windows OSX, coming soon
  32         Introduced new style CCC3D project files (as of now each CC3D simulation can be stored as a self-contened directory containing all the files necessaruy to run simulations). All file locations are w.r.t to directory containing main CC3D project file *.cc3d        
  33         Introduced new storage place. By default all the simulations results are now saved to <homeDirectory>/CC3DWorkspace
  34         Added CC3D project management tool to Twedit ++
  35         Added CC3D simulation wizard to Twedit
  36         Added new boundary condition specification and a llowed mixed BC for most of the PDE's (Kernel and AdvectionDivffusion solver are not included in this change)
  37         
  38         
  39         
  40      Bug Fixes:   
  41         Fixed the following problem:
  42         
  43         SWIG has problems correctly generating/handling STL iterators (or in general any iterators) 
  44         Once there are more than one SWIG-generated modules loaded in Python and each of those modules contains STL containers
  45         then iterators generated by SWIG () like those returneb by itervalues, iter, iterator iterkeys etc) will caus segfault during iteration
  46         This is well documented below and here:
  47 
  48         http://permalink.gmane.org/gmane.comp.programming.swig.devel/20140 
  49         //here is a reference found on the web to the bug in Swig
  50         // # 1. Workaround for SWIG bug #1863647: Ensure that the PySwigIterator class
  51         // #    (SwigPyIterator in 1.3.38 or later) is renamed with a module-specific
  52         // #    prefix, to avoid collisions when using multiple modules
  53         // # 2. If module names contain '.' characters, SWIG emits these into the CPP
  54         // #    macros used in the director header. Work around this by replacing them
  55         // #    with '_'. A longer term fix is not to call our modules "IMP.foo" but
  56         // #    to say %module(package=IMP) foo but this doesn't work in SWIG stable
  57         // #    as of 1.3.36 (Python imports incorrectly come out as 'import foo'
  58         // #    rather than 'import IMP.foo'). See also IMP bug #41 at
  59         // #    https://salilab.org/imp/bugs/show_bug.cgi?id=41
  60 
  61         The bottom line is that instead of relying on SWIG to generate iterators for you it is much better to write your own iterator wrapper like the one included 
  62         in the CC3D code.
  63         This is a bit of the overhead but not too much and if necessary it can be further simplified (for the convenience of coding)        
  64         
  65         SteadyStateDiffusionSolver
  66         Fixed instability issues associated with floats - Change solver to work with doubles
  67         
  68 Version 3.6.1
  69 
  70     Additions:
  71         TO BE ADDED
  72         
  73         
  74      Bug Fixes:   
  75         TO BE ADDED
  76 Version 3.6.2
  77 
  78     Additions:
  79         
  80         Added CC3DML Helper to Twedit       
  81         GPU Diffusion solver
  82         
  83         
  84      Bug Fixes:   
  85      
  86 Version 3.7.0
  87 
  88     Additions:
  89         
  90         GPU Reaction-Diffusion Solvers (explicit and implicit)
  91         RoadRunner-basedSBMLsolvers
  92         Simplified and improved Steppable API (backward compatibility maintained)
  93         Numpy-based syntax for field manipulation    
  94         Demo integration with Dolfin- works on linux only
  95         
  96      Bug Fixes:   
  97      
  98 Version 3.7.1
  99 
 100     Additions:
 101         LLVM-based RoadRunner as a backend for SBML Solver
 102         Parameter Scans
 103         Improved Twedit
 104         On Windows switched compilers from VS2008 to VS 2010
 105         Added Serialization of SBMLSolver objects
 106         Fixed memory leaks in the Player
 107         Added proper cleanup functions to Simulator
 108         
 109      Bug Fixes:   
 110         Fixed sneaky bug related to cell inventory ordering - affected windows only and when cells were deleted it could cause CC3D crash. Same for FocalPOintPLasticity plugin ordering of the links was buggy on windows. 
 111         

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