fixed generatino of offsets for hex lattice. Before offsets weer incorerctly generated for a 3D lattice which was less than 9 pizels wide in the z direction > this i is fairly minor problem but it is fixed no
fixed diffusion solver on hex lattice with non periodic bc conditions. For no flux BC total amount of chemical is preserved on hex lattice. BC are implemented in slightly different way now for hex lattice but this is a correct way as opposed to incorrect way in previous versions
Fixed DiffusionSolver and Reaction Diffusion solvers. BEfore on hex lattice with no fluxc boundary conditions solvers were leaking chemical. I fixed how boundary cionditions are calculated for both hex and Cartesian lattice. There si an opportunity to improve performance a but here by getting rid of boundaryConditionInit function but this is really minor stuff. I leave it for now because when periodic BCs are used this function is still needed. I will get rid of this fcn in the next code iteration
Fixed GPU diffusion solver to behave exactly as CPU one and have corerct implementation of BC's on all types of lattices
cleaned up solver code
cleaned up the code
cleaned up th code
Improved SBML solver by adding simulate options, turning off dynamic python properties, using empty output list etc. Still need to write better accessor functions
commented out debug statements
fixed bug in part of the cmake file dealing with version number - minor thing
fixed how options in roadrunner should be handled. Fixed serialization to include new options
added options to SBML solver eamples - they help with numerical instabilities during SBML integration
added min/max function to Field3D objects - implemented in .i SWIG file. Later we can move it to C++ if necessary
Replaced Flexible Diffusion solver with Diffusion solver in the Demos
Replaced old style blob initializer with new style
replace VirtualProcessingUnit with Number of processor in simulation files
updated twedi++ python helper
fixed player crash when accessing unknown custom field i.e. the one that has not been stored in the CC3D settings
fixed player's rendering of vector field in 2D on hex lattice
added VTK function wrapper which releases GIL - necessary if one wants to do non-blocking VTK data point reads using VTK provided functions. The trick was to write requested functionaluity in C++ and then wrap this function usign SWIG with threads=1 option enabled in SWIG