Cadet

Minor changes:
- Inlet concentration now returns the actual inlet concentration instead of the concentration in the first axial cell.
- Outlet and inlet concentrations of a unit operation are assigned with respect to flow direction.
- Add a colloidal binding model developed by the group of Lenhoff at University of Delaware
- Pore and surface diffusion coefficients may depend on concentration (i.e., support for nonlinear pore and surface diffusion)
- Generalized ion exchange binding model now uses separate normalization concentrations for the pH dependent terms
- Make ADSORPTION_MODEL optional in unit operations (defaults to NONE)
- Many bugfixes

Major internal changes:
- Add SUNDIALS 3.2.1 to distribution and optionally support external SUNDIALS code
- Fix many compiler warnings on Linux and MacOS
- Require a C++17 compiler
- Support binary distribution of Intel oneTBB

Major changes:
- Dynamic flow rates: Flow rates can depend on time (cubic polynomial)
- Performance optimization for acyclic systems of unit operations: Force serial or parallel mode by setting `LINEAR_SOLUTION_MODE`
- Particle geometries: Add support for cylinders and slabs

Minor changes:
- Fix convergence order problem for rapid-equilibrium binding with surface diffusion
- Parallelize consistent initialization on system level
- Extended mobile phase modulators binding model with linear binding for selected components
- Fix ParameterFit Matlab class
- Fix reactions in CSTR
- Fix reactions in DPFR / non-binding LRM

Non-breaking changes in the file format:
- Allows `CONNECTIONS` list to have 3 additional columns for flow rate polynomial coefficients if `CONNECTIONS_INCLUDE_DYNAMIC_FLOW` is enabled.

Major internal changes:
- Improved CMake build system
- Remove ADOL-C from distribution
- Fix Travis and AppVeyor CI
- Split ModelSystemImpl.cpp into multiple files

Major changes:
- Fix backwards incompatible file format change (addition of _PORT_XYZ_
to dataset names)
- Fix Matlab interface bugs (ports, StirredTankModel)

Minor changes:
- Fix Windows build problems
- Update build instructions
- Fix bug when using equidistant particle discretization and core-shell
beads
- Minor fixes and improvements

Major changes:
- Added dynamic reaction terms to all unit operation models.
- `IS_KINETIC` field of binding models can now be set on per-bound-state basis.

Minor changes:
- Added radial column position to external function interface.
- Added progress bar to cadet-cli. The bar is enabled by calling `cadet-cli --progress`.

Non-breaking changes in the file format:
- Allows `CONNECTIONS` list to have 5 columns (port indices are omitted) in case of missing multi-port unit operations. A 7 column list can be used if `CONNECTIONS_INCLUDE_PORTS` is enabled.

Major internal changes:
- Modernized CMake build system.
- Refactored scratch memory interface and added thread local storage.
- Simplified AD library.
- Removed timeFactor and time transformation.
- Moved consistent initialization from binding models to unit operations.

Major changes:
- Add 2D general rate model variant.
- Add support for multiple ports in unit operations.
- Parameter multiplexing for initial conditions and particle-type dependent parameters (including binding models). This allows, for example, to specify just one value for all particle types.

Minor changes:
- Make axial dispersion coefficient component-dependent in all column models.

Breaking changes in the file format:
- `CONNECTIONS` list is now 7 columns wide (2 additional columns for source and destination ports).
- `SOLUTION_OUTLET`, `SOLUTION_INLET`, `SOLDOT_OUTLET`, `SOLDOT_INLET`, `SENS_OUTLET`, `SENS_INLET`, `SENSDOT_OUTLET`, `SENSDOT_INLET` now return the solution for all unit operation ports. When `SPLIT_PORTS_DATA` and `SPLIT_COMPONENTS_DATA` are both disabled, a 3d array is returned. When `SPLIT_PORTS_DATA` is enabled, the usual 2d arrays (`SPLIT_COMPONENTS_DATA` disabled) or many 1d arrays (`SPLIT_COMPONENTS_DATA` enabled) are returned as usual.

Non-breaking changes in the file format:
- Add support for returning discretization node coordinates (useful for plotting) in `/output/coordinates`. This is enabled by setting `/input/return/unit_XXX/WRITE_COORDINATES` to 1.
- Add several options to control parameter multiplexing for breaking ties or correcting automatic inference.

Major internal changes:
- Refactoring of convection dispersion operator code.
- Add compressed sparse matrix and support for sparse direct solvers (SuperLU, UMFPACK). The Matlab MEX interface automatically uses Matlab's UMFPACK library.
- Added and fixed bugs in tests.
- Refactoring of some function signatures by grouping common parameters into structs.

Major changes:
- Add multiple particle type support to LRMP and CSTR unit operations
- Allow particle volume fractions to depend on the axial coordinate in LRMP and GRM models.

Internal changes:
- Added more tests (e.g., for flux part of Jacobian)