Cadet

Major changes:
- Add a command line tool to convert input files between formats (JSON, HDF5, XML).
- Make initial conditions true parameters which can be used for sensitivities.
- Improve file format documentation layout.
- Fix problems when using externally dependent binding models with multithreading.
- Add support for multiple particle types in the GRM.
- Add support for core shell particles in GRM.

Non-breaking changes in the file format:
- Additional field `PAR_CORERADIUS` for core shell particle support.
- Additional field `PAR_TYPE_VOLFRAC` and groups `adsorption_XYZ` for multiple particle type support.

Major internal changes:
- Add support for SUNDIALS v3.0.0 and above.
- Update CATCH to CATCH2.
- Add continuous integration (Travis CI and AppVeyor CI).
- Unify file IO.
- Fix a lot of bugs (e.g., memory related, consistent initialization).
- Binding models use a custom template processor pre-build step to save boilerplate code.

Major changes:
- Add variable volume continuous stirred-tank reactor model (supports binding for batch uptake experiments).
- Add lumped rate model without pores (e.g., equilibrium dispersive model, DPFR, PFR).
- Add lumped rate model with pores.
- Add support for size exclusion chromatography (models can be run without binding model, `PORE_ACCESSIBILITY` provides component dependent porosities).
- Add a lot of tests for various vital parts (Jacobians, parameter sensitivities).
- Add row equilibration to consistent initialization (nonlinear solvers, linear systems) for improved precision.
- Fix a lot of bugs.
- Add JSON as input file format to cadet-cli.
- Improve documentation.

Breaking changes in the file format:
- In output datasets: `SOLUTION_PARTICLE` no longer contains mobile and solid phase, but only the mobile phase. The same holds for `SOLDOT_PARTICLE`, `SENS_PARTICLE`, `SENSDOT_PARTICLE`.
- Added `SOLUTION_SOLID` (`SOLDOT_SOLID`, `SENS_SOLID`, `SENSDOT_SOLID`) output dataset which stores the solid phase.
- Added `WRITE_XYZ_SOLID` field to `/input/return/unit_ABC` for configuring whether the solid phase is returned.
- In return configuration rename `WRITE_XYZ_COLUMN_ABC` to `WRITE_XYZ_ABC` (e.g., `WRITE_SOLUTION_COLUMN_INLET` -> `WRITE_SOLUTION_INLET`). Note that the old return configuration fields are still supported for compatibility, but this may change at any time.
- In output datasets rename `XYZ_COLUMN_ABC` to `XYZ_ABC` (e.g., `SENSDOT_COLUMN_OUTLET` -> `SENSDOT_OUTLET`).
- In `/meta` change `FILE_FORMAT` version field from string to int. Versions of the type Major.Minor.Patch are assumed to have only two digits for each part. This number is encoded in an int by concatenating the parts (e.g., „02.12.78" -> 21278).
- In return configuration rename `WRITE_XYZ_COLUMN` to `WRITE_XYZ_BULK` (e.g., `WRITE_SENS_COLUMN` -> `WRITE_SENS_BULK`).
- In output datasets rename `XYZ_COLUMN` to `XYZ_BULK` (e.g., `SOLDOT_COLUMN` -> `SOLDOT_BULK`).
- In `/meta` rename `SIMTIME` to `TIME_SIM`.

Non-breaking changes in the file format:
- In return configuration add `WRITE_XYZ_VOLUME` (e.g., `WRITE_SOLUTION_VOLUME`) to indicate that the volume should be returned if it is available (e.g., CSTR).
- In output datasets add `XYZ_VOLUME` datasets (e.g., `SOLUTION_VOLUME`).
- Expose some time integrator (IDAS) settings to the user (e.g., number of Newton iterations, sensitivity error test).

Major internal changes:
- Change state ordering from component-major to cell-major in the bulk block of the GRM.
- Reduce duplicated and boilerplate code (especially in binding models).
- Changes in some internal interfaces necessitated by CSTR implementation.

Besides some minor fixes, the following multi-state binding models are introduced in this release:
- Multi-state steric mass action (multi-state SMA)
- Simplified multi-state SMA
- Multi-component spreading

The Windows version is built with [Visual Studio 2017](https://www.visualstudio.com/downloads/) and CADET requires the corresponding runtime files in order to run. Almost all systems will already have these files. However, if CADET does not work on your system, your system might not have those runtime libraries. In this case, you can download them for free from [Microsoft](https://go.microsoft.com/fwlink/?LinkId=746572).

CADET has been extended to support networks of unit operations. Many more changes have been made and the most important ones are listed below.
Note that the interface has changed and *breaking changes* had to be introduced.

Major changes:
- Full support for strongly coupled networks of unit operations (CADET now natively simulates SMB and other multi-column processes)
- Support for backwards flow in General Rate Model
- Replace OpenMP parallelization by Intel Threading Building Blocks
- Add some behavior tests using the CATCH unit testing framework
- Extended documentation (improved manual)
- Improved CMake build system

CADET has been (almost fully) rewritten with a complete new OOP / code
architecture. The rewrite enables and eases the implementation of new
features in the near future and has improved stability as well as
performance of the simulation.

Major highlights:
- Completely new code architecture
- Increased single- and multi-core performance
- Improved documentation (quality and quantity)
- Improved MATLAB interface and examples
- Preparations for upcoming features (networks of unit operations and
support of reaction terms)
- Consistent initialization of the DAE solver
- Modernized CMake build system
- Native support of joined parameters via AD

Unfortunately, the _changes are breaking_, that is, users have to migrate
their code to the new version.

The Windows version is built with [Visual Studio 2015](https://www.visualstudio.com/downloads/) and CADET requires the corresponding runtime files in order to run. Almost all systems will already have these files. However, if CADET does not work on your system, your system might not have those runtime libraries. In this case, you can download them for free from [Microsoft](https://www.microsoft.com/en-us/download/details.aspx?id=48145).

Bug fix release:
- Fix ignored number of threads setting.
- Fix ignored sensitivity output mode (WRITE_SENS_ALL).

No breaking changes.