Release of version 3.0.0

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 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.

.gitignore

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+.DS_Store
+*.m~
+*.asv
+*._*
+*.*~
+*.mexmaci64
+*.mexa64
+*.mexw64
+*.mexw32
+*.dll
+*.dylib
+*.so
+doc/doxy/html
+doc/tex/*.aux
+doc/tex/*.fdb_latexmk
+doc/tex/*.bbl
+doc/tex/*.bcf
+doc/tex/*.run.xml
+doc/tex/*.out
+doc/tex/*.blg
+doc/tex/*.lot
+doc/tex/*.lof
+doc/tex/*.toc
+doc/tex/*.log
+doc/tex/*.idx
+doc/tex/*.ind
+doc/tex/*.gitinfo
+doc/tex/*.synctex.gz
+doc/tex/*.pdf
+doc/tex/docs/*.aux

AUTHORS

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+Eric von Lieres (Forschungszentrum Juelich GmbH, IBG-1: Biotechnology, Juelich, Germany): Supervision, concepts, first Matlab implementation, user interface design
+Joel Andersson (Forschungszentrum Juelich GmbH, IBG-1: Biotechnology, Juelich, Germany): Domain decomposition (GRM), linear solver (GRM), first C implementation
+Sebastian Schnittert (Forschungszentrum Juelich GmbH, IBG-1: Biotechnology, Juelich, Germany): First C++ implementation, first Matlab interface, first file format
+Andreas Püttmann (Forschungszentrum Juelich GmbH, IBG-1: Biotechnology, Juelich, Germany): Parameter sensitivities, Jacobians via AD, AD techniques (block- & band-compression)
+Samuel Leweke (Forschungszentrum Juelich GmbH, IBG-1: Biotechnology, Juelich, Germany): Complete rewrite of v3.0 from scratch, build system, code & framework design and architecture, Matlab interface, file format, frontends (MEX, CLI), domain decomposition (multi-unit systems), reactions

BUILD-LINUX.md

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+# Prerequisites
+
+* CMake (>= 3.1.0)
+* GCC >= 4.7 or Clang >= 3.3
+* Optional: MATLAB R2009a or greater
+* Optional: Git
+
+Assumed directory structure:
+
+<pre>
+&lt;ROOT&gt;
+   |-libs
+   |   |- sundials
+   |   |- hdf5
+   |-code
+   |-cadet
+   |-build
+</pre>
+
+Note that the version numbers of the files and packages below are subject to change and will not always reflect the most recent version.
+
+# Build dependencies
+
+## HDF5
+
+You can either build HDF5 yourself or rely on the packages provided by your Linux distribution.
+
+Obtain HDF5 from your distribution:
+* Install the development package of your distribution (e.g., `libhdf5-dev` for Ubuntu and Debian, `hdf5-devel` OpenSUSE)
+* Additional postfixes or prefixes in the library names (e.g., Debian uses `libhdf5_serial.*` instead of `libhdf5.*`) can cause troubles when CMake is trying to find HDF5. If this is the case, you can circumvent this by using symlinks `ln -s libhdf5_serial.* libhdf5.*`. However, this can later cause troubles because other packages might contain this file.
+
+Build HDF5 yourself:
+* Download CMake-enabled source from https://support.hdfgroup.org/HDF5/release/cmakebuild.html or https://support.hdfgroup.org/HDF5/release/cmakebuild5110.html
+* Unzip and make sure that the directory path does not contain blank spaces
+* Open a terminal and change to the unzipped directory
+* Execute `ctest -S HDF5config.cmake,BUILD_GENERATOR=Unix,INSTALLDIR="<ROOT>/Libs/hdf5" -C Release -V`
+* Extract the created `HDF5-1.10.0-patch1-Linux.tar.gz` file to `<ROOT>/Libs/hdf5` such that you have `<ROOT>/Libs/hdf5/lib`
+
+## SUNDIALS
+
+* Download SUNDIALS source from http://computation.llnl.gov/projects/sundials/sundials-software
+* Unzip
+* Open a terminal and change to the parent directory of the unzipped directory
+* Create a new folder `sundialsbuild` and change to it
+* Execute `cmake -DCMAKE_INSTALL_PREFIX="<ROOT>/Libs/sundials" -DEXAMPLES_ENABLE=OFF -DOPENMP_ENABLE=ON -DBUILD_SHARED_LIBS=OFF -DCMAKE_C_FLAGS=-fPIC ../sundials-2.7.0/`
+* Execute `make install`
+* Delete the folder `sundialsbuild` (e.g., execute `rm -rf sundialsbuild` in the parent directory of `sundialsbuild`)
+
+## LAPACK
+
+You can either use a LAPACK implementation provided by your distribution or install the freely available [Intel MKL](https://software.intel.com/sites/campaigns/nest/) which is very fast and probably faster than your distribution's implementation.
+
+Obtain LAPACK from your distribution:
+* Install the packages (LAPACK and BLAS) of your distribution (e.g., `liblapack3`, `liblapack-dev`, `libblas3`, `libblas-dev` for Ubuntu and Debian). Note that some packages only provide reference (i.e., slow) implementations and others (e.g., ATLAS, GOTO) perform much faster.
+
+# Build CADET
+
+* Download release of CADET or checkout from git
+* Place the source in `<ROOT>/code` and create the directory `<ROOT>/build`
+* Open a terminal and change to `<ROOT>/build`
+* If you have built HDF5 yourself, execute `export HDF5_ROOT=<ROOT>/Libs/hdf5`
+* Execute `export SUNDIALS_ROOT=<ROOT>/Libs/sundials`
+* Using standard LAPACK: Execute `cmake -DCMAKE_INSTALL_PREFIX="<ROOT>/cadet" ../code/`
+
+    Using MKL (sequential): Execute `cmake -DCMAKE_INSTALL_PREFIX="<ROOT>/cadet" -DCMAKE_LIBRARY_PATH="<MKL_ROOT>/lib/intel64" -DBLA_VENDOR=Intel10_64lp_seq ../code/`
+
+    Using MKL (parallel): Execute `cmake -DCMAKE_INSTALL_PREFIX="<ROOT>/cadet" -DCMAKE_LIBRARY_PATH="<MKL_ROOT>/lib/intel64" -DBLA_VENDOR=Intel10_64lp ../code/`
+* If CMake was not able to locate Matlab, execute `export MATLAB_ROOT=/path/to/my/MATLAB/R2016a` and try to run CMake again
+* Execute `make`
+* Execute `make install`
+

BUILD-OSX.md

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+# Prerequisites
+
+* CMake (>= 3.1.0)
+* GCC >= 4.7 or Clang >= 3.3
+* Optional: MATLAB R2009a or greater
+* Optional: Git
+
+Assumed directory structure:
+
+<pre>
+&lt;ROOT&gt;
+   |-libs
+   |   |- sundials
+   |   |- hdf5
+   |-code
+   |-cadet
+   |-build
+</pre>
+
+Note that the version numbers of the files and packages below are subject to change and will not always reflect the most recent version.
+
+Also note that you have to use the same compiler for all packages. This is especially important if some of the packages are installed via a package manager such as [Homebrew](http://brew.sh/) which uses the system compiler (Clang).
+
+# Build dependencies
+
+## HDF5
+
+You can either build HDF5 yourself or rely on the `hdf5` package of [Homebrew](http://brew.sh/).
+
+Obtain HDF5 from Homebrew:
+* Open a terminal and execute `brew install hdf5`
+* Homebrew has installed HDF5 to `/usr/local`
+
+Build HDF5 yourself:
+* Download CMake-enabled source from https://support.hdfgroup.org/HDF5/release/cmakebuild.html or https://support.hdfgroup.org/HDF5/release/cmakebuild5110.html
+* Unzip and make sure that the directory path does not contain blank spaces
+* Open a terminal and change to the unzipped directory
+* Execute `ctest -S HDF5config.cmake,BUILD_GENERATOR=Unix,INSTALLDIR="<ROOT>/Libs/hdf5" -C Release -V`
+* Extract the created `HDF5-1.10.0-patch1-Darwin.tar.gz` file to `<ROOT>/Libs/hdf5` such that you have `<ROOT>/Libs/hdf5/lib`
+
+## SUNDIALS
+
+You can either build SUNDIALS yourself or rely on the `hdf5` package of [Homebrew](http://brew.sh/).
+
+Obtain SUNDIALS from Homebrew:
+* Open a terminal and execute `brew install sundials`
+* Homebrew has installed SUNDIALS to `/usr/local`
+
+Build SUNDIALS yourself:
+* Download SUNDIALS source from http://computation.llnl.gov/projects/sundials/sundials-software
+* Unzip
+* Open a terminal and change to the parent directory of the unzipped directory
+* Create a new folder `sundialsbuild` and change to it
+* Execute `cmake -DCMAKE_INSTALL_PREFIX="<ROOT>/Libs/sundials" -DEXAMPLES_ENABLE=OFF -DOPENMP_ENABLE=ON -DBUILD_SHARED_LIBS=OFF -DCMAKE_C_FLAGS=-fPIC ../sundials-2.7.0/`
+* Execute `make install`
+* Delete the folder `sundialsbuild` (e.g., execute `rm -rf sundialsbuild` in the parent directory of `sundialsbuild`)
+
+## LAPACK
+
+You can either use the native LAPACK implementation provided by Mac OS X (vecLib, Accelerate) or install the freely available [Intel MKL](https://software.intel.com/sites/campaigns/nest/) which is very fast and probably faster than Accelerate.
+
+# Build CADET
+
+* Download release of CADET or checkout from git
+* Place the source in `<ROOT>/code` and create the directory `<ROOT>/build`
+* Open a terminal and change to `<ROOT>/build`
+* If you have built HDF5 yourself, execute `export HDF5_ROOT=<ROOT>/Libs/hdf5`
+* If you have built SUNDIALS yourself, execute `export SUNDIALS_ROOT=<ROOT>/Libs/sundials`
+* Using standard LAPACK: Execute `cmake -DCMAKE_INSTALL_PREFIX="<ROOT>/cadet" ../code/`
+
+    Using MKL (sequential): Execute `cmake -DCMAKE_INSTALL_PREFIX="<ROOT>/cadet" -DCMAKE_LIBRARY_PATH="<MKL_ROOT>/lib/intel64_win" -DBLA_VENDOR=Intel10_64lp_seq ../code/`
+
+    Using MKL (parallel): Execute `cmake -DCMAKE_INSTALL_PREFIX="<ROOT>/cadet" -DCMAKE_LIBRARY_PATH="<MKL_ROOT>/lib/intel64_win" -DBLA_VENDOR=Intel10_64lp ../code/`
+* Execute `make`
+* Execute `make install`
+

BUILD-WINDOWS.md

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+# Prerequisites
+
+* CMake (>= 3.1.0)
+* Microsoft Visual Studio 2015 (Community Edition, or better)
+* Optional: MATLAB R2009a or greater
+* Optional: Git
+
+Assumed directory structure:
+
+<pre>
+&lt;ROOT&gt;
+   |-Libs
+   |   |- sundials
+   |   |- hdf5
+   |   |- lapack
+   |-code
+   |-cadet
+   |-build
+</pre>
+
+Note that the version numbers of the files and packages below are subject to change and will not always reflect the most recent version.
+
+# Build dependencies
+
+## HDF5
+
+* Make sure that no HDF5 libraries are installed (remove already existing HDF5 installations)
+* Download CMake-enabled source from https://support.hdfgroup.org/HDF5/release/cmakebuild.html or https://support.hdfgroup.org/HDF5/release/cmakebuild5110.html
+* Unzip and make sure that the directory path does not contain blank spaces
+* Open VS2015x64 Command Prompt and change to the unzipped directory
+* Execute `ctest -S HDF5config.cmake,BUILD_GENERATOR=VS201564,INSTALLDIR="<ROOT>\Libs\hdf5" -C Release -V`
+* Extract the created `HDF5-1.8.17-win64.zip` file to `<ROOT>/Libs/hdf5` such that you have `<ROOT>/Libs/hdf5/lib`
+* We need to remove the `lib` prefix of the `.lib` files in `<ROOT>/Libs/hdf5/lib` (i.e., rename `libhdf5.lib` to `hdf5.lib`). Change to `<ROOT>/Libs/hdf5/lib` and execute `rename "lib*" "///*"`
+
+## SUNDIALS
+
+* Download SUNDIALS source from http://computation.llnl.gov/projects/sundials/sundials-software
+* Unzip
+* Open VS2015x64 Command Prompt and change to the parent directory of the unzipped directory
+* Create a new folder `sundialsbuild` and change to it
+* Execute `cmake -DCMAKE_INSTALL_PREFIX="<ROOT>\Libs\sundials" -DEXAMPLES_ENABLE=OFF -DOPENMP_ENABLE=ON -DBUILD_SHARED_LIBS=OFF -G "Visual Studio 14 Win64" -DCMAKE_C_FLAGS="/GL" -DCMAKE_STATIC_LINKER_FLAGS="/LTCG" ..\sundials-2.7.0\`
+* Execute `msbuild.exe INSTALL.vcxproj /p:Configuration=Release;Platform=x64`
+
+## LAPACK
+
+In the following, CLAPACK is built and used. You can also install the freely available [Intel MKL](https://software.intel.com/sites/campaigns/nest/) which is very fast and certainly much faster than CLAPACK.
+
+* Download `clapack-3.2.1-CMAKE.tgz` from https://icl.cs.utk.edu/lapack-for-windows/clapack/index.html#build and unzip
+* Open VS2015x64 Command Prompt and change to the parent directory of the unzipped directory
+* Create a new folder `clapackbuild` and change to it
+* Execute `cmake -DCMAKE_INSTALL_PREFIX="<ROOT>\Libs\clapack" -G "Visual Studio 14 Win64" -DCMAKE_C_FLAGS="/GL" -DCMAKE_CXX_FLAGS="/GL" -DCMAKE_STATIC_LINKER_FLAGS="/LTCG" ..\clapack-3.2.1-`
+* Execute `msbuild.exe CLAPACK.sln /p:Configuration=Release;Platform=x64`
+* Execute `msbuild.exe INSTALL.vcxproj /p:Configuration=Release;Platform=x64`
+* Rename `<ROOT>\Libs\clapack\lib\libf2c.lib` to `<ROOT>\Libs\clapack\lib\f2c.lib`
+
+# Build CADET
+
+* Download release of CADET or checkout from git
+* Place the source in `<ROOT>\code` and create the directory `<ROOT>\build`
+* Open VS2015x64 Command Prompt and change to `<ROOT>\build`
+* Execute `set SUNDIALS_ROOT=<ROOT>\Libs\sundials`
+* Execute `set HDF5_ROOT=<ROOT>\Libs\hdf5`
+* Using CLAPACK: Execute `cmake -DCMAKE_INSTALL_PREFIX="<ROOT>\cadet" -DBUILD_TESTS=OFF -DCMAKE_LIBRARY_PATH="<ROOT>\Libs\clapack\lib" -G "Visual Studio 14 Win64" -DBLA_VENDOR=CLAPACK ..\code\`
+
+    Using MKL (sequential): Execute `cmake -DCMAKE_INSTALL_PREFIX="<ROOT>\cadet" -DBUILD_TESTS=OFF -DCMAKE_LIBRARY_PATH="<MKL_ROOT>\compilers_and_libraries_2016\windows\mkl\lib\intel64_win" -G "Visual Studio 14 Win64" -DBLA_VENDOR=Intel10_64lp_seq ..\code\`
+
+    Using MKL (parallel): Execute `cmake -DCMAKE_INSTALL_PREFIX="<ROOT>\cadet" -DBUILD_TESTS=OFF -DCMAKE_LIBRARY_PATH="<MKL_ROOT>\compilers_and_libraries_2016\windows\mkl\lib\intel64_win" -G "Visual Studio 14 Win64" -DBLA_VENDOR=Intel10_64lp ..\code\`
+* Execute `msbuild.exe CadetFramework.sln /p:Configuration=Release;Platform=x64`
+* Execute `msbuild.exe INSTALL.vcxproj /p:Configuration=Release;Platform=x64`
+