Update documentation (#193)

* Add radial flow models documentation
* Update DG documentation
* Fix FV boundary model documentation
* Fix surface diffusion salt dependence documentation
* Update citing: Selected applications moved to website, only cite
CADET-Core (extension) publications on github

Co-authored-by: Eric von Lieres <[email protected]>

BUILD-LINUX.md

@@ -48,11 +48,14 @@ sudo apt -y install liblapack3 liblapack-dev libblas3 libblas-dev
 
 - Open a terminal and change to `CADET/build`
 - If using MKL, execute `export MKLROOT=/opt/intel/mkl`
-- Using standard LAPACK: Execute `cmake -DCMAKE_INSTALL_PREFIX="../install" ../`
+- To compile:
+	- Using standard LAPACK: Execute `cmake -DCMAKE_INSTALL_PREFIX="../install" ../`
 
-    - Using MKL (sequential): Execute `cmake -DCMAKE_INSTALL_PREFIX="../install" -DBLA_VENDOR=Intel10_64lp_seq ../`
+	- Using MKL (sequential): Execute `cmake -DCMAKE_INSTALL_PREFIX="../install" -DBLA_VENDOR=Intel10_64lp_seq ../`
 
-    - Using MKL (parallel): Execute `cmake -DCMAKE_INSTALL_PREFIX="../install" -DBLA_VENDOR=Intel10_64lp ../`
+	- Using MKL (parallel): Execute `cmake -DCMAKE_INSTALL_PREFIX="../install" -DBLA_VENDOR=Intel10_64lp ../`
 
-- Execute `make`
-- Execute `make install`
+- To build:
+	- Execute `make`
+- To install:
+	- Execute `make install`

CONTRIBUTORS.md

@@ -8,12 +8,14 @@
 * Andreas Püttmann (Forschungszentrum Juelich GmbH, IBG-1: Biotechnology, Juelich, Germany): Parameter sensitivities, Jacobians via AD, AD techniques (block- & band-compression)
 * [Samuel Leweke](https://github.com/sleweke) (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, 2D general rate model (paid by GE Healthcare), multiple particle types (paid by GE Healthcare)
 * [William Heymann](https://github.com/immudzen) (Forschungszentrum Juelich GmbH, IBG-1: Biotechnology, Juelich, Germany): Networks of unit operations, compiler flag optimization
-Salah Azzouzi (Forschungszentrum Juelich GmbH, IBG-1: Biotechnology, Juelich, Germany): Core-shell particles (paid by GE Healthcare)
+* Salah Azzouzi (Forschungszentrum Juelich GmbH, IBG-1: Biotechnology, Juelich, Germany): Core-shell particles (paid by GE Healthcare)
 * [Johannes Schmölder](https://github.com/schmoelder) (Forschungszentrum Juelich GmbH, IBG-1: Biotechnology, Juelich, Germany)
 * [Jayghosh Rao](https://github.com/jayghoshter) (Forschungszentrum Juelich GmbH, IBG-1: Biotechnology, Juelich, Germany)
 * [Jazib Hassan](https://github.com/jazib-hassan-juelich) (Forschungszentrum Juelich GmbH, IBG-1: Biotechnology, Juelich, Germany)
-* [Jan Breuer](https://github.com/jbreue16) (Forschungszentrum Juelich GmbH, IBG-1: Biotechnology, Juelich, Germany)
+* [Jan Breuer](https://github.com/jbreue16) (Forschungszentrum Juelich GmbH, IBG-1: Biotechnology, Juelich, Germany): Spatial DG discretizations (LRM, LRMP, GRM)
 * [Ronald Jäpel](https://github.com/ronald-jaepel) (Forschungszentrum Juelich GmbH, IBG-1: Biotechnology, Juelich, Germany)
+* [Hannah Lanzrath](https://github.com/hannahlanzrath) (Forschungszentrum Juelich GmbH, IBG-1: Biotechnology, Juelich, Germany)
+* [Antonia Berger](https://github.com/AntoniaBerger) (Forschungszentrum Juelich GmbH, IBG-1: Biotechnology, Juelich, Germany)
 
 ## Funding Acknowledgement
 

README.rst

@@ -15,8 +15,8 @@ CADET
 
 - **Website (including documentation):** https://cadet.github.io
 - **Forum:** https://forum.cadet-web.de
-- **Source:** https://github.com/modsim/cadet
-- **Bug reports:** https://github.com/modsim/cadet/issues
+- **Source:** https://github.com/cadet/cadet-core
+- **Bug reports:** https://github.com/cadet/cadet-core/issues
 - **Demo:** https://www.cadet-web.de 
 - **Newsletter:** https://cadet-web.de/newsletter/
 
@@ -55,22 +55,10 @@ Therefore, we kindly ask that any publications or projects leveraging the capabi
 
 - Püttmann, A.; Schnittert, S.; Naumann, U.; von Lieres, E.: `Fast and accurate parameter sensitivities for the general rate model of column liquid chromatography <http://dx.doi.org/10.1016/j.compchemeng.2013.04.021>`_, Computers and Chemical Engineering **56** (2013), 46–57.
 
-**Selected applications:**
-
-- Heymann, W.; Glaser, J.; Schlegel, F.; Johnson, W.; Rolandi, P.; von Lieres, E.: `Advanced score system and automated search strategies for parameter estimation in mechanistic chromatography modeling <https://doi.org/10.1016/j.chroma.2021.462693>`_, Journal of Chromatography A **1661** (2022): 462693.
-
-- He, Q.-L.; Leweke, S.; von Lieres, E.: `Efficient numerical simulation of simulated moving bed chromatography with a single-column solver <http://doi.org/10.1016/j.compchemeng.2017.12.022>`_, Computers and Chemical Engineering **111** (2018), 183–198.
-
-- Freier, L.; von Lieres, E.: `Robust multi-objective global optimization of stochastic processes with a case study in gradient elution chromatography <http://doi.org/10.1002/biot.201700257>`_, Biotechnology Journal **13,1** (2018), 1700257.
-
-- Freier, L.; von Lieres, E.: [Multi-objective global optimization (MOGO): `Algorithm and case study in gradient elution chromatography <http://dx.doi.org/10.1002/biot.201600613>`_, Biotechnology Journal **12,7** (2017), 1600613.
-
-- Diedrich, J.; Heymann, W.; Leweke, S.; Kunert, C.; Johnson, W.; Hunt, S.; Todd, B.; von Lieres, E.: `Multi-state steric mass-action model and case study on complex high loading behavior of mAb on ion exchange tentacle resin <https://doi.org/10.1016/j.chroma.2017.09.039>`_, Journal of Chromatography A **1525** (2017), 60–70.
-
-- Püttmann, A.; Schnittert, S.; Leweke, S.; von Lieres, E.: `Utilizing algorithmic differentiation to efficiently compute chromatograms and parameter sensitivities <https://doi.org/10.1016/j.ces.2015.08.050>`_, Chemical Engineering Science, **139** (2016), 152–162.
-
 Additionally, to ensure reproducibility of your work, we recommend citing the zenodo doi corresponding to the specific CADET release that you used.
 
+Selected applications that demonstrate the capabilities and use-cases of CADET are highlighted in the `documentation <https://cadet.github.io>`_.
+
 Ongoing Development
 -------------------
 
@@ -79,7 +67,7 @@ We do our best to provide you with a stable API. However, CADET is actively deve
 Bugs
 ----
 
-Please report any bugs that you find `here <https://github.com/modsim/cadet/issues>`_. Or, even better, fork the repository on `GitHub <https://github.com/modsim/cadet>`_ and create a pull request (PR) with the fix. 
+Please report any bugs that you find `here <https://github.com/cadet/cadet-core/issues>`_. Or, even better, fork the repository on `GitHub <https://github.com/cadet/cadet-core>`_ and create a pull request (PR) with the fix. 
 
 Donations
 ---------
@@ -90,11 +78,11 @@ Donations
 License
 -------
 
-Released under GPL v3. License (see `LICENSE.txt <https://github.com/modsim/CADET/blob/master/LICENSE.txt>`_)::
+Released under GPL v3. License (see `LICENSE.txt <https://github.com/cadet/cadet-core/blob/master/LICENSE.txt>`_)::
 
 Acknowledgments
 ---------------
 
-Please refer to the `list of contributors <https://github.com/modsim/CADET/blob/master/CONTRIBUTORS.md>`_ who helped building and funding this project.
+Please refer to the `list of contributors <https://github.com/cadet/cadet-core/blob/master/CONTRIBUTORS.md>`_ who helped building and funding this project.
 
    Copyright (C) 2004-2024 CADET Authors

doc/README.md

@@ -1,7 +1,7 @@
 ## CADET Documentation
 
 
-To build the documentation locally, install sphinx and other dependencies by running
+To build the documentation locally, in the `doc` folder, install sphinx and other dependencies by running
 
 ```
 pip install -r requirements.txt

doc/index.rst

@@ -79,12 +79,30 @@ Donations
 Citing
 ------
 
-To cite CADET please use the following publication:
+Citing
+------------
+The development of CADET has been a collaborative effort, with multiple dedicated individuals contributing their expertise to create a powerful and versatile open-source software tool.
+Countless hours of hard work have been invested to provide the scientific community with a valuable resource.
+As an open-source project, CADET relies on the support and recognition from users and researchers to thrive.
+Therefore, we kindly ask that any publications or projects leveraging the capabilities of CADET acknowledge its creators and their contributions by citing an adequate selection of our publications.
+
+**General:**
+
+- Leweke, S.; von Lieres, E.: `Chromatography Analysis and Design Toolkit (CADET) <https://doi.org/10.1016/j.compchemeng.2018.02.025>`_, Computers and Chemical Engineering **113** (2018), 274–294.
+
+- von Lieres, E.; Andersson, J.: `A fast and accurate solver for the general rate model of column liquid chromatography <https://doi.org/10.1016/j.compchemeng.2010.03.008>`_, Computers and Chemical Engineering **34,8** (2010), 1180–1191.
+
+**Numerics:**
+
+- Breuer, J. M.; Leweke, S.; Schmölder, J.; Gassner, G.; von Lieres, E.: `Spatial discontinuous Galerkin spectral element method for a family of chromatography models in CADET <https://doi.org/10.1016/j.compchemeng.2023.108340>`_, Computers and Chemical Engineering **177** (2023), 108340.
+
+- Leweke, S.; von Lieres, E.: `Fast arbitrary order moments and arbitrary precision solution of the general rate model of column liquid chromatography with linear isotherm <http://dx.doi.org/10.1016/j.compchemeng.2015.09.009>`_, Computers and Chemical Engineering **84** (2016), 350–362.
+
+- Püttmann, A.; Schnittert, S.; Naumann, U.; von Lieres, E.: `Fast and accurate parameter sensitivities for the general rate model of column liquid chromatography <http://dx.doi.org/10.1016/j.compchemeng.2013.04.021>`_, Computers and Chemical Engineering **56** (2013), 46–57.
+
+Additionally, to ensure reproducibility of your work, we recommend citing the `zenodo doi <https://doi.org/10.5281/zenodo.8179015>`_ corresponding to the specific CADET release that you used.
 
-* Leweke, S.; von Lieres, E.: `Chromatography Analysis and Design Toolkit (CADET) <http://doi.org/10.1016/j.compchemeng.2018.02.025>`_, Computers and Chemical Engineering 113 (2018), 274–294.
-* Püttmann, A.; Schnittert, S.; Leweke, S.; von Lieres, E.: `Utilizing algorithmic differentiation to efficiently compute chromatograms and parameter sensitivities <http://doi.org/10.1016/j.ces.2015.08.050>`_, Chemical Engineering Science, 139 (2016), 152–162.
-* Püttmann, A.; Schnittert, S.; Naumann, U.; von Lieres, E.: `Fast and accurate parameter sensitivities for the general rate model of column liquid chromatography <http://doi.org/10.1016/j.compchemeng.2013.04.021>`_, Computers and Chemical Engineering 56,13 (2013), 46-57.
-* von Lieres, E.; Andersson, J.: `A fast and accurate solver for the general rate model of column liquid chromatography <http://doi.org/10.1016/j.compchemeng.2010.03.008>`_, Computers and Chemical Engineering 34,8 (2010), 1180–1191.
+Selected applications that demonstrate the capabilities and use-cases of CADET are highlighted `here <https://github.com/cadet/CADET-Core/tree/master/doc/publications.md>`_.
 
 Acknowledgments
 ---------------

doc/interface/flux_reconstruction.rst

@@ -1,4 +1,4 @@
-.. _flux_restruction_methods:
+.. _flux_reconstruction_methods:
 
 Flux reconstruction methods
 ===========================

doc/interface/parameter_dependencies.rst

@@ -73,7 +73,108 @@ Here, :math:`p_{dep}` is the dependent parameter and :math:`p_{on}` is the param
 Parameter-State Dependencies
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
+Currently, the dependence of surface diffusion on the particle liquid salt component is the only available parameter-state dependence.
+
 Group /input/model/unit_XXX
 ---------------------------
 
-Parameter-State Dependencies are not fully implemented yet.
+``PAR_SURFDIFFUSION_DEP``
+
+   Parameter dependence of :math:`\texttt{PAR_SURFDIFFUSION}` on the particle liquid salt component (i.e. component with index 0). Valid dependencies are:
+
+   - :math:`\texttt{NONE}` Original parameter is used unmodified.
+   - :math:`\texttt{LIQUID_SALT_EXPONENTIAL}` Original parameter is modified by exponential law of liquid phase salt concentration.
+   - :math:`\texttt{LIQUID_SALT_POWER}` Original parameter is modified by power law of liquid phase salt concentration.
+   - :math:`\texttt{LIQUID_SALT_COLLOIDAL_AFFINITY}` Original parameter is modified by colloidal binding affinity based on liquid phase salt concentration.
+
+   Optional: If left out, no parameter dependence is assumed and the original surface diffusion coefficients are used unmodified.
+
+   ================  =========================================
+   **Type:** string  **Length:** :math:`1 / \texttt{NPARTYPE}`
+   ================  =========================================
+
+``PAR_SURFDIFFUSION_EXPFACTOR``
+
+   Factor :math:`\texttt{p1}` in exponential law particle surface diffusion relation
+   :math:`D_{s, i, m} = \tilde{D}_{s, i, m} p_{1, i, m} exp \left(p_{2, i, m} c_{0}^{p} \right)`, where :math:`\tilde{D}_{s, i, m}` is the original surface diffusion coefficient.
+   Only required if :math:`\texttt{PAR_SURFDIFFUSION_DEP}` is :math:`\texttt{LIQUID_SALT_EXPONENTIAL}`.
+
+   ================  =========================  ===================================
+   **Type:** double  **Range:** :math:`\geq 0`  **Length:** :math:`\texttt{NBOUND}`
+   ================  =========================  ===================================
+
+   ``PAR_SURFDIFFUSION_EXPFACTOR``
+   :math:`D_{s, i, m} = \tilde{D}_{s, i, m} \left[  p_{4, i, m} \left( k_{i, m} \left( c_{0}^{p} \right) \right)^{p_{5, i, m}} p_{6, i, m} exp \left( p_{7, i, m} k_{i, m} \left( c_{0}^{p} \right) \right) \right]`
+   where :math:`\tilde{D}_{s, i, m}` is the original surface diffusion coefficient and 
+   :math:`k_{i, m} \left( c_{0}^{p} \right) = p_{1, i, m}\left( c_{0}^{p} \right)^{p_{2, i, m}} + p_{3, i, m}`.
+   Only required if :math:`\texttt{PAR_SURFDIFFUSION_DEP}` is :math:`\texttt{LIQUID_SALT_COLLOIDAL_AFFINITY}`.
+
+   ================  =============================  ===================================
+   **Type:** double  **Range:** :math:`\mathbb{R}`  **Length:** :math:`\texttt{NBOUND}`
+   ================  =============================  ===================================
+
+``PAR_SURFDIFFUSION_EXPARGMULT``
+
+   Factor :math:`\texttt{p2}` in exponential law particle surface diffusion relation
+   :math:`D_{s, i, m} = \tilde{D}_{s, i, m} p_{1, i, m} exp \left(p_{2, i, m} c_{0}^{p} \right)`
+   where :math:`\tilde{D}_{s, i, m}` is the original surface diffusion coefficient. Only required if :math:`\texttt{PAR_SURFDIFFUSION_DEP}` is :math:`\texttt{LIQUID_SALT_EXPONENTIAL}`.
+
+   ================  =============================  ===================================
+   **Type:** double  **Range:** :math:`\mathbb{R}`  **Length:** :math:`\texttt{NBOUND}`
+   ================  =============================  ===================================
+
+``PAR_SURFDIFFUSION_POWFACTOR``
+
+   Factor :math:`\texttt{p1}` in power law particle surface diffusion relation
+   :math:`D_{s, i, m} = \tilde{D}_{s, i, m} p_{1, i, m} \left( c_{0}^{p} \right)^{p_{2, i, m}}`
+   where :math:`\tilde{D}_{s, i, m}` is the original surface diffusion coefficient. Only required if :math:`\texttt{PAR_SURFDIFFUSION_DEP}` is :math:`\texttt{LIQUID_SALT_POWER}`.
+
+   ================  =========================  ===================================
+   **Type:** double  **Range:** :math:`\geq 0`  **Length:** :math:`\texttt{NBOUND}`
+   ================  =========================  ===================================
+
+``PAR_SURFDIFFUSION_POWEXP``
+
+   Fjactor :math:`\texttt{p2}` in power law particle surface diffusion relation
+   :math:`D_{s, i, m} = \tilde{D}_{s, i, m} p_{1, i, m} \left( c_{0}^{p} \right)^{p_{2, i, m}}`
+   where :math:`\tilde{D}_{s, i, m}` is the original surface diffusion coefficient. Only required if :math:`\texttt{PAR_SURFDIFFUSION_DEP}` is :math:`\texttt{LIQUID_SALT_POWER}`.
+
+   ================  =============================  ===================================
+   **Type:** double  **Range:** :math:`\mathbb{R}`  **Length:** :math:`\texttt{NBOUND}`
+   ================  =============================  ===================================
+
+``PAR_SURFDIFFUSION_LOGKEQFACTOR``
+
+   Factor :math:`\texttt{p1}` in colloidal affinity law particle surface diffusion relation
+   :math:`D_{s, i, m} = \tilde{D}_{s, i, m} \left[  p_{4, i, m} \left( k_{i, m} \left( c_{0}^{p} \right) \right)^{p_{5, i, m}} p_{6, i, m} exp \left( p_{7, i, m} k_{i, m} \left( c_{0}^{p} \right) \right) \right]`
+   where :math:`\tilde{D}_{s, i, m}` is the original surface diffusion coefficient and 
+   :math:`k_{i, m} \left( c_{0}^{p} \right) = p_{1, i, m}\left( c_{0}^{p} \right)^{p_{2, i, m}} + p_{3, i, m}`.
+   Only required if :math:`\texttt{PAR_SURFDIFFUSION_DEP}` is :math:`\texttt{LIQUID_SALT_COLLOIDAL_AFFINITY}`.
+
+   ================  =============================  ===================================
+   **Type:** double  **Range:** :math:`\mathbb{R}`  **Length:** :math:`\texttt{NBOUND}`
+   ================  =============================  ===================================
+
+``PAR_SURFDIFFUSION_LOGKEQEXP``
+
+   Factor :math:`\texttt{p2}` in colloidal affinity law particle surface diffusion relation
+   :math:`D_{s, i, m} = \tilde{D}_{s, i, m} \left[  p_{4, i, m} \left( k_{i, m} \left( c_{0}^{p} \right) \right)^{p_{5, i, m}} p_{6, i, m} exp \left( p_{7, i, m} k_{i, m} \left( c_{0}^{p} \right) \right) \right]`
+   where :math:`\tilde{D}_{s, i, m}` is the original surface diffusion coefficient and 
+   :math:`k_{i, m} \left( c_{0}^{p} \right) = p_{1, i, m}\left( c_{0}^{p} \right)^{p_{2, i, m}} + p_{3, i, m}`.
+   Only required if :math:`\texttt{PAR_SURFDIFFUSION_DEP}` is :math:`\texttt{LIQUID_SALT_COLLOIDAL_AFFINITY}`.
+
+   ================  =============================  ===================================
+   **Type:** double  **Range:** :math:`\mathbb{R}`  **Length:** :math:`\texttt{NBOUND}`
+   ================  =============================  ===================================
+
+``PAR_SURFDIFFUSION_LOGKEQCONST``
+
+   Factor :math:`\texttt{p3}` in colloidal affinity law particle surface diffusion relation
+   :math:`D_{s, i, m} = \tilde{D}_{s, i, m} \left[  p_{4, i, m} \left( k_{i, m} \left( c_{0}^{p} \right) \right)^{p_{5, i, m}} p_{6, i, m} exp \left( p_{7, i, m} k_{i, m} \left( c_{0}^{p} \right) \right) \right]`
+   where :math:`\tilde{D}_{s, i, m}` is the original surface diffusion coefficient and 
+   :math:`k_{i, m} \left( c_{0}^{p} \right) = p_{1, i, m}\left( c_{0}^{p} \right)^{p_{2, i, m}} + p_{3, i, m}`.
+   Only required if :math:`\texttt{PAR_SURFDIFFUSION_DEP}` is :math:`\texttt{LIQUID_SALT_COLLOIDAL_AFFINITY}`.
+
+   ================  =============================  ===================================
+   **Type:** double  **Range:** :math:`\mathbb{R}`  **Length:** :math:`\texttt{NBOUND}`
+   ================  =============================  ===================================