cadet · schmoelder · Feb 21, 2024 · Jul 27, 2023 · Jul 27, 2023 · Jul 27, 2023
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -0,0 +1,22 @@
+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# We recommend specifying your dependencies to enable reproducible builds:
+# https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
+python:
+  install:
+  - requirements: docs/requirements.txt
diff --git a/README.rst b/README.rst
@@ -4,11 +4,14 @@ CADET
 .. image:: https://img.shields.io/github/release/modsim/cadet.svg
    :target: https://github.com/modsim/CADET/releases
 
-.. image:: https://img.shields.io/github/downloads/modsim/cadet/latest/total.svg
-   :target: https://github.com/modsim/CADET/releases
-
 .. image:: https://github.com/modsim/CADET/actions/workflows/ci.yml/badge.svg
-   :target: https://github.com/modsim/CADET/actions
+   :target: https://github.com/modsim/CADET/actions/workflows/ci.yml
+
+.. image:: https://anaconda.org/conda-forge/cadet/badges/downloads.svg
+   :target: https://anaconda.org/conda-forge/cadet
+
+.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.8179015.svg
+   :target: https://doi.org/10.5281/zenodo.8179015
 
 - **Website (including documentation):** https://cadet.github.io
 - **Forum:** https://forum.cadet-web.de
@@ -31,6 +34,42 @@ Optionally, use `mamba <https://github.com/mamba-org/mamba>`_ which uses a faste
 
 `Additional information <https://cadet.github.io/master/getting_started/installation>`_ and a `tutorial <https://cadet.github.io/master/getting_started/tutorials/breakthrough>`_ are available to guide you through the installation and the first steps of using CADET.
 
+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.
+
+**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.
 
 Ongoing Development
 -------------------

diff --git a/cmake/Modules/FindCADET.cmake b/cmake/Modules/FindCADET.cmake
@@ -1,7 +1,7 @@
 # =============================================================================
 #  CADET
 #  
-#  Copyright © 2008-2022: The CADET Authors
+#  Copyright © 2008-2024: The CADET Authors
 #            Please see the AUTHORS and CONTRIBUTORS file.
 #  
 #  All rights reserved. This program and the accompanying materials

diff --git a/cmake/Modules/FindSUNDIALS.cmake b/cmake/Modules/FindSUNDIALS.cmake
@@ -1,7 +1,7 @@
 # =============================================================================
 #  CADET
 #  
-#  Copyright © 2008-2022: The CADET Authors
+#  Copyright © 2008-2024: The CADET Authors
 #            Please see the AUTHORS and CONTRIBUTORS file.
 #  
 #  All rights reserved. This program and the accompanying materials

diff --git a/cmake/Modules/FindSuperLU.cmake b/cmake/Modules/FindSuperLU.cmake
@@ -1,7 +1,7 @@
 # =============================================================================
 #  CADET
 #  
-#  Copyright © 2008-2022: The CADET Authors
+#  Copyright © 2008-2024: The CADET Authors
 #            Please see the AUTHORS and CONTRIBUTORS file.
 #  
 #  All rights reserved. This program and the accompanying materials

diff --git a/cmake/Modules/FindUMFPACK.cmake b/cmake/Modules/FindUMFPACK.cmake
@@ -1,7 +1,7 @@
 # =============================================================================
 #  CADET
 #  
-#  Copyright © 2008-2022: The CADET Authors
+#  Copyright © 2008-2024: The CADET Authors
 #            Please see the AUTHORS and CONTRIBUTORS file.
 #  
 #  All rights reserved. This program and the accompanying materials

diff --git a/cmake/Modules/MatlabTBBversion.cpp b/cmake/Modules/MatlabTBBversion.cpp
@@ -1,7 +1,7 @@
 // =============================================================================
 //  CADET
 //  
-//  Copyright © 2008-2022: The CADET Authors
+//  Copyright © 2008-2024: The CADET Authors
 //            Please see the AUTHORS and CONTRIBUTORS file.
 //  
 //  All rights reserved. This program and the accompanying materials

diff --git a/doc/index.rst b/doc/index.rst
@@ -7,14 +7,14 @@
 .. image:: https://img.shields.io/github/release/modsim/cadet.svg
    :target: https://github.com/modsim/CADET/releases
 
-.. image:: https://img.shields.io/github/downloads/modsim/cadet/latest/total.svg
-   :target: https://github.com/modsim/CADET/releases
+.. image:: https://github.com/modsim/CADET/actions/workflows/ci.yml/badge.svg
+   :target: https://github.com/modsim/CADET/actions/workflows/ci.yml
 
-.. image:: https://img.shields.io/travis/modsim/CADET/master.svg?logo=travis&maxAge=3600)
-   :target: https://travis-ci.org/modsim/CADET
+.. image:: https://anaconda.org/conda-forge/cadet/badges/downloads.svg
+   :target: https://anaconda.org/conda-forge/cadet
 
-.. image:: https://img.shields.io/appveyor/ci/sleweke/cadet/master.svg?logo=appveyor&maxAge=3600svg=true
-   :target: https://ci.appveyor.com/project/sleweke/cadet
+.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.8179015.svg
+   :target: https://doi.org/10.5281/zenodo.8179015
 
 |
 

diff --git a/doc/interface/binding/bi_steric_mass_action.rst b/doc/interface/binding/bi_steric_mass_action.rst
@@ -5,6 +5,8 @@ Bi Steric Mass Action
 
 **Group /input/model/unit_XXX/adsorption – ADSORPTION_MODEL = BI_STERIC_MASS_ACTION**
 
+For information on model equations, refer to :ref:`bi_steric_mass_action_model`.
+
 
 ``IS_KINETIC``
    Selects kinetic or quasi-stationary adsorption mode: 1 = kinetic, 0 =

diff --git a/doc/interface/binding/extended_mobile_phase_modulator_langmuir.rst b/doc/interface/binding/extended_mobile_phase_modulator_langmuir.rst
@@ -5,6 +5,8 @@ Extended Mobile Phase Modulator Langmuir
 
 **Group /input/model/unit_XXX/adsorption – ADSORPTION_MODEL = EXTENDED_MOBILE_PHASE_MODULATOR**
 
+For information on model equations, refer to :ref:`extended_mobile_phase_modulator_langmuir_model`.
+
 
 ``IS_KINETIC``
    Selects kinetic or quasi-stationary adsorption mode: 1 = kinetic, 0 =

diff --git a/doc/interface/binding/freundlich_ldf.rst b/doc/interface/binding/freundlich_ldf.rst
@@ -5,6 +5,8 @@ Freundlich LDF
 
 **Group /input/model/unit_XXX/adsorption – ADSORPTION_MODEL = FREUNDLICH_LDF**
 
+For information on model equations, refer to :ref:`freundlich_ldf_model`.
+
 
 ``IS_KINETIC``
    Selects kinetic or quasi-stationary adsorption mode: 1 = kinetic, 0 =

diff --git a/doc/interface/binding/generalized_ion_exchange.rst b/doc/interface/binding/generalized_ion_exchange.rst
@@ -5,6 +5,8 @@ Generalized Ion Exchange
 
 **Group /input/model/unit_XXX/adsorption – ADSORPTION_MODEL = GENERALIZED_ION_EXCHANGE**
 
+For information on model equations, refer to :ref:`generalized_ion_exchange_model`.
+
 
 ``IS_KINETIC``
    Selects kinetic or quasi-stationary adsorption mode: 1 = kinetic, 0 =

diff --git a/doc/interface/binding/hic_constant_water_activity.rst b/doc/interface/binding/hic_constant_water_activity.rst
@@ -5,6 +5,8 @@ HIC Constant Water Activity
 
 **Group /input/model/unit_XXX/adsorption – ADSORPTION_MODEL = HIC_CONSTANT_WATER_ACTIVITY**
 
+For information on model equations, refer to :ref:`hic_constant_water_activity_model`.
+
 
 ``IS_KINETIC``
    Selects kinetic or quasi-stationary adsorption mode: 1 = kinetic, 0 =

diff --git a/doc/interface/binding/hic_water_on_hydrophobic_surfaces.rst b/doc/interface/binding/hic_water_on_hydrophobic_surfaces.rst
@@ -5,6 +5,8 @@ HIC Water on Hydrophobic Surfaces
 
 **Group /input/model/unit_XXX/adsorption – ADSORPTION_MODEL = HIC_WATER_ON_HYDROPHOBIC_SURFACES**
 
+For information on model equations, refer to :ref:`hic_water_on_hydrophobic_surfaces_model`.
+
 
 ``IS_KINETIC``
    Selects kinetic or quasi-stationary adsorption mode: 1 = kinetic, 0 =

diff --git a/doc/interface/binding/index.rst b/doc/interface/binding/index.rst
@@ -52,10 +52,13 @@ This group also takes precedence over a possibly existing ``/input/model/unit_XX
 
     linear
     multi_component_langmuir
-    multi_component_bi_langmuir
-    multi_component_anti_langmuir
+    multi_component_langmuir_ldf
+    multi_component_langmuir_ldf_liquid_phase
     mobile_phase_modulator_langmuir
     extended_mobile_phase_modulator_langmuir
+    multi_component_bi_langmuir
+    multi_component_bi_langmuir_ldf
+    multi_component_anti_langmuir
     multi_component_spreading
     steric_mass_action
     multi_state_steric_mass_action
@@ -64,7 +67,7 @@ This group also takes precedence over a possibly existing ``/input/model/unit_XX
     generalized_ion_exchange
     saska
     self_association
-    kumar_langmuir
+    freundlich_ldf
     hic_water_on_hydrophobic_surfaces
     hic_constant_water_activity
 
diff --git a/doc/interface/binding/linear.rst b/doc/interface/binding/linear.rst
@@ -5,6 +5,8 @@ Linear
 
 **Group /input/model/unit_XXX/adsorption – ADSORPTION_MODEL = LINEAR**
 
+For information on model equations, refer to :ref:`linear_model`.
+
 
 ``IS_KINETIC``
    Selects kinetic or quasi-stationary adsorption mode: 1 = kinetic, 0 =

diff --git a/doc/interface/binding/mobile_phase_modulator_langmuir.rst b/doc/interface/binding/mobile_phase_modulator_langmuir.rst
@@ -5,6 +5,8 @@ Mobile Phase Modulator Langmuir
 
 **Group /input/model/unit_XXX/adsorption – ADSORPTION_MODEL = MOBILE_PHASE_MODULATOR**
 
+For information on model equations, refer to :ref:`mobile_phase_modulator_langmuir_model`.
+
 
 ``IS_KINETIC``
    Selects kinetic or quasi-stationary adsorption mode: 1 = kinetic, 0 =

diff --git a/doc/interface/binding/multi_component_anti_langmuir.rst b/doc/interface/binding/multi_component_anti_langmuir.rst
@@ -5,6 +5,8 @@ Multi Component Anti-Langmuir
 
 **Group /input/model/unit_XXX/adsorption – ADSORPTION_MODEL = MULTI_COMPONENT_ANTILANGMUIR**
 
+For information on model equations, refer to :ref:`multi_component_anti_langmuir_model`.
+
 
 ``IS_KINETIC``
    Selects kinetic or quasi-stationary adsorption mode: 1 = kinetic, 0 =

diff --git a/doc/interface/binding/multi_component_bi_langmuir.rst b/doc/interface/binding/multi_component_bi_langmuir.rst
@@ -5,6 +5,8 @@ Multi Component Bi-Langmuir
 
 **Group /input/model/unit_XXX/adsorption – ADSORPTION_MODEL = MULTI_COMPONENT_BILANGMUIR**
 
+For information on model equations, refer to :ref:`multi_component_bi_langmuir_model`.
+
 
 ``IS_KINETIC``
    Selects kinetic or quasi-stationary adsorption mode: 1 = kinetic, 0 =

diff --git a/doc/interface/binding/multi_component_bi_langmuir_ldf.rst b/doc/interface/binding/multi_component_bi_langmuir_ldf.rst
@@ -5,6 +5,8 @@ Multi Component Bi-Langmuir LDF
 
 **Group /input/model/unit_XXX/adsorption – ADSORPTION_MODEL = MULTI_COMPONENT_BILANGMUIR_LDF**
 
+For information on model equations, refer to :ref:`multi_component_bi_langmuir_ldf_model`.
+
 
 ``IS_KINETIC``
    Selects kinetic or quasi-stationary adsorption mode: 1 = kinetic, 0 =

diff --git a/doc/interface/binding/multi_component_langmuir.rst b/doc/interface/binding/multi_component_langmuir.rst
@@ -5,6 +5,8 @@ Multi Component Langmuir
 
 **Group /input/model/unit_XXX/adsorption – ADSORPTION_MODEL = MULTI_COMPONENT_LANGMUIR**
 
+For information on model equations, refer to :ref:`multi_component_langmuir_model`.
+
 
 ``IS_KINETIC``
    Selects kinetic or quasi-stationary adsorption mode: 1 = kinetic, 0 =

diff --git a/doc/interface/binding/multi_component_langmuir_ldf.rst b/doc/interface/binding/multi_component_langmuir_ldf.rst
@@ -5,6 +5,8 @@ Multi Component Langmuir LDF
 
 **Group /input/model/unit_XXX/adsorption – ADSORPTION_MODEL = MULTI_COMPONENT_LANGMUIR_LDF**
 
+For information on model equations, refer to :ref:`multi_component_langmuir_ldf_model`.
+
 
 ``IS_KINETIC``
    Selects kinetic or quasi-stationary adsorption mode: 1 = kinetic, 0 =

diff --git a/doc/interface/binding/multi_component_langmuir_ldf_liquid_phase.rst b/doc/interface/binding/multi_component_langmuir_ldf_liquid_phase.rst
@@ -5,6 +5,8 @@ Multi Component Langmuir LDF Liquid Phase
 
 **Group /input/model/unit_XXX/adsorption – ADSORPTION_MODEL = MULTI_COMPONENT_LANGMUIR_LDF_LIQUID_PHASE**
 
+For information on model equations, refer to :ref:`multi_component_langmuir_ldf_liquid_phase_model`.
+
 
 ``IS_KINETIC``
    Selects kinetic or quasi-stationary adsorption mode: 1 = kinetic, 0 =

diff --git a/doc/interface/binding/multi_component_spreading.rst b/doc/interface/binding/multi_component_spreading.rst
@@ -5,6 +5,8 @@ Multi Component Spreading
 
 **Group /input/model/unit_XXX/adsorption – ADSORPTION_MODEL = MULTI_COMPONENT_SPREADING**
 
+For information on model equations, refer to :ref:`multi_component_spreading_model`.
+
 
 ``IS_KINETIC``
    Selects kinetic or quasi-stationary adsorption mode: 1 = kinetic, 0 =

diff --git a/doc/interface/binding/multi_state_steric_mass_action.rst b/doc/interface/binding/multi_state_steric_mass_action.rst
@@ -5,6 +5,8 @@ Multi-State Steric Mass Action
 
 **Group /input/model/unit_XXX/adsorption – ADSORPTION_MODEL = MULTISTATE_STERIC_MASS_ACTION**
 
+For information on model equations, refer to :ref:`multi_state_steric_mass_action_model`.
+
 
 ``IS_KINETIC``
    Selects kinetic or quasi-stationary adsorption mode: 1 = kinetic, 0 =

diff --git a/doc/interface/binding/saska.rst b/doc/interface/binding/saska.rst
@@ -5,6 +5,8 @@ Saska
 
 **Group /input/model/unit_XXX/adsorption – ADSORPTION_MODEL = SASKA**
 
+For information on model equations, refer to :ref:`saska_model`.
+
 
 ``IS_KINETIC``
    Selects kinetic or quasi-stationary adsorption mode: 1 = kinetic, 0 =

diff --git a/doc/interface/binding/self_association.rst b/doc/interface/binding/self_association.rst
@@ -5,6 +5,8 @@ Self Association
 
 **Group /input/model/unit_XXX/adsorption – ADSORPTION_MODEL = SELF_ASSOCIATION**
 
+For information on model equations, refer to :ref:`self_association_model`.
+
 
 ``IS_KINETIC``
    Selects kinetic or quasi-stationary adsorption mode: 1 = kinetic, 0 =

diff --git a/doc/interface/binding/simplified_multi_state_steric_mass_action.rst b/doc/interface/binding/simplified_multi_state_steric_mass_action.rst
@@ -5,6 +5,8 @@ Simplified Multi-State Steric Mass Action
 
 **Group /input/model/unit_XXX/adsorption – ADSORPTION_MODEL = SIMPLIFIED_MULTISTATE_STERIC_MASS_ACTION**
 
+For information on model equations, refer to :ref:`simplified_multi_state_steric_mass_action_model`.
+
 
 ``IS_KINETIC``
    Selects kinetic or quasi-stationary adsorption mode: 1 = kinetic, 0 =

diff --git a/doc/interface/binding/steric_mass_action.rst b/doc/interface/binding/steric_mass_action.rst
@@ -5,6 +5,8 @@ Steric Mass Action
 
 **Group /input/model/unit_XXX/adsorption – ADSORPTION_MODEL = STERIC_MASS_ACTION**
 
+For information on model equations, refer to :ref:`steric_mass_action_model`.
+
 
 ``IS_KINETIC``
    Selects kinetic or quasi-stationary adsorption mode: 1 = kinetic, 0 =

diff --git a/doc/interface/consistent_initialization.rst b/doc/interface/consistent_initialization.rst
@@ -5,6 +5,7 @@ Nonlinear solver for consistent initialization
 
 Group /input/model/unit_XXX/discretization/consistency_solver - Nonlinear consistency solver paramters
 ------------------------------------------------------------------------------------------------------
+
 ``SOLVER_NAME``
 
 Name of the solver. Available solvers are ``LEVMAR``, ``ATRN_RES``, ``ATRN_ERR``, and ``COMPOSITE``.