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+++ b/joss.06963/10.21105.joss.06963.crossref.xml
@@ -0,0 +1,231 @@
+
+
+
+ 20241030151253-f2a06a390fe9800579bda985adb4c40be88793ea
+ 20241030151253
+
+ JOSS Admin
+ admin@theoj.org
+
+ The Open Journal
+
+
+
+
+ Journal of Open Source Software
+ JOSS
+ 2475-9066
+
+ 10.21105/joss
+ https://joss.theoj.org
+
+
+
+
+ 10
+ 2024
+
+
+ 9
+
+ 102
+
+
+
+ OpenCCM: An Open-Source Continuous Compartmental
+Modelling Package
+
+
+
+ Alexandru Andrei
+ Vasile
+
+ Department of Chemical Engineering, University of Waterloo, Ontario, Canada
+
+ https://orcid.org/0000-0002-0233-0172
+
+
+ Matthew Peres
+ Tino
+
+ Department of Chemical Engineering, University of Waterloo, Ontario, Canada
+
+ https://orcid.org/0009-0005-6832-1761
+
+
+ Yuvraj
+ Aseri
+
+ Department of Chemical Engineering, University of Waterloo, Ontario, Canada
+
+ https://orcid.org/0009-0008-4703-3711
+
+
+ Nasser Mohieddin
+ Abukhdeir
+
+ Department of Chemical Engineering, University of Waterloo, Ontario, Canada
+ Department of Physics and Astronomy, University of Waterloo, Ontario, Canada
+ Waterloo Institute for Nanotechnology, University of Waterloo, Ontario, Canada
+
+ https://orcid.org/0000-0002-1772-0376
+
+
+
+ 10
+ 30
+ 2024
+
+
+ 6963
+
+
+ 10.21105/joss.06963
+
+
+ http://creativecommons.org/licenses/by/4.0/
+ http://creativecommons.org/licenses/by/4.0/
+ http://creativecommons.org/licenses/by/4.0/
+
+
+
+ Software archive
+ 10.5281/zenodo.13988255
+
+
+ GitHub review issue
+ https://github.com/openjournals/joss-reviews/issues/6963
+
+
+
+ 10.21105/joss.06963
+ https://joss.theoj.org/papers/10.21105/joss.06963
+
+
+ https://joss.theoj.org/papers/10.21105/joss.06963.pdf
+
+
+
+
+
+ Cantera: An object-oriented software toolkit
+for chemical kinetics, thermodynamics, and transport
+processes
+ Goodwin
+ 10.5281/zenodo.8137090
+ 2023
+ Goodwin, D. G., Moffat, H. K.,
+Schoegl, I., Speth, R. L., & Weber, B. W. (2023). Cantera: An
+object-oriented software toolkit for chemical kinetics, thermodynamics,
+and transport processes. https://www.cantera.org.
+https://doi.org/10.5281/zenodo.8137090
+
+
+ Compartment modelling
+software
+ Quintessa
+ Quintessa. (n.d.). Compartment
+modelling software. Quintessa; Online. Retrieved January 3, 2024, from
+https://www.quintessa.org/software/AMBER
+
+
+ OpenFOAM v12 user guide
+ Greenshields
+ 2024
+ Greenshields, C. (2024). OpenFOAM v12
+user guide. The OpenFOAM Foundation.
+https://doc.cfd.direct/openfoam/user-guide-v12
+
+
+ OpenCMP: An Open-Source Computational
+Multiphysics Package
+ Monte
+ Journal of Open Source
+Software
+ 73
+ 7
+ 10.21105/joss.03742
+ 2475-9066
+ 2022
+ Monte, E. J., Vasile, A. A., Lowman,
+J., & Abukhdeir, N. M. (2022). OpenCMP: An Open-Source Computational
+Multiphysics Package. Journal of Open Source Software, 7(73), 3742.
+https://doi.org/10.21105/joss.03742
+
+
+ A flow alignment-informed method for
+compartmental modelling
+ Vasile
+ Computers & Chemical
+Engineering
+ 185
+ 10.1016/j.compchemeng.2024.108650
+ 0098-1354
+ 2024
+ Vasile, A. A., Aucoin, M. G., Budman,
+H., & Abukhdeir, N. M. (2024). A flow alignment-informed method for
+compartmental modelling. Computers & Chemical Engineering, 185,
+108650.
+https://doi.org/10.1016/j.compchemeng.2024.108650
+
+
+ Compartmental modelling in chemical
+engineering: A critical review
+ Jourdan
+ Chemical Engineering Science
+ 210
+ 10.1016/j.ces.2019.115196
+ 0009-2509
+ 2019
+ Jourdan, N., Neveux, T., Potier, O.,
+Kanniche, M., Wicks, J., Nopens, I., Rehman, U., & Le Moullec, Y.
+(2019). Compartmental modelling in chemical engineering: A critical
+review. Chemical Engineering Science, 210, 115196.
+https://doi.org/10.1016/j.ces.2019.115196
+
+
+ Model reduction methods
+ Chinesta
+ Encyclopedia of computational mechanics
+second edition
+ 10.1002/9781119176817.ecm2110
+ 9781119176817
+ 2017
+ Chinesta, F., Huerta, A., Rozza, G.,
+& Willcox, K. (2017). Model reduction methods. In Encyclopedia of
+computational mechanics second edition (pp. 1–36). John Wiley &
+Sons, Ltd.
+https://doi.org/10.1002/9781119176817.ecm2110
+
+
+ Model Order Reduction: Volume 3
+Applications
+ 10.1515/9783110499001
+ 2020
+ Benner, P., Schilders, W.,
+Grivet-Talocia, S., Quarteroni, A., Rozza, G., & Miguel Silveira, L.
+(Eds.). (2020). Model Order Reduction: Volume 3 Applications. De
+Gruyter. https://doi.org/10.1515/9783110499001
+
+
+ The paraview guide: A parallel visualization
+application
+ Ayachit
+ 2015
+ Ayachit, U. (2015). The paraview
+guide: A parallel visualization application. Kitware,
+Inc.
+
+
+
+
+
+
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+
+
+
+
+
+
+
+Journal of Open Source Software
+JOSS
+
+2475-9066
+
+Open Journals
+
+
+
+6963
+10.21105/joss.06963
+
+OpenCCM: An Open-Source Continuous
+Compartmental Modelling Package
+
+
+
+https://orcid.org/0000-0002-0233-0172
+
+Vasile
+Alexandru Andrei
+
+
+
+
+https://orcid.org/0009-0005-6832-1761
+
+Tino
+Matthew Peres
+
+
+
+
+https://orcid.org/0009-0008-4703-3711
+
+Aseri
+Yuvraj
+
+
+
+
+https://orcid.org/0000-0002-1772-0376
+
+Abukhdeir
+Nasser Mohieddin
+
+
+
+
+*
+
+
+
+Department of Chemical Engineering, University of Waterloo,
+Ontario, Canada
+
+
+
+
+Department of Physics and Astronomy, University of
+Waterloo, Ontario, Canada
+
+
+
+
+Waterloo Institute for Nanotechnology, University of
+Waterloo, Ontario, Canada
+
+
+
+
+* E-mail:
+
+9
+102
+6963
+
+Authors of papers retain copyright and release the
+work under a Creative Commons Attribution 4.0 International License (CC
+BY 4.0)
+2022
+The article authors
+
+Authors of papers retain copyright and release the work under
+a Creative Commons Attribution 4.0 International License (CC BY
+4.0)
+
+
+
+Python
+compartmental modelling
+reduced order modelling
+model order reduction
+computational fluid dynamics
+
+
+
+
+
+ Summary
+
OpenCCM is a compartmental modelling
+ (Jourdan
+ et al., 2019) software package based on recently developed
+ fully automated flow alignment compartmentalization methods
+ (Vasile
+ et al., 2024). It is primarily intended for large-scale
+ flow-based processes with weak coupling between composition changes,
+ e.g., through (bio)chemical reactions, and convective mass transport
+ in the system. Compartmental modelling is an important approach used
+ to develop reduced-order models
+ (Benner
+ et al., 2020;
+ Chinesta
+ et al., 2017) using a priori knowledge of process hydrodynamics
+ (Jourdan
+ et al., 2019). Compartmental modelling methods, such as those
+ implemented in OpenCCM, enable simulations of
+ these processes with far less computational complexity while still
+ capturing the key aspects of process dynamics.
+
OpenCCM integrates with two multiphysics
+ simulation software packages, OpenCMP
+ (Monte
+ et al., 2022) and OpenFOAM
+ (Greenshields,
+ 2024), allowing for ease of transferring simulation data for
+ compartmentalization. Additionally, it provides users with built-in
+ functionality for computing residence times and exporting for use in
+ other simulation or visualization software, including
+ ParaView
+ (Ayachit,
+ 2015). Post-processing methods are included for mapping
+ simulation results from compartment domains to the original simulation
+ domain, which are useful for visualization purposes and for further
+ simulations in using other software (e.g., multi-scale modelling).
+
+
+ Statement of Need
+
Simulation-based design and analysis continue to be widely applied
+ in the research and development of physicochemical processes.
+ Processes with large differences in characteristic time and length
+ scales result in the infeasibility of direct multiphysics simulations
+ due to computational limitations. This imposes significant
+ computational costs, which severely reduce the utility of these
+ simulations for entire classes of processes. Compartmental modeling is
+ well-suited for such applications because it enables the generatation
+ of reduced-order models which are less computationally demanding,
+ frequently by orders of magnitude, compared to direct continuum
+ mechanical simulations. This is enabled by taking advantage, when
+ present, of weak couplings between the short and long-time-scale
+ dynamic phenomena.
+
However, several barriers prevent the more widespread use of
+ compartmental models. The largest of these is the lack of software for
+ automating the generation compartmental models. Closed-source software
+ packages, specifically AMBER
+ (Quintessa,
+ n.d.), exists for manually creating and solving well-mixed
+ compartment networks. However, the cost of these packages are
+ prohibitive for much of the research community and it lacks automated
+ compartmentalization. Open-source software,
+ Cantera
+ (Goodwin
+ et al., 2023), also exists to solve compartment networks.
+ However, it does not incorporate flow information, when available,
+ either from direct observation or continuum mechanical simulations.
+ Furthermore, neither of these software allow for the usage and direct
+ transfer of flow information from continuum mechanical simulations,
+ such as computational fluid dynamics (CFD) simulations, which are
+ typically feasible over short (hydrodynamic) time scales.
+
The overall aim of OpenCCM is to fill the
+ need for an open-source compartmental modeling package that is
+ user-friendly, compatible with a variety of simulation package
+ back-ends (e.g., OpenFOAM and
+ OpenCMP), and which fits into the user’s
+ existing simulation and post-processing software toolchain, i.e.,
+ ParaView.
+
+
+ Features
+
+
+
+
+
+
+
+
+
FEATURE
+
DESCRIPTION
+
+
+
+
+
Model support
+
Accepts OpenCMP
+ (Monte
+ et al., 2022) and OpenFOAM
+ (Greenshields,
+ 2024) results
Linear, non-linear, and reversible arbitrary
+ reactions
+
+
+
+
1st Order upwinding finite-difference-based
+
+
+
+
Adaptive time-stepping
+
+
+
————————-
+
————————————————————————————-
+
+
+
Post-Processing
+
Residence time distribution
+
+
+
————————-
+
————————————————————————————-
+
+
+
Output
+
Intermediary mesh format
+
+
+
+
Labeled compartments in Paraview
+ format
+
+
+
+
Concentrations from CM simulations in both
+ Paraview and simulation package
+ format
+
+
+
————————-
+
————————————————————————————-
+
+
+
Performance
+
Multi-threading
+
+
+
+
Caching of intermediary results to speed up subsequent
+ runs
+
+
+
+
+
+
+ User Interface
+
The OpenCCM Python package can be used via
+ text-based configuration files centred around the command line
+ interface (CLI), where each simulation run/project is self-contained
+ in a project directory. In addition to the
+ OpenCCM configuration files, the required
+ contents include flow information from one of two open-source
+ simulation packages: OpenCMP or
+ OpenFOAM. For OpenCMP
+ three files are required:
+
+
+
+
The OpenCMP config file,
+
+
+
+
The mesh on which the simulation was run, and
+
+
+
+
The .sol solution file containing the velocity profile to
+ create the compartmental model.
+
+
+
For OpenFOAM, two sub-directories are
+ required:
+
+
+
+
The constant/ directory, which contains
+ the mesh information in ASCII format,
+
+
+
+
A directory containing the simulation results, which will be
+ used to create the compartmental model saved in ASCII format.
+
+
+
The path to the solution directory is specified in the
+ OpenCCM configuration file and the
+ constant/ directory is assumed to be in the
+ same parent folder. OpenCCM will create several
+ output directories: log/, which contains
+ detailed debugging information (if enabled);
+ cache/, which contains intermediary files; and
+ output_ccm/, which contains both simulation
+ results of the compartmental model (in various user-specified formats)
+ and ParaView files for visualization.
+
A sample config file, CONFIG, which outlines
+ the available parameters, is included in the main directory. An
+ excerpt of it, showing the compartmental modeling parameters, is shown
+ below. Square brackets indicate parameters with default values along
+ with those values indicated inside the brackets.
+ [COMPARTMENT MODELLING]
+# Whether to use PFRs-in-series or a CSTR to model each compartment.
+model = PFR
+# Volumetric flow through a single facet
+# below which the flow is considered 0.
+flow_threshold_facet = [1e-15]
+# Volumetric flow threshold through a surface
+# below which the flow is considered 0.
+flow_threshold = [1e-15]
+# Maximum allowable difference (in % of compartment volume)
+# between connections to merge them into one location.
+dist_threshold = [5 / 100]
+# Absolute tolerances for checking that mass is conserved
+# after the flow optimization is performed.
+atol_opt = [1e-2]
+
+
+ Reaction Configuration File
+
The chemical reaction parser in OpenCCM
+ reads and parses the reaction configuration files and can handle
+ general reaction equations of the form,
+
aA + bB + [...] -> cC + dD + [...]
+
with associated numeric rate constants. It intentionally does not
+ support the standard <-> symbol for
+ reversible chemical reactions, so that each independent reaction has
+ an explicitly defined rate constant. Therefore, a reversible reaction
+ must be written as two independent forward reactions, each with its
+ own rate constant. Each species label can contain
+ letters and numbers, but cannot contain brackets or special
+ characters, e.g., “(”, “)”, “+”, “-”, “^”. Kinetic rate constants must
+ be expressed as positive real numbers in standard or scientific
+ notation. Additionally, each reaction/rate pair must have a unique
+ identifier (i.e., R1, R2). For example, the
+ reversible reaction,
+
+
+ 2NaCl+CaCO3⇔Na2CO3+CaCl2
+
with
+
+ kf=5e−2
+ and
+
+ kr=2
+ (chosen to be dimensionless for example). A configuration file for
+ this reversible reaction may then be:
where R1 and R2 are the reaction
+ identifiers for the forward and reverse reactions,
+ respectively.
+
An example reaction config file,
+ CONFIG_REACTIONS, is provided in the main
+ package directory.
+
+
+ Examples of Usage
+
Several examples are provided in the OpenCCM
+ documentation, which demonstrates the using of both
+ OpenCMP and OpenFOAM
+ simulation-based flow information for compartmentalization. One
+ example, located in
+ examples/OpenCMP/pipe_with_recird_2d/, uses the
+ geometry from
+ (Vasile
+ et al., 2024) and shows how to execute the needed CFD
+ simulation for flow information (both using
+ OpenCMP and OpenFOAM),
+ create/visualize the compartmental model results, and compare the
+ predicted RTD to the reference result directly from CFD
+ simulation.
+
For this illustrative example, the steady-state hydrodynamic
+ flow-profile is obtained by running the OpenCMP
+ simulation through the run_OpenCMP.py script in
+ the folder. The resulting flow profile was opened in
+ ParaView and a line integral convolution
+ visualization of the velocity field is shown below, coloured by
+ velocity magnitude.
+
+
Visualization of hydrodynamics from CFD simulation with
+ line integral convolutions indicating local flow direction and color
+ corresponding to velocity magnitude.
+
+
+
The underlying velocity field data is then processed using
+ OpenCCM to generate a network of compartments
+ by executing the run_compartment.py script. The
+ figure below shows each element of the original mesh coloured
+ according to the compartment to which it belongs.
+
+
Visualization of flow-informed compartmentalization with
+ coloring corresponding to compartment number.
+
+
+
That network of compartments is further processed, as each
+ compartment is represented by a series of plug-flow reactors (PFRs).
+ The resulting network (graph) of PFRs is shown in the figure below.
+ Nodes are the centres of the PFRs and edges are connections (flows)
+ between PFRs.
+
+
Undirectly graph of the compartment network resulting
+ from both (i) flow-information compartmentalization and (ii) the use
+ of spatially-varying compartment approximations
+ (PFRs).
+
+
+
+ RTD Curves
+
The residence time distribution (RTD) curve from both the CFD and
+ compartmental model (CM) simulations is computed using the script in
+ the supplementary material of
+ (Vasile
+ et al., 2024).
+
+
Residence time distribution curves for CFD and CM
+ simulations.
+
+
+
+
+ Reactions
+
Finally, to demonstrate how to simulate chemical reaction, an
+ example is included using the reversible reaction system from
+ above:
+
+
+ 2NaCl+CaCO3⇔Na2CO3+CaCl2
+
with
+
+ kf=5e−2
+ and
+
+ kr=2
+ as the forward and backward rate constants (chosen to be
+ dimensionless for example). All species have an initial
+ dimensionless concentration of
+
+ 0
+ and have inlet boundary dimensionless concentration values of
+
+
+ [NaCl]=[CaCO3]=1
+ and
+
+ [Na2CO3]=[CaCl2]=0.
+ The equations and conditions have already been specified, and the
+ simulation can be run by using the
+ run_compartment_w_rxn.py script. Note that
+ when this script is run multiple times, computational times
+ following the first will be much shorter in that the compartmental
+ model is pre-computed (stored within the project directory).
+
To analyze the results, the equilibrium values for this
+ reversible system are calculated as follows:
where x is the change in
+
+
+ CaCO3,
+ in dimensionless units.
+
The expected equilibrium concentrations for the four species are:
+
+
+ [NaCl]=0.7706,
+
+
+ [CaCO3]=0.8853,
+
+
+ [Na2CO3]=0.1147,
+ and
+
+ [CaCl2]=0.1147.
+ Based on the figures below and from direct inspection of the CM
+ simulation results, correct steady-state values are obtained at the
+ reactor outlet.
+
+ Input/Output Concentrations for NaCl.
+
+
+ Input/Output Concentrations for CaCO3.
+
+
+ Input/Output Concentrations for Na2CO3.
+
+
+ Input/Output Concentrations for CaCl2.
+
+
To output the ParaView visualizations,
+ change output_VTK to
+ True in the CONFIG
+ file and re-run the simulation.
+
+
+
+ Acknowledgements
+
This research was supported by the Natural Sciences and Engineering
+ Research Council of Canada (NSERC) and the Digital Research Alliance
+ of Canada.
+
+
+
+
+
+
+
+
+ GoodwinDavid G.
+ MoffatHarry K.
+ SchoeglIngmar
+ SpethRaymond L.
+ WeberBryan W.
+
+ Cantera: An object-oriented software toolkit for chemical kinetics, thermodynamics, and transport processes
+ https://www.cantera.org
+ 2023
+ 10.5281/zenodo.8137090
+
+
+
+
+
+ Quintessa
+
+ Compartment modelling software
+ Quintessa; Online
+ 20240103
+ https://www.quintessa.org/software/AMBER
+
+
+
+
+
+ GreenshieldsChristopher
+
+ OpenFOAM v12 user guide
+ The OpenFOAM Foundation
+ London, UK
+ 2024
+ https://doc.cfd.direct/openfoam/user-guide-v12
+
+
+
+
+
+ MonteElizabeth Julia
+ VasileAlexandru Andrei
+ LowmanJames
+ AbukhdeirNasser Mohieddin
+
+ OpenCMP: An Open-Source Computational Multiphysics Package
+ Journal of Open Source Software
+ 202205
+ 20230523
+ 7
+ 73
+ 2475-9066
+ 10.21105/joss.03742
+ 3742
+
+
+
+
+
+
+ VasileAlexandru Andrei
+ AucoinMarc G.
+ BudmanHector
+ AbukhdeirNasser Mohieddin
+
+ A flow alignment-informed method for compartmental modelling
+ Computers & Chemical Engineering
+ 2024
+ 185
+ 0098-1354
+ https://www.sciencedirect.com/science/article/pii/S0098135424000681
+ 10.1016/j.compchemeng.2024.108650
+ 108650
+
+
+
+
+
+
+ JourdanNicolas
+ NeveuxThibaut
+ PotierOlivier
+ KannicheMohamed
+ WicksJim
+ NopensIngmar
+ RehmanUsman
+ Le MoullecYann
+
+ Compartmental modelling in chemical engineering: A critical review
+ Chemical Engineering Science
+ 2019
+ 210
+ 0009-2509
+ https://www.sciencedirect.com/science/article/pii/S0009250919306888
+ 10.1016/j.ces.2019.115196
+ 115196
+
+
+
+
+
+
+ ChinestaFrancisco
+ HuertaAntonio
+ RozzaGianluigi
+ WillcoxKaren
+
+ Model reduction methods
+ Encyclopedia of computational mechanics second edition
+ John Wiley & Sons, Ltd
+ 2017
+ 9781119176817
+ https://onlinelibrary.wiley.com/doi/abs/10.1002/9781119176817.ecm2110
+ 10.1002/9781119176817.ecm2110
+ 1
+ 36
+
+
+
+
+ Model Order Reduction: Volume 3 Applications
+
+ BennerPeter
+ SchildersWil
+ Grivet-TalociaStefano
+ QuarteroniAlfio
+ RozzaGianluigi
+ Miguel SilveiraLuís
+
+ De Gruyter
+ 2020
+ 20230814
+ 10.1515/9783110499001
+
+
+
+
+
+ AyachitUtkarsh
+
+ The paraview guide: A parallel visualization application
+ Kitware, Inc.
+ 2015
+
+
+
+
+
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