Adds examples for CPC paper (#26)

Co-authored-by: Pierre Jolivet <prj-@users.noreply.github.com>

Author: cmdoug

examples/README.md

@@ -21,19 +21,20 @@ This folder contains example implementations that reproduce selected results fro
 
 | Folder | Description | Citation |
 | :--- | :--- | :--- |
-| [brokof_etal_2024](https://github.com/cmdoug/ff-bifbox/tree/main/examples/brokof_etal_2024) | stability and resolvent analysis of a reacting compressible flow in a duct with acoustic characteristic boundary conditions | Brokof, P., Douglas, C. M., & Polifke, W. (2024). The role of hydrodynamic shear in the thermoacoustic response of slit flames. _Proceedings of the Combustion Institute_, 40(1), 105362. doi:[10.1016/j.proci.2024.105362](https://doi.org/10.1016/j.proci.2024.105362). |
-| [chevalier_etal_2024](https://github.com/cmdoug/ff-bifbox/tree/main/examples/chevalier_etal_2024)| resolvent analysis of swirling jet mean flow with Spalart--Allmaras turbulence model | Chevalier, Q., Douglas, C., & Lesshafft, L. (2024). Resolvent analysis of swirling turbulent jets. _Theoretical and Computational Fluid Dynamics_. doi:[10.1007/s00162-024-00704-2](https://doi.org/10.1007/s00162-024-00704-2). |
-| [douglas_2024](https://github.com/cmdoug/ff-bifbox/tree/main/examples/douglas_2024) | analysis of various outflow boundary conditions for swirling flows | Douglas, C. M. (2024). A balanced outflow boundary condition for swirling flows. _Theoretical and Compuational Fluid Dynamics_. doi:[10.1007/s00162-024-00701-5](https://doi.org/10.1007/s00162-024-00701-5). |
-| [douglas_etal_2021](https://github.com/cmdoug/ff-bifbox/tree/main/examples/douglas_etal_2021) | bifurcation analysis of an incompressible axisymmetric swirling jet with axisymmetry breaking | Douglas, C. M., Emerson, B. L., & Lieuwen, T. C. (2021). Nonlinear dynamics of fully developed swirling jets. _Journal of Fluid Mechanics_, 924, A14. doi:[10.1017/jfm.2021.615](https://doi.org/10.1017/jfm.2021.615). |
-| [douglas_etal_2022](https://github.com/cmdoug/ff-bifbox/tree/main/examples/douglas_etal_2022) | bifurcation analysis of an incompressible axisymmetric swirling annular jet with coordinate transformation and axisymmetry breaking | Douglas, C. M., Emerson, B. L., & Lieuwen, T. C. (2022). Dynamics and bifurcations of laminar annular swirling and non-swirling jets. _Journal of Fluid Mechanics_, 943, A35. doi:[10.1017/jfm.2022.453](https://doi.org/10.1017/jfm.2022.453). |
-| [douglas_etal_2023](https://github.com/cmdoug/ff-bifbox/tree/main/examples/douglas_etal_2023) | bifurcation analysis of a reacting weakly-compressible axisymmetric jet with axisymmetry breaking | Douglas, C. M., Polifke, W., & Lesshafft, L. (2023). Flash-back, blow-off, and symmetry breaking of premixed conical flames. _Combustion and Flame_, 258(2), 113060. doi:[10.1016/j.combustflame.2023.113060](https://doi.org/10.1016/j.combustflame.2023.113060). |
-| [fani_etal_2018](https://github.com/cmdoug/ff-bifbox/tree/main/examples/fani_etal_2018) | bifurcation analysis of a compressible 2-D flow over a cylinder with reflective symmetry breaking | Fani, A., Citro, V., Giannetti, F., & Auteri, F. (2018). Computation of the bluff-body sound generation by a self-consistent mean flow formulation. _Physics of Fluids_, 30(3), 036102. doi:[10.1063/1.4997536](https://doi.org/10.1063/1.4997536). |
-| [FK_problem](https://github.com/cmdoug/ff-bifbox/tree/main/examples/FK_problem) | bifurcation analysis of Frank–Kamenetskii thermal runaway (explosion) in a cylinderical vessel | I. B. Zeldovich, G. I. Barenblatt, V. B. Librovich, G. M. Makhviladze, _Mathematical theory of combustion and explosions_, 1985. |
-| [garnaud_2012](https://github.com/cmdoug/ff-bifbox/tree/main/examples/garnaud_2012) | resolvent analysis of an incompressible axisymmetric laminar jet | Garnaud, X. (2012). _Modes, transient dynamics and forced response of circular jets_. [Doctoral dissertation, Ecole Polytechnique], HAL ID:[tel-00740133](https://theses.hal.science/tel-00740133). |
-| [marquet_larsson_2015](https://github.com/cmdoug/ff-bifbox/tree/main/examples/marquet_larsson_2015) | bifurcation analysis of an incompressible 3-D flow over a thin flat plate with coordinate transformation and multiple symmetries | Marquet, O., & Larsson, M. (2015). Global wake instabilities of low aspect-ratio flat-plates. _European Journal of Mechanics - B/Fluids_, 49(B), 400-412. doi:[10.1016/j.euromechflu.2014.05.005](https://doi.org/10.1016/j.euromechflu.2014.05.005). |
-| [meliga_etal_2012](https://github.com/cmdoug/ff-bifbox/tree/main/examples/meliga_etal_2012) | bifurcation analysis of an axisymmetric incompressible Grabowski--Berger vortex with axisymmetry breaking and weakly nonlinear analysis | Meliga, P., Gallaire, F., & Chomaz, J.-M. (2012). A weakly nonlinear mechanism for mode selection in swirling jets. _Journal of Fluid Mechanics_, 699, 216–262. doi:[10.1017/jfm.2012.93](https://doi.org/10.1017/jfm.2012.93). |
-| [moreno-boza_etal_2018](https://github.com/cmdoug/ff-bifbox/tree/main/examples/moreno-boza_etal_2018) | analysis of puffing instability in an axisymmetric non-premixed pool flame | Moreno-Boza, D., Coenen, W., Carpio, J., Sánchez A.L., & Williams, F.A. (2018). On the critical conditions for pool-fire puffing. _Combustion and Flame_, 192, 426-438. doi:[10.1016/j.combustflame.2018.02.011](https://doi.org/10.1016/j.combustflame.2018.02.011). |
-| [moulin_etal_2019](https://github.com/cmdoug/ff-bifbox/tree/main/examples/moulin_etal_2019) | stability analysis of a 3-D incompressible flow over a thin flat plate using the mAL preconditioner | Moulin, J., Jolivet, P., & Marquet, O. (2019). Augmented Lagrangian preconditioner for large-scale hydrodynamic stability analysis. _Computer Methods in Applied Mechanics and Engineering_, 351, 718-743. doi:[10.1016/j.cma.2019.03.052](https://doi.org/10.1016/j.cma.2019.03.052). |
-| [pralits_etal_2010](https://github.com/cmdoug/ff-bifbox/tree/main/examples/pralits_etal_2010) | bifurcation analysis of an incompressible 2-D flow over a rotating cylinder | Pralits, J. O., Brandt, L., & Giannetti, F. (2010). Instability and sensitivity of the flow around a rotating circular cylinder. _Journal of Fluid Mechanics_, 650, 513–536. doi:[10.1017/S0022112009993764](https://doi.org/10.1017/S0022112009993764). |
-| [sipp_lebedev_2007](https://github.com/cmdoug/ff-bifbox/tree/main/examples/sipp_lebedev_2007) | bifurcation analysis of the incompressible 2-D flows over a cylinder and open cavity with weakly nonlinear analysis | Sipp, D., & Lebedev, A. (2007). Global stability of base and mean flows: a general approach and its applications to cylinder and open cavity flows. _Journal of Fluid Mechanics_, 593, 333–358. doi:[10.1017/S0022112007008907](https://doi.org/10.1017/S0022112007008907). |
-| [wang_etal_2024](https://github.com/cmdoug/ff-bifbox/tree/main/examples/wang_etal_2024) | global linear and nonlinear analysis of an axisymmetric lean premixed V-flame in a weakly-compressible annular jet | Wang, C., Douglas, C., Guan, Y., Xu. C, & Lesshafft, L. (2024). Onset of global instability in a premixed annular V-flame. _Journal of Fluid Mechanics_, 998, A23. doi:[10.1017/jfm.2024.869](https://doi.org/10.1017/jfm.2024.869). |
+| [brokof_etal_2024](./brokof_etal_2024) | stability and resolvent analysis of a reacting compressible flow in a duct with acoustic characteristic boundary conditions | Brokof, P., Douglas, C. M., & Polifke, W. (2024). The role of hydrodynamic shear in the thermoacoustic response of slit flames. _Proceedings of the Combustion Institute_, 40(1), 105362. doi:[10.1016/j.proci.2024.105362](https://doi.org/10.1016/j.proci.2024.105362). |
+| [chevalier_etal_2024](./chevalier_etal_2024)| resolvent analysis of swirling jet mean flow with Spalart--Allmaras turbulence model | Chevalier, Q., Douglas, C., & Lesshafft, L. (2024). Resolvent analysis of swirling turbulent jets. _Theoretical and Computational Fluid Dynamics_. doi:[10.1007/s00162-024-00704-2](https://doi.org/10.1007/s00162-024-00704-2). |
+| [douglas_2024](./douglas_2024) | analysis of various outflow boundary conditions for swirling flows | Douglas, C. M. (2024). A balanced outflow boundary condition for swirling flows. _Theoretical and Computational Fluid Dynamics_. doi:[10.1007/s00162-024-00701-5](https://doi.org/10.1007/s00162-024-00701-5). |
+| [douglas_etal_2021](./douglas_etal_2021) | bifurcation analysis of an incompressible axisymmetric swirling jet with axisymmetry breaking | Douglas, C. M., Emerson, B. L., & Lieuwen, T. C. (2021). Nonlinear dynamics of fully developed swirling jets. _Journal of Fluid Mechanics_, 924, A14. doi:[10.1017/jfm.2021.615](https://doi.org/10.1017/jfm.2021.615). |
+| [douglas_etal_2022](./douglas_etal_2022) | bifurcation analysis of an incompressible axisymmetric swirling annular jet with coordinate transformation and axisymmetry breaking | Douglas, C. M., Emerson, B. L., & Lieuwen, T. C. (2022). Dynamics and bifurcations of laminar annular swirling and non-swirling jets. _Journal of Fluid Mechanics_, 943, A35. doi:[10.1017/jfm.2022.453](https://doi.org/10.1017/jfm.2022.453). |
+| [douglas_etal_2023](./douglas_etal_2023) | bifurcation analysis of a reacting weakly-compressible axisymmetric jet with axisymmetry breaking | Douglas, C. M., Polifke, W., & Lesshafft, L. (2023). Flash-back, blow-off, and symmetry breaking of premixed conical flames. _Combustion and Flame_, 258(2), 113060. doi:[10.1016/j.combustflame.2023.113060](https://doi.org/10.1016/j.combustflame.2023.113060). |
+| [douglas_jolivet_2026](./douglas_jolivet_2026) | bifurcation analysis of a 3-D Brusselator system, a 3-D plate buckling system, and a 2-D compressible Navier--Stokes system | Douglas, C. M., & Jolivet, P. (2026). ff-bifbox: A scalable, open-source toolbox for bifurcation analysis of nonlinear PDEs. _Computer Physics Communications_, (accepted manuscript). doi:[10.48550/arXiv.2509.18429](https://doi.org/10.48550/arXiv.2509.18429). |
+| [fani_etal_2018](./fani_etal_2018) | bifurcation analysis of a compressible 2-D flow over a cylinder with reflective symmetry breaking | Fani, A., Citro, V., Giannetti, F., & Auteri, F. (2018). Computation of the bluff-body sound generation by a self-consistent mean flow formulation. _Physics of Fluids_, 30(3), 036102. doi:[10.1063/1.4997536](https://doi.org/10.1063/1.4997536). |
+| [FK_problem](./FK_problem) | bifurcation analysis of Frank–Kamenetskii thermal runaway (explosion) in a cylinderical vessel | \Zeldovich, I. B., Barenblatt, G. I., Librovich, V. B., & Makhviladze, G. M. _Mathematical theory of combustion and explosions_, 1985. |
+| [garnaud_2012](./garnaud_2012) | resolvent analysis of an incompressible axisymmetric laminar jet | Garnaud, X. (2012). _Modes, transient dynamics and forced response of circular jets_. [Doctoral dissertation, Ecole Polytechnique], HAL ID:[tel-00740133](https://theses.hal.science/tel-00740133). |
+| [marquet_larsson_2015](./marquet_larsson_2015) | bifurcation analysis of an incompressible 3-D flow over a thin flat plate with coordinate transformation and multiple symmetries | Marquet, O., & Larsson, M. (2015). Global wake instabilities of low aspect-ratio flat-plates. _European Journal of Mechanics - B/Fluids_, 49(B), 400-412. doi:[10.1016/j.euromechflu.2014.05.005](https://doi.org/10.1016/j.euromechflu.2014.05.005). |
+| [meliga_etal_2012](./meliga_etal_2012) | bifurcation analysis of an axisymmetric incompressible Grabowski--Berger vortex with axisymmetry breaking and weakly nonlinear analysis | Meliga, P., Gallaire, F., & Chomaz, J.-M. (2012). A weakly nonlinear mechanism for mode selection in swirling jets. _Journal of Fluid Mechanics_, 699, 216–262. doi:[10.1017/jfm.2012.93](https://doi.org/10.1017/jfm.2012.93). |
+| [moreno-boza_etal_2018](./moreno-boza_etal_2018) | analysis of puffing instability in an axisymmetric non-premixed pool flame | Moreno-Boza, D., Coenen, W., Carpio, J., Sánchez, A. L., & Williams, F.A. (2018). On the critical conditions for pool-fire puffing. _Combustion and Flame_, 192, 426-438. doi:[10.1016/j.combustflame.2018.02.011](https://doi.org/10.1016/j.combustflame.2018.02.011). |
+| [moulin_etal_2019](./moulin_etal_2019) | stability analysis of a 3-D incompressible flow over a thin flat plate using the mAL preconditioner | Moulin, J., Jolivet, P., & Marquet, O. (2019). Augmented Lagrangian preconditioner for large-scale hydrodynamic stability analysis. _Computer Methods in Applied Mechanics and Engineering_, 351, 718-743. doi:[10.1016/j.cma.2019.03.052](https://doi.org/10.1016/j.cma.2019.03.052). |
+| [pralits_etal_2010](./pralits_etal_2010) | bifurcation analysis of an incompressible 2-D flow over a rotating cylinder | Pralits, J. O., Brandt, L., & Giannetti, F. (2010). Instability and sensitivity of the flow around a rotating circular cylinder. _Journal of Fluid Mechanics_, 650, 513–536. doi:[10.1017/S0022112009993764](https://doi.org/10.1017/S0022112009993764). |
+| [sipp_lebedev_2007](./sipp_lebedev_2007) | bifurcation analysis of the incompressible 2-D flows over a cylinder and open cavity with weakly nonlinear analysis | Sipp, D., & Lebedev, A. (2007). Global stability of base and mean flows: a general approach and its applications to cylinder and open cavity flows. _Journal of Fluid Mechanics_, 593, 333–358. doi:[10.1017/S0022112007008907](https://doi.org/10.1017/S0022112007008907). |
+| [wang_etal_2024](./wang_etal_2024) | global linear and nonlinear analysis of an axisymmetric lean premixed V-flame in a weakly-compressible annular jet | Wang, C., Douglas, C. M., Guan, Y., Xu C., & Lesshafft, L. (2024). Onset of global instability in a premixed annular V-flame. _Journal of Fluid Mechanics_, 998, A23. doi:[10.1017/jfm.2024.869](https://doi.org/10.1017/jfm.2024.869). |