Switch documentation citations to Doxygen BibTeX cite system

Replace manual HTML anchor references and inline text citations across
all docs with Doxygen native cite command backed by a central
references.bib file. This auto-generates a Bibliography page and
provides clickable citation links throughout the documentation.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

Author: sbryngelson

.typos.toml

@@ -30,4 +30,4 @@ unknwn = "unknwn"     # typo for "unknown" - tests unknown param detection
 tru = "tru"           # typo for "true" in "when_tru" - tests dependency keys
 
 [files]
-extend-exclude = ["docs/documentation/references*", "tests/", "toolchain/cce_simulation_workgroup_256.sh", "build-docs/"]
+extend-exclude = ["docs/documentation/references*", "docs/references.bib", "tests/", "toolchain/cce_simulation_workgroup_256.sh", "build-docs/"]

CMakeLists.txt

@@ -720,6 +720,7 @@ if (MFC_DOCUMENTATION)
         set(DOXYGEN_HTML_OUTPUT      "\"${CMAKE_CURRENT_BINARY_DIR}/${target}\"")
         set(DOXYGEN_MATHJAX_CODEFILE "\"${CMAKE_CURRENT_SOURCE_DIR}/docs/config.js\"")
         set(DOXYGEN_PROJECT_LOGO     "\"${CMAKE_CURRENT_SOURCE_DIR}/docs/res/icon.ico\"")
+        set(DOXYGEN_CITE_BIB_FILES   "\"${CMAKE_CURRENT_SOURCE_DIR}/docs/references.bib\"")
         set(DOXYGEN_IMAGE_PATH       "\"${CMAKE_CURRENT_SOURCE_DIR}/docs/res\"\
                                       \"${CMAKE_CURRENT_SOURCE_DIR}/docs/${target}\"")
 

docs/Doxyfile.in

@@ -740,7 +740,7 @@ LAYOUT_FILE            =
 # LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the
 # search path. See also \cite for info how to create references.
 
-CITE_BIB_FILES         =
+CITE_BIB_FILES         = @DOXYGEN_CITE_BIB_FILES@
 
 #---------------------------------------------------------------------------
 # Configuration options related to warning and progress messages

docs/documentation/case.md

@@ -2,74 +2,6 @@
 
 # References
 
-- <a id="Allaire02">Allaire, G., Clerc, S., and Kokh, S. (2002). A five-equation model for the simulation of interfaces between compressible fluids. Journal of Computational Physics, 181(2):577–616.</a>
+All references cited throughout the MFC documentation are managed via BibTeX and rendered automatically by Doxygen.
 
-- <a id="Ando10">Ando, K. (2010). Effects of polydispersity in bubbly flows. PhD thesis, California Institute of Technology.</a>
-
-- <a id="Balsara00">Balsara, D. S. and Shu, C.-W. (2000). Monotonicity preserving weighted essentially non-oscillatory schemes with increasingly high order of accuracy. Journal of Computational Physics, 160(2):405–452.</a>
-
-- <a id="Batten97">Batten, P., Clarke, N., Lambert, C., and Causon, D. M. (1997). On the choice of wavespeeds for the hllc riemann solver. SIAM Journal on Scientific Computing, 18(6):1553–1570.</a>
-
-- <a id="Bryngelson19">Bryngelson, S. H., Schmidmayer, K., Coralic, V., Meng, J. C., Maeda, K., and Colonius, T. (2019). Mfc: An open-source high-order multi-component, multi-phase, and multi-scale compressible flow solver. arXiv preprint arXiv:1907.10512.</a>
-
-- <a id="Cao24">Cao A. and. Sch&auml;fer F. (2024). Information Geometric Regularization of the Barotropic Euler Equations. arXiv preprint arXiv:2308.14127.</a>
-
-- <a id="Chen22">Chen, S. S., Li, J. P., Li, Z., Yuan, W., & Gao, Z. H. (2022). Anti-dissipation pressure correction under low Mach numbers for Godunov-type schemes. Journal of Computational Physics, 456, 111027. </a>
-
-- <a id="Childs12">Childs, H., Brugger, E., Whitlock, B., Meredith, J., Ahern, S., Pugmire, D., Biagas, K., Miller, M., Harrison, C., Weber, G. H., Krishnan, H., Fogal, T., Sanderson, A., Garth, C., Bethel, E. W., Camp, D., R¨ubel, O., Durant, M., Favre, J. M., and Navr´atil, P. (2012). VisIt: An End-User Tool For Visualizing and Analyzing Very Large Data. In High Performance Visualization–Enabling Extreme-Scale Scientific Insight, pages 357–372.</a>
-
-- <a id="Coralic15">Coralic, V. (2015). Simulation of shock-induced bubble collapse with application to vascular injury in shockwave lithotripsy. PhD thesis, California Institute of Technology.</a>
-
-- <a id="Coralic14">Coralic, V. and Colonius, T. (2014). Finite-volume weno scheme for viscous compressible multicomponent flows. Journal of computational physics, 274:95–121.</a>
-
-- <a id="Gottlieb98">Gottlieb, S. and Shu, C.-W. (1998). Total variation diminishing runge-kutta schemes. Mathematics of computation of the American Mathematical Society, 67(221):73–85.</a>
-
-- <a id="Guo23">Guo, H., Jiang, P., Ye, L., & Zhu, Y. (2023). An efficient and low-divergence method for generating inhomogeneous and anisotropic turbulence with arbitrary spectra. Journal of Fluid Mechanics, 970, A2.</a>
-
-- <a id="Henrick05">Henrick, A. K., Aslam, T. D., and Powers, J. M. (2005). Mapped weighted essentially nonoscillatory schemes: achieving optimal order near critical points. Journal of Computational Physics, 207(2):542–567.</a>
-
-- <a id="Borges08">Borges, R., Carmona, M., Costa, B., and Don, W. S. (2008). An improved weighted essentially non-oscillatory scheme for hyperbolic conservation laws. Journal of computational physics, 227(6):3191–3211.</a>
-
-- <a id="Fu16">Fu, L., Hu, X. Y., and Adams, N. A. (2016). A family of high-order targeted ENO schemes for compressible-fluid simulations. Journal of Computational Physics, 305:333–359.</a>
-
-- <a id="Johnsen08">Johnsen, E. (2008). Numerical simulations of non-spherical bubble collapse: With applications to shockwave lithotripsy. PhD thesis, California Institute of Technology.</a>
-
-- <a id="Maeda17">Maeda, K. and Colonius, T. (2017). A source term approach for generation of one-way acoustic waves in the euler and navier–stokes equations. Wave Motion, 75:36–49.</a>
-
-- <a id="Maeda18">Maeda, K. and Colonius, T. (2018). Eulerian–lagrangian method for simulation of cloud cavitation. Journal of computational physics, 371:994–1017.</a>
-
-- <a id="Meng16">Meng, J. C. C. (2016). Numerical simulations of droplet aerobreakup. PhD thesis, California Institute of Technology.</a>
-
-- <a id="Michalke64"> Michalke, A. (1964). On the inviscid instability of the hyperbolictangent velocity profile. Journal of Fluid Mechanics, 19(4), 543-556.</a>
-
-- <a id="Pirozzoli13">Pirozzoli, S., and Colonius, T. (2013). Generalized characteristic relaxation boundary conditions for unsteady compressible flow simulations. Journal of Computational Physics, 248:109-126.</a>
-
-- <a id="Preston07">Preston, A., Colonius, T., and Brennen, C. (2007). A reduced-order model of diffusive effects on the dynamics of bubbles. Physics of Fluids, 19(12):123302.</a>
-
-- <a id="Saurel09">Saurel, R., Petitpas, F., and Berry, R. A. (2009). Simple and efficient relaxation methods for interfaces separating compressible fluids, cavitating flows and shocks in multiphase mixtures. journal of Computational Physics, 228(5):1678–1712</a>
-
-- <a id="Schmidmayer19">Schmidmayer, K., Bryngelson, S. H., and Colonius, T. (2019). An assessment of multicomponent flow models and interface capturing schemes for spherical bubble dynamics. arXiv preprint arXiv:1903.08242.</a>
-
-- <a id="Suresh97">Suresh, A. and Huynh, H. (1997). Accurate monotonicity-preserving schemes with runge–kutta time stepping. Journal of Computational Physics, 136(1):83–99.</a>
-
-- <a id="Tam05">Tam, C. K., Ju, H., Jones, M. G., Watson, W. R., and Parrott, T. L. (2005). A computational and experimental study of slit resonators. Journal of Sound and Vibration, 284(3-5), 947-984.</a>
-
-- <a id="Thompson87">Thompson, K. W. (1987). Time dependent boundary conditions for hyperbolic systems. Journal of computational physics, 68(1):1–24.</a>
-
-- <a id="Thompson90">Thompson, K. W. (1990). Time-dependent boundary conditions for hyperbolic systems, ii. Journal of computational physics, 89(2):439–461.</a>
-
-- <a id="Thornber08">Thornber, B., Mosedale, A., Drikakis, D., Youngs, D., & Williams, R. J. (2008). An improved reconstruction method for compressible flows with low Mach number features. Journal of computational Physics, 227(10), 4873-4894.</a>
-
-- <a id="Titarev04">Titarev, V. A. and Toro, E. F. (2004). Finite-volume weno schemes for three-dimensional conservation laws. Journal of Computational Physics, 201(1):238–260.</a>
-
-- <a id="Tiwari13">Tiwari, A., Freund, J. B., and Pantano, C. (2013). A diffuse interface model with immiscibility preservation. Journal of computational physics, 252:290–309.</a>
-
-- <a id="Toro13">Toro, E. F. (2013). Riemann solvers and numerical methods for fluid dynamics: a practical introduction. Springer Science & Business Media.</a>
-
-- <a id="Miyoshi05">Miyoishi, T., and Kusano, K. (2005). A multi-state HLL approximate Riemann solver for ideal magnetohydrodynamics. Journal of Computational Physics, 208(1), 315-344.</a>
-
-- <a id="Dedner02">Dedner, A., Kemm, F., Kröner, D., Munz, C. D., Schnitzer, T., & Wesenberg, M. (2002). Hyperbolic divergence cleaning for the MHD equations. Journal of Computational Physics, 175(2), 645-673.</a>
-
-- <a id="Cao19">Cao, S., Zhang, Y., Liao, D., Zhong, P., and Wang, K. G. (2019). Shock-induced damage and dynamic fracture in cylindrical bodies submerged in liquid. International Journal of Solids and Structures, 169:55–71. Elsevier.</a>
-
-- <a id="Xu2019">Xu, W., Gao, Y., Deng, Y., Liu, J., and Liu, C. (2019). An explicit expression for the calculation of the Rortex vector. Physics of Fluids, 31(9)..</a>
+See the \ref citelist "Bibliography" for the full list of cited works.

docs/documentation/equations.md

@@ -40,7 +40,7 @@ For many cases, this step will require resizing the render view window.
 VisIt is an alternative open-source interactive parallel visualization and graphical analysis tool for viewing scientific data.
 Versions of VisIt after 2.6.0 have been confirmed to work with the MFC databases for some parallel environments.
 Nevertheless, installation and configuration of VisIt can be environment-dependent and are left to the user.
-Further remarks on parallel flow visualization, analysis, and processing of the MFC database using VisIt can also be found in [Coralic (2015)](@ref references) and [Meng (2016)](@ref references).
+Further remarks on parallel flow visualization, analysis, and processing of the MFC database using VisIt can also be found in \cite Coralic15 and \cite Meng16.
 
 The user can launch VisIt and open the index files under `/silo_hdf5/root`.
 Once the database is loaded, flow field variables contained in the database can be added to the plot.