Add citations

Add citations in the "Statement of Need" section with papers published with meshes from HOHQMesh.

paper.bib

@@ -1,10 +1,10 @@
 %% This BibTeX bibliography file was created using BibDesk.
 %% https://bibdesk.sourceforge.io/
 
-%% Created for David Kopriva at 2024-10-18 16:54:49 -0700
+%% Created for David Kopriva at 2024-10-29 13:34:44 -0700 
 
 
-%% Saved with string encoding Unicode (UTF-8)
+%% Saved with string encoding Unicode (UTF-8) 
 
 
 
@@ -14,24 +14,24 @@ @misc{fischer2008nek5000
 	date-modified = {2024-10-18 16:54:48 -0700},
 	title = {NEK fast high-order scalable CFD NEK: Fast high-order scalable {CFD}},
 	url = {https://nek5000.mcs.anl.gov},
-	year = {2008}}
+	year = {2008},
+	bdsk-url-1 = {https://nek5000.mcs.anl.gov}}
 
 @misc{kopriva2024hohqmesh,
-  title={{HOHQM}esh: An All Quadrilateral/Hexahedral Unstructured Mesh Generator for High Order Elements},
-  author={Kopriva, David A and Winters, Andrew R and Schlottke-Lakemper, Michael
-          and Schoonover, Joseph A and Ranocha, Hendrik},
-  year={2024},
-  howpublished={\url{https://github.com/trixi-framework/HOHQMesh}},
-  doi={10.5281/zenodo.13959058}
-}
+	author = {Kopriva, David A and Winters, Andrew R and Schlottke-Lakemper, Michael and Schoonover, Joseph A and Ranocha, Hendrik},
+	doi = {10.5281/zenodo.13959058},
+	howpublished = {\url{https://github.com/trixi-framework/HOHQMesh}},
+	title = {{HOHQM}esh: An All Quadrilateral/Hexahedral Unstructured Mesh Generator for High Order Elements},
+	year = {2024},
+	bdsk-url-1 = {https://doi.org/10.5281/zenodo.13959058}}
 
 @misc{kopriva2024hohqmeshjl,
-  title={{HOHQM}esh.jl: A Julia frontend to the Fortran-based HOHQMesh mesh generator for high order elements},
-  author={Kopriva, David A and Winters, Andrew R and Schlottke-Lakemper, Michael and Ranocha, Hendrik},
-  year={2024},
-  howpublished={\url{https://github.com/trixi-framework/HOHQMesh.jl}},
-  doi={10.5281/zenodo.13959071}
-}
+	author = {Kopriva, David A and Winters, Andrew R and Schlottke-Lakemper, Michael and Ranocha, Hendrik},
+	doi = {10.5281/zenodo.13959071},
+	howpublished = {\url{https://github.com/trixi-framework/HOHQMesh.jl}},
+	title = {{HOHQM}esh.jl: A Julia frontend to the Fortran-based HOHQMesh mesh generator for high order elements},
+	year = {2024},
+	bdsk-url-1 = {https://doi.org/10.5281/zenodo.13959071}}
 
 @article{Martire:2021xt,
 	abstract = {{We introduce SPECFEM2D-DG, an open-source, time-domain, hybrid Galerkin software modelling the propagation of seismic and acoustic waves in coupled solid--fluid systems. For the solid part, the visco-elastic system from the routinely used SPECFEM2D software is used to simulate linear seismic waves subject to attenuation. For the fluid part, SPECFEM2D-DG includes two extensions to the acoustic part of SPECFEM2D, both relying on the Navier--Stokes equations to model high-frequency acoustics, infrasound and gravity waves in complex atmospheres. The first fluid extension, SPECFEM2D-DG-FNS, was introduced in 2017 by Brissaud, Martin, Garcia, and Komatitsch; it features a nonlinear Full Navier--Stokes (FNS) approach discretized with a discontinuous Galerkin numerical scheme. In this contribution, we focus only on introducing a second fluid extension, SPECFEM2D-DG-LNS, based on the same numerical method but rather relying on the Linear Navier--Stokes (LNS) equations. The three main modules of SPECFEM2D-DG all use the spectral element method (SEM). For both fluid extensions (FNS and LNS), two-way mechanical coupling conditions preserve the Riemann problem solution at the fluid--solid interface. Absorbing outer boundary conditions (ABCs) derived from the perfectly matched layers' approach is proposed for the LNS extension. The SEM approach supports complex topographies and unstructured meshes. The LNS equations allow the use of range-dependent atmospheric models, known to be crucial for the propagation of infrasound at regional scales. The LNS extension is verified using the method of manufactured solutions, and convergence is numerically characterized. The mechanical coupling conditions at the fluid--solid interface (between the LNS and elastodynamics systems of equations) are verified against theoretical reflection-transmission coefficients. The ABCs in the LNS extension are tested and prove to yield satisfactory energy dissipation. In an example case study, we model infrasonic waves caused by quakes occurring under various topographies; we characterize the acoustic scattering conditions as well as the apparent acoustic radiation pattern. Finally, we discuss the example case and conclude by describing the capabilities of this software. SPECFEM2D-DG is open-source and is freely available online on GitHub.}},
@@ -291,30 +291,33 @@ @book{Karniadakis:2005fj
 	author = {George Em Karniadakis and Spencer J. Sherwin},
 	date-added = {2024-10-10 08:42:26 -0700},
 	date-modified = {2024-10-10 08:42:26 -0700},
+	doi = {10.1093/acprof:oso/9780198528692.001.0001},
 	publisher = {Oxford University Press},
 	title = {Spectral/hp Element Methods for Computational Fluid Dynamics},
 	year = {2005},
-	doi={10.1093/acprof:oso/9780198528692.001.0001}}
+	bdsk-url-1 = {https://doi.org/10.1093/acprof:oso/9780198528692.001.0001}}
 
 @book{Hestahven:1008th,
 	author = {J.S. Hesthaven and T. Warburton},
 	date-added = {2024-10-10 08:41:53 -0700},
 	date-modified = {2024-10-10 08:41:53 -0700},
+	doi = {10.1007/978-0-387-72067-8},
 	publisher = {Springer},
 	title = {Nodal Discontinuous {G}alerkin Methods: Algorithms, Analysis, and Applications},
 	year = {2008},
-	doi={10.1007/978-0-387-72067-8}}
+	bdsk-url-1 = {https://doi.org/10.1007/978-0-387-72067-8}}
 
 @book{Kopriva:2009nx,
 	author = {David A. Kopriva},
 	date-added = {2024-10-10 08:41:39 -0700},
 	date-modified = {2024-10-10 08:41:39 -0700},
+	doi = {10.1007/978-90-481-2261-5},
 	month = {May},
 	publisher = {Springer},
 	series = {Scientific Computation},
 	title = {Implementing Spectral Methods for Partial Differential Equations},
 	year = {2009},
-	doi={10.1007/978-90-481-2261-5}}
+	bdsk-url-1 = {https://doi.org/10.1007/978-90-481-2261-5}}
 
 @book{Deville:2002fk,
 	author = {M.O. Deville and P.F. Fischer and E.H. Mund},
@@ -326,14 +329,15 @@ @book{Deville:2002fk
 
 @article{ainsworth2004,
 	author = {Ainsworth, Mark},
+	doi = {10.1016/j.jcp.2004.01.004},
 	journal = {Journal of Computational Physics},
 	number = {1},
 	pages = {106--130},
 	publisher = {Elsevier},
 	title = {Dispersive and dissipative behaviour of high order discontinuous {G}alerkin finite element methods},
 	volume = {198},
 	year = {2004},
-	doi={10.1016/j.jcp.2004.01.004}}
+	bdsk-url-1 = {https://doi.org/10.1016/j.jcp.2004.01.004}}
 
 @article{bezanson2017julia,
 	author = {Bezanson, Jeff and Edelman, Alan and Karpinski, Stefan and Shah, Viral B},
@@ -437,19 +441,8 @@ @online{eriksson2024laplacian
 	year = {2024},
 	bdsk-url-1 = {https://doi.org/10.48550/arXiv.2404.09050}}
 
-@article{klose2020assessing,
-	author = {Klose, Bjoern F and Jacobs, Gustaaf B and Kopriva, David A},
-	doi = {10.1016/j.compfluid.2020.104557},
-	journal = {Computers \& Fluids},
-	pages = {104557},
-	publisher = {Elsevier},
-	title = {Assessing standard and kinetic energy conserving volume fluxes in discontinuous Galerkin formulations for marginally resolved Navier-Stokes flows},
-	volume = {205},
-	year = {2020},
-	bdsk-url-1 = {https://doi.org/10.1016/j.compfluid.2020.104557}}
-
 @article{PhysRevFluids.9.053901,
-	author = {Marbona, Himpu and Rodr\‘{\i}guez, Daniel and Mart\’{\i}nez-Cava, Alejandro and Valero, Eusebio},
+	author = {Marbona, Himpu and Rodr\`{\i}guez, Daniel and Mart\'{\i}nez-Cava, Alejandro and Valero, Eusebio},
 	doi = {10.1103/PhysRevFluids.9.053901},
 	issue = {5},
 	journal = {Phys. Rev. Fluids},
@@ -465,9 +458,10 @@ @article{PhysRevFluids.9.053901
 	bdsk-url-2 = {https://doi.org/10.1103/PhysRevFluids.9.053901}}
 
 @phdthesis{wintermeyer2018,
+	author = {Niklas Wintermeyer},
+	month = {November},
 	school = {Universit{\"a}t zu K{\"o}ln},
 	title = {A novel entropy stable discontinuous {G}alerkin spectral element method for the shallow water equations on {GPU}s},
+	url = {https://kups.ub.uni-koeln.de/9234/},
 	year = {2018},
-	month = {November},
-	author = {Niklas Wintermeyer},
-	url = {https://kups.ub.uni-koeln.de/9234/}}
+	bdsk-url-1 = {https://kups.ub.uni-koeln.de/9234/}}

paper.md

@@ -59,6 +59,8 @@ The advantages not withstanding, a major impediment to the application of SEMs h
 In 2002 Sherwin and Peiro [@Sherwin:2002vx] wrote:  "The development of robust unstructured high-order methods is currently limited by the inability to consistently generate valid computational meshes for complex geometries without user intervention." This has remained true particularly for quadrilateral and hexahedral meshes.
 For these reasons, HOHQMesh was developed to generate all-quadrilateral and extruded hexahedral meshes suitable for use with spectral element methods. HOHQMesh is a direct quadrilateral mesher, which generates quadrilateral elements by the subdivision method of Schneiders [@schneiders2000algorithms] rather than indirectly from a triangular mesh or by curving a low order mesh. It also sizes and curves the elements based on the length scales in the model, rather than try to modify an existing low order mesh.
 
+Examples of meshes generated by HOHQMesh have been published in [@winters2014high], [@kopriva2016geometry], [@acosta2020simulation], [@manzanero2020entropy], [@ersing2024entropy], [@ranocha2024robustness], [@PhysRevFluids.9.053901], plus [@wintermeyer2018] and [@eriksson2024laplacian].
+
 # Features
 
 HOHQMesh is designed to require minimal input from the user through the use of a control file. The model defines the geometry in terms of an outer and inner boundary curves.