Add more references and some urls/dois (#795)

- Add references to workstream paper and dof distribution paper
 - Add urls and dois to existing references

docs/make.jl

@@ -93,7 +93,7 @@ bibtex_plugin = CitationBibliography(
         #     "gallery/topology_optimization.md",
         # ],
         "devdocs/index.md",
-        "bibliography.md",
+        "references.md",
         ],
     plugins = [
         bibtex_plugin,

docs/src/assets/references.bib

@@ -6,6 +6,8 @@ @article{JanHacJun2019regularizedthermotopopt
   number={9},
   pages={991--1017},
   year={2019},
+  url={https://doi.org/10.1002/nme.5988},
+  doi={10.1002/nme.5988},
   publisher={Wiley Online Library}
 }
 @article{BlaJanJun2022taylorwlsthermotopopt,
@@ -15,5 +17,43 @@ @article{BlaJanJun2022taylorwlsthermotopopt
   volume={393},
   pages={114698},
   year={2022},
+  url={https://doi.org/10.1016/j.cma.2022.114698},
+  doi={10.1016/j.cma.2022.114698},
   publisher={Elsevier}
 }
+@article{Turcksin2016,
+  author={Turcksin, Bruno and Kronbichler, Martin and Bangerth, Wolfgang},
+  title={WorkStream -- A Design Pattern for Multicore-Enabled Finite Element Computations},
+  year={2016},
+  issue_date={March 2017},
+  publisher={Association for Computing Machinery},
+  address={New York, NY, USA},
+  volume={43},
+  number={1},
+  issn={0098-3500},
+  url={https://doi.org/10.1145/2851488},
+  doi={10.1145/2851488},
+  journal={ACM Trans. Math. Softw.},
+  month={aug},
+  articleno={2},
+  numpages={29},
+  keywords={Finite element algorithms, assembly, pipeline software pattern}
+}
+@article{Scroggs2022,
+author = {Scroggs, Matthew W. and Dokken, J\o{}rgen S. and Richardson, Chris N. and Wells, Garth N.},
+title = {Construction of Arbitrary Order Finite Element Degree-of-Freedom Maps on Polygonal and Polyhedral Cell Meshes},
+year = {2022},
+issue_date = {June 2022},
+publisher = {Association for Computing Machinery},
+address = {New York, NY, USA},
+volume = {48},
+number = {2},
+issn = {0098-3500},
+url = {https://doi.org/10.1145/3524456},
+doi = {10.1145/3524456},
+journal = {ACM Trans. Math. Softw.},
+month = {may},
+articleno = {18},
+numpages = {23},
+keywords = {Finite element methods, polyhedral cells, degrees-of-freedom}
+}

docs/src/references.md

@@ -0,0 +1,14 @@
+# References
+
+```@bibliography
+```
+
+```@raw html
+<!--
+```
+Workaround for https://github.com/JuliaDocs/DocumenterCitations.jl/issues/39
+ - [Turcksin2016](@cite)
+ - [Scroggs2022](@cite)
+```@raw html
+-->
+```

src/Dofs/DofHandler.jl

@@ -582,18 +582,15 @@ element B in the example.
 
 In addition, we also have to preverse the ordering at each dof location.
 
-For more details we refer to [1] as we follow the methodology described therein.
-
-[1] Scroggs, M. W., Dokken, J. S., Richardson, C. N., & Wells, G. N. (2022).
-    Construction of arbitrary order finite element degree-of-freedom maps on
-    polygonal and polyhedral cell meshes. ACM Transactions on Mathematical
-    Software (TOMS), 48(2), 1-23.
+For more details we refer to Scroggs et al. [Scroggs2022](@cite) as we follow the methodology
+described therein.
 
-    !!!TODO Citation via DocumenterCitations.jl.
-
-    !!!TODO Investigate if we can somehow pass the interpolation into this function in a typestable way.
+# References
+ - [Scroggs2022](@cite) Scroggs et al. ACM Trans. Math. Softw. 48 (2022).
 """
 @inline function permute_and_push!(cell_dofs::Vector{Int}, dofs::StepRange{Int,Int}, orientation::PathOrientationInfo, adjust_during_distribution::Bool)
+    # TODO Investigate if we can somehow pass the interpolation into this function in a
+    # typestable way.
     n_copies = step(dofs)
     @assert n_copies > 0
     if adjust_during_distribution && !orientation.regular

src/Grid/coloring.jl

@@ -174,8 +174,7 @@ ret = [
 
 Two different algorithms are available, specified with the `alg` keyword argument:
  - `alg = ColoringAlgorithm.WorkStream` (default): Three step algorithm from
-   [*WorkStream*](https://www.math.colostate.edu/%7Ebangerth/publications/2013-pattern.pdf)
-   , albeit with a greedy coloring in the second step. Generally results in more colors than
+   Turcksin et al. [Turcksin2016](@cite), albeit with a greedy coloring in the second step. Generally results in more colors than
    `ColoringAlgorithm.Greedy`, however the cells are more equally distributed among the colors.
  - `alg = ColoringAlgorithm.Greedy`: greedy algorithm that works well for structured quadrilateral grids such as
    e.g. quadrilateral grids from `generate_grid`.
@@ -192,6 +191,9 @@ The resulting colors can be visualized using [`vtk_cell_data_colors`](@ref).
         cellid => color for (color, cellids) in enumerate(final_colors) for cellid in cellids
     )
     ```
+
+# References
+ - [Turcksin2016](@cite) Turcksin et al. ACM Trans. Math. Softw. 43 (2016).
 """
 function create_coloring(g::AbstractGrid, cellset=1:getncells(g); alg::ColoringAlgorithm.T=ColoringAlgorithm.WorkStream)
     incidence_matrix = create_incidence_matrix(g, cellset)