Merge #141

141: Use bib, reduce duplicate docs r=charleskawczynski a=charleskawczynski

This PR uses the bibliography and reduces some duplicate docs

Co-authored-by: Charles Kawczynski <[email protected]>

Author: bors[bot]

docs/refs.bib

@@ -171,3 +171,47 @@ @article{ARS1997
 	year = {1997},
 	pages = {151--167}
 }
+
+@article{Sandu2019,
+    title={A class of multirate infinitesimal gark methods},
+    author={Sandu, Adrian},
+    journal={SIAM Journal on Numerical Analysis},
+    volume={57},
+    number={5},
+    pages={2300--2327},
+    year={2019},
+    publisher={SIAM},
+    doi={10.1137/18M1205492}
+}
+
+@article{Bank1985,
+    title={Transient simulation of silicon devices and circuits},
+    author={R. E. Bank and W. M. Coughran and W. Fichtner and
+            E. H. Grosse and D. J. Rose and R. K. Smith},
+    journal={IEEE Transactions on Computer-Aided Design of Integrated
+             Circuits and Systems},
+    volume={4},
+    number={4},
+    pages={436-451},
+    year={1985},
+    publisher={IEEE},
+    doi={10.1109/TCAD.1985.1270142}
+}
+
+@techreport{KennedyCarpenter2016,
+    title = {Diagonally implicit Runge-Kutta methods for ordinary
+             differential equations. A review},
+             author = {C. A. Kennedy and M. H. Carpenter},
+    institution = {National Aeronautics and Space Administration},
+    year = {2016},
+    number = {NASA/TM–2016–219173},
+    address = {Langley Research Center, Hampton, VA}
+}
+
+@article{RobertsSarsharSandu2018arxiv,
+    title={Coupled Multirate Infinitesimal GARK Schemes for Stiff Systems with
+            Multiple Time Scales},
+    author={Roberts, Steven and Sarshar, Arash and Sandu, Adrian},
+    journal={arXiv preprint arXiv:1812.00808},
+    year={2019}
+}

src/solvers/MultirateInfinitesimalGARKDecoupledImplicit.jl

@@ -42,18 +42,7 @@ The available concrete implementations are:
   - [`MRIGARKESDIRK24LSA`](@ref)
 
 ### References
-
-    @article{Sandu2019,
-        title={A class of multirate infinitesimal gark methods},
-        author={Sandu, Adrian},
-        journal={SIAM Journal on Numerical Analysis},
-        volume={57},
-        number={5},
-        pages={2300--2327},
-        year={2019},
-        publisher={SIAM},
-        doi={10.1137/18M1205492}
-    }
+ - [Sandu2019](@cite)
 """
 mutable struct MRIGARKDecoupledImplicit{T, RT, AT, Nstages, NΓ, FS, Nx, Ny, Nx_Ny, BE} <: AbstractODESolver
     "time step"
@@ -325,29 +314,8 @@ The free parameter `δ` can take any values for accuracy.
 
 ### References
 
-    @article{Bank1985,
-        title={Transient simulation of silicon devices and circuits},
-        author={R. E. Bank and W. M. Coughran and W. Fichtner and
-                E. H. Grosse and D. J. Rose and R. K. Smith},
-        journal={IEEE Transactions on Computer-Aided Design of Integrated
-                 Circuits and Systems},
-        volume={4},
-        number={4},
-        pages={436-451},
-        year={1985},
-        publisher={IEEE},
-        doi={10.1109/TCAD.1985.1270142}
-    }
-
-    @techreport{KennedyCarpenter2016,
-        title = {Diagonally implicit Runge-Kutta methods for ordinary
-                 differential equations. A review},
-                 author = {C. A. Kennedy and M. H. Carpenter},
-        institution = {National Aeronautics and Space Administration},
-        year = {2016},
-        number = {NASA/TM–2016–219173},
-        address = {Langley Research Center, Hampton, VA}
-    }
+ - [Bank1985](@cite)
+ - [KennedyCarpenter2016](@cite)
 """
 function MRIGARKESDIRK23LSA(slowrhs!, implicitsolve!, fastsolver, Q; dt, t0 = 0, δ = 0)
     T = real(eltype(Q))

src/solvers/MultirateInfinitesimalGARKExplicit.jl

@@ -79,18 +79,8 @@ The available concrete implementations are:
   - [`MRIGARKERK45aSandu`](@ref)
 
 ### References
+ - [Sandu2019](@cite)
 
-    @article{Sandu2019,
-        title={A class of multirate infinitesimal gark methods},
-        author={Sandu, Adrian},
-        journal={SIAM Journal on Numerical Analysis},
-        volume={57},
-        number={5},
-        pages={2300--2327},
-        year={2019},
-        publisher={SIAM},
-        doi={10.1137/18M1205492}
-    }
 """
 mutable struct MRIGARKExplicit{T, RT, AT, Nstages, NΓ, FS, Nstages_sq} <: AbstractODESolver
     "time step"

test/ode_tests_convergence.jl

@@ -189,14 +189,7 @@ const ArrayType = CuArray
         end
 
         #=
-        Test problem (4.2) from RobertsSarsharSandu2018arxiv
-        @article{RobertsSarsharSandu2018arxiv,
-          title={Coupled Multirate Infinitesimal GARK Schemes for Stiff Systems with
-                 Multiple Time Scales},
-          author={Roberts, Steven and Sarshar, Arash and Sandu, Adrian},
-          journal={arXiv preprint arXiv:1812.00808},
-          year={2019}
-        }
+        Test problem (4.2) from [RobertsSarsharSandu2018arxiv](@cite)
 
         Note: The actual rates are all over the place with this test and passing largely
               depends on final dt size
@@ -356,7 +349,7 @@ const ArrayType = CuArray
             end
         end
 
-        # Simple 3-rate problem based on test of RobertsSarsharSandu2018arxiv
+        # Simple 3-rate problem based on test of [RobertsSarsharSandu2018arxiv](@cite)
         #
         # NOTE: Since we have no theory to say this ODE solver is accurate, the rates
         #      suggest that things are really only 2nd order.
@@ -488,20 +481,7 @@ const ArrayType = CuArray
             end
         end
 
-        #=
-        Test problem (8.2) from Sandu (2019) for MRI-GARK Schemes
-            @article{Sandu2019,
-                title={A class of multirate infinitesimal gark methods},
-                author={Sandu, Adrian},
-                journal={SIAM Journal on Numerical Analysis},
-                volume={57},
-                number={5},
-                pages={2300--2327},
-                year={2019},
-                publisher={SIAM},
-                doi={10.1137/18M1205492}
-            }
-        =#
+        #= Test problem (8.2) from [Sandu2019](@cite) for MRI-GARK Schemes =#
         @testset "2-rate problem" begin
             ω = 20
             λf = -10

test/problems.jl

@@ -209,19 +209,7 @@ function kpr_sol(u0, param, t)
 end
 
 """
-Test problem (4.2) from RobertsSarsharSandu2018arxiv
-
-# TODO: move this to bibliography
-
-```
-@article{RobertsSarsharSandu2018arxiv,
-    title={Coupled Multirate Infinitesimal GARK Schemes for Stiff Systems with
-            Multiple Time Scales},
-    author={Roberts, Steven and Sarshar, Arash and Sandu, Adrian},
-    journal={arXiv preprint arXiv:1812.00808},
-    year={2019}
-}
-```
+Test problem (4.2) from [RobertsSarsharSandu2018arxiv](@cite)
 
 Note: The actual rates are all over the place with this test and passing largely
         depends on final dt size