Merge #1687

1687: Extract remaining citations r=charleskawczynski a=charleskawczynski ### Description Extracts remaining references/citations to `docs/bibliography.bib`. Co-authored-by: Charles Kawczynski <kawczynski.charles@gmail.com>
CliMA · Nov 20, 2020 · 1c498cc · 1c498cc
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diff --git a/docs/bibliography.bib b/docs/bibliography.bib
diff --git a/docs/src/Theory/Atmos/Microphysics.md b/docs/src/Theory/Atmos/Microphysics.md
diff --git a/docs/src/Theory/Common/SurfaceFluxes.md b/docs/src/Theory/Common/SurfaceFluxes.md
@@ -16,19 +16,7 @@ This module provides a means to compute surface fluxes given several variables,
 
 ## References
 
-- Businger, Joost A., et al. "Flux-profile relationships in the atmospheric surface
-  layer." Journal of the atmospheric Sciences 28.2 (1971): 181-189.
-
-- Nishizawa, S., and Y. Kitamura. "A Surface Flux Scheme Based on the Monin-Obukhov
-  Similarity for Finite Volume Models." Journal of Advances in Modeling Earth Systems
-  10.12 (2018): 3159-3175.
-
-- Businger, Joost A., et al. "Flux-profile relationships in the atmospheric surface
-  layer." Journal of the atmospheric Sciences 28.2 (1971): 181-189.
-  doi: [10.1175/1520-0469(1971)028<0181:FPRITA>2.0.CO;2](https://doi.org/10.1175/1520-0469(1971)028<0181:FPRITA>2.0.CO;2)
-
-- Byun, Daewon W. "On the analytical solutions of flux-profile relationships for the
-  atmospheric surface layer." Journal of Applied Meteorology 29.7 (1990): 652-657.
-
-- Wyngaard, John C. "Modeling the planetary boundary layer-Extension to the stable case."
-  Boundary-Layer Meteorology 9.4 (1975): 441-460.
+- [Businger1971](@cite)
+- [Nishizawa2018](@cite)
+- [Byun1990](@cite)
+- [Wyngaard1975](@cite)
diff --git a/experiments/AtmosGCM/GCMDriver/baroclinicwave_problem.jl b/experiments/AtmosGCM/GCMDriver/baroclinicwave_problem.jl
@@ -1,9 +1,5 @@
 # This file establishes the default initial conditions, boundary conditions and sources
-# for the baroclinicwave_problem experiment, following
-#
-# Ullrich, P. A., Melvin, T., Jablonowski, C., and Staniforth, A.:
-# A proposed baroclinic wave test case for deep- and shallow atmosphere
-# dynamical cores, Q. J. Roy. Meteor. Soc., 140, 1590-1602, doi:10.1002/qj.2241, 2014.
+# for the baroclinicwave_problem experiment, following [Ullrich2014](@cite)
 
 # Override default CLIMAParameters for consistency with literature on this case
 CLIMAParameters.Planet.press_triple(::EarthParameterSet) = 610.78

diff --git a/experiments/AtmosLES/bomex_model.jl b/experiments/AtmosLES/bomex_model.jl
@@ -22,29 +22,7 @@
 # 3) Collapsed experiment design
 # 4) Updates to generally keep this in sync with master
 
-@article{doi:10.1175/1520-0469(2003)60<1201:ALESIS>2.0.CO;2,
-author = {Siebesma, A. Pier and Bretherton,
-          Christopher S. and Brown,
-          Andrew and Chlond,
-          Andreas and Cuxart,
-          Joan and Duynkerke,
-          Peter G. and Jiang,
-          Hongli and Khairoutdinov,
-          Marat and Lewellen,
-          David and Moeng,
-          Chin-Hoh and Sanchez,
-          Enrique and Stevens,
-          Bjorn and Stevens,
-          David E.},
-title = {A Large Eddy Simulation Intercomparison Study of Shallow Cumulus Convection},
-journal = {Journal of the Atmospheric Sciences},
-volume = {60},
-number = {10},
-pages = {1201-1219},
-year = {2003},
-doi = {10.1175/1520-0469(2003)60<1201:ALESIS>2.0.CO;2},
-URL = {https://journals.ametsoc.org/doi/abs/10.1175/1520-0469%282003%2960%3C1201%3AALESIS%3E2.0.CO%3B2},
-eprint = {https://journals.ametsoc.org/doi/pdf/10.1175/1520-0469%282003%2960%3C1201%3AALESIS%3E2.0.CO%3B2}
+[Siebesma2003](@cite)
 =#
 
 using ArgParse

diff --git a/experiments/AtmosLES/convective_bl_model.jl b/experiments/AtmosLES/convective_bl_model.jl
@@ -5,17 +5,7 @@
 # Convective Boundary Layer LES case (Kitamura et al, 2016).
 
 ## ### Convective Boundary Layer LES
-## @article{Nishizawa2018,
-## author={Nishizawa, S and Kitamura, Y},
-## title={A Surface Flux Scheme Based on the Monin-Obukhov Similarity for Finite Volume Models},
-## journal={Journal of Advances in Modeling Earth Systems},
-## year={2018},
-## volume={10},
-## number={12},
-## pages={3159-3175},
-## doi={10.1029/2018MS001534},
-## url={https://doi.org/10.1029/2018MS001534},
-## }
+## [Nishizawa2018](@cite)
 #
 # To simulate the experiment, type in
 #

diff --git a/experiments/AtmosLES/dycoms.jl b/experiments/AtmosLES/dycoms.jl
@@ -109,10 +109,8 @@ function flux_radiation!(
 """
   DYCOMSRadiation <: RadiationModel
 
-Stevens et. al (2005) approximation of longwave radiative fluxes in DYCOMS.
-Analytical description as a function of the liquid water path and inversion height zᵢ
-
-* Stevens, B. et. al. (2005) "Evaluation of Large-Eddy Simulations via Observations of Nocturnal Marine Stratocumulus". Mon. Wea. Rev., 133, 1443–1462, https://doi.org/10.1175/MWR2930.1
+## References
+ - [Stevens2005](@cite)
 """
 struct DYCOMSRadiation{FT} <: RadiationModel
     "mass absorption coefficient `[m^2/kg]`"
@@ -210,23 +208,9 @@ end
 
 """
   Initial Condition for DYCOMS_RF01 LES
-@article{doi:10.1175/MWR2930.1,
-author = {Stevens, Bjorn and Moeng, Chin-Hoh and Ackerman,
-          Andrew S. and Bretherton, Christopher S. and Chlond,
-          Andreas and de Roode, Stephan and Edwards, James and Golaz,
-          Jean-Christophe and Jiang, Hongli and Khairoutdinov,
-          Marat and Kirkpatrick, Michael P. and Lewellen, David C. and Lock, Adrian and
-          Maeller, Frank and Stevens, David E. and Whelan, Eoin and Zhu, Ping},
-title = {Evaluation of Large-Eddy Simulations via Observations of Nocturnal Marine Stratocumulus},
-journal = {Monthly Weather Review},
-volume = {133},
-number = {6},
-pages = {1443-1462},
-year = {2005},
-doi = {10.1175/MWR2930.1},
-URL = {https://doi.org/10.1175/MWR2930.1},
-eprint = {https://doi.org/10.1175/MWR2930.1}
-}
+
+## References
+ - [Stevens2005](@cite)
 """
 function init_dycoms!(problem, bl, state, aux, localgeo, t)
     FT = eltype(state)

diff --git a/experiments/AtmosLES/schar_scalar_advection.jl b/experiments/AtmosLES/schar_scalar_advection.jl
@@ -24,24 +24,7 @@ struct EarthParameterSet <: AbstractEarthParameterSet end
 const param_set = EarthParameterSet()
 
 ### Citation
-#@article{
-#    author = {Schär, Christoph and 
-#              Leuenberger, Daniel and 
-#              Fuhrer, Oliver and 
-#              Lüthi, Daniel and 
-#              Girard, Claude},
-#    title = "{A New Terrain-Following Vertical Coordinate Formulation 
-#              for Atmospheric Prediction Models}",
-#    journal = {Monthly Weather Review},
-#    volume = {130},
-#    number = {10},
-#    pages = {2459-2480},
-#    year = {2002},
-#    month = {10},
-#    issn = {0027-0644},
-#    doi = {10.1175/1520-0493(2002)130<2459:ANTFVC>2.0.CO;2},
-#    url = {https://doi.org/10.1175/1520-0493(2002)130<2459:ANTFVC>2.0.CO;2},
-#}
+# [Schar2002](@cite)
 
 # ## [Initial Conditions]
 function init_schar!(problem, bl, state, aux, localgeo, t)

diff --git a/experiments/AtmosLES/stable_bl_model.jl b/experiments/AtmosLES/stable_bl_model.jl
@@ -2,22 +2,9 @@
 #=
 # This experiment file establishes the initial conditions, boundary conditions,
 # source terms and simulation parameters (domain size + resolution) for the
-# GABLS LES case (Beare et al, 2006; Kosovic and Curry, 2000).
+# GABLS LES case ([Beare2006](@cite); [Kosovic2000](@cite)).
 #
-## @article{10.1175/1520-0469(2000)057<1052:ALESSO>2.0.CO;2,
-##     author = {Kosović, Branko and Curry, Judith A.},
-##     title = "{A Large Eddy Simulation Study of a Quasi-Steady,
-##               Stably Stratified Atmospheric Boundary Layer}",
-##     journal = {Journal of the Atmospheric Sciences},
-##     volume = {57},
-##     number = {8},
-##     pages = {1052-1068},
-##     year = {2000},
-##     month = {04},
-##     issn = {0022-4928},
-##     doi = {10.1175/1520-0469(2000)057<1052:ALESSO>2.0.CO;2},
-##     url = {https://doi.org/10.1175/1520-0469(2000)057<1052:ALESSO>2.0.CO;2},
-## }
+## [Kosovic2000](@cite)
 #
 # To simulate the experiment, type in
 #

diff --git a/experiments/AtmosLES/taylor_green.jl b/experiments/AtmosLES/taylor_green.jl
@@ -42,28 +42,10 @@ import ClimateMachine.Atmos: flux_second_order!
 """
     Initial Condition for Taylor-Green vortex (LES)
 
-@article{taylorGreen1937,
-author = {Taylor, G. I. and Green, A. E.},
-title = {Mechanisms of production of small eddies from large ones},
-journal = {Proc. Roy. Soc. A},
-volume = {158}
-number = {895},
-year = {1937},
-doi={doi.org/10.1098/rspa.1937.0036},
-}
-@article{rafeiEtAl2018,
-author = {Rafei, M.E. and K\"on\"oszy, L. and Rana, Z.},
-title = {Investigation of Numerical Dissipation in Classicaland Implicit Large Eddy Simulations,
-journal = {Aerospace},
-year = {2018},
-}
-@article{bullJameson2014,
-author = {Bull, J.R. and Jameson, A.},
-title = {Simulation of the Compressible {Taylor Green} Vortex
-using High-Order Flux Reconstruction Schemes},
-journal = {AIAA Aviation 7th AIAA theoretical fluid mechanics conference},
-year = {2014},
-}
+## References:
+ - [Taylor1937](@cite)
+ - [Rafei2018](@cite)
+ - [Bull2014](@cite)
 """
 function init_greenvortex!(problem, bl, state, aux, localgeo, t)
     (x, y, z) = localgeo.coord

diff --git a/src/Atmos/Model/AtmosModel.jl b/src/Atmos/Model/AtmosModel.jl
@@ -955,12 +955,9 @@ the AtmosModel. For more information on this particular implementation,
 see Chapter 10.4 in the provided reference below.
 
 ## References
-    @book{toro2013riemann,
-        title={Riemann solvers and numerical methods for fluid dynamics: a practical introduction},
-        author={Toro, Eleuterio F},
-        year={2013},
-        publisher={Springer Science & Business Media}
-    }
+
+ - [Toro2013](@cite)
+
 """
 function numerical_flux_first_order!(
     ::HLLCNumericalFlux,

diff --git a/src/Common/Spectra/power_spectrum_gcm.jl b/src/Common/Spectra/power_spectrum_gcm.jl
@@ -8,8 +8,8 @@ The snapshots of these spectra should be averaged to obtain a time-average.
 The input velocities must be interpolated to a Gaussian grid.
 
 # References
-- A. Wiin-Nielsen (1967) On the annual variation and spectral distribution of atmospheric energy, Tellus, 19:4, 540-559, DOI: 10.3402/tellusa.v19i4.9822
-- Koshyk, J. N., and K. Hamilton, 2001: The Horizontal Kinetic Energy Spectrum and Spectral Budget Simulated by a High-Resolution Troposphere–Stratosphere–Mesosphere GCM. J. Atmos. Sci., 58, 329–348, https://doi.org/10.1175/1520-0469(2001)058<0329:THKESA>2.0.CO;2.
+- [Wiin1967](@cite)
+- [Koshyk2001](@cite)
 
 # Arguments
 - var_grid: variable (typically u or v) on a Gausian (lon, lat, z) grid to be transformed
@@ -73,7 +73,7 @@ end
 - mass_weight: weight for mass-weighted calculations
 
 # References
-Baer, F., 1972: An Alternate Scale Representation of Atmospheric Energy Spectra. J. Atmos. Sci., 29, 649–664, https://doi.org/10.1175/1520-0469(1972)029<0649:AASROA>2.0.CO;2
+ - [Baer1972](@cite)
 """
 function power_spectrum_2d(::AtmosGCMConfigType, var_grid, mass_weight)
     #  initialize spherical mesh variables

diff --git a/src/Common/Spectra/spherical_helper.jl b/src/Common/Spectra/spherical_helper.jl
@@ -195,7 +195,7 @@ pfield = F(λ, η)             # Input variable on Gaussian grid Float64[nλ, n
 
 # References
 - Ehrendorfer, M., Spectral Numerical Weather Prediction Models, Appendix B, Society for Industrial and Applied Mathematics, 2011
-- A. Wiin-Nielsen (1967) On the annual variation and spectral distribution of atmospheric energy, Tellus, 19:4, 540-559, DOI: 10.3402/tellusa.v19i4.9822
+- [Wiin1967](@cite)
 """
 function trans_grid_to_spherical!(
     mesh::SpectralSphericalMesh,

diff --git a/src/Common/SurfaceFluxes/SurfaceFluxes.jl b/src/Common/SurfaceFluxes/SurfaceFluxes.jl
@@ -10,17 +10,7 @@
     - exchange coefficients
 
 ## References
-
-@article{nishizawa2018surface,
-  title={A Surface Flux Scheme Based on the Monin-Obukhov Similarity for Finite Volume Models},
-  author={Nishizawa, S and Kitamura, Y},
-  journal={Journal of Advances in Modeling Earth Systems},
-  volume={10},
-  number={12},
-  pages={3159--3175},
-  year={2018},
-  publisher={Wiley Online Library}
-}
+ - [Nishizawa2018](@cite)
 
 """
 module SurfaceFluxes

diff --git a/src/Common/SurfaceFluxes/UniversalFunctions.jl b/src/Common/SurfaceFluxes/UniversalFunctions.jl
@@ -85,18 +85,11 @@ c_h(uf::AUF) = c_h(uf.param_set, uf)
 
 # Reference
 
-    Nishizawa, S., and Y. Kitamura. "A Surface Flux
-    Scheme Based on the Monin‐Obukhov Similarity for
-    Finite Volume Models." Journal of Advances in
-    Modeling Earth Systems 10.12 (2018): 3159-3175.
-    Appendix A.
+ - [Nishizawa2018](@cite)
 
 # Original research
 
-    Businger, Joost A., et al. "Flux-profile
-    relationships in the atmospheric surface layer."
-    Journal of the atmospheric Sciences 28.2 (1971):
-    181-189.
+ - [Businger1971](@cite)
 
 # Equations in reference:
 
@@ -232,12 +225,8 @@ end
 """
     Gryanik <: AbstractUniversalFunction{FT}
 
-# Reference
-    Gryanik, Vladimir M., et al. "New modified and extended
-    stability functions for the stable boundary layer based
-    on SHEBA and parametrizations of bulk transfer coefficients
-    for climate models." Journal of the Atmospheric Sciences
-    (2020).
+# References
+ - [Gryanik2020](@cite)
 
 # Equations in reference:
 
@@ -319,11 +308,8 @@ end
 """
     Grachev <: AbstractUniversalFunction{FT}
 
-# Reference:
-    Grachev, A. A., E. L. Andreas, C. W. Fairall, P. S. Guest, and
-    P. O. G. Persson, 2007a: SHEBA flux–profile relationships in
-    the stable atmospheric boundary layer. Bound.-Layer Meteor.,
-    124, 315–333, https://doi.org/10.1007/s10546-007-9177-6.
+# References
+ - [Grachev2007](@cite)
 
 Equations in reference:
 

diff --git a/src/Common/TurbulenceClosures/TurbulenceClosures.jl b/src/Common/TurbulenceClosures/TurbulenceClosures.jl
@@ -511,29 +511,15 @@ $(DocStringExtensions.FIELDS)
 
 # Smagorinsky Model Reference
 
-See [smagorinsky1963](@cite)
+See [Smagorinsky1963](@cite)
 
 # Lilly Model Reference
-    article{doi:10.1111/j.2153-3490.1962.tb00128.x,
-      author = {LILLY, D. K.},
-      title = {On the numerical simulation of buoyant convection},
-      journal = {Tellus},
-      volume = {14},
-      number = {2},
-      pages = {148-172},
-      doi = {10.1111/j.2153-3490.1962.tb00128.x},
-      url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/j.2153-3490.1962.tb00128.x},
-      eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.2153-3490.1962.tb00128.x},
-      year = {1962}
-      }
 
+See [Lilly1962](@cite)
 
 # Brunt-Väisälä Frequency Reference
-    Brunt-Vaisala frequency N² defined as in equation (1b) in
-      Durran, D.R. and J.B. Klemp, 1982:
-      On the Effects of Moisture on the Brunt-Väisälä Frequency.
-      J. Atmos. Sci., 39, 2152–2158,
-      https://doi.org/10.1175/1520-0469(1982)039<2152:OTEOMO>2.0.CO;2
+
+See [Durran1982](@cite)
 
 """
 struct SmagorinskyLilly{FT} <: TurbulenceClosureModel
@@ -651,16 +637,7 @@ $(DocStringExtensions.FIELDS)
 
 # Reference
 
-    @article{Vreman2004,
-      title={An eddy-viscosity subgrid-scale model for turbulent shear flow: Algebraic theory and applications},
-      author={Vreman, AW},
-      journal={Physics of fluids},
-      volume={16},
-      number={10},
-      pages={3670--3681},
-      year={2004},
-      publisher={AIP}
-    }
+ - [Vreman2004](@cite)
 """
 struct Vreman{FT} <: TurbulenceClosureModel
     "Smagorinsky Coefficient [dimensionless]"
@@ -756,18 +733,7 @@ $(DocStringExtensions.FIELDS)
 
 # Reference
 
-    @article{
-        doi:10.1063/1.5037039,
-        author = {Vreugdenhil,Catherine A.  and Taylor,John R. },
-        title = {Large-eddy simulations of stratified plane Couette flow using the anisotropic minimum-dissipation model},
-        journal = {Physics of Fluids},
-        volume = {30},
-        number = {8},
-        pages = {085104},
-        year = {2018},
-        doi = {10.1063/1.5037039},
-        URL = {https://doi.org/10.1063/1.5037039}
-    }
+See [Vreugdenhil2018](@cite)
 
 """
 struct AnisoMinDiss{FT} <: TurbulenceClosureModel