From a72cbf7697d6ca2c09c38a1ca4a198b99eed943d Mon Sep 17 00:00:00 2001 From: Charles Kawczynski Date: Mon, 2 Nov 2020 11:01:52 -0800 Subject: [PATCH] Extract more citations, polish format --- docs/bibliography.bib | 1393 +++++++++-------- docs/src/Theory/Atmos/Microphysics.md | 80 +- docs/src/Theory/Common/SurfaceFluxes.md | 8 +- experiments/AtmosLES/bomex_model.jl | 2 +- experiments/AtmosLES/convective_bl_model.jl | 2 +- experiments/AtmosLES/dycoms.jl | 4 +- .../AtmosLES/schar_scalar_advection.jl | 2 +- experiments/AtmosLES/stable_bl_model.jl | 4 +- src/Atmos/Model/AtmosModel.jl | 2 +- src/Common/Spectra/power_spectrum_gcm.jl | 6 +- src/Common/SurfaceFluxes/SurfaceFluxes.jl | 2 +- .../SurfaceFluxes/UniversalFunctions.jl | 8 +- .../TurbulenceClosures/TurbulenceClosures.jl | 10 +- src/Driver/SolverTypes/IMEXSolverType.jl | 2 +- src/Driver/SolverTypes/MultirateSolverType.jl | 6 +- src/Numerics/DGMethods/NumericalFluxes.jl | 2 +- src/Numerics/Mesh/BrickMesh.jl | 2 +- src/Numerics/Mesh/Elements.jl | 6 +- src/Numerics/Mesh/Filters.jl | 2 +- src/Numerics/Mesh/Metrics.jl | 2 +- src/Numerics/Mesh/Topologies.jl | 2 +- .../ODESolvers/AdditiveRungeKuttaMethod.jl | 6 +- .../ODESolvers/LowStorageRungeKuttaMethod.jl | 2 +- ...irateInfinitesimalGARKDecoupledImplicit.jl | 2 +- .../MultirateInfinitesimalGARKExplicit.jl | 2 +- .../ODESolvers/MultirateRungeKuttaMethod.jl | 2 +- ...rongStabilityPreservingRungeKuttaMethod.jl | 10 +- .../SystemSolvers/columnwise_lu_solver.jl | 33 +- .../generalized_conjugate_residual_solver.jl | 2 +- .../generalized_minimal_residual_solver.jl | 2 +- .../Parameterizations/Microphysics/KM_ice.jl | 2 +- .../Microphysics/KinematicModel.jl | 4 +- .../Microphysics/runtests.jl | 6 +- .../advection_diffusion/advection_sphere.jl | 4 +- .../density_current_model.jl | 2 +- .../ODESolvers/ode_tests_convergence.jl | 8 +- tutorials/Atmos/densitycurrent.jl | 4 +- tutorials/Atmos/heldsuarez.jl | 2 +- 38 files changed, 832 insertions(+), 808 deletions(-) diff --git a/docs/bibliography.bib b/docs/bibliography.bib index 857f71895a3..fcbe51239b1 100644 --- a/docs/bibliography.bib +++ b/docs/bibliography.bib @@ -1,511 +1,544 @@ -@article{arabas2015, - title={libcloudph++ 1.0: a single-moment bulk, double-moment bulk, and particle-based warm-rain microphysics library in C++}, - author={Arabas, Sylwester and Jaruga, Anna and Pawlowska, Hanna and Grabowski, Wojciech W}, - journal={Geoscientific Model Development}, - volume={8}, - number={6}, - pages={1677--1707}, - year={2015}, - publisher={Copernicus GmbH} -} - -@article{baer1972, - title={An alternate scale representation of atmospheric energy spectra}, - author={Baer, Ferdinand}, - journal={Journal of the Atmospheric Sciences}, - volume={29}, - number={4}, - pages={649--664}, - year={1972} +# The citation keys have been formatted as: +# Last author name (titlecase), followed by +# (no characters in-between) the year. + +@article{Arabas2015, + title = {libcloudph++ 1.0: a single-moment bulk, double-moment bulk, and particle-based warm-rain microphysics library in C++}, + author = {Arabas, Sylwester and Jaruga, Anna and Pawlowska, Hanna and Grabowski, Wojciech W}, + journal = {Geoscientific Model Development}, + volume = {8}, + number = {6}, + url = {https://www.geosci-model-dev.net/8/1677/2015/}, + doi = {10.5194/gmd-8-1677-2015}, + pages = {1677--1707}, + year = {2015}, + publisher = {Copernicus GmbH} +} + +@article{Baer1972, + title = {An alternate scale representation of atmospheric energy spectra}, + author = {Baer, Ferdinand}, + journal = {Journal of the Atmospheric Sciences}, + volume = {29}, + number = {4}, + url = {https://doi.org/10.1175/1520-0469(1972)029<0649:AASROA>2.0.CO;2}, + pages = {649--664}, + year = {1972} } @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} -} - -@article{beare2006, - title={An intercomparison of large-eddy simulations of the stable boundary layer}, - author={Beare, Robert J and Macvean, Malcolm K and Holtslag, Albert AM and Cuxart, Joan and Esau, Igor and Golaz, Jean-Christophe and Jimenez, Maria A and Khairoutdinov, Marat and Kosovic, Branko and Lewellen, David and others}, - journal={Boundary-Layer Meteorology}, - volume={118}, - number={2}, - pages={247--272}, - year={2006}, - publisher={Springer} -} - -@article{berrut2004, - title={Barycentric lagrange interpolation}, - author={Berrut, Jean-Paul and Trefethen, Lloyd N}, - journal={SIAM review}, - volume={46}, - number={3}, - pages={501--517}, - year={2004}, - publisher={SIAM} -} - -@inproceedings{boyd1996, - title={The erfc-log filter and the asymptotics of the Euler and Vandeven sequence accelerations}, - author={Boyd, JP}, - booktitle={Proceedings of the Third International Conference on Spectral and High Order Methods}, - pages={267--276}, - year={1996}, - organization={Houston Math. J} -} - - -@article{businger1971, - title={Flux-profile relationships in the atmospheric surface layer}, - author={Businger, Joost A and Wyngaard, John C and Izumi, Yꎬ and Bradley, Edward F}, - journal={Journal of the atmospheric Sciences}, - volume={28}, - number={2}, - pages={181--189}, - year={1971} -} - -@article{byun1990, - title={On the analytical solutions of flux-profile relationships for the atmospheric surface layer}, - author={Byun, Daewon W}, - journal={Journal of Applied Meteorology}, - volume={29}, - number={7}, - pages={652--657}, - year={1990} -} - -@article{desai2019, - title={Aerosol-Mediated Glaciation of Mixed-Phase Clouds: Steady-State Laboratory Measurements}, - author={Desai, Neel and Chandrakar, KK and Kinney, G and Cantrell, W and Shaw, RA}, - journal={Geophysical Research Letters}, - volume={46}, - number={15}, - pages={9154--9162}, - year={2019}, - publisher={Wiley Online Library} -} - -@article{doms2011, - title={A Description of the Nonhydrostatic Regional COSMO model. Part I: Dynamics and Numerics}, - author={Doms, G{\"u}nther and Baldauf, M}, - journal={Deutscher Wetterdienst, Offenbach}, - volume={-1}, - year={2011} -} - -@article{durran1982, - title={On the effects of moisture on the Brunt-V{\"a}is{\"a}l{\"a} frequency}, - author={Durran, Dale R and Klemp, Joseph B}, - journal={Journal of the Atmospheric Sciences}, - volume={39}, - number={10}, - pages={2152--2158}, - year={1982} -} - -@article{carpenter1990, - title={Application of the piecewise parabolic method (PPM) to meteorological modeling}, - author={Carpenter Jr, Richard L and Droegemeier, Kelvin K and Woodward, Paul R and Hane, Carl E}, - journal={Monthly Weather Review}, - volume={118}, - number={3}, - pages={586--612}, - year={1990} -} - -@article{eisenstat1983, - title={Variational iterative methods for nonsymmetric systems of linear equations}, - author={Eisenstat, Stanley C and Elman, Howard C and Schultz, Martin H}, - journal={SIAM Journal on Numerical Analysis}, - volume={20}, - number={2}, - pages={345--357}, - year={1983}, - publisher={SIAM} -} - -@article{giraldo2013, - title={Implicit-explicit formulations of a three-dimensional nonhydrostatic unified model of the atmosphere ({NUMA})}, - author={Giraldo, Francis X and Kelly, James F and Constantinescu, Emil M}, - journal={SIAM Journal on Scientific Computing}, - volume={35}, - number={5}, - pages={B1162--B1194}, - year={2013}, - publisher={SIAM} -} - -@article{grabowski1996, - title={Two-time-level semi-Lagrangian modeling of precipitating clouds}, - author={Grabowski, Wojciech W and Smolarkiewicz, Piotr K}, - journal={Monthly weather review}, - volume={124}, - number={3}, - pages={487--497}, - year={1996} -} - -@article{grabowski1998, - title={Toward cloud resolving modeling of large-scale tropical circulations: A simple cloud microphysics parameterization}, - author={Grabowski, Wojciech W}, - journal={Journal of the Atmospheric Sciences}, - volume={55}, - number={21}, - pages={3283--3298}, - year={1998} -} - -@article{grachev2007sheba, - title={SHEBA flux--profile relationships in the stable atmospheric boundary layer}, - author={Grachev, Andrey A and Andreas, Edgar L and Fairall, Christopher W and Guest, Peter S and Persson, P Ola G}, - journal={Boundary-layer meteorology}, - volume={124}, - number={3}, - pages={315--333}, - year={2007}, - publisher={Springer} -} - -@article{gryanik2020, - title={New modified and extended stability functions for the stable boundary layer based on SHEBA and parametrizations of bulk transfer coefficients for climate models}, - author={Gryanik, Vladimir M and L{\"u}pkes, Christof and Grachev, Andrey and Sidorenko, Dmitry}, - journal={Journal of the Atmospheric Sciences}, - volume={-1}, - year={2020} -} - -@article{harrington1995, - title={Parameterization of ice crystal conversion processes due to vapor deposition for mesoscale models using double-moment basis functions. Part I: Basic formulation and parcel model results}, - author={Harrington, Jerry Y and Meyers, Michael P and Walko, Robert L and Cotton, William R}, - journal={Journal of the atmospheric sciences}, - volume={52}, - number={23}, - pages={4344--4366}, - year={1995} -} - -@article{held1994, - title={A proposal for the intercomparison of the dynamical cores of atmospheric general circulation models}, - author={Held, Isaac M and Suarez, Max J}, - journal={Bulletin of the American Meteorological society}, - volume={75}, - number={10}, - pages={1825--1830}, - year={1994}, - publisher={American Meteorological Society} + 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} +} + +@article{Beare2006, + title = {An intercomparison of large-eddy simulations of the stable boundary layer}, + author = {Beare, Robert J and Macvean, Malcolm K and Holtslag, Albert AM and Cuxart, Joan and Esau, Igor and Golaz, Jean-Christophe and Jimenez, Maria A and Khairoutdinov, Marat and Kosovic, Branko and Lewellen, David and others}, + journal = {Boundary-Layer Meteorology}, + volume = {118}, + number = {2}, + 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}, + pages = {247--272}, + month = {04}, + year = {2006}, + publisher = {Springer} +} + +@article{Berrut2004, + title = {Barycentric lagrange interpolation}, + author = {Berrut, Jean-Paul and Trefethen, Lloyd N}, + journal = {SIAM review}, + volume = {46}, + number = {3}, + pages = {501--517}, + year = {2004}, + url = {https://doi.org/10.1137/S0036144502417715}, + publisher = {SIAM} +} + +@inproceedings{Boyd1996, + title = {The erfc-log filter and the asymptotics of the Euler and Vandeven sequence accelerations}, + author = {Boyd, JP}, + booktitle = {Proceedings of the Third International Conference on Spectral and High Order Methods}, + pages = {267--276}, + year = {1996}, + organization = {Houston Math. J} +} + +@article{Businger1971, + title = {Flux-profile relationships in the atmospheric surface layer}, + author = {Businger, Joost A and Wyngaard, John C and Izumi, Yꎬ and Bradley, Edward F}, + journal = {Journal of the atmospheric Sciences}, + volume = {28}, + number = {2}, + url = {https://doi.org/10.1175/1520-0469(1971)028<0181:FPRITA>2.0.CO;2}, + pages = {181--189}, + year = {1971} +} + +@article{Byun1990, + title = {On the analytical solutions of flux-profile relationships for the atmospheric surface layer}, + author = {Byun, Daewon W}, + journal = {Journal of Applied Meteorology}, + volume = {29}, + number = {7}, + pages = {652--657}, + year = {1990} +} + +@article{Desai2019, + title = {Aerosol-Mediated Glaciation of Mixed-Phase Clouds: Steady-State Laboratory Measurements}, + author = {Desai, Neel and Chandrakar, KK and Kinney, G and Cantrell, W and Shaw, RA}, + journal = {Geophysical Research Letters}, + volume = {46}, + number = {15}, + pages = {9154--9162}, + year = {2019}, + publisher = {Wiley Online Library} +} + +@article{Doms2011, + title = {A Description of the Nonhydrostatic Regional COSMO model. Part I: Dynamics and Numerics}, + author = {Doms, G{\"u}nther and Baldauf, M}, + journal = {Deutscher Wetterdienst, Offenbach}, + volume = {-1}, + year = {2011} +} + +@article{Durran1982, + title = {On the effects of moisture on the Brunt-V{\"a}is{\"a}l{\"a} frequency}, + author = {Durran, Dale R and Klemp, Joseph B}, + journal = {Journal of the Atmospheric Sciences}, + volume = {39}, + number = {10}, + url = {https://doi.org/10.1175/1520-0469(1982)039<2152:OTEOMO>2.0.CO;2}, + pages = {2152--2158}, + year = {1982} +} + +@article{Carpenter1990, + title = {Application of the piecewise parabolic method (PPM) to meteorological modeling}, + author = {Carpenter Jr, Richard L and Droegemeier, Kelvin K and Woodward, Paul R and Hane, Carl E}, + journal = {Monthly Weather Review}, + volume = {118}, + number = {3}, + url = {https://doi.org/10.1175/1520-0493(1990)118<0586:AOTPPM>2.0.CO;2}, + pages = {586--612}, + year = {1990} +} + +@article{Eisenstat1983, + title = {Variational iterative methods for nonsymmetric systems of linear equations}, + author = {Eisenstat, Stanley C and Elman, Howard C and Schultz, Martin H}, + journal = {SIAM Journal on Numerical Analysis}, + volume = {20}, + number = {2}, + pages = {345--357}, + year = {1983}, + publisher = {SIAM} +} + +@book{GolubVanLoan2013, + title = {Matrix Computations}, + author = {Gene H. Golub and Charles F. Van Loan}, + edition = {4th}, + isbn = {9781421407944}, + publisher = {Johns Hopkins University Press}, + address = {Baltimore, MD, USA}, + url = {http://www.cs.cornell.edu/cv/GVL4/golubandvanloan.htm}, + year = 2013 +} + +@article{Giraldo2013, + title = {Implicit-explicit formulations of a three-dimensional nonhydrostatic unified model of the atmosphere ({NUMA})}, + author = {Giraldo, Francis X and Kelly, James F and Constantinescu, Emil M}, + journal = {SIAM Journal on Scientific Computing}, + volume = {35}, + number = {5}, + pages = {B1162--B1194}, + year = {2013}, + publisher = {SIAM} +} + +@article{Grabowski1996, + title = {Two-time-level semi-Lagrangian modeling of precipitating clouds}, + author = {Grabowski, Wojciech W and Smolarkiewicz, Piotr K}, + journal = {Monthly weather review}, + volume = {124}, + number = {3}, + url = {https://doi.org/10.1175/1520-0493(1996)124<0487:TTLSLM>2.0.CO;2}, + pages = {487--497}, + year = {1996} +} + +@article{Grabowski1998, + title = {Toward cloud resolving modeling of large-scale tropical circulations: A simple cloud microphysics parameterization}, + author = {Grabowski, Wojciech W}, + journal = {Journal of the Atmospheric Sciences}, + volume = {55}, + number = {21}, + pages = {3283--3298}, + url = {https://journals.ametsoc.org/doi/pdf/10.1175/1520-0469%281998%29055%3C3283%3ATCRMOL%3E2.0.CO%3B2}, + year = {1998} +} + +@article{Grachev2007, + title = {SHEBA flux--profile relationships in the stable atmospheric boundary layer}, + author = {Grachev, Andrey A and Andreas, Edgar L and Fairall, Christopher W and Guest, Peter S and Persson, P Ola G}, + journal = {Boundary-layer meteorology}, + volume = {124}, + number = {3}, + pages = {315--333}, + year = {2007}, + url = {https://doi.org/10.1007/s10546-007-9177-6}, + publisher = {Springer} +} + +@article{Gryanik2020, + title = {New modified and extended stability functions for the stable boundary layer based on SHEBA and parametrizations of bulk transfer coefficients for climate models}, + author = {Gryanik, Vladimir M and L{\"u}pkes, Christof and Grachev, Andrey and Sidorenko, Dmitry}, + journal = {Journal of the Atmospheric Sciences}, + volume = {-1}, + year = {2020} +} + +@article{Harrington1995, + title = {Parameterization of ice crystal conversion processes due to vapor deposition for mesoscale models using double-moment basis functions. Part I: Basic formulation and parcel model results}, + author = {Harrington, Jerry Y and Meyers, Michael P and Walko, Robert L and Cotton, William R}, + journal = {Journal of the atmospheric sciences}, + volume = {52}, + number = {23}, + pages = {4344--4366}, + year = {1995} +} + +@article{Held1994, + title = {A proposal for the intercomparison of the dynamical cores of atmospheric general circulation models}, + author = {Held, Isaac M and Suarez, Max J}, + journal = {Bulletin of the American Meteorological society}, + volume = {75}, + number = {10}, + pages = {1825--1830}, + year = {1994}, + url = {https://doi.org/10.1175/1520-0477(1994)075<1825:APFTIO>2.0.CO;2}, + publisher = {American Meteorological Society} } @article{Heun1900, - title = {Neue Methoden zur approximativen Integration der - Differentialgleichungen einer unabh\"{a}ngigen Ver\"{a}nderlichen}, - author = {Heun, Karl}, - journal = {Z. Math. Phys}, - volume = {45}, - pages = {23--38}, - year = {1900} -} - -@article{kaul2015, - title={Sensitivities in large-eddy simulations of mixed-phase Arctic stratocumulus clouds using a simple microphysics approach}, - author={Kaul, Colleen M and Teixeira, Jo{\~a}o and Suzuki, Kentaroh}, - journal={Monthly Weather Review}, - volume={143}, - number={11}, - pages={4393--4421}, - year={2015} -} - -@article{karrer2020, - title={Ice Particle Properties Inferred from Aggregation Modelling}, - author={Karrer, M and Seifert, A and Siewert, C and Ori, D and von Lerber, A and Kneifel, S}, - journal={Journal of Advances in Modeling Earth Systems}, - pages={e2020MS002066}, - volume={-1}, - year={2020}, - publisher={Wiley Online Library} -} - -@article{kennedy2019, - title={Higher-order additive Runge--Kutta schemes for ordinary - differential equations}, - author={Kennedy, Christopher A and Carpenter, Mark H}, - journal={Applied Numerical Mathematics}, - volume={136}, - pages={183--205}, - year={2019}, - publisher={Elsevier} + title = {Neue Methoden zur approximativen Integration der + Differentialgleichungen einer unabh\"{a}ngigen Ver\"{a}nderlichen}, + author = {Heun, Karl}, + journal = {Z. Math. Phys}, + volume = {45}, + pages = {23--38}, + year = {1900} +} + +@article{Kaul2015, + title = {Sensitivities in large-eddy simulations of mixed-phase Arctic stratocumulus clouds using a simple microphysics approach}, + author = {Kaul, Colleen M and Teixeira, Jo{\~a}o and Suzuki, Kentaroh}, + journal = {Monthly Weather Review}, + volume = {143}, + number = {11}, + pages = {4393--4421}, + year = {2015} +} + +@article{Karrer2020, + title = {Ice Particle Properties Inferred from Aggregation Modelling}, + author = {Karrer, M and Seifert, A and Siewert, C and Ori, D and von Lerber, A and Kneifel, S}, + journal = {Journal of Advances in Modeling Earth Systems}, + pages = {e2020MS002066}, + volume = {-1}, + year = {2020}, + publisher = {Wiley Online Library} +} + +@article{Kennedy2019, + title = {Higher-order additive Runge--Kutta schemes for ordinary differential equations}, + author = {Kennedy, Christopher A and Carpenter, Mark H}, + journal = {Applied Numerical Mathematics}, + volume = {136}, + pages = {183--205}, + year = {2019}, + publisher = {Elsevier} } @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{kessler1995, - title={On the continuity and distribution of water substance in atmospheric circulations}, - author={Kessler, Edwin}, - journal={Atmospheric research}, - volume={38}, - number={1-4}, - pages={109--145}, - year={1995}, - publisher={Elsevier} -} - -@article{khvorostyanov2002, - title={Terminal velocities of droplets and crystals: Power laws with continuous parameters over the size spectrum}, - author={Khvorostyanov, Vitaly I and Curry, Judith A}, - journal={Journal of the atmospheric sciences}, - volume={59}, - number={11}, - pages={1872--1884}, - year={2002} + 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{Kessler1995, + title = {On the continuity and distribution of water substance in atmospheric circulations}, + author = {Kessler, Edwin}, + journal = {Atmospheric research}, + volume = {38}, + number = {1-4}, + pages = {109--145}, + year = {1995}, + publisher = {Elsevier} +} + +@article{Khvorostyanov2002, + title = {Terminal velocities of droplets and crystals: Power laws with continuous parameters over the size spectrum}, + author = {Khvorostyanov, Vitaly I and Curry, Judith A}, + journal = {Journal of the atmospheric sciences}, + volume = {59}, + number = {11}, + pages = {1872--1884}, + year = {2002} } @article{KnothWensch2014, - title={Generalized split-explicit Runge--Kutta methods for the compressible Euler equations}, - author={Knoth, Oswald and Wensch, Joerg}, - journal={Monthly Weather Review}, - volume={142}, - number={5}, - pages={2067--2081}, - year={2014} -} - -@article{kopriva2006, - title={Metric identities and the discontinuous spectral element method on curvilinear meshes}, - author={Kopriva, David A}, - journal={Journal of Scientific Computing}, - volume={26}, - number={3}, - pages={301}, - year={2006}, - publisher={Springer} -} - -@article{koshyk2001, - title={The horizontal kinetic energy spectrum and spectral budget simulated by a high-resolution troposphere--stratosphere--mesosphere GCM}, - author={Koshyk, John N and Hamilton, Kevin}, - journal={Journal of the atmospheric sciences}, - volume={58}, - number={4}, - pages={329--348}, - year={2001} -} - -@article{kosovic2000, - title={A large eddy simulation study of a quasi-steady, stably stratified atmospheric boundary layer}, - author={Kosovi{\'c}, Branko and Curry, Judith A}, - journal={Journal of the atmospheric sciences}, - volume={57}, - number={8}, - pages={1052--1068}, - year={2000} -} - -@article{lauritzen2012, - title={A standard test case suite for two-dimensional linear transport on the sphere}, - author={Lauritzen, Peter Hjort and Skamarock, William C and Prather, MJ and Taylor, MA}, - journal={Geoscientific Model Development}, - volume={5}, - number={3}, - pages={887--901}, - year={2012} -} - -@article{lilly1962, - title={On the numerical simulation of buoyant convection}, - author={Lilly, Douglas K}, - journal={Tellus}, - volume={14}, - number={2}, - pages={148--172}, - year={1962}, - publisher={Wiley Online Library} -} - -@article{marshall1948, - title={The distribution of raindrops with size}, - author={Marshall, John S and Palmer, W Mc K}, - journal={Journal of meteorology}, - volume={5}, - number={4}, - pages={165--166}, - year={1948} -} - -@book{mason2010, - title={Physics of clouds}, - author={Mason, Basil John}, - year={2010}, - publisher={Clarendon Press} -} - -@article{morrison2008, - title={A new two-moment bulk stratiform cloud microphysics scheme in the Community Atmosphere Model, version 3 (CAM3). Part I: Description and numerical tests}, - author={Morrison, Hugh and Gettelman, Andrew}, - journal={Journal of Climate}, - volume={21}, - number={15}, - pages={3642--3659}, - year={2008} -} - -@article{muhlbauer2013, - title={Reexamination of the state of the art of cloud modeling shows real improvements}, - author={Muhlbauer, Andreas and Grabowski, Wojciech W and Malinowski, Szymon P and Ackerman, Thomas P and Bryan, George H and Lebo, Zachary J and Milbrandt, Jason A and Morrison, Hugh and Ovchinnikov, Mikhail and Tessendorf, Sarah and others}, - journal={Bulletin of the American Meteorological Society}, - volume={94}, - number={5}, - pages={ES45--ES48}, - year={2013}, - publisher={American Meteorological Society} -} - -@article{niegemann2012, - title={Efficient low-storage Runge--Kutta schemes with optimized stability regions}, - author={Niegemann, Jens and Diehl, Richard and Busch, Kurt}, - journal={Journal of Computational Physics}, - volume={231}, - number={2}, - pages={364--372}, - year={2012}, - publisher={Elsevier} -} - -@article{nishizawa2018, - 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} -} - -@article{ogura1971, - title={Numerical simulation of the life cycle of a thunderstorm cell}, - author={Ogura, Yoshimitsu and Takahashi, Tsutomu}, - journal={Mon. Wea. Rev}, - volume={99}, - number={12}, - pages={895--911}, - year={1971}, - publisher={Citeseer} -} - -@article{ralston1962, - title={Runge-Kutta methods with minimum error bounds}, - author={Ralston, Anthony}, - journal={Mathematics of computation}, - volume={16}, - number={80}, - pages={431--437}, - year={1962}, - doi={10.1090/S0025-5718-1962-0150954-0} -} - -@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}, - volume={-1}, - year={2019} -} - -@article{RonchiIaconoPaolucci1996, - title={The ``cubed sphere'': a new method for the solution of partial - differential equations in spherical geometry}, - author={Ronchi, C. and Iacono, R. and Paolucci, P. S.}, - journal={Journal of Computational Physics}, - volume={124}, - number={1}, - pages={93--114}, - year={1996}, - doi={10.1006/jcph.1996.0047} -} - -@article{rutledge1983, - title={The mesoscale and microscale structure and organization of clouds and precipitation in midlatitude cyclones. VIII: A model for the “seeder-feeder” process in warm-frontal rainbands}, - author={Rutledge, Steven A and Hobbs, Peterv}, - journal={Journal of the Atmospheric Sciences}, - volume={40}, - number={5}, - pages={1185--1206}, - year={1983} -} - -@article{rutledge1984, - title={The mesoscale and microscale structure and organization of clouds and precipitation in midlatitude cyclones. XII: A diagnostic modeling study of precipitation development in narrow cold-frontal rainbands}, - author={Rutledge, Steven A and Hobbs, Peter V}, - journal={Journal of the Atmospheric Sciences}, - volume={41}, - number={20}, - pages={2949--2972}, - year={1984} -} - -@article{saad1986gmres, - title={GMRES: A generalized minimal residual algorithm for solving nonsymmetric linear systems}, - author={Saad, Youcef and Schultz, Martin H}, - journal={SIAM Journal on scientific and statistical computing}, - volume={7}, - number={3}, - pages={856--869}, - year={1986}, - publisher={SIAM} -} - -@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{schar2002, - title={A new terrain-following vertical coordinate formulation for atmospheric prediction models}, - author={Sch{\"a}r, Christoph and Leuenberger, Daniel and Fuhrer, Oliver and L{\"u}thi, Daniel and Girard, Claude}, - journal={Monthly Weather Review}, - volume={130}, - number={10}, - pages={2459--2480}, - year={2002} -} - -@article{SchlegelKnothArnoldWolke2012, - title={Implementation of multirate time integration methods for air - pollution modelling}, - author={Schlegel, M and Knoth, O and Arnold, M and Wolke, R}, - journal={Geoscientific Model Development}, - volume={5}, - number={6}, - pages={1395--1405}, - year={2012}, - publisher={Copernicus GmbH} + title = {Generalized split-explicit Runge--Kutta methods for the compressible Euler equations}, + author = {Knoth, Oswald and Wensch, Joerg}, + journal = {Monthly Weather Review}, + volume = {142}, + number = {5}, + pages = {2067--2081}, + year = {2014} +} + +@article{Kopriva2006, + title = {Metric identities and the discontinuous spectral element method on curvilinear meshes}, + author = {Kopriva, David A}, + journal = {Journal of Scientific Computing}, + volume = {26}, + number = {3}, + pages = {301}, + year = {2006}, + url = {https://doi.org/10.1007/s10915-005-9070-8}, + publisher = {Springer} +} + +@article{Koshyk2001, + title = {The horizontal kinetic energy spectrum and spectral budget simulated by a high-resolution troposphere--stratosphere--mesosphere GCM}, + author = {Koshyk, John N and Hamilton, Kevin}, + journal = {Journal of the atmospheric sciences}, + volume = {58}, + number = {4}, + url = {https://doi.org/10.1175/1520-0469(2001)058<0329:THKESA>2.0.CO;2}, + pages = {329--348}, + year = {2001} +} + +@article{Kosovic2000, + title = {A large eddy simulation study of a quasi-steady, stably stratified atmospheric boundary layer}, + author = {Kosovi{\'c}, Branko and Curry, Judith A}, + journal = {Journal of the atmospheric sciences}, + volume = {57}, + number = {8}, + pages = {1052--1068}, + year = {2000} +} + +@article{Lauritzen2012, + title = {A standard test case suite for two-dimensional linear transport on the sphere}, + author = {Lauritzen, Peter Hjort and Skamarock, William C and Prather, MJ and Taylor, MA}, + journal = {Geoscientific Model Development}, + volume = {5}, + number = {3}, + url = {https://www.geosci-model-dev.net/5/887/2012/}, + doi = {10.5194/gmd-5-887-2012}, + pages = {887--901}, + year = {2012} +} + +@article{Lilly1962, + title = {On the numerical simulation of buoyant convection}, + author = {Lilly, Douglas K}, + journal = {Tellus}, + volume = {14}, + number = {2}, + pages = {148--172}, + year = {1962}, + publisher = {Wiley Online Library} +} + +@article{Marshall1948, + title = {The distribution of raindrops with size}, + author = {Marshall, John S and Palmer, W Mc K}, + journal = {Journal of meteorology}, + volume = {5}, + number = {4}, + pages = {165--166}, + year = {1948} +} + +@book{Mason2010, + title = {Physics of clouds}, + author = {Mason, Basil John}, + year = {2010}, + publisher = {Clarendon Press} +} + +@article{Morrison2008, + title = {A new two-moment bulk stratiform cloud microphysics scheme in the Community Atmosphere Model, version 3 (CAM3). Part I: Description and numerical tests}, + author = {Morrison, Hugh and Gettelman, Andrew}, + journal = {Journal of Climate}, + volume = {21}, + number = {15}, + pages = {3642--3659}, + year = {2008} +} + +@article{Muhlbauer2013, + title = {Reexamination of the state of the art of cloud modeling shows real improvements}, + author = {Muhlbauer, Andreas and Grabowski, Wojciech W and Malinowski, Szymon P and Ackerman, Thomas P and Bryan, George H and Lebo, Zachary J and Milbrandt, Jason A and Morrison, Hugh and Ovchinnikov, Mikhail and Tessendorf, Sarah and others}, + journal = {Bulletin of the American Meteorological Society}, + volume = {94}, + number = {5}, + doi = {doi:10.1175/BAMS-D-12-00188.1}, + pages = {ES45--ES48}, + year = {2013}, + publisher = {American Meteorological Society} +} + +@article{Niegemann2012, + title = {Efficient low-storage Runge--Kutta schemes with optimized stability regions}, + author = {Niegemann, Jens and Diehl, Richard and Busch, Kurt}, + journal = {Journal of Computational Physics}, + volume = {231}, + number = {2}, + pages = {364--372}, + year = {2012}, + publisher = {Elsevier} +} + +@article{Nishizawa2018, + 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}, + url = {https://doi.org/10.1029/2018MS001534}, + doi = {10.1029/2018MS001534}, + pages = {3159--3175}, + year = {2018}, + publisher = {Wiley Online Library} +} + +@article{Ogura1971, + title = {Numerical simulation of the life cycle of a thunderstorm cell}, + author = {Ogura, Yoshimitsu and Takahashi, Tsutomu}, + journal = {Mon. Wea. Rev}, + volume = {99}, + number = {12}, + pages = {895--911}, + year = {1971}, + publisher = {Citeseer} +} + +@article{Ralston1962, + title = {Runge-Kutta methods with minimum error bounds}, + author = {Ralston, Anthony}, + journal = {Mathematics of computation}, + volume = {16}, + number = {80}, + pages = {431--437}, + year = {1962}, + doi = {10.1090/S0025-5718-1962-0150954-0} +} + +@article{Roberts2018, + 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}, + volume = {-1}, + year = {2019} +} + +@article{Ronchi1996, + title = {The ``cubed sphere``: a new method for the solution of partial differential equations in spherical geometry}, + author = {Ronchi, C. and Iacono, R. and Paolucci, P. S.}, + journal = {Journal of Computational Physics}, + volume = {124}, + number = {1}, + pages = {93--114}, + year = {1996}, + url = {https://linkinghub.elsevier.com/retrieve/pii/S0021999196900479}, + doi = {10.1006/jcph.1996.0047} +} + +@article{Rutledge1983, + title = {The mesoscale and microscale structure and organization of clouds and precipitation in midlatitude cyclones. VIII: A model for the “seeder-feeder” process in warm-frontal rainbands}, + author = {Rutledge, Steven A and Hobbs, Peterv}, + journal = {Journal of the Atmospheric Sciences}, + volume = {40}, + number = {5}, + pages = {1185--1206}, + year = {1983} +} + +@article{Rutledge1984, + title = {The mesoscale and microscale structure and organization of clouds and precipitation in midlatitude cyclones. XII: A diagnostic modeling study of precipitation development in narrow cold-frontal rainbands}, + author = {Rutledge, Steven A and Hobbs, Peter V}, + journal = {Journal of the Atmospheric Sciences}, + volume = {41}, + number = {20}, + pages = {2949--2972}, + year = {1984} +} + +@article{Saad1986, + title = {GMRES: A generalized minimal residual algorithm for solving nonsymmetric linear systems}, + author = {Saad, Youcef and Schultz, Martin H}, + journal = {SIAM Journal on scientific and statistical computing}, + volume = {7}, + number = {3}, + pages = {856--869}, + year = {1986}, + publisher = {SIAM} +} + +@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{Schar2002, + title = {A new terrain-following vertical coordinate formulation for atmospheric prediction models}, + author = {Sch{\"a}r, Christoph and Leuenberger, Daniel and Fuhrer, Oliver and L{\"u}thi, Daniel and Girard, Claude}, + journal = {Monthly Weather Review}, + volume = {130}, + number = {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}, + pages = {2459--2480}, + month = {10}, + year = {2002} +} + +@article{Schlegel2012, + title = {Implementation of multirate time integration methods for air pollution modelling}, + author = {Schlegel, M and Knoth, O and Arnold, M and Wolke, R}, + journal = {Geoscientific Model Development}, + volume = {5}, + number = {6}, + pages = {1395--1405}, + year = {2012}, + publisher = {Copernicus GmbH} } @article{Schlegel2009, @@ -521,183 +554,201 @@ @article{Schlegel2009 journal = {Journal of Computational and Applied Mathematics} } -@article{seifert2006, - title={A two-moment cloud microphysics parameterization for mixed-phase clouds. Part 1: Model description}, - author={Seifert, Axel and Beheng, Klaus Dieter}, - journal={Meteorology and atmospheric physics}, - volume={92}, - number={1-2}, - pages={45--66}, - year={2006}, - publisher={Springer} -} - -@article{shu1988, - title={Efficient implementation of essentially non-oscillatory shock-capturing schemes}, - author={Shu, Chi-Wang and Osher, Stanley}, - journal={Journal of computational physics}, - volume={77}, - number={2}, - pages={439--471}, - year={1988}, - publisher={Elsevier} -} - -@article{siebesma2003, - title={A large eddy simulation intercomparison study of shallow cumulus convection}, - 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 others}, - journal={Journal of the Atmospheric Sciences}, - volume={60}, - number={10}, - pages={1201--1219}, - year={2003} -} - -@inproceedings{skilling2004, - title={Programming the Hilbert curve}, - author={Skilling, John}, - booktitle={AIP Conference Proceedings}, - volume={707}, - number={1}, - pages={381--387}, - year={2004}, - organization={American Institute of Physics} -} - -@article{smagorinsky1963, - title={General circulation experiments with the primitive equations: I. The basic experiment}, - author={Smagorinsky, Joseph}, - journal={Monthly weather review}, - volume={91}, - number={3}, - pages={99--164}, - year={1963} -} - -@article{spiteri2002, - title={A new class of optimal high-order strong-stability-preserving time discretization methods}, - author={Spiteri, Raymond J and Ruuth, Steven J}, - journal={SIAM Journal on Numerical Analysis}, - volume={40}, - number={2}, - pages={469--491}, - year={2002}, - publisher={SIAM} -} - -@article{stevens2005, - title={Evaluation of large-eddy simulations via observations of nocturnal marine stratocumulus}, - 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 others}, - journal={Monthly weather review}, - volume={133}, - number={6}, - pages={1443--1462}, - year={2005} -} - -@article{straka1993, - title={Numerical solutions of a non-linear density current: A benchmark solution and comparisons}, - author={Straka, Jerry M and Wilhelmson, Robert B and Wicker, Louis J and Anderson, John R and Droegemeier, Kelvin K}, - journal={International Journal for Numerical Methods in Fluids}, - volume={17}, - number={1}, - pages={1--22}, - year={1993}, - publisher={Wiley Online Library} +@article{Seifert2006, + title = {A two-moment cloud microphysics parameterization for mixed-phase clouds. Part 1: Model description}, + author = {Seifert, Axel and Beheng, Klaus Dieter}, + journal = {Meteorology and atmospheric physics}, + volume = {92}, + number = {1-2}, + pages = {45--66}, + year = {2006}, + publisher = {Springer} +} + +@article{Shu1988, + title = {Efficient implementation of essentially non-oscillatory shock-capturing schemes}, + author = {Shu, Chi-Wang and Osher, Stanley}, + journal = {Journal of computational physics}, + volume = {77}, + number = {2}, + pages = {439--471}, + year = {1988}, + publisher = {Elsevier} +} + +@article{Siebesma2003, + title = {A large eddy simulation intercomparison study of shallow cumulus convection}, + 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 others}, + journal = {Journal of the Atmospheric Sciences}, + volume = {60}, + number = {10}, + eprint = {https://journals.ametsoc.org/doi/pdf/10.1175/1520-0469%282003%2960%3C1201%3AALESIS%3E2.0.CO%3B2}, + 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}, + pages = {1201--1219}, + year = {2003} +} + +@inproceedings{Skilling2004, + title = {Programming the Hilbert curve}, + author = {Skilling, John}, + booktitle = {AIP Conference Proceedings}, + volume = {707}, + number = {1}, + pages = {381--387}, + year = {2004}, + url = {https://doi.org/10.1063/1.1751381}, + organization = {American Institute of Physics} +} + +@article{Smagorinsky1963, + title = {General circulation experiments with the primitive equations: I. The basic experiment}, + author = {Smagorinsky, Joseph}, + journal = {Monthly weather review}, + volume = {91}, + number = {3}, + doi = {10.1111/j.2153-3490.1962.tb00128.x}, + pages = {99--164}, + 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 = {1963} +} + +@article{Spiteri2002, + title = {A new class of optimal high-order strong-stability-preserving time discretization methods}, + author = {Spiteri, Raymond J and Ruuth, Steven J}, + journal = {SIAM Journal on Numerical Analysis}, + volume = {40}, + number = {2}, + pages = {469--491}, + year = {2002}, + publisher = {SIAM} +} + +@article{Stevens2005, + title = {Evaluation of large-eddy simulations via observations of nocturnal marine stratocumulus}, + 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 others}, + journal = {Monthly weather review}, + volume = {133}, + number = {6}, + url = {https://doi.org/10.1175/MWR2930.1}, + doi = {10.1175/MWR2930.1}, + eprint = {https://doi.org/10.1175/MWR2930.1}, + pages = {1443--1462}, + year = {2005} +} + +@article{Straka1993, + title = {Numerical solutions of a non-linear density current: A benchmark solution and comparisons}, + author = {Straka, Jerry M and Wilhelmson, Robert B and Wicker, Louis J and Anderson, John R and Droegemeier, Kelvin K}, + journal = {International Journal for Numerical Methods in Fluids}, + volume = {17}, + number = {1}, + doi = {10.1002/fld.1650170103}, + url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/fld.1650170103}, + eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/fld.1650170103}, + pages = {1--22}, + year = {1993}, + publisher = {Wiley Online Library} } @article{Tomita2008, - doi = {10.1137/070692273}, - year = {2008}, - month = {jan}, - publisher = {Society for Industrial and Applied Mathematics ({SIAM})}, - volume = {30}, - number = {6}, - pages = {2755--2776}, - author = {Hirofumi Tomita and Koji Goto and Masaki Satoh}, - title = {A New Approach to Atmospheric General Circulation Model: Global Cloud Resolving Model {NICAM} and its Computational Performance}, - journal = {{SIAM} Journal on Scientific Computing} -} - -@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} -} - -@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} -} - -@article{vreugdenhil2018, - title={Large-eddy simulations of stratified plane Couette flow using the anisotropic minimum-dissipation model}, - author={Vreugdenhil, Catherine A and Taylor, John R}, - journal={Physics of Fluids}, - volume={30}, - number={8}, - pages={085104}, - year={2018}, - publisher={AIP Publishing LLC} -} - -@article{wang2006, - title={Probability distributions of angle of approach and relative velocity for colliding droplets in a turbulent flow}, - author={Wang, Lian-Ping and Franklin, Charmaine N and Ayala, Orlando and Grabowski, Wojciech W}, - journal={Journal of the atmospheric sciences}, - volume={63}, - number={3}, - pages={881--900}, - year={2006} -} - -@article{wiin1967, - title={On the annual variation and spectral distribution of atmospheric energy 1}, - author={WIIN-NIELSEN, Aksel}, - journal={Tellus}, - volume={19}, - number={4}, - pages={540--559}, - year={1967}, - publisher={Wiley Online Library} -} - -@article{williamson1992, - title={A standard test set for numerical approximations to the shallow water equations in spherical geometry}, - author={Williamson, David L and Drake, John B and Hack, James J and Jakob, R{\"u}diger and Swarztrauber, Paul N}, - journal={Journal of Computational Physics}, - volume={102}, - number={1}, - pages={211--224}, - year={1992}, - publisher={Elsevier} -} - -@article{wood2005, - title={Drizzle in stratiform boundary layer clouds. Part II: Microphysical aspects}, - author={Wood, R}, - journal={Journal of the atmospheric sciences}, - volume={62}, - number={9}, - pages={3034--3050}, - year={2005} -} - -@article{wyngaard1975, - title={Modeling the planetary boundary layer—extension to the stable case}, - author={Wyngaard, John C}, - journal={Boundary-Layer Meteorology}, - volume={9}, - number={4}, - pages={441--460}, - year={1975}, - publisher={Springer} + doi = {10.1137/070692273}, + year = {2008}, + month = {jan}, + publisher = {Society for Industrial and Applied Mathematics ({SIAM})}, + volume = {30}, + number = {6}, + pages = {2755--2776}, + author = {Hirofumi Tomita and Koji Goto and Masaki Satoh}, + title = {A New Approach to Atmospheric General Circulation Model: Global Cloud Resolving Model {NICAM} and its Computational Performance}, + journal = {{SIAM} Journal on Scientific Computing} +} + +@book{Toro2013, + title = {Riemann solvers and numerical methods for fluid dynamics: a practical introduction}, + author = {Toro, Eleuterio F}, + year = {2013}, + publisher = {Springer Science & Business Media} +} + +@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} +} + +@article{Vreugdenhil2018, + title = {Large-eddy simulations of stratified plane Couette flow using the anisotropic minimum-dissipation model}, + author = {Vreugdenhil, Catherine A and Taylor, John R}, + journal = {Physics of Fluids}, + volume = {30}, + number = {8}, + pages = {085104}, + year = {2018}, + url = {https://doi.org/10.1063/1.5037039}, + doi = {10.1063/1.5037039}, + publisher = {AIP Publishing LLC} +} + +@article{Wang2006, + title = {Probability distributions of angle of approach and relative velocity for colliding droplets in a turbulent flow}, + author = {Wang, Lian-Ping and Franklin, Charmaine N and Ayala, Orlando and Grabowski, Wojciech W}, + journal = {Journal of the atmospheric sciences}, + volume = {63}, + number = {3}, + pages = {881--900}, + year = {2006} +} + +@article{Wiin1967, + title = {On the annual variation and spectral distribution of atmospheric energy 1}, + author = {WIIN-NIELSEN, Aksel}, + journal = {Tellus}, + volume = {19}, + number = {4}, + doi = {10.3402/tellusa.v19i4.9822}, + pages = {540--559}, + year = {1967}, + publisher = {Wiley Online Library} +} + +@article{Williamson1992, + title = {A standard test set for numerical approximations to the shallow water equations in spherical geometry}, + author = {Williamson, David L and Drake, John B and Hack, James J and Jakob, R{\"u}diger and Swarztrauber, Paul N}, + journal = {Journal of Computational Physics}, + volume = {102}, + number = {1}, + doi = {10.1016/S0021-9991(05)80016-6}, + url = {https://doi.org/10.1016/S0021-9991(05)80016-6}, + pages = {211--224}, + year = {1992}, + publisher = {Elsevier} +} + +@article{Wood2005, + title = {Drizzle in stratiform boundary layer clouds. Part II: Microphysical aspects}, + author = {Wood, R}, + journal = {Journal of the atmospheric sciences}, + volume = {62}, + number = {9}, + pages = {3034--3050}, + year = {2005} +} + +@article{Wyngaard1975, + title = {Modeling the planetary boundary layer—extension to the stable case}, + author = {Wyngaard, John C}, + journal = {Boundary-Layer Meteorology}, + volume = {9}, + number = {4}, + pages = {441--460}, + year = {1975}, + publisher = {Springer} } diff --git a/docs/src/Theory/Atmos/Microphysics.md b/docs/src/Theory/Atmos/Microphysics.md index 11b05d47f16..694a079aa09 100644 --- a/docs/src/Theory/Atmos/Microphysics.md +++ b/docs/src/Theory/Atmos/Microphysics.md @@ -3,9 +3,9 @@ The `Microphysics.jl` module describes a 1-moment bulk parameterization of cloud microphysical processes. The module is based on the ideas of - [kessler1995](@cite), - [grabowski1998](@cite) - and [kaul2015](@cite). + [Kessler1995](@cite), + [Grabowski1998](@cite) + and [Kaul2015](@cite). The cloud microphysics variables are expressed as specific humidities: - `q_tot` - total water specific humidity, @@ -78,12 +78,12 @@ With that said, the assumption about the shape of the particles is used three |``m_e^{ice}`` | exponent in ``m(r)`` for ice | - | ``3`` | | | | | | | | |``r_0^{sno}`` | typical snow crystal radius | ``m`` | ``10^{-3} `` | | -|``m_0^{sno}`` | coefficient in ``m(r)`` for snow | ``kg`` | ``0.1 \, r_0^2`` | eq (6b) [grabowski1998](@cite) | -|``m_e^{sno}`` | exponent in ``m(r)`` for snow | - | ``2`` | eq (6b) [grabowski1998](@cite) | -|``a_0^{sno}`` | coefficient in ``a(r)`` for snow | ``m^2`` | ``0.3 \pi \, r_0^2`` | ``\alpha`` in eq(16b) [grabowski1998](@cite).| +|``m_0^{sno}`` | coefficient in ``m(r)`` for snow | ``kg`` | ``0.1 \, r_0^2`` | eq (6b) [Grabowski1998](@cite) | +|``m_e^{sno}`` | exponent in ``m(r)`` for snow | - | ``2`` | eq (6b) [Grabowski1998](@cite) | +|``a_0^{sno}`` | coefficient in ``a(r)`` for snow | ``m^2`` | ``0.3 \pi \, r_0^2`` | ``\alpha`` in eq(16b) [Grabowski1998](@cite).| |``a_e^{sno}`` | exponent in ``a(r)`` for snow | - | ``2`` | | -|``v_0^{sno}`` | coefficient in ``v_{term}(r)`` for snow | ``\frac{m}{s}`` | ``2^{9/4} r_0^{1/4}`` | eq (6b) [grabowski1998](@cite) | -|``v_e^{sno}`` | exponent in ``v_{term}(r)`` for snow | - | ``0.25`` | eq (6b) [grabowski1998](@cite) | +|``v_0^{sno}`` | coefficient in ``v_{term}(r)`` for snow | ``\frac{m}{s}`` | ``2^{9/4} r_0^{1/4}`` | eq (6b) [Grabowski1998](@cite) | +|``v_e^{sno}`` | exponent in ``v_{term}(r)`` for snow | - | ``0.25`` | eq (6b) [Grabowski1998](@cite) | where: - ``\rho_{water}`` is the density of water, @@ -112,15 +112,15 @@ where: It would be great to replace the above simple power laws with more accurate relationships. For example: - [khvorostyanov2002](@cite) + [Khvorostyanov2002](@cite) or - [karrer2020](@cite) + [Karrer2020](@cite) ## Assumed particle size distributions The particle size distributions are assumed to follow Marshall-Palmer distribution - [marshall1948](@cite) + [Marshall1948](@cite) eq. 1: ```math \begin{equation} @@ -148,10 +148,10 @@ package and are shown in the table below. | symbol | definition | units | default value | reference | |-----------------|----------------------------------------------|--------------------|-------------------------------------------|------------| -|``n_{0}^{rai}`` | rain drop size distribution parameter | ``\frac{1}{m^4}`` | ``16 \cdot 10^6`` | eq (2) [marshall1948](@cite) | -|``n_{0}^{ice}`` | cloud ice size distribution parameter | ``\frac{1}{m^4}`` | ``2 \cdot 10^7`` | bottom of page 4396 [kaul2015](@cite) | -|``\mu^{sno}`` | snow size distribution parameter coefficient | ``\frac{1}{m^4}`` | ``4.36 \cdot 10^9 \, \rho_0^{\nu^{sno}}`` | eq (A1) [kaul2015](@cite) | -|``\nu^{sno}`` | snow size distribution parameter exponent | ``-`` | ``0.63`` | eq (A1) [kaul2015](@cite) | +|``n_{0}^{rai}`` | rain drop size distribution parameter | ``\frac{1}{m^4}`` | ``16 \cdot 10^6`` | eq (2) [Marshall1948](@cite) | +|``n_{0}^{ice}`` | cloud ice size distribution parameter | ``\frac{1}{m^4}`` | ``2 \cdot 10^7`` | bottom of page 4396 [Kaul2015](@cite) | +|``\mu^{sno}`` | snow size distribution parameter coefficient | ``\frac{1}{m^4}`` | ``4.36 \cdot 10^9 \, \rho_0^{\nu^{sno}}`` | eq (A1) [Kaul2015](@cite) | +|``\nu^{sno}`` | snow size distribution parameter exponent | ``-`` | ``0.63`` | eq (A1) [Kaul2015](@cite) | The ``\lambda`` parameter is defined as ```math @@ -199,19 +199,19 @@ They consist of: | symbol | definition | units | default value | reference | |----------------------------|-----------------------------------------------------------|--------------------------|------------------------|-----------| -|``C_{drag}`` | rain drop drag coefficient | - | ``0.55`` | ``C_{drag}`` is such that the mass averaged terminal velocity is close to [grabowski1996](@cite) | +|``C_{drag}`` | rain drop drag coefficient | - | ``0.55`` | ``C_{drag}`` is such that the mass averaged terminal velocity is close to [Grabowski1996](@cite) | |``\tau_{cond\_evap}`` | cloud water condensation/evaporation timescale | ``s`` | ``10`` | | |``\tau_{dep\_sub}`` | cloud ice deposition/sublimation timescale | ``s`` | ``10`` | | -|``\tau_{acnv}`` | cloud to rain water autoconversion timescale | ``s`` | ``10^3`` | eq (5a) [grabowski1996](@cite) | -|``q_{liq\_threshold}`` | cloud to rain water autoconversion threshold | - | ``5 \cdot 10^{-4}`` | eq (5a) [grabowski1996](@cite) | -|``r_{is}`` | threshold particle radius between ice and snow | ``m`` | ``62.5 \cdot 10^{-6}`` | abstract [harrington1995](@cite) | -|``E_{lr}`` | collision efficiency between rain drops and cloud droplets| - | ``0.8`` | eq (16a) [grabowski1998](@cite) | -|``E_{ls}`` | collision efficiency between snow and cloud droplets | - | ``0.1`` | Appendix B [rutledge1983](@cite) | -|``E_{ir}`` | collision efficiency between rain drops and cloud ice | - | ``1`` | Appendix B [rutledge1984](@cite) | -|``E_{is}`` | collision efficiency between snow and cloud ice | - | ``0.1`` | bottom page 3649 [morrison2008](@cite) | -|``E_{rs}`` | collision efficiency between rain drops and snow | - | ``1`` | top page 3650 [morrison2008](@cite) | -|``a_{vent}^{rai}, b_{vent}^{rai}`` | rain drop ventilation factor coefficients | - | ``1.5 \;``,``\; 0.53`` | chosen such that at ``q_{tot}=15 g/kg`` and ``T=288K`` the evap. rate is close to empirical evap. rate in [grabowski1996](@cite) | -|``a_{vent}^{sno}, b_{vent}^{sno}`` | snow ventilation factor coefficients | - | ``0.65 \;``,``\; 0.44``| eq (A19) [kaul2015](@cite) | +|``\tau_{acnv}`` | cloud to rain water autoconversion timescale | ``s`` | ``10^3`` | eq (5a) [Grabowski1996](@cite) | +|``q_{liq\_threshold}`` | cloud to rain water autoconversion threshold | - | ``5 \cdot 10^{-4}`` | eq (5a) [Grabowski1996](@cite) | +|``r_{is}`` | threshold particle radius between ice and snow | ``m`` | ``62.5 \cdot 10^{-6}`` | abstract [Harrington1995](@cite) | +|``E_{lr}`` | collision efficiency between rain drops and cloud droplets| - | ``0.8`` | eq (16a) [Grabowski1998](@cite) | +|``E_{ls}`` | collision efficiency between snow and cloud droplets | - | ``0.1`` | Appendix B [Rutledge1983](@cite) | +|``E_{ir}`` | collision efficiency between rain drops and cloud ice | - | ``1`` | Appendix B [Rutledge1984](@cite) | +|``E_{is}`` | collision efficiency between snow and cloud ice | - | ``0.1`` | bottom page 3649 [Morrison2008](@cite) | +|``E_{rs}`` | collision efficiency between rain drops and snow | - | ``1`` | top page 3650 [Morrison2008](@cite) | +|``a_{vent}^{rai}, b_{vent}^{rai}`` | rain drop ventilation factor coefficients | - | ``1.5 \;``,``\; 0.53`` | chosen such that at ``q_{tot}=15 g/kg`` and ``T=288K`` the evap. rate is close to empirical evap. rate in [Grabowski1996](@cite) | +|``a_{vent}^{sno}, b_{vent}^{sno}`` | snow ventilation factor coefficients | - | ``0.65 \;``,``\; 0.44``| eq (A19) [Kaul2015](@cite) | |``K_{therm}`` | thermal conductivity of air | ``\frac{J}{m \; s \; K}``| ``2.4 \cdot 10^{-2}`` | | |``\nu_{air}`` | kinematic viscosity of air | ``\frac{m^2}{s}`` | ``1.6 \cdot 10^{-5}`` | | |``D_{vapor}`` | diffusivity of water vapor | ``\frac{m^2}{s}`` | ``2.26 \cdot 10^{-5}`` | | @@ -220,7 +220,7 @@ They consist of: The ventilation factor parameterizes the increase in the mass and heat exchange for falling particles. -Following [seifert2006](@cite) +Following [Seifert2006](@cite) eq. 24 the ventilation factor is defined as: ```math \begin{equation} @@ -261,7 +261,7 @@ F(r) = a_{vent} + ## Terminal velocity The mass weighted terminal velocity ``v_t`` is defined following -[ogura1971](@cite): +[Ogura1971](@cite): ```math \begin{equation} v_t = \frac{\int_0^\infty n(r) \, m(r) \, v_{term}(r) \, dr} @@ -285,9 +285,9 @@ Integrating over the assumed Marshall-Palmer distribution and using the be size and flow dependent. In general we should implement these terminal velocity parameterizations: - [khvorostyanov2002](@cite) + [Khvorostyanov2002](@cite) or - [karrer2020](@cite) + [Karrer2020](@cite) ## Cloud water condensation/evaporation @@ -326,14 +326,14 @@ where: available condensation nuclei, turbulence intensity, etc. See works by [prof Raymond Shaw](https://www.mtu.edu/physics/department/faculty/shaw/) for hints. - In particular, [desai2019](@cite). + In particular, [Desai2019](@cite). ## Rain autoconversion Rain autoconversion defines the rate of conversion form cloud liquid water to rain water due to collisions between cloud droplets. It is parameterized following - [kessler1995](@cite): + [Kessler1995](@cite): ```math \begin{equation} @@ -350,7 +350,7 @@ where: This is the simplest possible autoconversion parameterization. It would be great to implement others and test the impact on precipitation. See for example - [wood2005](@cite) + [Wood2005](@cite) Table 1 for other simple choices. ## Snow autoconversion @@ -359,7 +359,7 @@ Snow autoconversion defines the rate of conversion form cloud ice to snow due the growth of cloud ice by water vapor deposition. It is defined as the change of mass of cloud ice for cloud ice particles larger than threshold ``r_{is}``. -See [harrington1995](@cite) +See [Harrington1995](@cite) for derivation. ```math @@ -375,7 +375,7 @@ The ``\frac{dm}{dt}`` is obtained by solving the water vapor diffusion equation in spherical coordinates and linking the changes in temperature at the drop surface to the changes in saturated vapor pressure via the Clausius-Clapeyron equation, following - [mason2010](@cite). + [Mason2010](@cite). For the simplest case of spherical particles and not taking into account ventilation effects: @@ -421,7 +421,7 @@ Finally the snow autoconversion rate is computed as For non-spherical particles the mass rate of growth should be multiplied by a function depending on the particle aspect ratio. For functions proposed for different crystal habitats see - [harrington1995](@cite) Appendix B. + [Harrington1995](@cite) Appendix B. ## Accretion @@ -538,7 +538,7 @@ There are two additional assumptions that we make to integrate - We assume that ``a(r_i, r_j) = \pi (r_i + r_j)^2``. This corresponds to a geometric formulation of the collision kernel, aka cylindrical formulation, see - [wang2006](@cite) + [Wang2006](@cite) for discussion. The eq.(\ref{eq:accr_sr1}) can then be integrated as: @@ -699,21 +699,21 @@ const rain_param_set = RainParameterSet() const ice_param_set = IceParameterSet() const snow_param_set = SnowParameterSet() -# eq. 5d in [grabowski1996](@cite) +# eq. 5d in [Grabowski1996](@cite) function terminal_velocity_empirical(q_rai::DT, q_tot::DT, ρ::DT, ρ_air_ground::DT) where {DT<:Real} rr = q_rai / (DT(1) - q_tot) vel = DT(14.34) * ρ_air_ground^DT(0.5) * ρ^-DT(0.3654) * rr^DT(0.1346) return vel end -# eq. 5b in [grabowski1996](@cite) +# eq. 5b in [Grabowski1996](@cite) function accretion_empirical(q_rai::DT, q_liq::DT, q_tot::DT) where {DT<:Real} rr = q_rai / (DT(1) - q_tot) rl = q_liq / (DT(1) - q_tot) return DT(2.2) * rl * rr^DT(7/8) end -# eq. 5c in [grabowski1996](@cite) +# eq. 5c in [Grabowski1996](@cite) function rain_evap_empirical(q_rai::DT, q::PhasePartition, T::DT, p::DT, ρ::DT) where {DT<:Real} ts_neq = PhaseNonEquil_ρTq(param_set, ρ, T, q) diff --git a/docs/src/Theory/Common/SurfaceFluxes.md b/docs/src/Theory/Common/SurfaceFluxes.md index d68817c80ed..9506687387a 100644 --- a/docs/src/Theory/Common/SurfaceFluxes.md +++ b/docs/src/Theory/Common/SurfaceFluxes.md @@ -16,7 +16,7 @@ This module provides a means to compute surface fluxes given several variables, ## References -- [businger1971](@cite) -- [nishizawa2018](@cite) -- [byun1990](@cite) -- [wyngaard1975](@cite) +- [Businger1971](@cite) +- [Nishizawa2018](@cite) +- [Byun1990](@cite) +- [Wyngaard1975](@cite) diff --git a/experiments/AtmosLES/bomex_model.jl b/experiments/AtmosLES/bomex_model.jl index 2a90db88852..659949e5a76 100644 --- a/experiments/AtmosLES/bomex_model.jl +++ b/experiments/AtmosLES/bomex_model.jl @@ -22,7 +22,7 @@ # 3) Collapsed experiment design # 4) Updates to generally keep this in sync with master -[siebesma2003](@cite) +[Siebesma2003](@cite) =# using ArgParse diff --git a/experiments/AtmosLES/convective_bl_model.jl b/experiments/AtmosLES/convective_bl_model.jl index 05278ef3ceb..4c0e22b153e 100644 --- a/experiments/AtmosLES/convective_bl_model.jl +++ b/experiments/AtmosLES/convective_bl_model.jl @@ -5,7 +5,7 @@ # Convective Boundary Layer LES case (Kitamura et al, 2016). ## ### Convective Boundary Layer LES -## [nishizawa2018](@cite) +## [Nishizawa2018](@cite) # # To simulate the experiment, type in # diff --git a/experiments/AtmosLES/dycoms.jl b/experiments/AtmosLES/dycoms.jl index c556e778d79..110c136cfa0 100755 --- a/experiments/AtmosLES/dycoms.jl +++ b/experiments/AtmosLES/dycoms.jl @@ -83,7 +83,7 @@ function flux_radiation!( DYCOMSRadiation <: RadiationModel ## References - - [stevens2005](@cite) + - [Stevens2005](@cite) """ struct DYCOMSRadiation{FT} <: RadiationModel "mass absorption coefficient `[m^2/kg]`" @@ -175,7 +175,7 @@ end Initial Condition for DYCOMS_RF01 LES ## References - - [stevens2005](@cite) + - [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 index faac99b135f..e90705a8bef 100755 --- a/experiments/AtmosLES/schar_scalar_advection.jl +++ b/experiments/AtmosLES/schar_scalar_advection.jl @@ -24,7 +24,7 @@ struct EarthParameterSet <: AbstractEarthParameterSet end const param_set = EarthParameterSet() ### Citation -# [schar2002](@cite) +# [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 index f42b066cacc..98edf722503 100755 --- a/experiments/AtmosLES/stable_bl_model.jl +++ b/experiments/AtmosLES/stable_bl_model.jl @@ -2,9 +2,9 @@ #= # This experiment file establishes the initial conditions, boundary conditions, # source terms and simulation parameters (domain size + resolution) for the -# GABLS LES case ([beare2006](@cite); [kosovic2000](@cite)). +# GABLS LES case ([Beare2006](@cite); [Kosovic2000](@cite)). # -## [kosovic2000](@cite) +## [Kosovic2000](@cite) # # To simulate the experiment, type in # diff --git a/src/Atmos/Model/AtmosModel.jl b/src/Atmos/Model/AtmosModel.jl index 3f68ae71b01..e1d627831ad 100644 --- a/src/Atmos/Model/AtmosModel.jl +++ b/src/Atmos/Model/AtmosModel.jl @@ -938,7 +938,7 @@ see Chapter 10.4 in the provided reference below. ## References - - [toro2013riemann](@cite) + - [Toro2013](@cite) """ function numerical_flux_first_order!( diff --git a/src/Common/Spectra/power_spectrum_gcm.jl b/src/Common/Spectra/power_spectrum_gcm.jl index e5bc3d69d49..1f0eddf92ae 100644 --- 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 -- [wiin1967](@cite) -- [koshyk2001](@cite) +- [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 - - [baer1972](@cite) + - [Baer1972](@cite) """ function power_spectrum_2d(::AtmosGCMConfigType, var_grid, mass_weight) # initialize spherical mesh variables diff --git a/src/Common/SurfaceFluxes/SurfaceFluxes.jl b/src/Common/SurfaceFluxes/SurfaceFluxes.jl index abfd8e17c6e..5bb6391325f 100644 --- a/src/Common/SurfaceFluxes/SurfaceFluxes.jl +++ b/src/Common/SurfaceFluxes/SurfaceFluxes.jl @@ -10,7 +10,7 @@ - exchange coefficients ## References - - [nishizawa2018](@cite) + - [Nishizawa2018](@cite) """ module SurfaceFluxes diff --git a/src/Common/SurfaceFluxes/UniversalFunctions.jl b/src/Common/SurfaceFluxes/UniversalFunctions.jl index 62b2daec72a..504a5da1fc0 100644 --- a/src/Common/SurfaceFluxes/UniversalFunctions.jl +++ b/src/Common/SurfaceFluxes/UniversalFunctions.jl @@ -85,11 +85,11 @@ c_h(uf::AUF) = c_h(uf.param_set, uf) # Reference - - [nishizawa2018](@cite) + - [Nishizawa2018](@cite) # Original research - - [businger1971](@cite) + - [Businger1971](@cite) # Equations in reference: @@ -226,7 +226,7 @@ end Gryanik <: AbstractUniversalFunction{FT} # References - - [gryanik2020](@cite) + - [Gryanik2020](@cite) # Equations in reference: @@ -309,7 +309,7 @@ end Grachev <: AbstractUniversalFunction{FT} # References - - [grachev2007sheba](@cite) + - [Grachev2007](@cite) Equations in reference: diff --git a/src/Common/TurbulenceClosures/TurbulenceClosures.jl b/src/Common/TurbulenceClosures/TurbulenceClosures.jl index 71fb2eefd13..13de04e39e5 100644 --- a/src/Common/TurbulenceClosures/TurbulenceClosures.jl +++ b/src/Common/TurbulenceClosures/TurbulenceClosures.jl @@ -511,15 +511,15 @@ $(DocStringExtensions.FIELDS) # Smagorinsky Model Reference -See [smagorinsky1963](@cite) +See [Smagorinsky1963](@cite) # Lilly Model Reference -See [lilly1962](@cite) +See [Lilly1962](@cite) # Brunt-Väisälä Frequency Reference -See [durran1982](@cite) +See [Durran1982](@cite) """ struct SmagorinskyLilly{FT} <: TurbulenceClosureModel @@ -637,7 +637,7 @@ $(DocStringExtensions.FIELDS) # Reference - - [vreman2004](@cite) + - [Vreman2004](@cite) """ struct Vreman{FT} <: TurbulenceClosureModel "Smagorinsky Coefficient [dimensionless]" @@ -733,7 +733,7 @@ $(DocStringExtensions.FIELDS) # Reference -See [vreugdenhil2018](@cite) +See [Vreugdenhil2018](@cite) """ struct AnisoMinDiss{FT} <: TurbulenceClosureModel diff --git a/src/Driver/SolverTypes/IMEXSolverType.jl b/src/Driver/SolverTypes/IMEXSolverType.jl index 2f8391110bf..452a406af21 100644 --- a/src/Driver/SolverTypes/IMEXSolverType.jl +++ b/src/Driver/SolverTypes/IMEXSolverType.jl @@ -61,7 +61,7 @@ where `n` is now only the nonlinear tendency. discretizing the original PDE directly. ### References - - [giraldo2013](@cite) + - [Giraldo2013](@cite) """ struct IMEXSolverType{DS, ST} <: AbstractSolverType # The type of discrete splitting to apply to the right-hand side diff --git a/src/Driver/SolverTypes/MultirateSolverType.jl b/src/Driver/SolverTypes/MultirateSolverType.jl index 25313c3b494..de77b223807 100644 --- a/src/Driver/SolverTypes/MultirateSolverType.jl +++ b/src/Driver/SolverTypes/MultirateSolverType.jl @@ -55,7 +55,7 @@ fast and slow dynamics respectively, depending on the state `Q`. discretizing the original PDE directly. ### References - - [SchlegelKnothArnoldWolke2012](@cite) + - [Schlegel2012](@cite) """ struct MultirateSolverType{DS} <: AbstractSolverType # The type of discrete splitting to apply to the right-hand side @@ -131,7 +131,7 @@ of a similar implementations include the following references. ### References - - [SchlegelKnothArnoldWolke2012](@cite) + - [Schlegel2012](@cite) - [Schlegel2009](@cite) """ function solversetup( @@ -208,7 +208,7 @@ Examples of similar multirate-HEVI approaches include the following references. ### References - - [doms2011](@cite) + - [Doms2011](@cite) - [Tomita2008](@cite) # Comments: diff --git a/src/Numerics/DGMethods/NumericalFluxes.jl b/src/Numerics/DGMethods/NumericalFluxes.jl index b493cc40d4a..6daffd9f4d2 100644 --- a/src/Numerics/DGMethods/NumericalFluxes.jl +++ b/src/Numerics/DGMethods/NumericalFluxes.jl @@ -337,7 +337,7 @@ based on the underlying balance law. Requires a custom implementation for the balance law. - - [toro2013riemann](@cite) + - [Toro2013](@cite) """ struct HLLCNumericalFlux <: NumericalFluxFirstOrder end diff --git a/src/Numerics/Mesh/BrickMesh.jl b/src/Numerics/Mesh/BrickMesh.jl index 0ef1e9b981c..0c40cc77ffc 100644 --- a/src/Numerics/Mesh/BrickMesh.jl +++ b/src/Numerics/Mesh/BrickMesh.jl @@ -35,7 +35,7 @@ where the 15-bit Hilbert integer = `A B C D E F G H I J K L M N O` is stored in `H` This function is based on public domain code from John Skilling which can be -found in [skilling2004](@cite). +found in [Skilling2004](@cite). """ function hilbertcode(Y::AbstractArray{T}; bits = 8 * sizeof(T)) where {T} # Below is Skilling's AxestoTranspose diff --git a/src/Numerics/Mesh/Elements.jl b/src/Numerics/Mesh/Elements.jl index d1af2268870..80b8e3fc6e6 100644 --- a/src/Numerics/Mesh/Elements.jl +++ b/src/Numerics/Mesh/Elements.jl @@ -30,7 +30,7 @@ end returns the barycentric weights associated with the array of points `r` Reference: - [berrut2004](@cite) + [Berrut2004](@cite) """ function baryweights(r::AbstractVector{T}) where {T} Np = length(r) @@ -56,7 +56,7 @@ returns the spectral differentiation matrix for a polynomial defined on the points `r` with associated barycentric weights `wb` Reference: - - [berrut2004](@cite) + - [Berrut2004](@cite) """ function spectralderivative( r::AbstractVector{T}, @@ -90,7 +90,7 @@ returns the polynomial interpolation matrix for interpolating between the points `rsrc` (with associated barycentric weights `wbsrc`) and `rdst` Reference: - - [berrut2004](@cite) + - [Berrut2004](@cite) """ function interpolationmatrix( rsrc::AbstractVector{T}, diff --git a/src/Numerics/Mesh/Filters.jl b/src/Numerics/Mesh/Filters.jl index d0975c06101..69e702218ce 100644 --- a/src/Numerics/Mesh/Filters.jl +++ b/src/Numerics/Mesh/Filters.jl @@ -183,7 +183,7 @@ the filter starts with polynomial order `Nc`, and `alpha` is a parameter controlling the smallest value of the filter function. ### References - - [boyd1996](@cite) + - [Boyd1996](@cite) """ struct BoydVandevenFilter <: AbstractSpectralFilter "filter matrix" diff --git a/src/Numerics/Mesh/Metrics.jl b/src/Numerics/Mesh/Metrics.jl index 9212cac3623..53c8640e697 100644 --- a/src/Numerics/Mesh/Metrics.jl +++ b/src/Numerics/Mesh/Metrics.jl @@ -227,7 +227,7 @@ arrays `sJ`, `n1`, `n2`, and `n3` should be of size `Nq^2 * nface * nelem` with The curl invariant formulation of Kopriva (2006), equation 37, is used. Reference: - - [kopriva2006](@cite) + - [Kopriva2006](@cite) """ function computemetric!( x1, diff --git a/src/Numerics/Mesh/Topologies.jl b/src/Numerics/Mesh/Topologies.jl index eb2e9e06739..51f448d30aa 100644 --- a/src/Numerics/Mesh/Topologies.jl +++ b/src/Numerics/Mesh/Topologies.jl @@ -922,7 +922,7 @@ end Given points `(a, b, c)` on the surface of a cube, warp the points out to a spherical shell of radius `R` based on the equiangular gnomonic grid proposed by -[RonchiIaconoPaolucci1996](@cite) +[Ronchi1996](@cite) """ function cubedshellwarp(a, b, c, R = max(abs(a), abs(b), abs(c))) diff --git a/src/Numerics/ODESolvers/AdditiveRungeKuttaMethod.jl b/src/Numerics/ODESolvers/AdditiveRungeKuttaMethod.jl index 8864a2d4f49..88ab2e03a14 100644 --- a/src/Numerics/ODESolvers/AdditiveRungeKuttaMethod.jl +++ b/src/Numerics/ODESolvers/AdditiveRungeKuttaMethod.jl @@ -757,7 +757,7 @@ This uses the second-order-accurate 3-stage additive Runge--Kutta scheme of Giraldo, Kelly and Constantinescu (2013). ### References - - [giraldo2013](@cite) + - [Giraldo2013](@cite) """ function ARK2GiraldoKellyConstantinescu( F, @@ -824,7 +824,7 @@ This uses the fifth-order-accurate 8-stage additive Runge--Kutta scheme of Kennedy and Carpenter (2013). ### References - - [kennedy2019](@cite) + - [Kennedy2019](@cite) """ function ARK548L2SA2KennedyCarpenter( F, @@ -968,7 +968,7 @@ This uses the fourth-order-accurate 7-stage additive Runge--Kutta scheme of Kennedy and Carpenter (2013). ### References - - [kennedy2019](@cite) + - [Kennedy2019](@cite) """ function ARK437L2SA1KennedyCarpenter( F, diff --git a/src/Numerics/ODESolvers/LowStorageRungeKuttaMethod.jl b/src/Numerics/ODESolvers/LowStorageRungeKuttaMethod.jl index 576ee56a2e0..628374add70 100644 --- a/src/Numerics/ODESolvers/LowStorageRungeKuttaMethod.jl +++ b/src/Numerics/ODESolvers/LowStorageRungeKuttaMethod.jl @@ -344,7 +344,7 @@ This uses the fourth-order, 14-stage, low-storage, Runge--Kutta scheme of Niegemann, Diehl, and Busch (2012) with optimized stability region ### References - - [niegemann2012](@cite) + - [Niegemann2012](@cite) """ function LSRK144NiegemannDiehlBusch( F, diff --git a/src/Numerics/ODESolvers/MultirateInfinitesimalGARKDecoupledImplicit.jl b/src/Numerics/ODESolvers/MultirateInfinitesimalGARKDecoupledImplicit.jl index d7ccd5c5bc7..9a50914f5a4 100644 --- a/src/Numerics/ODESolvers/MultirateInfinitesimalGARKDecoupledImplicit.jl +++ b/src/Numerics/ODESolvers/MultirateInfinitesimalGARKDecoupledImplicit.jl @@ -43,7 +43,7 @@ The available concrete implementations are: - [`MRIGARKESDIRK46aSandu`](@ref) ### References - - [sandu2019](@cite) + - [Sandu2019](@cite) """ mutable struct MRIGARKDecoupledImplicit{ T, diff --git a/src/Numerics/ODESolvers/MultirateInfinitesimalGARKExplicit.jl b/src/Numerics/ODESolvers/MultirateInfinitesimalGARKExplicit.jl index 5d3a518cf16..68901c51c5c 100644 --- a/src/Numerics/ODESolvers/MultirateInfinitesimalGARKExplicit.jl +++ b/src/Numerics/ODESolvers/MultirateInfinitesimalGARKExplicit.jl @@ -84,7 +84,7 @@ The available concrete implementations are: - [`MRIGARKERK45aSandu`](@ref) ### References - - [sandu2019](@cite) + - [Sandu2019](@cite) """ mutable struct MRIGARKExplicit{T, RT, AT, Nstages, NΓ, FS, Nstages_sq} <: AbstractODESolver diff --git a/src/Numerics/ODESolvers/MultirateRungeKuttaMethod.jl b/src/Numerics/ODESolvers/MultirateRungeKuttaMethod.jl index 916cdf824d9..1443946ea9d 100644 --- a/src/Numerics/ODESolvers/MultirateRungeKuttaMethod.jl +++ b/src/Numerics/ODESolvers/MultirateRungeKuttaMethod.jl @@ -22,7 +22,7 @@ solvers. This is based on Currently only the low storage RK methods can be used as slow solvers ### References - - [SchlegelKnothArnoldWolke2012](@cite) + - [Schlegel2012](@cite) """ mutable struct MultirateRungeKutta{SS, FS, RT} <: AbstractODESolver "slow solver" diff --git a/src/Numerics/ODESolvers/StrongStabilityPreservingRungeKuttaMethod.jl b/src/Numerics/ODESolvers/StrongStabilityPreservingRungeKuttaMethod.jl index 6b98df47b08..756c026e030 100644 --- a/src/Numerics/ODESolvers/StrongStabilityPreservingRungeKuttaMethod.jl +++ b/src/Numerics/ODESolvers/StrongStabilityPreservingRungeKuttaMethod.jl @@ -197,7 +197,7 @@ of Shu and Osher (1988) (also known as Heun's method.) Exact choice of coefficients from wikipedia page for Heun's method :) ### References - - [shu1988](@cite) + - [Shu1988](@cite) - [Heun1900](@cite) """ function SSPRK22Heuns(F, Q::AT; dt = 0, t0 = 0) where {AT <: AbstractArray} @@ -228,8 +228,8 @@ of Shu and Osher (1988) (also known as Ralstons's method.) Exact choice of coefficients from wikipedia page for Heun's method :) ### References - - [shu1988](@cite) - - [ralston1962](@cite) + - [Shu1988](@cite) + - [Ralston1962](@cite) """ function SSPRK22Ralstons(F, Q::AT; dt = 0, t0 = 0) where {AT <: AbstractArray} T = eltype(Q) @@ -258,7 +258,7 @@ This uses the third-order, 3-stage, strong-stability-preserving, Runge--Kutta sc of Shu and Osher (1988) ### References - - [shu1988](@cite) + - [Shu1988](@cite) """ function SSPRK33ShuOsher(F, Q::AT; dt = 0, t0 = 0) where {AT <: AbstractArray} T = eltype(Q) @@ -287,7 +287,7 @@ This uses the third-order, 4-stage, strong-stability-preserving, Runge--Kutta sc of Spiteri and Ruuth (1988) ### References - - [spiteri2002](@cite) + - [Spiteri2002](@cite) """ function SSPRK34SpiteriRuuth( F, diff --git a/src/Numerics/SystemSolvers/columnwise_lu_solver.jl b/src/Numerics/SystemSolvers/columnwise_lu_solver.jl index 49c31031b97..bfb4b6cd058 100644 --- a/src/Numerics/SystemSolvers/columnwise_lu_solver.jl +++ b/src/Numerics/SystemSolvers/columnwise_lu_solver.jl @@ -525,16 +525,7 @@ is stored as ### Reference - @book{GolubVanLoan, - title = {Matrix Computations}, - author = {Gene H. Golub and Charles F. Van Loan}, - edition = {4th}, - isbn = {9781421407944}, - publisher = {Johns Hopkins University Press}, - address = {Baltimore, MD, USA}, - url = {http://www.cs.cornell.edu/cv/GVL4/golubandvanloan.htm}, - year = 2013 - } + - [GolubVanLoan2013](@cite) """ band_lu_kernel! @kernel function band_lu_kernel!(A) @@ -592,16 +583,7 @@ eband - 1`. ### Reference - @book{GolubVanLoan, - title = {Matrix Computations}, - author = {Gene H. Golub and Charles F. Van Loan}, - edition = {4th}, - isbn = {9781421407944}, - publisher = {Johns Hopkins University Press}, - address = {Baltimore, MD, USA}, - url = {http://www.cs.cornell.edu/cv/GVL4/golubandvanloan.htm}, - year = 2013 - } + - [GolubVanLoan2013](@cite) """ band_forward_kernel! @kernel function band_forward_kernel!(b, LU) @@ -685,16 +667,7 @@ eband - 1`. ### Reference - @book{GolubVanLoan, - title = {Matrix Computations}, - author = {Gene H. Golub and Charles F. Van Loan}, - edition = {4th}, - isbn = {9781421407944}, - publisher = {Johns Hopkins University Press}, - address = {Baltimore, MD, USA}, - url = {http://www.cs.cornell.edu/cv/GVL4/golubandvanloan.htm}, - year = 2013 - } + - [GolubVanLoan2013](@cite) """ band_back_kernel! @kernel function band_back_kernel!(b, LU) diff --git a/src/Numerics/SystemSolvers/generalized_conjugate_residual_solver.jl b/src/Numerics/SystemSolvers/generalized_conjugate_residual_solver.jl index 0ec8a4f1940..6c7f9cfe9c4 100644 --- a/src/Numerics/SystemSolvers/generalized_conjugate_residual_solver.jl +++ b/src/Numerics/SystemSolvers/generalized_conjugate_residual_solver.jl @@ -19,7 +19,7 @@ This uses the restarted Generalized Conjugate Residual method of Eisenstat (1983 ## References - - [eisenstat1983](@cite) + - [Eisenstat1983](@cite) """ mutable struct GeneralizedConjugateResidual{K, T, AT} <: AbstractIterativeSystemSolver diff --git a/src/Numerics/SystemSolvers/generalized_minimal_residual_solver.jl b/src/Numerics/SystemSolvers/generalized_minimal_residual_solver.jl index 60341ef862d..5d1fc479395 100644 --- a/src/Numerics/SystemSolvers/generalized_minimal_residual_solver.jl +++ b/src/Numerics/SystemSolvers/generalized_minimal_residual_solver.jl @@ -18,7 +18,7 @@ This uses the restarted Generalized Minimal Residual method of Saad and Schultz ## References - - [saad1986gmres](@cite) + - [Saad1986](@cite) """ mutable struct GeneralizedMinimalResidual{M, MP1, MMP1, T, AT} <: diff --git a/test/Atmos/Parameterizations/Microphysics/KM_ice.jl b/test/Atmos/Parameterizations/Microphysics/KM_ice.jl index 391db432b73..f3fed1a0c2e 100644 --- a/test/Atmos/Parameterizations/Microphysics/KM_ice.jl +++ b/test/Atmos/Parameterizations/Microphysics/KM_ice.jl @@ -98,7 +98,7 @@ function init_kinematic_eddy!(eddy_model, state, aux, localgeo, t, spline_fun) state.ρq_rai = ρ * FT(0) state.ρq_sno = ρ * FT(0) - # [grabowski1998](@cite) + # [Grabowski1998](@cite) # velocity (derivative of streamfunction) # This is actually different than what comes out from taking a # derivative of Ψ from the paper. I have sin(π/2/X(x-xc)). diff --git a/test/Atmos/Parameterizations/Microphysics/KinematicModel.jl b/test/Atmos/Parameterizations/Microphysics/KinematicModel.jl index 92497abb67d..4863f22cc44 100644 --- a/test/Atmos/Parameterizations/Microphysics/KinematicModel.jl +++ b/test/Atmos/Parameterizations/Microphysics/KinematicModel.jl @@ -1,8 +1,8 @@ # The set-up was designed for the # 8th International Cloud Modelling Workshop -# ([muhlbauer2013](@cite)) +# ([Muhlbauer2013](@cite)) # -# See chapter 2 in [arabas2015](@cite) for setup details: +# See chapter 2 in [Arabas2015](@cite) for setup details: using Dates using DocStringExtensions diff --git a/test/Atmos/Parameterizations/Microphysics/runtests.jl b/test/Atmos/Parameterizations/Microphysics/runtests.jl index 0a8ee9657e8..ed001b4ce0b 100644 --- a/test/Atmos/Parameterizations/Microphysics/runtests.jl +++ b/test/Atmos/Parameterizations/Microphysics/runtests.jl @@ -84,7 +84,7 @@ end end @testset "RainFallSpeed" begin - # eq. 5d in [grabowski1996](@cite) + # eq. 5d in [Grabowski1996](@cite) function terminal_velocity_empir( q_rai::FT, q_tot::FT, @@ -190,7 +190,7 @@ end @testset "RainLiquidAccretion" begin - # eq. 5b in [grabowski1996](@cite) + # eq. 5b in [Grabowski1996](@cite) function accretion_empir(q_rai::FT, q_liq::FT, q_tot::FT) where {FT <: Real} rr = q_rai / (FT(1) - q_tot) rl = q_liq / (FT(1) - q_tot) @@ -240,7 +240,7 @@ end @testset "RainEvaporation" begin - # eq. 5c in [grabowski1996](@cite) + # eq. 5c in [Grabowski1996](@cite) function rain_evap_empir( prs::AbstractParameterSet, q_rai::FT, diff --git a/test/Numerics/DGMethods/advection_diffusion/advection_sphere.jl b/test/Numerics/DGMethods/advection_diffusion/advection_sphere.jl index 1636f3a4e6a..df639a6239d 100644 --- a/test/Numerics/DGMethods/advection_diffusion/advection_sphere.jl +++ b/test/Numerics/DGMethods/advection_diffusion/advection_sphere.jl @@ -29,7 +29,7 @@ const output = parse(Bool, lowercase(get(ENV, "JULIA_CLIMA_OUTPUT", "false"))) include("advection_diffusion_model.jl") -# This is a setup similar to the one presented in [williamson1992](@cite) +# This is a setup similar to the one presented in [Williamson1992](@cite) struct SolidBodyRotation <: AdvectionDiffusionProblem end function init_velocity_diffusion!( ::SolidBodyRotation, @@ -57,7 +57,7 @@ end finaltime(::SolidBodyRotation) = 1 u_scale(::SolidBodyRotation) = 2π -# This is a setup similar to the one presented in [lauritzen2012](@cite) +# This is a setup similar to the one presented in [Lauritzen2012](@cite) struct ReversingDeformationalFlow <: AdvectionDiffusionProblem end init_velocity_diffusion!( ::ReversingDeformationalFlow, diff --git a/test/Numerics/DGMethods/compressible_Navier_Stokes/density_current_model.jl b/test/Numerics/DGMethods/compressible_Navier_Stokes/density_current_model.jl index 631ba632937..0757a954842 100644 --- a/test/Numerics/DGMethods/compressible_Navier_Stokes/density_current_model.jl +++ b/test/Numerics/DGMethods/compressible_Navier_Stokes/density_current_model.jl @@ -51,7 +51,7 @@ const timeend = 10dt """ # Reference -See [straka1993](@cite) +See [Straka1993](@cite) """ function Initialise_Density_Current!( problem, diff --git a/test/Numerics/ODESolvers/ode_tests_convergence.jl b/test/Numerics/ODESolvers/ode_tests_convergence.jl index f72c52ae002..8bfee6ce9e5 100644 --- a/test/Numerics/ODESolvers/ode_tests_convergence.jl +++ b/test/Numerics/ODESolvers/ode_tests_convergence.jl @@ -234,12 +234,12 @@ const ArrayType = ClimateMachine.array_type() end #= - Test problem (4.2) from [RobertsSarsharSandu2018arxiv](@cite) + Test problem (4.2) from [Roberts2018](@cite) Note: The actual rates are all over the place with this test and passing largely depends on final dt size =# - @testset "2-rate ODE from RobertsSarsharSandu2018arxiv" begin + @testset "2-rate ODE from Roberts2018" begin ω = 100 λf = -10 λs = -1 @@ -422,7 +422,7 @@ const ArrayType = ClimateMachine.array_type() end end - # Simple 3-rate problem based on test of RobertsSarsharSandu2018arxiv + # Simple 3-rate problem based on test of [Roberts2018](@cite) # # NOTE: Since we have no theory to say this ODE solver is accurate, the rates # suggest that things are really only 2nd order. @@ -567,7 +567,7 @@ const ArrayType = ClimateMachine.array_type() end #= - Test problem (8.2) from [sandu2019](@cite) for MRI-GARK Schemes + Test problem (8.2) from [Sandu2019](@cite) for MRI-GARK Schemes =# @testset "2-rate problem" begin ω = 20 diff --git a/tutorials/Atmos/densitycurrent.jl b/tutorials/Atmos/densitycurrent.jl index 64499c3d8e4..8c7a167d77a 100644 --- a/tutorials/Atmos/densitycurrent.jl +++ b/tutorials/Atmos/densitycurrent.jl @@ -299,7 +299,7 @@ end # # ## References # -# - [straka1993](@cite) -# - [carpenter1990](@cite) +# - [Straka1993](@cite) +# - [Carpenter1990](@cite) main() diff --git a/tutorials/Atmos/heldsuarez.jl b/tutorials/Atmos/heldsuarez.jl index d196463a337..cf12af29357 100644 --- a/tutorials/Atmos/heldsuarez.jl +++ b/tutorials/Atmos/heldsuarez.jl @@ -307,4 +307,4 @@ result = ClimateMachine.invoke!( # ## References # -# - [held1994](@cite) +# - [Held1994](@cite)