--- manual/manual_references.bib 2006/11/17 01:33:05 1.31 +++ manual/manual_references.bib 2011/06/27 02:09:19 1.44 @@ -1,7 +1,9 @@ +@string{angl = {Ann.\ Glaciol.}} @string{arfm = {Annu.~Rev.~Fluid Mech.}} @string{bams = {Bull.~Am.~Met.~Soc.}} @string{blm = {Bound.~Layer~Meteorol.}} @string{climd = {Clim.~Dynamics}} +@string{cch = {Clim.\ Change}} @string{jgr = {J.~Geophys.~Res.}} @string{ijrs = {Int.~J.~Remote Sensing}} @string{jas = {J.~Atmos.~Sci.}} @@ -32,6 +34,7 @@ @string{estec = {European Space Research and Technology Centre (ESTEC)}} @string{esa = {European Space Agency (ESA)}} +@string{eos = {Eos~Trans.\ AGU}} @Article{bis-eta:92, author = {C.H. Bishof and G.F. Corliss and L. Green and @@ -131,6 +134,17 @@ pages = {1367--1387}, } +@ARTICLE{durr:91, + author = {Dale R. Durran}, + title = {The Third-Order Adams-Bashforth Method: An Attractive Alternative + to Leapfrog Time Differencing}, + journal = mwr, + year = {1991}, + volume = {119}, + pages = {702-720}, +} + + @ARTICLE{dutk-etal:06, author = {S. Dutkiewicz and M.J. Follows and P. Heimbach and J. Marshall}, title = {Controls on ocean productivity and air-sea carbon flux: @@ -202,8 +216,29 @@ note = {in press}, } +@Article{fer-eta:05, + author = {D. Ferreira and J. Marshall and P. Heimbach}, + year = 2005, + title = {Estimating Eddy Stresses by Fitting Dynamics to Observations + using a Residual-Mean Ocean Circulation Model and Its Adjoint}, + journal = jpo, + volume = {35}, + pages = {1891--1910}, + } + +@Article{gas-eta:90, + author = {P. Gaspar and Y. Gr\'egoris and J.-M. Lefevre}, + year = 1990, + title = {A Simple Eddy Kinetic Energy Model for Simulations of the + Oceanic Vertical Mixing: Tests at Station Papa and Long-Term + Upper Ocean Study Site}, + journal = jgr, + volume = {95 (C9)}, + pages = {16,179--16,193}, + } + @Article{gen-mcw:90, - author = {P.R. Gent and J.C. McWilliams}, + author = {P. R. Gent and J. C. McWilliams}, year = 1990, title = {Isopycnal mixing in ocean circulation models}, journal = jpo, @@ -212,11 +247,9 @@ } @Article{gen-eta:95, - author = {P.R. Gent and J. Willebrand and T.J. McDougall - and J.C. McWilliams}, + author = {P. R. Gent and J. Willebrand and T. J. McDougall and J. C. McWilliams}, year = 1995, - title = {Parameterizing eddy-induced tracer transports in - ocean circulation models}, + title = {Parameterizing eddy-induced tracer transports in ocean circulation models}, journal = jpo, volume = {25}, pages = {463--474}, @@ -351,7 +384,7 @@ } @ARTICLE{hib80, - AUTHOR = "W. D. {Hibler, III}", + author = {Hibler, III, William D.}, TITLE = "Modeling a Variable Thickness Sea Ice Cover", JOURNAL = mwr, YEAR = 1980, @@ -405,8 +438,7 @@ @Article{lar-eta:94, author = {W.G. Large and J.C. McWilliams and S.C. Doney}, year = 1994, - title = {Oceanic vertical mixing: A review and a model - with nonlocal boundary layer parameterization}, + title = {Oceanic vertical mixing: A review and a model with nonlocal boundary layer parameterization}, journal = {Rev.~Geophys.}, volume = {32}, pages = {363--403}, @@ -488,12 +520,15 @@ } @ARTICLE{losc-heim:06, - author = {M. Losch and P. Heimbach}, - title = {Adjoint sensitivity of an ocean general circulation model - to bottom topography}, - journal = jpo, - year = {2006}, - volume = {{in press}}, + author = {Martin Losch and Patrick Heimbach}, + title = {Adjoint Sensitivity of an Ocean General Circulation + Model to Bottom Topography}, + journal = jpo, + year = 2007, + volume = 37, + doi = {10.1175/JPO3017.1}, + number = 2, + pages = {377--393}, url = {http://mitgcm.org/pdfs/Los2006a.pdf}, } @@ -543,7 +578,7 @@ pages = {5,753--5,766}, } -@Article{mars-sha:98, +@Article{mars-eta:98, author = {J. Marshall and H. Jones and C. Hill}, year = 1998, title = {Efficient ocean modeling using @@ -555,13 +590,14 @@ doi = {10.1016/S0924-7963\%2898\%2900008-6}, } -@Article{mcw:96, - author = {J. McWilliams}, - year = 1996, - title = {Modeling the oceanic general circulation}, - journal = arfm, - volume = {28}, - pages = {215--248}, +@Article{mol:09, + author = {Andrea Molod}, + year = 2009, + title = {Running {GCM} physics and dynamics on different grids: + algorithm and tests}, + journal = tel, + volume = {61A}, + pages = {381--393}, } %% Rew, R. K., G. P. Davis, S. Emmerson, and H. Davies @@ -572,6 +608,34 @@ %% http://www.unidata.ucar.edu/packages/netcdf/guidec. NetCDF User's %% Guide for Fortran 90 and NetCDF User's Guide for Fortran 77 are %% also available. + +@incollection{naum-etal:06, + Author = {U. Naumann and J. Utke and P. Heimbach and C. Hill and D. Ozyurt and C. Wunsch and M. Fagan and N. Tallent and M. Strout}, + Booktitle = {European Conference on Computational Fluid Dynamics ECCOMAS CFD 2006}, + Editor = {{P. Wesseling, E. O~nate and J. Periaux}}, + Pages = {~}, + Publisher = {TU Delft}, + Title = {Adjoint code by source transformation with OpenAD/F}, + Year = {2006}} + +@Article{orl:76, + author = {I. Orlanski}, + year = 1976, + title = {A simple boundary condition for unbounded hyperbolic flows}, + journal = jcp, + volume = {21}, + pages = {251--269}, + } + +@Article{pal-rom:97, + author = {T. Paluszkiewicz and R.D. Romea}, + year = 1997, + title = {A one-dimensional model for the parameterization + of deep convection in the ocean}, + journal = dao, + volume = {26}, + pages = {95--130}, + } @TechReport{rew:97, author = {R. K. Rew and G. P. Davis and S. Emmerson and H. Davies}, @@ -619,6 +683,15 @@ address = {Berlin (Germany)}, } +@article{utke-etal:08, + Author = {J. Utke and U. Naumann and M. Fagan and N. Tallent and M. Strout and P. Heimbach and C. Hill and D. Ozyurt and C. Wunsch}, + Date-Modified = {2007-11-19 10:15:08 -0500}, + Journal = {{ACM} Transactions on Mathematical Software}, + Pages = {~}, + Title = {OpenAD/F: A modular open source tool for automatic differentiation of Fortran codes}, + Volume = {34(4)}, + Year = {2008}} + @Article{DaSilva94, author = {A. da Silva and A. C. Young and S. Levitus}, year = 1994, @@ -631,7 +704,7 @@ url = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/}, } -@techreport{sta-eta:97, +@techreport{stam-etal:97, author = {D. Stammer and C. Wunsch and R. Giering and Q. Zhang and J. Marotzke and J. Marshall and C. Hill}, @@ -647,7 +720,7 @@ address = {Cambridge (MA), USA}, } -@ARTICLE{stam-eta:01, +@ARTICLE{stam-etal:02, author = {D. Stammer and C. Wunsch and R. Giering and C. Eckert and P. Heimbach and J. Marotzke and A. Adcroft and C.N. Hill and J. Marshall}, title = {The global ocean circulation and transports during 1992 -- 1997, estimated from ocean observations and a general circulation model.}, journal = jgr, @@ -873,6 +946,19 @@ doi = {10.1175/MWR2823.1}, } +@inproceedings{adcroft:04c, + author = {Adcroft, A. and C. Hill and J.-M. Campin and J. Marshall + and P. Heimbach}, + title = {Overview of the Formulation and Numerics of the {MIT}GCM}, + booktitle = {Proceedings of the ECMWF seminar series on Numerical Methods, + Recent developments in numerical methods for atmosphere and + ocean modelling}, + year = 2004, + pages = {139-149}, + url = {http://mitgcm.org/pdfs/ECMWF2004-Adcroft.pdf}, + publisher = ecmwf +} + @Article{marshall:04, author = {Marshall, J. and A. Adcroft and J.-M. Campin and C. Hill and A. White}, title = {Atmosphere-Ocean Modeling Exploiting Fluid Isomorphisms}, @@ -885,9 +971,8 @@ } @Article{visbeck:97, - author = {Visbeck, M., J. Marshall, T. Haine, and M. Spall}, - title = {Specification of eddy transfer coefficients in - coarse-resolution ocean circulation models}, + author = {M. Visbeck and J. Marshall and T. Haine and M. Spall}, + title = {Specification of eddy transfer coefficients in coarse-resolution ocean circulation models}, journal = jpo, year = 1997, volume = 27, @@ -1027,7 +1112,7 @@ @Article{griffies:00, author = {Griffies, S.,M. and Hallberg, R.,W.}, - title = {Biharmonic friction with a Smagorinsky-like viscosity for + title = {Biharmonic friction with a {Smagorinsky}-like viscosity for use in large-scale eddy-permitting ocean models}, journal = mwr, year = 2000, @@ -1056,8 +1141,47 @@ pages = {221-244} } +@Article{Cox87, + author = {M. D. Cox}, + title = {An isopycnal diffusion in a z-coordinate ocean model}, + journal = {Ocean modelling}, + year = 1987, + volume = 74, + pages = {1-5 (Unpublished manuscript)} +} + +@Article{gretal:98, + author = {S. M. Griffies and A. Gnanadesikan and R. C. Pacanowski and V. Larichev and J. K. Dukowicz and R. D. Smith}, + title = {Isoneutral diffusion in a z-coordinate ocean model}, + journal = jpo, + year = 1998, + volume = 28, + pages = {805-830} +} + +@ARTICLE{gr:98, + author = {S. M. Griffies}, + title = {The {Gent-McWilliams} Skew Flux}, + journal = jpo, + year = 1998, + volume = 28, + pages = {831-841} +} + + +@Article{gkw:91, + author = {R. Gerdes and C. Koberle and J. Willebrand}, + title = {The influence of numerical advection schemes on the results of ocean general circulation models}, + journal = climd, + year = 1991, + volume = 5, + number = 4, + pages = {211-226}, + doi = {10.1007/BF00210006} +} + @Article{dm:95, - author = {Danabasoglu, G. and McWilliams J.C.}, + author = {G. Danabasoglu and J. C. McWilliams}, title = {Sensitivity of the global ocean circulation to parameterizations of mesoscale tracer transports}, journal = jclim, year = 1995, @@ -1067,7 +1191,7 @@ } @Article{ldd:97, - author = {Large, W.G. and Danabasoglu, G. and Doney, S.C. and McWilliams, J.C.}, + author = {W. G. Large and G. Danabasoglu and S. D. Doney and J. C. McWilliams}, title = {Sensitivity to surface forcing and boundary layer mixing in a global ocean model: Annual-mean climatology}, journal = jpo, year = 1997, @@ -1077,9 +1201,8 @@ } @Article{gkw:99, - author = {Gerdes R. and Koberle C. and Beckmann A. and Herrmann P. and Willebrand J.}, - title = {Mechanisms for spreading of Mediterranean water in - coarse-resolution numerical models}, + author = {R. Gerdes and C. Koberle and A. Beckmann and P. Herrmann and J. Willebrand}, + title = {Mechanisms for spreading of Mediterranean water in coarse-resolution numerical models}, journal = jpo, year = 1999, volume = 29, @@ -1183,7 +1306,7 @@ } @ARTICLE{zha98a, - AUTHOR = "J. Zhang and W. D. {Hibler, III} and M. Steele + AUTHOR = "J. Zhang and Hibler, III, W. D. and M. Steele and D. A. Rothrock", TITLE = "Arctic ice-ocean modeling with and without climate restoring", JOURNAL = jpo, @@ -1212,7 +1335,7 @@ } @ARTICLE{hib79, - AUTHOR = "W. D. {Hibler, III}", + author = {Hibler, III, W. D.}, TITLE = "A Dynamic Thermodynamic Sea Ice Model", JOURNAL = jpo, YEAR = 1979, @@ -1221,7 +1344,7 @@ } @ARTICLE{fla92, - AUTHOR = "G. M. Flato and W. D. {Hibler, III}", + AUTHOR = "G. M. Flato and Hibler, III, W. D.", TITLE = "Modeling pack ice as a cavitating fluid", JOURNAL = jpo, YEAR = 1992, @@ -1235,7 +1358,18 @@ JOURNAL = jpo, YEAR = 1997, VOLUME = 27, - PAGES = "1849-1867" + PAGES = "1849--1867" +} + +@Article{hun01, + author = {Elizabeth C. Hunke}, + title = {Viscous-Plastic Sea Ice Dynamics with the {EVP} + Model: Linearization Issues}, + journal = jcp, + year = 2001, + volume = 170, + pages = {18--38}, + doi = {10.1006/jcph.2001.6710} } @ARTICLE{zha00, @@ -1244,7 +1378,7 @@ JOURNAL = jgr, YEAR = 2000, VOLUME = 105, - PAGES = "3325-3338" + PAGES = "3325--3338" } @Article{Shapiro_70, @@ -1604,10 +1738,303 @@ volume = {126}, pages = {991-1000} } + @TechReport{MPI-std-20, - author = {{Message Passing Interface Forum}}}, + author = {{Message Passing Interface Forum}}, title = {{MPI}: A Message-Passing Interface standard (version 2.0)}, institution = {mpi-forum.org}, year = {1998}, } +@Article{cam08, + author = {Jean-Michel Campin and John Marshall and David + Ferreira}, + title = {Sea-Ice Ocean Coupling Using a Rescaled Vertical + Coordinate z$^\ast$}, + journal = om, + volume = 24, + number = {1--2}, + pages = {1--14}, + doi = {10.1016/j.ocemod.2008.05.005}, + year = 2008 +} + +@Article{geiger98, + author = {Cathleen A. 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