--- manual/manual_references.bib 2005/09/23 01:03:47 1.25 +++ manual/manual_references.bib 2011/03/02 13:18:42 1.42 @@ -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 @@ -71,6 +74,18 @@ Argonne (ILL), 90439; USA}, note = {http://www.mcs.anl.gov/autodiff/}, } + +@ARTICLE{bugi-hill:06, + author = {V. Bugnion and C. Hill}, + title = {Equilibration mechanisms in an adjoint ocean general + circulation model}, + journal = {Ocean Dynamics}, + year = {2006}, + volume = {56}, + number = {1}, + pages = {51-61}, + doi = {10.1007/s10236-005-0052-z}, +} @techreport{bis-roh:97, author = {C. Bishof and L. Roh}, @@ -118,6 +133,28 @@ volume = {120}, 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: + An adjoint model sensitivity study}, + journal = grl, + year = {2006}, + volume = {33}, + pages = {L02603}, + doi = {10.1029/2005GL024987}, +} @Article{err:97, author = {R.M. Errico}, @@ -179,6 +216,27 @@ 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}, year = 1990, @@ -328,7 +386,7 @@ } @ARTICLE{hib80, - AUTHOR = "W. D. {Hibler, III}", + author = {Hibler, III, William D.}, TITLE = "Modeling a Variable Thickness Sea Ice Cover", JOURNAL = mwr, YEAR = 1980, @@ -358,6 +416,15 @@ pages = {658-669} } +@Article{jam-oze:86, + author = {B.M. Jamart and J. Ozer}, + year = {1986}, + title = {Numerical boundary layers and spurious residual flows}, + journal = jgr, + volume = {91}, + pages = {10,621-10,631} + } + @book{kas-eta:00, author = {P. Kasibhatla and M. Heimann and P. Rayner and N. Mahowald and R.G. Prinn and D.E. Hartley}, @@ -454,6 +521,20 @@ pages = {38 pp.}, address = {Delft (NL)}, } + +@ARTICLE{losc-heim:06, + 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}, +} + @Article{maro-wun:93, author = {J. Marotzke and C. Wunsch}, @@ -500,7 +581,7 @@ 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 @@ -508,15 +589,18 @@ journal = jms, volume = {18}, pages = {115--134}, + url = {http://mitgcm.org/pdfs/journal_of_marine_systems_1998.pdf}, + 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 @@ -527,6 +611,34 @@ %% 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}, @@ -574,6 +686,15 @@ 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, @@ -583,9 +704,10 @@ publisher = {U.S. Department of Commerce}, address = {Washington, D.C. (USA)}, note = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/}, + 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}, @@ -601,17 +723,16 @@ address = {Cambridge (MA), USA}, } -@Article{sta-eta:01, - author = {D. Stammer and C. Wunsch and R. Giering and - C. Eckert and P. Heimbach and J. Marotzke and - A. Adcroft and C. Hill and J. Marshall}, - year = 2001, - title = {The global ocean circulation during 1992 -- 1997, - estimated from ocean observations and a general - circulation model}, - journal = jgr, - note = {in press}, - } +@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, + year = {2002a}, + volume = {107(C9)}, + pages = {3118}, + doi = {10.1029/2001JC000888}, +} + @Article{Stommel66, author = {H. Stommel}, @@ -777,7 +898,8 @@ year = 1997, volume = 102, number = {C3}, - pages = {5733-5752} + pages = {5733-5752}, + url = {http://mitgcm.org/pdfs/96JC02775.pdf}, } @Article{marshall:97b, @@ -788,7 +910,8 @@ year = 1997, volume = 102, number = {C3}, - pages = {5753-5766} + pages = {5753-5766}, + url = {http://mitgcm.org/pdfs/96JC02776.pdf}, } @Article{adcroft:97, @@ -798,7 +921,9 @@ journal = mwr, year = 1997, volume = 125, - pages = {2293-2315} + pages = {2293-2315}, + url = {http://mitgcm.org/pdfs/mwr_1997.pdf}, + doi = {10.1175/1520-0493\%281997\%29125<2293:ROTBSC>2.0.CO;2}, } @Article{adcroft:04a, @@ -808,7 +933,8 @@ journal = om, year = 2004, volume = 7, - pages = {269-284} + pages = {269-284}, + doi = {10.1016/j.ocemod.2003.09.003}, } @Article{adcroft:04b, @@ -818,7 +944,22 @@ journal = mwr, year = 2004, volume = 132, - pages = {2845-2863} + pages = {2845-2863}, + url = {http://mitgcm.org/pdfs/mwr_2004.pdf}, + 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, @@ -827,7 +968,9 @@ journal = mwr, year = 2004, volume = 132, - pages = {2882-2894} + pages = {2882-2894}, + url = {http://mitgcm.org/pdfs/a_o_iso.pdf}, + doi = {10.1175/MWR2835.1}, } @Article{visbeck:97, @@ -854,15 +997,6 @@ pages = {1-51} } -@Article{marshall:98, - author = {J. Marshall and H. Jones and C. Hill}, - title = {Efficient ocean modeling using non-hydrostatic algorithms}, - journal = {JMR}, - year = 1998, - volume = 18, - pages = {115-134} -} - @Article{mjn:99, author = {Marshall, J., Jamous, D and J. Nilsson}, title = {Reconciling `thermodynamic' and `dynamic' methods of @@ -890,7 +1024,9 @@ journal = mwr, year = 1999, volume = 127, - pages = {1928-1936} + pages = {1928-1936}, + url = {http://mitgcm.org/pdfs/mwr_1999.pdf}, + doi = {10.1175/1520-0493\%281999\%29127<1928:ANTOTC>2.0.CO;2}, } @InProceedings{hill:99, @@ -1064,9 +1200,9 @@ } @Article{molteni:03, - author = {K. M. Trenberth and J. Olson and W. G. Large}, - title = {Atmospheric simulations using a GCM with simplified physical - parametrization, I model climatology and variability in + author = {F. Molteni}, + title = {Atmospheric simulations using a {GCM} with simplified physical + parametrization, {I}: Model climatology and variability in multidecadal experiments}, journal = climd, year = 2003, @@ -1136,7 +1272,7 @@ } @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, @@ -1165,7 +1301,7 @@ } @ARTICLE{hib79, - AUTHOR = "W. D. {Hibler, III}", + author = {Hibler, III, W. D.}, TITLE = "A Dynamic Thermodynamic Sea Ice Model", JOURNAL = jpo, YEAR = 1979, @@ -1174,7 +1310,7 @@ } @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, @@ -1188,7 +1324,18 @@ 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, @@ -1197,7 +1344,7 @@ JOURNAL = jgr, YEAR = 2000, VOLUME = 105, - PAGES = "3325-3338" + PAGES = "3325--3338" } @Article{Shapiro_70, @@ -1557,3 +1704,289 @@ volume = {126}, pages = {991-1000} } + +@TechReport{MPI-std-20, + 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. Geiger and Hibler, III, William D. and + Stephen F. Ackley}, + title = {Large-Scale Sea Ice Drift and Deformation: + {C}omparison between Models and Observations in the + Western {W}eddell {S}ea during 1992}, + journal = jgr, + year = 1998, + volume = 103, + number = {C10}, + pages = {21893--21913} +} + +@InCollection{hibler84, + author = {Hibler, III, William D.}, + title = {The role of sea ice dynamics in modeling CO{$_2$} + increases}, + booktitle = {Climate processes and climate sensitivity}, + pages = {238--253}, + publisher = {AGU}, + year = 1984, + editor = {J. E. Hansen and T. Takahashi}, + volume = 29, + series = {Geophysical Monograph}, + address = {Washington, D.C.} +} + +@Article{hibler87, + author = {Hibler, III, William D. and Kirk Bryan}, + title = {A Diagnostic Ice-Ocean Model}, + journal = jpo, + year = 1987, + volume = 17, + number = 7, + pages = {987--1015} +} + +@InCollection{hibler95, + author = {Hibler, III, William D. and Chi F. Ip}, + title = {The effect of sea ice rheology on {A}rcitc buoy + drift}, + booktitle = {Ice Mechanics}, + pages = {255--264}, + publisher = {Am. Soc. of Mech. Eng.}, + year = 1995, + editor = {John P. Dempsey and Y. D. S. Rajapakse}, + volume = 204, + series = {AMD}, + address = {New York} +} + +@Article{hibler97, + author = {Hibler, III, William D. and Erland M. Schulson}, + title = {On Modeling Sea-Ice Fracture and Flow in Numerical + Investigations of Climate}, + journal = angl, + year = 1997, + volume = 25, + pages = {26--32} +} + +@Article{hundsdorfer94, + author = {Willem Hundsdorfer and R. A. 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Rothrock}, + title = {Modeling Global Sea Ice with a Thickness and + Enthalpy Distribution Model in Generalized + Curvilinear Coordinates}, + journal = mwr, + year = 2003, + volume = 131, + number = 5, + pages = {845--861} +} + +@Article{beckmann99, + author = {Aike Beckmann and Hartmut H. Hellmer and Ralph + Timmermann}, + title = {A Numerical Model of the {W}eddell {S}ea: + Large-Scale Circulation and Water Mass Distribution}, + journal = jgr, + year = 1999, + volume = 104, + number = {C10}, + pages = {23,375--23,392} +} + +@Article{grosfeld97, + author = {Klaus Grosfeld and R{\"u}diger Gerdes and J{\"u}rgen + Determann}, + title = {Thermohaline Circulation and Interaction between Ice + Shelf Cavities and the Adjacent Open Water}, + journal = jgr, + year = 1997, + volume = 102, + number = {C7}, + pages = {15,595--15,610} +} + +@Article{hellmer89, + author = {Hartmut H. Hellmer and Dirk J. 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Holland}, + title = {The Role of Meltwater Advection in the Formulation + of Conservative Boundary Conditions at an Ice-Ocean + Interface}, + journal = jpo, + year = 2001, + volume = 31, + pages = {285--296}} + +@Article{losch08, + author = {Martin Losch}, + title = {Modeling Ice Shelf Cavities in a z-Coordinate Ocean + General Circulation Model}, + journal = jgr, + year = 2008, + volume = 113, + number = {C08043}, + doi = {10.1029/2007JC004368} +} + +@Article{Dutay02, + author = {Dutay, J.-C. and J.L. Bullister and S.C. Doney and J.C. Orr + and R. Najjar and K. Caldeira and J.-M. Campin and H. Drange and M. Follows + and Y. Gao and N. Gruber and M.W. Hecht and A. Ishida and F. Joos and K. Lindsay + and G. Madec and E. Maier-Reimer and J.C. Marshall and R.J. Matear and P. Monfray + and A. Mouchet and G.-K. Plattner and J. sarmiento and R. Schlitzer and R. Slater + and I.J. Totterdell and M.-F. Weirig and Y. Yammanaka and A. Yool}, + year = 2002, + title = {Evaluation of ocean model ventilation with CFC-11: + comparison of 13 global ocean models}, + journal = om, + volume = {4}, number= {}, month = {}, + pages = {89-120} + } + +@Article{marsh06, + author = {Marshall, John and Emily Shuckburgh and Helen Jones and Chris Hill}, + year = 2006, + title = {Estimates and Implications of Surface Eddy Diffusivity + in the Southern Ocean Derived from Tracer Transport}, + journal = jpo, + volume = {36}, number= {}, month = {}, + pages = {1806-1821} + } + +@InProceedings{hoe-hill:99, + author = {Hoe, James C. and Chris Hill and Alistair Adcroft}, + title = {A Personal Supercomputer for Climate Research}, + booktitle = {In Proceedings of the ACM/IEEE Super-Computing Confrence}, + year = 1999, + pages = {10.1109/SC.1999}, + publisher = {IEEE}, +} + +@Article{stevens:90, + author = {Stevens, D. 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