--- manual/manual_references.bib 2005/08/31 18:51:42 1.24 +++ manual/manual_references.bib 2008/02/11 21:40:13 1.34 @@ -5,8 +5,10 @@ @string{jgr = {J.~Geophys.~Res.}} @string{ijrs = {Int.~J.~Remote Sensing}} @string{jas = {J.~Atmos.~Sci.}} +@string{jam = {J.~Appl.~Meteor.}} @string{jpo = {J.~Phys.~Oceanogr.}} @string{jclim = {J.~Clim.}} +@string{jcp = {J.~Comput.~Phys.}} @string{ieee = {IEEE Trans.~Geosci. Remote Sensing}} @string{jfm = {J.~Fluid Mech.}} @string{jaot = {J.~Atmos.~Ocean.~Technol.}} @@ -69,6 +71,18 @@ 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}, @@ -116,6 +130,28 @@ 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}, @@ -177,6 +213,16 @@ 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{gen-mcw:90, author = {P.R. Gent and J.C. McWilliams}, year = 1990, @@ -356,6 +402,15 @@ 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}, @@ -452,6 +507,17 @@ pages = {38 pp.}, address = {Delft (NL)}, } + +@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}}, + url = {http://mitgcm.org/pdfs/Los2006a.pdf}, +} + @Article{maro-wun:93, author = {J. Marotzke and C. Wunsch}, @@ -498,7 +564,7 @@ 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 @@ -506,6 +572,8 @@ 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, @@ -526,6 +594,15 @@ %% 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}} + @TechReport{rew:97, author = {R. K. Rew and G. P. Davis and S. Emmerson and H. Davies}, title = {{NetCDF User's Guide for C, FORTRAN 77, and FORTRAN 90}, @@ -572,6 +649,15 @@ 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, @@ -581,9 +667,10 @@ 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}, @@ -599,17 +686,16 @@ 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}, @@ -771,32 +857,36 @@ author = {Marshall, J. and C. Hill and L. Perelman and A. Adcroft}, title = {Hydrostatic, quasi-hydrostatic, and nonhydrostatic ocean modeling}, - journal = {JGR}, + journal = jgr, year = 1997, volume = 102, number = {C3}, - pages = {5733-5752} + pages = {5733-5752}, + url = {http://mitgcm.org/pdfs/96JC02775.pdf}, } @Article{marshall:97b, author = {Marshall, J. and A. Adcroft and C. Hill and L. Perelman and C. Heisey}, title = {A finite-volume, incompressible Navier Stokes model for studies of the ocean on parallel computers}, - journal = {JGR}, + journal = jgr, year = 1997, volume = 102, number = {C3}, - pages = {5753-5766} + pages = {5753-5766}, + url = {http://mitgcm.org/pdfs/96JC02776.pdf}, } @Article{adcroft:97, author = {Adcroft, A.J. and Hill, C.N. and J. Marshall}, title = {Representation of topography by shaved cells in a height coordinate ocean model}, - journal = {MWR}, + 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, @@ -806,7 +896,8 @@ journal = om, year = 2004, volume = 7, - pages = {269-284} + pages = {269-284}, + doi = {10.1016/j.ocemod.2003.09.003}, } @Article{adcroft:04b, @@ -816,7 +907,22 @@ 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, @@ -825,14 +931,16 @@ 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, author = {Visbeck, M., J. Marshall, T. Haine, and M. Spall}, title = {Specification of eddy transfer coefficients in coarse-resolution ocean circulation models}, - journal = {JPO}, + journal = jpo, year = 1997, volume = 27, number = 3, @@ -852,15 +960,6 @@ 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 @@ -885,10 +984,12 @@ author = {Adcroft, A., Hill C. and J. Marshall}, title = {A new treatment of the Coriolis terms in C-grid models at both high and low resolutions}, - journal = {MWR}, + 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, @@ -903,7 +1004,7 @@ @Article{wardle:00, author = {Wardle R. and Marshall J.}, title = {Representation of eddies in primitive equation models by a PV flux}, - journal = {JPO}, + journal = jpo, year = 2000, volume = 30, number = 10, @@ -920,7 +1021,7 @@ } @Article{adcroft:02, - author = {Adcroft et al.}, + author = {Adcroft, A., et~al.}, title = {Energy conversion in discrete numerical models}, journal = om, year = 2002, @@ -942,7 +1043,7 @@ author = {Miller, M. J. and White, A. A.}, title = {On the non-hydrostatic equations in pressure and sigma coordiantes}, - journal = {qjrms}, + journal = qjrms, year = 1984, volume = 110, pages = {515-533} @@ -951,7 +1052,7 @@ @Article{white:89, author = {White, A. A.}, title = {An extended version of a nonhydrostatic, pressure coordiante model}, - journal = {qjrms}, + journal = qjrms, year = 1989, volume = 115, pages = {1243-1251} @@ -980,7 +1081,7 @@ author = {Griffies, S.,M. and Hallberg, R.,W.}, title = {Biharmonic friction with a Smagorinsky-like viscosity for use in large-scale eddy-permitting ocean models}, - journal = {MWR}, + journal = mwr, year = 2000, volume = 128, number = 8, @@ -991,7 +1092,7 @@ author = {Wajsowicz, R.}, title = {A CONSISTENT FORMULATION OF THE ANISOTROPIC STRESS TENSOR FOR USE IN MODELS OF THE LARGE-SCALE OCEAN CIRCULATION}, - journal = {JCP}, + journal = jcp, year = 1993, volume = 105, number = 2, @@ -1010,7 +1111,7 @@ @Article{dm:95, author = {Danabasoglu, G. and McWilliams J.C.}, title = {Sensitivity of the global ocean circulation to parameterizations of mesoscale tracer transports}, - journal = {JC}, + journal = jclim, year = 1995, volume = 8, number = 12, @@ -1020,7 +1121,7 @@ @Article{ldd:97, author = {Large, W.G. and Danabasoglu, G. and Doney, S.C. and McWilliams, J.C.}, title = {Sensitivity to surface forcing and boundary layer mixing in a global ocean model: Annual-mean climatology}, - journal = {JPO}, + journal = jpo, year = 1997, volume = 27, number = 11, @@ -1031,7 +1132,7 @@ 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}, - journal = {JPO}, + journal = jpo, year = 1999, volume = 29, number = 8, @@ -1062,9 +1163,9 @@ } @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, @@ -1237,7 +1338,7 @@ title = {Mechanisms of air-sea CO$_2$ flux variability in the Equatorial Pacific and the North Atlantic}, journal = {Global Biogeochemical Cycles}, - year = {}, + year = {2004}, OPTkey = {}, volume = {18}, number = {doi:10.1029/2003GB002179}, @@ -1555,3 +1656,10 @@ 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}, +} +