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1 mlosch 1.36 @string{angl = {Ann.\ Glaciol.}}
2 heimbach 1.1 @string{arfm = {Annu.~Rev.~Fluid Mech.}}
3     @string{bams = {Bull.~Am.~Met.~Soc.}}
4     @string{blm = {Bound.~Layer~Meteorol.}}
5 jmc 1.14 @string{climd = {Clim.~Dynamics}}
6 mlosch 1.36 @string{cch = {Clim.\ Change}}
7 heimbach 1.1 @string{jgr = {J.~Geophys.~Res.}}
8     @string{ijrs = {Int.~J.~Remote Sensing}}
9     @string{jas = {J.~Atmos.~Sci.}}
10 jmc 1.25 @string{jam = {J.~Appl.~Meteor.}}
11 heimbach 1.1 @string{jpo = {J.~Phys.~Oceanogr.}}
12     @string{jclim = {J.~Clim.}}
13 jmc 1.25 @string{jcp = {J.~Comput.~Phys.}}
14 heimbach 1.1 @string{ieee = {IEEE Trans.~Geosci. Remote Sensing}}
15     @string{jfm = {J.~Fluid Mech.}}
16     @string{jaot = {J.~Atmos.~Ocean.~Technol.}}
17     @string{jms = {J.~Mar.~Sys.}}
18 jmc 1.14 @string{om = {Ocean Modelling}}
19 heimbach 1.1 @string{gaos = {Global Atmos.~Ocean System}}
20     @string{grl = {Geophys.~Res.~Lett.}}
21     @string{dsr = {Deep Sea Res.}}
22     @string{dao = {Dyn.~Atmos.~Oceans}}
23     @string{mwr = {Mon.~Wea.~Rev.}}
24     @string{qjrms = {{Q.~J.~R.~Meteorol.~Soc.}}}
25     @string{tel = {Tellus}}
26     @string{cup = {Cambridge University Press}}
27     @string{esapub = {ESA Publications Division, ESTEC, Noordwijk (NL)}}
28     @string{ifremer = {IFREMER/CERSAT}}
29     @string{igarss = {IEEE Press, Piscataway, N.J., USA}}
30     @string{dnmi = {The Norwegian Meteorological Institute (DNMI)}}
31     @string{dkrz = {Deutsches Klimarechenzentrum (DKRZ)}}
32     @string{mpi = {MPI f\"ur Meteorologie}}
33     @string{ecmwf = {ECMWF}}
34     @string{estec = {European Space Research and Technology Centre
35     (ESTEC)}}
36     @string{esa = {European Space Agency (ESA)}}
37 mlosch 1.36 @string{eos = {Eos~Trans.\ AGU}}
38 heimbach 1.1
39     @Article{bis-eta:92,
40     author = {C.H. Bishof and G.F. Corliss and L. Green and
41     A. Griewank and K. Haigler and P. Newman},
42     year = 1992,
43     title = {Automatic differentiation of advanced GFD codes
44     for multidisciplinary design},
45     journal = {Journal on Computing Systems in Engineering},
46     volume = {3},
47     pages = {625--638},
48     }
49    
50     @incollection{bis:94,
51     author = {C.H. Bishof},
52     year = 1994,
53     title = {Automatic differentiation, tangent linear models
54     and pseudo-adjoints},
55     booktitle = {High Performance Computing in the Geosciences},
56     series = {Series C: Mathematical and Physical Sciences},
57     pages = {59--80},
58     editor = {F.X. {Le Dimet}},
59     publisher = {Kluwer},
60     address = {Dordrecht, NL},
61     }
62    
63     @techreport{bis-eta:94,
64     author = {C. Bishof and A. Carle and P. Khademi and
65     A. Maurer},
66     year = 1994,
67     title = {The ADIFOR 2.0 system for the automatic
68     differentiation of FORTRAN 77 programs},
69     institution = {Argonne National Laboratory, Mathematics and
70     Computer Science Division},
71     type = {Argonne Preprint},
72     number = {ANL-MCS-P981-1194},
73     address = {ANL; 9700 South Cass Ave.;
74     Argonne (ILL), 90439; USA},
75     note = {http://www.mcs.anl.gov/autodiff/},
76     }
77 cnh 1.29
78     @ARTICLE{bugi-hill:06,
79     author = {V. Bugnion and C. Hill},
80     title = {Equilibration mechanisms in an adjoint ocean general
81     circulation model},
82     journal = {Ocean Dynamics},
83     year = {2006},
84     volume = {56},
85     number = {1},
86     pages = {51-61},
87     doi = {10.1007/s10236-005-0052-z},
88     }
89 heimbach 1.1
90     @techreport{bis-roh:97,
91     author = {C. Bishof and L. Roh},
92     year = 1997,
93     title = {ADIC: An extensible automatic differentiation tool
94     for ANSI-C},
95     institution = {Argonne National Laboratory, Mathematics and
96     Computer Science Division},
97     type = {Argonne Preprint},
98     number = {ANL-MCS-P626-1196},
99     address = {ANL; 9700 South Cass Ave.;
100     Argonne (ILL), 90439; USA},
101     note = {http://www.mcs.anl.gov/autodiff/},
102     }
103    
104     @Article{cou-tal:87,
105     author = {P. Courtier and O. Talagrand},
106     year = 1987,
107     title = {Variational assimilation of meteorological
108     observations with the adjoint vorticity equation.
109     II: Numerical results},
110     journal = qjrms,
111     volume = {113},
112     pages = {1329--1347},
113     }
114    
115     @Article{cou-tal:90,
116     author = {P. Courtier and O. Talagrand},
117     year = 1990,
118     title = {Variational assimilation of meteorological
119     observations with direct and adjoint shallow-water
120     equations},
121     journal = tel,
122     volume = {42A},
123     pages = {531--549},
124     }
125    
126     @Article{cou-eta:94,
127     author = {P. Courtier and J.-N. Th{\'e}paut and
128     A. Hollingsworth},
129     year = 1994,
130     title = {A strategy for operational implementation of
131     4-D-VAR using an incremental approach},
132     journal = qjrms,
133     volume = {120},
134     pages = {1367--1387},
135     }
136 cnh 1.29
137 jmc 1.33 @ARTICLE{durr:91,
138     author = {Dale R. Durran},
139     title = {The Third-Order Adams-Bashforth Method: An Attractive Alternative
140     to Leapfrog Time Differencing},
141     journal = mwr,
142     year = {1991},
143     volume = {119},
144     pages = {702-720},
145     }
146    
147    
148 cnh 1.29 @ARTICLE{dutk-etal:06,
149     author = {S. Dutkiewicz and M.J. Follows and P. Heimbach and J. Marshall},
150     title = {Controls on ocean productivity and air-sea carbon flux:
151     An adjoint model sensitivity study},
152     journal = grl,
153     year = {2006},
154     volume = {33},
155     pages = {L02603},
156     doi = {10.1029/2005GL024987},
157     }
158 heimbach 1.1
159     @Article{err:97,
160     author = {R.M. Errico},
161     year = 1997,
162     title = {What is an adjoint model},
163     journal = bams,
164     volume = {78},
165     pages = {2577--2591},
166     }
167    
168     @Article{far-moo:92,
169     author = {B.F. Farrell and A.M. Moore},
170     year = {1992},
171     title = {An adjoint method for obtaining the most rapidly
172     growing perturbation to oceanic flows},
173     journal = jpo,
174     volume = {22},
175     pages = {338--349},
176     }
177    
178     @Article{far-ioa:96a,
179     author = {B.F. Farrell and P. Ioannou},
180     year = {1996a},
181     title = {Generalized stability theory. Part I:
182     Autonomous operators},
183     journal = jas,
184     volume = {53},
185     pages = {2025--2040},
186     }
187    
188     @Article{far-ioa:96b,
189     author = {B.F. Farrell and P. Ioannou},
190     year = {1996b},
191     title = {Generalized stability theory. Part I:
192     Nonautonomous operators},
193     journal = jas,
194     volume = {53},
195     pages = {2041--2053},
196     }
197    
198     @techreport{fau-pap:98,
199     author = {C. Faure and Y. Papegay},
200     year = 1998,
201     title = {Odyss{\'e}e User's Guide. Version 1.7},
202     institution = {Institut National de Recherche en Informatique
203     et en Automatique},
204     type = {Rapport Technique},
205     number = {0224},
206     address = {INRIA; 2004, route des Luciolis, B.P. 93;
207     06902 Sophia Antipolis Cedex; France},
208     note = {http://www-sop.inria.fr/safir/SAM/Odyssee/odyssee.html},
209     }
210    
211     @Article{fau:00,
212     author = {C. Faure},
213     year = {2000},
214     title = {Adjoining strategies for multi-layered programs},
215     journal = {Optimisation Methods and Software},
216     note = {in press},
217     }
218    
219 dfer 1.34 @Article{fer-eta:05,
220     author = {D. Ferreira and J. Marshall and P. Heimbach},
221     year = 2005,
222     title = {Estimating Eddy Stresses by Fitting Dynamics to Observations
223     using a Residual-Mean Ocean Circulation Model and Its Adjoint},
224     journal = jpo,
225     volume = {35},
226     pages = {1891--1910},
227     }
228    
229 jmc 1.39 @Article{gas-eta:90,
230     author = {P. Gaspar and Y. Gr\'egoris and J.-M. Lefevre},
231     year = 1990,
232     title = {A Simple Eddy Kinetic Energy Model for Simulations of the
233     Oceanic Vertical Mixing: Tests at Station Papa and Long-Term
234     Upper Ocean Study Site},
235     journal = jgr,
236     volume = {95 (C9)},
237     pages = {16,179--16,193},
238     }
239    
240 heimbach 1.1 @Article{gen-mcw:90,
241     author = {P.R. Gent and J.C. McWilliams},
242     year = 1990,
243     title = {Isopycnal mixing in ocean circulation models},
244     journal = jpo,
245     volume = {20},
246     pages = {150--155},
247     }
248    
249     @Article{gen-eta:95,
250     author = {P.R. Gent and J. Willebrand and T.J. McDougall
251     and J.C. McWilliams},
252     year = 1995,
253     title = {Parameterizing eddy-induced tracer transports in
254     ocean circulation models},
255     journal = jpo,
256     volume = {25},
257     pages = {463--474},
258     }
259    
260     @Article{gie-kam:98,
261     author = {R. Giering and T. Kaminski},
262     year = 1998,
263     title = {Recipes for adjoint code construction},
264     journal = {ACM Transactions on Mathematical Software},
265     volume = 24,
266     pages = {437--474},
267     }
268    
269     @techreport{gie:99,
270     author = {R. Giering},
271     year = 1999,
272     title = {Tangent linear and Adjoint Model Compiler.
273     Users manual 1.4 (TAMC Version 5.2)},
274     institution = {Massachusetts Institute of Technology},
275     type = {Report},
276     number = {~},
277     address = {MIT/EAPS; 77 Massachusetts Ave.; Cambridge (MA)
278     02139; USA},
279     note = {http://puddle.mit.edu/$\sim$ralf/tamc/tamc.html},
280     }
281    
282     @incollection{gie:00,
283     author = {R. Giering},
284     editor = {P. Kasibhatla and M. Heimann and P. Rayner and
285     N. Mahowald and R.G. Prinn and D.E. Hartley},
286     year = 2000,
287     booktitle = {Inverse methods in global biogeochemical cycles},
288     title = {Tangent linear and adjoint biogeochemical models},
289     publisher = {American Geophysical Union},
290     series = {Geophysical Monograph},
291     volume = {114},
292     address = {Washington, DC},
293     pages = {33--48},
294     }
295    
296     @Article{gil-lem:89,
297     author = {J.C. Gilbert and C. Lemar\'echal},
298     year = 1989,
299     title = {Some numerical experiments with variable-storage
300     quasi-Newton algorithms},
301     journal = {Math. Programming},
302     volume = {45},
303     pages = {407--435},
304     }
305    
306     @book{gil-eta:81,
307     author = {P.E. Gill and W. Murray and M.H. Wright},
308     title = {Practical optimization},
309     year = 1981,
310     publisher = {Academic Press},
311     address = {London},
312     pages = {401 pp.},
313     }
314    
315 heimbach 1.11 @incollection{gri:89,
316     author = {A. Griewank},
317     year = 1989,
318     title = {On automatic differentiation},
319     booktitle = {Mathematical Programming: Recent Developments and
320     Applications},
321     pages = {83--108},
322     editor = {M. Iri and K. Tanabe},
323     publisher = {Kluwer},
324     address = {Dordrecht, NL},
325     }
326    
327     @Article{gri:92,
328     author = {A.~Griewank},
329     title = {Achieving logarithmic growth of temporal and spatial
330     complexity in reverse {A}utomatic {D}ifferentiation},
331     journal = {Optimization Methods and Software},
332     year = {1992},
333     volume = {1},
334     pages = {35--54}
335     }
336    
337 heimbach 1.1 @book{gri:00,
338     author = {A. Griewank},
339     title = {Evaluating Derivatives. Principles and Techniques
340     of Algorithmic Differentiation},
341     year = 2000,
342     series = {Frontiers in Applied Mathematics},
343     volume = {19},
344     publisher = {SIAM},
345     address = {Philadelphia},
346     pages = {369 pp.},
347     }
348    
349     @Article{hal-eta:82,
350     author = {M.C.G. Hall and D.G. Caccuci and M.E. Schlesinger},
351     year = 1982,
352     title = {Sensitivity analysis of a radiative-convective
353     model by the adjoint method},
354     journal = jas,
355     volume = {39},
356     pages = {2038--3050},
357     }
358 cnh 1.6
359     @Article{Haney,
360     author = {R.L. Haney},
361     title = {Surface thermal boundary conditions for ocean
362     circulation models},
363     journal = jpo,
364     year = 1971,
365     volume = 1,
366     pages = {241--248}
367     }
368 heimbach 1.1
369 cnh 1.16 @Article{held-suar:94,
370     author = {I.M. Held and M.J. Suarez},
371     year = {1994},
372     title = {A proposal for the intercomparison of the dynamical cores of atmospheric general circulation models},
373     journal = {Bulletin of the American Meteorological Society},
374     volume = {75(10)},
375     pages = {1825-1830}
376     }
377    
378 heimbach 1.1 @Article{hil-eta:01,
379     author = {C. Hill and M. Follows and V. Bugnion and
380     J. Marshall},
381 cnh 1.10 year = {2002},
382 heimbach 1.1 title = {Spatial and Temporal Impacts of ocean general
383     circulation on carbon sequestration},
384 cnh 1.6 journal = {Global Biogeochemical Cycles},
385 heimbach 1.1 note = {submitted},
386     }
387 cnh 1.6
388 edhill 1.15 @ARTICLE{hib80,
389 mlosch 1.36 author = {Hibler, III, William D.},
390 edhill 1.15 TITLE = "Modeling a Variable Thickness Sea Ice Cover",
391     JOURNAL = mwr,
392     YEAR = 1980,
393     VOLUME = 1,
394     PAGES = "1943-1973"
395     }
396    
397 cnh 1.6 @Article{Holland75,
398     author = {W.R. Holland and L. B. Lin},
399     year = {1975a},
400     title = {On the origin of mesoscale eddies and their contribution
401     to the general circulation of the ocean. I. A preliminary
402     numerical experiment},
403     journal = jpo,
404     volume = {5},
405     pages = {642-657}
406     }
407    
408     @Article{hol-lin:75b,
409     author = {W.R. Holland and L. B. Lin},
410     year = {1975b},
411     title = {On the origin of mesoscale eddies and their contribution
412     to the general circulation of the ocean. II. A parameter
413     study},
414     journal = jpo,
415     volume = {5},
416     pages = {658-669}
417     }
418    
419 jmc 1.31 @Article{jam-oze:86,
420     author = {B.M. Jamart and J. Ozer},
421     year = {1986},
422     title = {Numerical boundary layers and spurious residual flows},
423     journal = jgr,
424     volume = {91},
425     pages = {10,621-10,631}
426     }
427    
428 heimbach 1.1 @book{kas-eta:00,
429     author = {P. Kasibhatla and M. Heimann and P. Rayner and
430     N. Mahowald and R.G. Prinn and D.E. Hartley},
431     year = 2000,
432     title = {Inverse methods in global biogeochemical cycles},
433     publisher = {American Geophysical Union},
434     series = {Geophysical Monograph},
435     volume = {114},
436     address = {Washington, DC},
437     pages = {324 pp.},
438     }
439    
440     @Article{lar-eta:94,
441     author = {W.G. Large and J.C. McWilliams and S.C. Doney},
442     year = 1994,
443     title = {Oceanic vertical mixing: A review and a model
444     with nonlocal boundary layer parameterization},
445     journal = {Rev.~Geophys.},
446     volume = {32},
447     pages = {363--403},
448     }
449    
450     @Article{lar-eta:97,
451     author = {W.G. Large and G. Danabasoglu and S.C. Doney
452     and J.C. McWilliams},
453     year = 1997,
454     title = {Sensitivity to surface forcing and boundary layer
455     mixing in a global ocean model: annual-mean
456     climatology},
457     journal = jpo,
458     volume = {27},
459     pages = {2418--2447},
460     }
461    
462     @Article{led-tal:86,
463     author = {F.-X. {Le Dimet} and O. Talagrand},
464     year = 1986,
465     title = {Variational algorithms for analysis and
466     assimilation of meteorological observations:
467     theoretical aspects},
468     journal = tel,
469     volume = {38A},
470     pages = {97--110},
471     }
472 cnh 1.6
473     @TechReport{lev:94a,
474     author = {S. Levitus and T.P.Boyer},
475     title = {{World Ocean Atlas 1994 Volume 3: Salinity}},
476     institution = {NOAA Atlas NESDIS 3},
477     year = 1994,
478     OPTkey = {},
479     OPTtype = {},
480     OPTnumber = {},
481     OPTaddress = {U.S. Department of Commerce, Washington D.C.},
482     OPTmonth = {},
483     OPTnote = {},
484     OPTannote = {}
485     }
486    
487    
488     @TechReport{Levitus94,
489     author = {S. Levitus and T.P.Boyer},
490     title = {{World Ocean Atlas 1994 Volume 4: Temperature}},
491     institution = {NOAA Atlas NESDIS 4},
492     year = 1994,
493     OPTkey = {},
494     OPTtype = {},
495     OPTnumber = {},
496     OPTaddress = {U.S. Department of Commerce, Washington D.C.},
497     OPTmonth = {},
498     OPTnote = {},
499     OPTannote = {}
500     }
501    
502 heimbach 1.1
503     @Article{lew-der:85,
504     author = {J. Lewis and J. Derber},
505     year = {1985},
506     title = {The use of adjoint equations to solve a variational
507     adjustment problem with advective constraints},
508     journal = {Tellus},
509     volume = {37A},
510     pages = {309--322},
511     }
512    
513     @techreport{lon:88,
514     author = {R.B. Long},
515     year = 1988,
516     title = {Notes on assimilating observations into
517     numerical models},
518     institution = {Delft Hydraulics},
519     type = {Report},
520     number = {~},
521     pages = {38 pp.},
522     address = {Delft (NL)},
523     }
524 cnh 1.29
525     @ARTICLE{losc-heim:06,
526 mlosch 1.42 author = {Martin Losch and Patrick Heimbach},
527     title = {Adjoint Sensitivity of an Ocean General Circulation
528     Model to Bottom Topography},
529     journal = jpo,
530     year = 2007,
531     volume = 37,
532     doi = {10.1175/JPO3017.1},
533     number = 2,
534     pages = {377--393},
535 cnh 1.29 url = {http://mitgcm.org/pdfs/Los2006a.pdf},
536     }
537    
538 heimbach 1.1
539     @Article{maro-wun:93,
540     author = {J. Marotzke and C. Wunsch},
541     year = 1993,
542     title = {Finding the steady state of a general circulation
543     model through data assimilation:
544     Application to the North Atlantic Ocean},
545     journal = jgr,
546     volume = {98, C11},
547     pages = {20,149--20,167},
548     }
549    
550     @Article{maro-eta:99,
551     author = {J. Marotzke and R. Giering and K.Q. Zhang and
552     D. Stammer and C. Hill and T. Lee},
553     year = 1999,
554     title = {Construction of the adjoint MIT ocean general
555     circulation model and application to Atlantic heat
556     transport variability},
557     journal = jgr,
558     volume = {104, C12},
559     pages = {29,529--29,547},
560     }
561    
562     @Article{mars-eta:97a,
563     author = {J. Marshall and C. Hill and L. Perelman and
564     A. Adcroft},
565     year = {1997a},
566     title = {Hydrostatic, quasi-hydrostatic and
567     nonhydrostatic ocean modeling},
568     journal = jgr,
569     volume = {102, C3},
570     pages = {5,733--5,752},
571     }
572    
573     @Article{mars-eta:97b,
574     author = {J. Marshall and A. Adcroft and C. Hill and
575     L. Perelman and C. Heisey},
576     year = {1997b},
577     title = {Hydrostatic, quasi-hydrostatic and
578     nonhydrostatic ocean modeling},
579     journal = jgr,
580     volume = {102, C3},
581     pages = {5,753--5,766},
582     }
583    
584 jmc 1.33 @Article{mars-eta:98,
585 heimbach 1.1 author = {J. Marshall and H. Jones and C. Hill},
586     year = 1998,
587     title = {Efficient ocean modeling using
588     non-hydrostatic algorithms},
589     journal = jms,
590     volume = {18},
591     pages = {115--134},
592 cnh 1.29 url = {http://mitgcm.org/pdfs/journal_of_marine_systems_1998.pdf},
593     doi = {10.1016/S0924-7963\%2898\%2900008-6},
594 heimbach 1.1 }
595    
596 jmc 1.38 @Article{mol:09,
597     author = {Andrea Molod},
598     year = 2009,
599     title = {Running {GCM} physics and dynamics on different grids:
600     algorithm and tests},
601     journal = tel,
602     volume = {61A},
603     pages = {381--393},
604 heimbach 1.1 }
605 edhill 1.13
606     %% Rew, R. K., G. P. Davis, S. Emmerson, and H. Davies
607     %% NetCDF User's Guide for C, An Interface for Data Access, Version 3, April 1997.
608     %% (Available from Unidata or in PostScript form by anonymous FTP from
609     %% ftp://ftp.unidata.ucar.edu/pub/netcdf/guidec.ps.Z). There is also
610     %% a hypertext version of the User's Guide available at
611     %% http://www.unidata.ucar.edu/packages/netcdf/guidec. NetCDF User's
612     %% Guide for Fortran 90 and NetCDF User's Guide for Fortran 77 are
613     %% also available.
614 jmc 1.38
615 heimbach 1.32 @incollection{naum-etal:06,
616     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},
617     Booktitle = {European Conference on Computational Fluid Dynamics ECCOMAS CFD 2006},
618     Editor = {{P. Wesseling, E. O~nate and J. Periaux}},
619     Pages = {~},
620     Publisher = {TU Delft},
621     Title = {Adjoint code by source transformation with OpenAD/F},
622     Year = {2006}}
623    
624 jmc 1.38 @Article{orl:76,
625     author = {I. Orlanski},
626     year = 1976,
627     title = {A simple boundary condition for unbounded hyperbolic flows},
628     journal = jcp,
629     volume = {21},
630     pages = {251--269},
631     }
632    
633 jmc 1.39 @Article{pal-rom:97,
634     author = {T. Paluszkiewicz and R.D. Romea},
635     year = 1997,
636     title = {A one-dimensional model for the parameterization
637     of deep convection in the ocean},
638     journal = dao,
639     volume = {26},
640     pages = {95--130},
641     }
642    
643 edhill 1.13 @TechReport{rew:97,
644     author = {R. K. Rew and G. P. Davis and S. Emmerson and H. Davies},
645     title = {{NetCDF User's Guide for C, FORTRAN 77, and FORTRAN 90},
646     An Interface for Data Access, Version 3},
647     institution = {Unidata Program Center},
648     type = {Report},
649     address = {Boulder, Colorado},
650     year = 1997,
651     note = {http://www.unidata.ucar.edu/packages/netcdf/},
652     }
653    
654    
655 heimbach 1.1 @Article{res-eta:98,
656     author = {J.M. Restrepo and G.K. Leaf and A. Griewank},
657     year = 1998,
658 cnh 1.5 title = {Circumventing storage limitations in variational
659 heimbach 1.1 data assimilation studies},
660     journal = {SIAM J. Sci. Comput.},
661     volume = {19},
662     pages = {1586--1605},
663     }
664    
665     @Article{ros-eta:93,
666     author = {N. Rostaing and S. Dalmas and A. Galligo},
667     year = 1993,
668     title = {Automatic differentiation in Odyss{\'e}e},
669     journal = {Tellus},
670     volume = {45A},
671     pages = {558--568},
672     }
673    
674     @incollection{she-and:89,
675     author = {J. Sheinbaum and D.L.T. Anderson},
676     year = 1989,
677     title = {Assimilation of XBT data using a variational
678     technique},
679     booktitle = {Oceanic circulation models:
680     Combining data and dynamics},
681     pages = {257--285},
682     series = {NATO ASI Series},
683     volume = {C 284},
684     editor = {{D.L.T. Anderson and J. Willebrand}},
685     publisher = {Springer-Verlag},
686     address = {Berlin (Germany)},
687     }
688 cnh 1.6
689 heimbach 1.32 @article{utke-etal:08,
690     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},
691     Date-Modified = {2007-11-19 10:15:08 -0500},
692     Journal = {{ACM} Transactions on Mathematical Software},
693     Pages = {~},
694     Title = {OpenAD/F: A modular open source tool for automatic differentiation of Fortran codes},
695     Volume = {34(4)},
696     Year = {2008}}
697    
698 cnh 1.6 @Article{DaSilva94,
699     author = {A. da Silva and A. C. Young and S. Levitus},
700     year = 1994,
701     title = {Atlas of Surface Marine Data 1994, Volume 1: Algorithms and Procedures},
702     journal = {NOAA Atlas NESDIS},
703     volume = {6},
704     publisher = {U.S. Department of Commerce},
705     address = {Washington, D.C. (USA)},
706     note = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/},
707 cnh 1.28 url = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/},
708 cnh 1.6 }
709 heimbach 1.1
710 heimbach 1.32 @techreport{stam-etal:97,
711 heimbach 1.1 author = {D. Stammer and C. Wunsch and R. Giering and
712 cnh 1.6 Q. Zhang and J. Marotzke and J. Marshall and
713 heimbach 1.1 C. Hill},
714     year = 1997,
715     title = {The global ocean circulation estimated from
716     TOPEX/POSEIDON altimetry and a general circulation
717     model},
718     institution = {Center for Global Change Science, Massachusetts
719     Institute of Technology},
720     type = {Technical Report},
721     number = {49},
722     pages = {40 pp.},
723     address = {Cambridge (MA), USA},
724     }
725    
726 heimbach 1.32 @ARTICLE{stam-etal:02,
727 cnh 1.29 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},
728     title = {The global ocean circulation and transports during 1992 -- 1997, estimated from ocean observations and a general circulation model.},
729     journal = jgr,
730     year = {2002a},
731     volume = {107(C9)},
732     pages = {3118},
733     doi = {10.1029/2001JC000888},
734     }
735    
736 cnh 1.6
737     @Article{Stommel66,
738     author = {H. Stommel},
739     year = 1948,
740     title = {The western intensification of wind-driven ocean currents},
741     journal = {Trans. Am. Geophys. Union},
742     volume = {29},
743     pages = {206},
744 heimbach 1.1 }
745    
746     @Article{tal-cou:87,
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748     year = 1987,
749     title = {Variational assimilation of meteorological
750     observations with the adjoint vorticity equation.
751     I: Theory},
752     journal = qjrms,
753     volume = {113},
754     pages = {1311--1328},
755     }
756    
757     @Article{tal:97,
758     author = {O. Talagrand},
759     year = 1997,
760     title = {Assimilation of observations, an introduction},
761     journal = {J.~Meteor.~Soc.~Japan},
762     volume = {75},
763     pages = {191--209},
764     }
765    
766     @book{tar:87,
767     author = {A. Tarantola},
768     title = {Inverse Problem Theory: Methods for data fitting
769     and model parameter estimation},
770     year = 1987,
771     publisher = {Elsevier},
772     address = {Amsterdam},
773     pages = {629 pp.},
774     }
775    
776     @techreport{tha:87,
777     author = {W.C. Thacker},
778     year = 1987,
779     title = {Three lectures on fitting numerical models to
780     observations},
781     institution = {GKSS},
782     type = {Report},
783     number = {87/E/65},
784     pages = {64 pp.},
785     address = {Geesthacht (D)},
786     }
787    
788     @Article{tha-lon:88,
789     author = {W.C. Thacker and R.B. Long},
790     year = 1988,
791     title = {Fitting dynamics to data},
792     journal = jgr,
793     volume = {93, C2},
794     pages = {1,227--1,240},
795     }
796    
797     @Article{tha:88,
798     author = {W.C. Thacker},
799     year = 1988,
800     title = {Fitting models to inadequate data by enforcing
801     spatial and temporal smoothness},
802     journal = jgr,
803     volume = {93},
804     pages = {10,655--10,665},
805     }
806    
807     @Article{tha:89,
808     author = {W.C. Thacker},
809     year = 1989,
810     title = {The role of the Hessian matrix in fitting models
811     to measurements},
812     journal = jgr,
813     volume = {94, C5},
814     pages = {6,177--6,196},
815     }
816    
817     @Article{tha-rag:94,
818     author = {W.C. Thacker and R. Raghunath},
819     year = 1994,
820     title = {The rigid lid's contribution to the ill-conditioning
821     of oceanic inverse problems},
822     journal = jgr,
823     volume = {99, C5},
824     pages = {10,131--10,141},
825     }
826    
827     @Article{tzi-tha:89,
828     author = {E. Tziperman and W.C. Thacker},
829     year = {1989},
830     title = {An optimal control / adjoint equation approach
831     to studying the ocean general circulation},
832     journal = jpo,
833     volume = {19},
834     pages = {1471--1485},
835     }
836    
837     @Article{tzi-eta:92a,
838     author = {E. Tziperman and W.C. Thacker and R.B. Long and
839     S. Hwang},
840     year = {1992a},
841     title = {Oceanic data analysis using a general circulation
842     model. I: Simulations},
843     journal = jpo,
844     volume = {22},
845     pages = {1434--1457},
846     }
847    
848     @Article{tzi-eta:92b,
849     author = {E. Tziperman and W.C. Thacker and R.B. Long and
850     S. Hwang and S.R. Rintoul},
851     year = {1992b},
852     title = {Oceanic data analysis using a general circulation
853     model. I: A North Atlantic model},
854     journal = jpo,
855     volume = {22},
856     pages = {1458--1485},
857     }
858    
859     @book{wun:96,
860     author = {C. Wunsch},
861     title = {The ocean circulation inverse problem},
862     year = 1996,
863     publisher = cup,
864     address = {Cambridge (UK)},
865     pages = {442 pp.},
866     }
867    
868     @Article{zha-mar:99,
869     author = {K.Q. Zhang and J. Marotzke},
870     year = 1999,
871     title = {The importance of open-boundary estimation for an
872     Indian Ocean GCM-data synthesis},
873     journal = {J.~Marine Res.},
874     volume = {57},
875     pages = {305--334},
876     }
877 adcroft 1.2
878    
879     @InCollection{hill:95,
880     author = {Hill, C. and J. Marshall},
881     title = {Application of a Parallel Navier-Stokes Model to
882     Ocean Circulation in Parallel Computational Fluid
883     Dynamics},
884     booktitle = {Implementations and Results Using Parallel
885     Computers},
886     pages = {545-552},
887     publisher = {Elsevier Science B.V.: New York},
888     year = 1995,
889     editor = {A. Ecer, J. Periaux, N. Satofuka and S. Taylor}
890     }
891    
892    
893     @Article{marshall:97a,
894 adcroft 1.4 author = {Marshall, J. and C. Hill and L. Perelman and A. Adcroft},
895 adcroft 1.2 title = {Hydrostatic, quasi-hydrostatic, and nonhydrostatic ocean
896     modeling},
897 jmc 1.25 journal = jgr,
898 adcroft 1.2 year = 1997,
899     volume = 102,
900     number = {C3},
901 cnh 1.29 pages = {5733-5752},
902     url = {http://mitgcm.org/pdfs/96JC02775.pdf},
903 adcroft 1.2 }
904    
905     @Article{marshall:97b,
906 cnh 1.10 author = {Marshall, J. and A. Adcroft and C. Hill and L. Perelman and C. Heisey},
907 adcroft 1.2 title = {A finite-volume, incompressible Navier Stokes model for
908     studies of the ocean on parallel computers},
909 jmc 1.25 journal = jgr,
910 adcroft 1.2 year = 1997,
911     volume = 102,
912     number = {C3},
913 cnh 1.29 pages = {5753-5766},
914     url = {http://mitgcm.org/pdfs/96JC02776.pdf},
915 adcroft 1.2 }
916    
917     @Article{adcroft:97,
918 adcroft 1.4 author = {Adcroft, A.J. and Hill, C.N. and J. Marshall},
919 adcroft 1.2 title = {Representation of topography by shaved cells in a height
920     coordinate ocean model},
921 jmc 1.25 journal = mwr,
922 adcroft 1.2 year = 1997,
923     volume = 125,
924 cnh 1.29 pages = {2293-2315},
925     url = {http://mitgcm.org/pdfs/mwr_1997.pdf},
926     doi = {10.1175/1520-0493\%281997\%29125<2293:ROTBSC>2.0.CO;2},
927 adcroft 1.2 }
928    
929 jmc 1.19 @Article{adcroft:04a,
930     author = {Adcroft, A. and J.-M. Campin},
931 jmc 1.14 title = {Re-scaled height coordinates for accurate representation
932     of free-surface flows in ocean circulation models},
933     journal = om,
934     year = 2004,
935 jmc 1.19 volume = 7,
936 cnh 1.28 pages = {269-284},
937     doi = {10.1016/j.ocemod.2003.09.003},
938 jmc 1.19 }
939    
940     @Article{adcroft:04b,
941     author = {Adcroft, A. and J.-M. Campin and C. Hill and J. Marshall},
942     title = {Implementation of an Atmosphere-Ocean General Circulation Model
943     on the Expanded Spherical Cube},
944     journal = mwr,
945     year = 2004,
946     volume = 132,
947 cnh 1.29 pages = {2845-2863},
948     url = {http://mitgcm.org/pdfs/mwr_2004.pdf},
949     doi = {10.1175/MWR2823.1},
950 jmc 1.19 }
951    
952 jmc 1.33 @inproceedings{adcroft:04c,
953     author = {Adcroft, A. and C. Hill and J.-M. Campin and J. Marshall
954     and P. Heimbach},
955 jmc 1.35 title = {Overview of the Formulation and Numerics of the {MIT}GCM},
956 jmc 1.33 booktitle = {Proceedings of the ECMWF seminar series on Numerical Methods,
957     Recent developments in numerical methods for atmosphere and
958     ocean modelling},
959     year = 2004,
960     pages = {139-149},
961     url = {http://mitgcm.org/pdfs/ECMWF2004-Adcroft.pdf},
962     publisher = ecmwf
963     }
964    
965 jmc 1.19 @Article{marshall:04,
966     author = {Marshall, J. and A. Adcroft and J.-M. Campin and C. Hill and A. White},
967     title = {Atmosphere-Ocean Modeling Exploiting Fluid Isomorphisms},
968     journal = mwr,
969     year = 2004,
970     volume = 132,
971 cnh 1.29 pages = {2882-2894},
972     url = {http://mitgcm.org/pdfs/a_o_iso.pdf},
973     doi = {10.1175/MWR2835.1},
974 jmc 1.14 }
975    
976 adcroft 1.2 @Article{visbeck:97,
977     author = {Visbeck, M., J. Marshall, T. Haine, and M. Spall},
978     title = {Specification of eddy transfer coefficients in
979     coarse-resolution ocean circulation models},
980 jmc 1.25 journal = jpo,
981 adcroft 1.2 year = 1997,
982     volume = 27,
983     number = 3,
984     pages = {381-402}
985     }
986    
987     @Article{shaw:98,
988     author = {Shaw; A. Arvind, Cho, K.-C., Hill, C., Johnson, R.P.
989     and Marshall, J.},
990     title = {A comparison of implicitly parallel multi-threaded and
991     data-parallel implementations of an ocean model based
992     on the Navier-Stokes equations},
993     journal = {J. of Parallel and Distributed Computing},
994     year = 1998,
995     volume = 48,
996     number = 1,
997     pages = {1-51}
998     }
999    
1000     @Article{mjn:99,
1001     author = {Marshall, J., Jamous, D and J. Nilsson},
1002     title = {Reconciling `thermodynamic' and `dynamic' methods of
1003     computation of water-mass transformation rates},
1004     journal = {DSR},
1005     year = 1999,
1006     volume = 46,
1007     pages = {545-572}
1008     }
1009    
1010     @Article{ms:99,
1011     author = {Marshall, J and F. Schott},
1012     title = {Open ocean deep convection: observations, models and theory},
1013     journal = {Rev. Geophys.},
1014     year = 1999,
1015     volume = 37,
1016     number = 1,
1017     pages = {1-64}
1018     }
1019    
1020     @Article{adcroft:99,
1021     author = {Adcroft, A., Hill C. and J. Marshall},
1022     title = {A new treatment of the Coriolis terms in C-grid models
1023     at both high and low resolutions},
1024 jmc 1.25 journal = mwr,
1025 adcroft 1.2 year = 1999,
1026     volume = 127,
1027 cnh 1.29 pages = {1928-1936},
1028     url = {http://mitgcm.org/pdfs/mwr_1999.pdf},
1029     doi = {10.1175/1520-0493\%281999\%29127<1928:ANTOTC>2.0.CO;2},
1030 adcroft 1.2 }
1031    
1032     @InProceedings{hill:99,
1033     author = {Chris Hill, Alistair Adcroft, Daniel Jamous and John Marshall},
1034     title = {A Strategy for Terascale Climate Modeling},
1035 cnh 1.8 booktitle = {In Proceedings of the Eighth ECMWF Workshop on the Use of Parallel Processors in Meteorology},
1036 cnh 1.9 year = 1999,
1037     pages = {406-425},
1038     publisher = {World Scientific},
1039 adcroft 1.2 }
1040    
1041     @Article{wardle:00,
1042     author = {Wardle R. and Marshall J.},
1043     title = {Representation of eddies in primitive equation models by a PV flux},
1044 jmc 1.25 journal = jpo,
1045 adcroft 1.2 year = 2000,
1046     volume = 30,
1047     number = 10,
1048     pages = {2481-2503}
1049     }
1050    
1051     @Article{ac:02,
1052     author = {Adcroft, A. and J.-M. Campin},
1053     title = {Comparison of finite volume schemes and direct-space-time
1054     methods for ocean circulation models},
1055 jmc 1.14 journal = om,
1056 adcroft 1.2 year = 2002,
1057     note = {in preparation}
1058     }
1059    
1060     @Article{adcroft:02,
1061 jmc 1.25 author = {Adcroft, A., et~al.},
1062 adcroft 1.2 title = {Energy conversion in discrete numerical models},
1063 jmc 1.14 journal = om,
1064 adcroft 1.2 year = 2002,
1065     note = {in preparation}
1066     }
1067    
1068     @InCollection{arakawa:77,
1069     author = {Arakawa, A. and Lamb, V.},
1070     title = {Computational Design of the Basic Dynamical Processes of
1071     the UCLA General Circulation Model},
1072     booktitle = {Methods in Computational Physics},
1073     pages = {174-267},
1074     publisher = {Academic Press},
1075     year = 1977,
1076     volume = 17
1077     }
1078    
1079 jmc 1.24 @Article{miller_white:84,
1080     author = {Miller, M. J. and White, A. A.},
1081     title = {On the non-hydrostatic equations in pressure
1082     and sigma coordiantes},
1083 jmc 1.25 journal = qjrms,
1084 jmc 1.24 year = 1984,
1085     volume = 110,
1086     pages = {515-533}
1087     }
1088    
1089     @Article{white:89,
1090     author = {White, A. A.},
1091     title = {An extended version of a nonhydrostatic, pressure coordiante model},
1092 jmc 1.25 journal = qjrms,
1093 jmc 1.24 year = 1989,
1094     volume = 115,
1095     pages = {1243-1251}
1096     }
1097    
1098 adcroft 1.2 @Article{adcroft:98,
1099     author = {Adcroft, A. and Marshall, D.},
1100 adcroft 1.3 title = {How slippery are piecewise-constant coastlines in numerical
1101     ocean models?},
1102 adcroft 1.2 journal = {Tellus},
1103 adcroft 1.3 year = 1998,
1104     volume = 50,
1105     number = 1,
1106     pages = {95-108}
1107     }
1108    
1109     @PhdThesis{adcroft:95,
1110     author = {Adcroft, A.},
1111     title = {Numerical Algorithms for use in a Dynamical Model of the
1112     Ocean},
1113     school = {Imperial College, London},
1114     year = 1995
1115     }
1116    
1117     @Article{griffies:00,
1118     author = {Griffies, S.,M. and Hallberg, R.,W.},
1119     title = {Biharmonic friction with a Smagorinsky-like viscosity for
1120     use in large-scale eddy-permitting ocean models},
1121 jmc 1.25 journal = mwr,
1122 adcroft 1.3 year = 2000,
1123     volume = 128,
1124     number = 8,
1125     pages = {2935-2946}
1126     }
1127    
1128     @Article{wajsowicz:93,
1129     author = {Wajsowicz, R.},
1130     title = {A CONSISTENT FORMULATION OF THE ANISOTROPIC STRESS TENSOR
1131     FOR USE IN MODELS OF THE LARGE-SCALE OCEAN CIRCULATION},
1132 jmc 1.25 journal = jcp,
1133 adcroft 1.3 year = 1993,
1134     volume = 105,
1135     number = 2,
1136     pages = {333-338}
1137     }
1138    
1139     @Article{campin:02,
1140 jmc 1.14 author = {Campin, J.-M. and A. Adcroft and C. Hill and J. Marshall},
1141 adcroft 1.3 title = {Conservation of properties in a free-surface model},
1142 jmc 1.14 journal = om,
1143     year = 2004,
1144     volume = 6,
1145     pages = {221-244}
1146 adcroft 1.4 }
1147    
1148     @Article{dm:95,
1149     author = {Danabasoglu, G. and McWilliams J.C.},
1150     title = {Sensitivity of the global ocean circulation to parameterizations of mesoscale tracer transports},
1151 jmc 1.25 journal = jclim,
1152 adcroft 1.4 year = 1995,
1153     volume = 8,
1154     number = 12,
1155     pages = {2967-2987}
1156     }
1157    
1158     @Article{ldd:97,
1159     author = {Large, W.G. and Danabasoglu, G. and Doney, S.C. and McWilliams, J.C.},
1160     title = {Sensitivity to surface forcing and boundary layer mixing in a global ocean model: Annual-mean climatology},
1161 jmc 1.25 journal = jpo,
1162 adcroft 1.4 year = 1997,
1163     volume = 27,
1164     number = 11,
1165     pages = {2418-2447}
1166     }
1167    
1168     @Article{gkw:99,
1169     author = {Gerdes R. and Koberle C. and Beckmann A. and Herrmann P. and Willebrand J.},
1170     title = {Mechanisms for spreading of Mediterranean water in
1171     coarse-resolution numerical models},
1172 jmc 1.25 journal = jpo,
1173 adcroft 1.4 year = 1999,
1174     volume = 29,
1175     number = 8,
1176     pages = {1682-1700}
1177     }
1178    
1179 jmc 1.17 @incollection{roe:85,
1180     author = {P.L. Roe},
1181     year = 1985,
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