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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 jmc 1.49 @string{cup = {Cambridge University Press}}
8     @string{dao = {Dyn.~Atmos.~Oceans}}
9     @string{dkrz = {Deutsches Klimarechenzentrum (DKRZ)}}
10     @string{dnmi = {The Norwegian Meteorological Institute (DNMI)}}
11     @string{dsr = {Deep Sea Res.}}
12     @string{ecmwf = {ECMWF}}
13     @string{eos = {Eos~Trans.\ AGU}}
14     @string{esa = {European Space Agency (ESA)}}
15     @string{esapub = {ESA Publications Division, ESTEC, Noordwijk (NL)}}
16     @string{estec = {European Space Research and Technology Centre (ESTEC)}}
17     @string{gaos = {Global Atmos.~Ocean System}}
18     @string{grl = {Geophys.~Res.~Lett.}}
19     @string{ieee = {IEEE Trans.~Geosci. Remote Sensing}}
20     @string{ifremer = {IFREMER/CERSAT}}
21     @string{igarss = {IEEE Press, Piscataway, N.J., USA}}
22     @string{jam = {J.~Appl.~Meteor.}}
23     @string{jaot = {J.~Atmos.~Ocean.~Technol.}}
24 heimbach 1.1 @string{jas = {J.~Atmos.~Sci.}}
25     @string{jclim = {J.~Clim.}}
26 jmc 1.25 @string{jcp = {J.~Comput.~Phys.}}
27 heimbach 1.1 @string{jfm = {J.~Fluid Mech.}}
28 jmc 1.49 @string{jgr = {J.~Geophys.~Res.}}
29     @string{ijrs = {Int.~J.~Remote Sensing}}
30 heimbach 1.1 @string{jms = {J.~Mar.~Sys.}}
31 jmc 1.49 @string{jpo = {J.~Phys.~Oceanogr.}}
32     @string{mpi = {MPI f\"ur Meteorologie}}
33     @string{mwr = {Mon.~Wea.~Rev.}}
34 jmc 1.14 @string{om = {Ocean Modelling}}
35 jmc 1.49 @string{ptrsl = {{Phil.~Trans.~R.~Soc.~Lond.}}}
36 heimbach 1.1 @string{qjrms = {{Q.~J.~R.~Meteorol.~Soc.}}}
37 jmc 1.49 @string{siscicom= {SIAM J.\ Sci.\ Comput.}}
38 heimbach 1.1 @string{tel = {Tellus}}
39    
40     @Article{bis-eta:92,
41     author = {C.H. Bishof and G.F. Corliss and L. Green and
42     A. Griewank and K. Haigler and P. Newman},
43     year = 1992,
44     title = {Automatic differentiation of advanced GFD codes
45     for multidisciplinary design},
46     journal = {Journal on Computing Systems in Engineering},
47     volume = {3},
48     pages = {625--638},
49     }
50 jmc 1.45
51 heimbach 1.1 @incollection{bis:94,
52     author = {C.H. Bishof},
53     year = 1994,
54     title = {Automatic differentiation, tangent linear models
55     and pseudo-adjoints},
56     booktitle = {High Performance Computing in the Geosciences},
57     series = {Series C: Mathematical and Physical Sciences},
58     pages = {59--80},
59     editor = {F.X. {Le Dimet}},
60     publisher = {Kluwer},
61     address = {Dordrecht, NL},
62     }
63 jmc 1.45
64 heimbach 1.1 @techreport{bis-eta:94,
65     author = {C. Bishof and A. Carle and P. Khademi and
66     A. Maurer},
67     year = 1994,
68     title = {The ADIFOR 2.0 system for the automatic
69     differentiation of FORTRAN 77 programs},
70     institution = {Argonne National Laboratory, Mathematics and
71     Computer Science Division},
72     type = {Argonne Preprint},
73     number = {ANL-MCS-P981-1194},
74 jmc 1.45 address = {ANL; 9700 South Cass Ave.;
75 heimbach 1.1 Argonne (ILL), 90439; USA},
76     note = {http://www.mcs.anl.gov/autodiff/},
77     }
78 cnh 1.29
79 mlosch 1.51 @Article{bouillon13,
80     author = {Sylvain Bouillon and Thierry Fichefet and Vincent
81     Legat and Gurvan Madec},
82     title = {The Elastic-Viscous-Plastic Method Revisited},
83 mlosch 1.52 journal = om,
84 mlosch 1.51 volume = 71,
85     number = 0,
86     pages = {2--12},
87     year = 2013,
88     note = {Arctic Ocean},
89     issn = {1463-5003},
90     doi = {10.1016/j.ocemod.2013.05.013},
91     url = {http://dx.doi.org/10.1016/j.ocemod.2013.05.013},
92     }
93 jmc 1.46 @ARTICLE{bryan:84,
94     author = {Kirk Bryan},
95     title = {Accelerating the convergence to equilibrium of Ocean-Climate Models},
96     journal = jpo,
97     year = {1984},
98     volume = {14},
99     number = {4},
100     pages = {666-673},
101     }
102    
103 cnh 1.29 @ARTICLE{bugi-hill:06,
104     author = {V. Bugnion and C. Hill},
105     title = {Equilibration mechanisms in an adjoint ocean general
106     circulation model},
107     journal = {Ocean Dynamics},
108     year = {2006},
109     volume = {56},
110     number = {1},
111     pages = {51-61},
112     doi = {10.1007/s10236-005-0052-z},
113     }
114 jmc 1.45
115 heimbach 1.1 @techreport{bis-roh:97,
116     author = {C. Bishof and L. Roh},
117     year = 1997,
118     title = {ADIC: An extensible automatic differentiation tool
119     for ANSI-C},
120     institution = {Argonne National Laboratory, Mathematics and
121     Computer Science Division},
122     type = {Argonne Preprint},
123     number = {ANL-MCS-P626-1196},
124 jmc 1.45 address = {ANL; 9700 South Cass Ave.;
125 heimbach 1.1 Argonne (ILL), 90439; USA},
126     note = {http://www.mcs.anl.gov/autodiff/},
127     }
128 jmc 1.45
129 mlosch 1.52 @Article{castro-morales14,
130     author = {Karel Castro-Morales and Frank Kauker and Martin
131     Losch and Stefan Hendricks and Kathrin Riemann-Campe
132     and R{\"u}diger Gerdes},
133     title = {Sensitivity of Simulated {A}rctic Sea Ice to
134     Realistic Ice Thickness Distributions and Snow
135     Parameterizations},
136     journal = jgr,
137     issn = {2169-9291},
138     year = 2014,
139     volume = 119,
140     number = 1,
141     pages = {559--571},
142     url = {http://dx.doi.org/10.1002/2013JC009342},
143     doi = {10.1002/2013JC009342},
144     }
145    
146 heimbach 1.1 @Article{cou-tal:87,
147     author = {P. Courtier and O. Talagrand},
148     year = 1987,
149 jmc 1.45 title = {Variational assimilation of meteorological
150 heimbach 1.1 observations with the adjoint vorticity equation.
151     II: Numerical results},
152     journal = qjrms,
153     volume = {113},
154     pages = {1329--1347},
155     }
156 jmc 1.45
157 heimbach 1.1 @Article{cou-tal:90,
158     author = {P. Courtier and O. Talagrand},
159     year = 1990,
160     title = {Variational assimilation of meteorological
161     observations with direct and adjoint shallow-water
162     equations},
163     journal = tel,
164     volume = {42A},
165     pages = {531--549},
166     }
167 jmc 1.45
168 heimbach 1.1 @Article{cou-eta:94,
169     author = {P. Courtier and J.-N. Th{\'e}paut and
170     A. Hollingsworth},
171     year = 1994,
172     title = {A strategy for operational implementation of
173     4-D-VAR using an incremental approach},
174     journal = qjrms,
175     volume = {120},
176     pages = {1367--1387},
177     }
178 cnh 1.29
179 jmc 1.33 @ARTICLE{durr:91,
180     author = {Dale R. Durran},
181     title = {The Third-Order Adams-Bashforth Method: An Attractive Alternative
182     to Leapfrog Time Differencing},
183     journal = mwr,
184     year = {1991},
185     volume = {119},
186     pages = {702-720},
187     }
188 jmc 1.45
189 jmc 1.33
190 cnh 1.29 @ARTICLE{dutk-etal:06,
191     author = {S. Dutkiewicz and M.J. Follows and P. Heimbach and J. Marshall},
192     title = {Controls on ocean productivity and air-sea carbon flux:
193     An adjoint model sensitivity study},
194     journal = grl,
195     year = {2006},
196     volume = {33},
197     pages = {L02603},
198     doi = {10.1029/2005GL024987},
199     }
200 jmc 1.45
201 heimbach 1.1 @Article{err:97,
202     author = {R.M. Errico},
203     year = 1997,
204     title = {What is an adjoint model},
205     journal = bams,
206     volume = {78},
207     pages = {2577--2591},
208     }
209 jmc 1.45
210 heimbach 1.1 @Article{far-moo:92,
211     author = {B.F. Farrell and A.M. Moore},
212     year = {1992},
213     title = {An adjoint method for obtaining the most rapidly
214     growing perturbation to oceanic flows},
215     journal = jpo,
216     volume = {22},
217     pages = {338--349},
218     }
219 jmc 1.45
220 heimbach 1.1 @Article{far-ioa:96a,
221     author = {B.F. Farrell and P. Ioannou},
222     year = {1996a},
223     title = {Generalized stability theory. Part I:
224     Autonomous operators},
225     journal = jas,
226     volume = {53},
227     pages = {2025--2040},
228     }
229 jmc 1.45
230 heimbach 1.1 @Article{far-ioa:96b,
231     author = {B.F. Farrell and P. Ioannou},
232     year = {1996b},
233     title = {Generalized stability theory. Part I:
234     Nonautonomous operators},
235     journal = jas,
236     volume = {53},
237     pages = {2041--2053},
238     }
239 jmc 1.45
240 heimbach 1.1 @techreport{fau-pap:98,
241     author = {C. Faure and Y. Papegay},
242     year = 1998,
243     title = {Odyss{\'e}e User's Guide. Version 1.7},
244     institution = {Institut National de Recherche en Informatique
245     et en Automatique},
246     type = {Rapport Technique},
247     number = {0224},
248     address = {INRIA; 2004, route des Luciolis, B.P. 93;
249     06902 Sophia Antipolis Cedex; France},
250     note = {http://www-sop.inria.fr/safir/SAM/Odyssee/odyssee.html},
251     }
252 jmc 1.45
253 heimbach 1.1 @Article{fau:00,
254     author = {C. Faure},
255     year = {2000},
256     title = {Adjoining strategies for multi-layered programs},
257     journal = {Optimisation Methods and Software},
258     note = {in press},
259     }
260 jmc 1.45
261 dfer 1.34 @Article{fer-eta:05,
262     author = {D. Ferreira and J. Marshall and P. Heimbach},
263     year = 2005,
264     title = {Estimating Eddy Stresses by Fitting Dynamics to Observations
265     using a Residual-Mean Ocean Circulation Model and Its Adjoint},
266     journal = jpo,
267     volume = {35},
268     pages = {1891--1910},
269     }
270    
271 gforget 1.55 @Article{for-eta:15,
272     author = {Forget, G. and Campin, J.-M. and Heimbach, P. and Hill, C. N. and Ponte, R. M and Wunsch, C.},
273     title = {{ECCO} version 4: an integrated framework for non-linear inverse modeling and global ocean state estimation},
274     journal = {Geoscientific Model Development},
275     volume = {8},
276     year = {2015},
277     number = {10},
278     pages = {3071--3104},
279     url = {http://www.geosci-model-dev.net/8/3071/2015/},
280     doi = {10.5194/gmd-8-3071-2015}
281     }
282    
283 jmc 1.39 @Article{gas-eta:90,
284 jmc 1.45 author = {P. Gaspar and Y. Gr\'egoris and J.-M. Lefevre},
285 jmc 1.39 year = 1990,
286 jmc 1.45 title = {A Simple Eddy Kinetic Energy Model for Simulations of the
287     Oceanic Vertical Mixing: Tests at Station Papa and Long-Term
288 jmc 1.39 Upper Ocean Study Site},
289     journal = jgr,
290     volume = {95 (C9)},
291     pages = {16,179--16,193},
292     }
293    
294 heimbach 1.1 @Article{gen-mcw:90,
295 dfer 1.44 author = {P. R. Gent and J. C. McWilliams},
296 heimbach 1.1 year = 1990,
297     title = {Isopycnal mixing in ocean circulation models},
298     journal = jpo,
299     volume = {20},
300     pages = {150--155},
301     }
302 jmc 1.45
303 heimbach 1.1 @Article{gen-eta:95,
304 dfer 1.44 author = {P. R. Gent and J. Willebrand and T. J. McDougall and J. C. McWilliams},
305 heimbach 1.1 year = 1995,
306 dfer 1.44 title = {Parameterizing eddy-induced tracer transports in ocean circulation models},
307 heimbach 1.1 journal = jpo,
308     volume = {25},
309     pages = {463--474},
310     }
311 jmc 1.45
312 heimbach 1.1 @Article{gie-kam:98,
313     author = {R. Giering and T. Kaminski},
314     year = 1998,
315     title = {Recipes for adjoint code construction},
316     journal = {ACM Transactions on Mathematical Software},
317     volume = 24,
318     pages = {437--474},
319     }
320    
321     @techreport{gie:99,
322     author = {R. Giering},
323     year = 1999,
324 jmc 1.45 title = {Tangent linear and Adjoint Model Compiler.
325 heimbach 1.1 Users manual 1.4 (TAMC Version 5.2)},
326     institution = {Massachusetts Institute of Technology},
327     type = {Report},
328     number = {~},
329     address = {MIT/EAPS; 77 Massachusetts Ave.; Cambridge (MA)
330     02139; USA},
331     note = {http://puddle.mit.edu/$\sim$ralf/tamc/tamc.html},
332     }
333 jmc 1.45
334 heimbach 1.1 @incollection{gie:00,
335     author = {R. Giering},
336     editor = {P. Kasibhatla and M. Heimann and P. Rayner and
337     N. Mahowald and R.G. Prinn and D.E. Hartley},
338     year = 2000,
339     booktitle = {Inverse methods in global biogeochemical cycles},
340     title = {Tangent linear and adjoint biogeochemical models},
341     publisher = {American Geophysical Union},
342     series = {Geophysical Monograph},
343     volume = {114},
344     address = {Washington, DC},
345     pages = {33--48},
346     }
347    
348     @Article{gil-lem:89,
349     author = {J.C. Gilbert and C. Lemar\'echal},
350     year = 1989,
351     title = {Some numerical experiments with variable-storage
352     quasi-Newton algorithms},
353     journal = {Math. Programming},
354     volume = {45},
355     pages = {407--435},
356     }
357 jmc 1.45
358 heimbach 1.1 @book{gil-eta:81,
359     author = {P.E. Gill and W. Murray and M.H. Wright},
360     title = {Practical optimization},
361     year = 1981,
362     publisher = {Academic Press},
363 jmc 1.45 address = {London},
364 heimbach 1.1 pages = {401 pp.},
365     }
366 jmc 1.45
367 heimbach 1.11 @incollection{gri:89,
368     author = {A. Griewank},
369     year = 1989,
370     title = {On automatic differentiation},
371     booktitle = {Mathematical Programming: Recent Developments and
372     Applications},
373     pages = {83--108},
374     editor = {M. Iri and K. Tanabe},
375     publisher = {Kluwer},
376     address = {Dordrecht, NL},
377     }
378 jmc 1.45
379 heimbach 1.11 @Article{gri:92,
380     author = {A.~Griewank},
381     title = {Achieving logarithmic growth of temporal and spatial
382     complexity in reverse {A}utomatic {D}ifferentiation},
383     journal = {Optimization Methods and Software},
384     year = {1992},
385     volume = {1},
386     pages = {35--54}
387     }
388    
389 heimbach 1.1 @book{gri:00,
390     author = {A. Griewank},
391     title = {Evaluating Derivatives. Principles and Techniques
392     of Algorithmic Differentiation},
393     year = 2000,
394     series = {Frontiers in Applied Mathematics},
395     volume = {19},
396     publisher = {SIAM},
397 jmc 1.45 address = {Philadelphia},
398 heimbach 1.1 pages = {369 pp.},
399     }
400 jmc 1.45
401 heimbach 1.1 @Article{hal-eta:82,
402     author = {M.C.G. Hall and D.G. Caccuci and M.E. Schlesinger},
403     year = 1982,
404     title = {Sensitivity analysis of a radiative-convective
405     model by the adjoint method},
406     journal = jas,
407     volume = {39},
408     pages = {2038--3050},
409     }
410 cnh 1.6
411     @Article{Haney,
412     author = {R.L. Haney},
413     title = {Surface thermal boundary conditions for ocean
414     circulation models},
415     journal = jpo,
416     year = 1971,
417     volume = 1,
418     pages = {241--248}
419     }
420 jmc 1.45
421 cnh 1.16 @Article{held-suar:94,
422     author = {I.M. Held and M.J. Suarez},
423     year = {1994},
424     title = {A proposal for the intercomparison of the dynamical cores of atmospheric general circulation models},
425     journal = {Bulletin of the American Meteorological Society},
426     volume = {75(10)},
427     pages = {1825-1830}
428     }
429 jmc 1.45
430 gforget 1.56
431     @article{heim-eta:11,
432     title = {Timescales and regions of the sensitivity of {Atlantic} meridional volume and heat transport: Toward observing system design},
433     author = {Heimbach, Patrick and Wunsch, Carl and Ponte, Rui M and Forget, Gael and Hill, Chris and Utke, Jean},
434     journal = {Deep Sea Research Part II: Topical Studies in Oceanography},
435     volume = {58},
436     number = {17},
437     pages = {1858--1879},
438     year = {2011},
439     publisher = {Elsevier}
440     }
441    
442 heimbach 1.1 @Article{hil-eta:01,
443 jmc 1.45 author = {C. Hill and M. Follows and V. Bugnion and
444 heimbach 1.1 J. Marshall},
445 cnh 1.10 year = {2002},
446 jmc 1.45 title = {Spatial and Temporal Impacts of ocean general
447 heimbach 1.1 circulation on carbon sequestration},
448 cnh 1.6 journal = {Global Biogeochemical Cycles},
449 heimbach 1.1 note = {submitted},
450     }
451 cnh 1.6
452 edhill 1.15 @ARTICLE{hib80,
453 mlosch 1.36 author = {Hibler, III, William D.},
454 edhill 1.15 TITLE = "Modeling a Variable Thickness Sea Ice Cover",
455     JOURNAL = mwr,
456     YEAR = 1980,
457     VOLUME = 1,
458     PAGES = "1943-1973"
459     }
460    
461 cnh 1.6 @Article{Holland75,
462     author = {W.R. Holland and L. B. Lin},
463     year = {1975a},
464 jmc 1.45 title = {On the origin of mesoscale eddies and their contribution
465     to the general circulation of the ocean. I. A preliminary
466 cnh 1.6 numerical experiment},
467     journal = jpo,
468     volume = {5},
469     pages = {642-657}
470     }
471    
472     @Article{hol-lin:75b,
473     author = {W.R. Holland and L. B. Lin},
474     year = {1975b},
475 jmc 1.45 title = {On the origin of mesoscale eddies and their contribution
476 cnh 1.6 to the general circulation of the ocean. II. A parameter
477     study},
478     journal = jpo,
479     volume = {5},
480     pages = {658-669}
481     }
482    
483 jmc 1.31 @Article{jam-oze:86,
484 jmc 1.45 author = {B.M. Jamart and J. Ozer},
485 jmc 1.31 year = {1986},
486 jmc 1.45 title = {Numerical boundary layers and spurious residual flows},
487 jmc 1.31 journal = jgr,
488     volume = {91},
489     pages = {10,621-10,631}
490     }
491    
492 heimbach 1.1 @book{kas-eta:00,
493     author = {P. Kasibhatla and M. Heimann and P. Rayner and
494     N. Mahowald and R.G. Prinn and D.E. Hartley},
495     year = 2000,
496     title = {Inverse methods in global biogeochemical cycles},
497     publisher = {American Geophysical Union},
498     series = {Geophysical Monograph},
499     volume = {114},
500     address = {Washington, DC},
501     pages = {324 pp.},
502     }
503    
504     @Article{lar-eta:94,
505     author = {W.G. Large and J.C. McWilliams and S.C. Doney},
506     year = 1994,
507 dfer 1.44 title = {Oceanic vertical mixing: A review and a model with nonlocal boundary layer parameterization},
508 heimbach 1.1 journal = {Rev.~Geophys.},
509     volume = {32},
510     pages = {363--403},
511     }
512 jmc 1.45
513 heimbach 1.1 @Article{lar-eta:97,
514 jmc 1.45 author = {W. G. Large and G. Danabasoglu and S. C. Doney
515     and J. C. McWilliams},
516 heimbach 1.1 year = 1997,
517     title = {Sensitivity to surface forcing and boundary layer
518 jmc 1.45 mixing in a global ocean model: Annual-mean climatology},
519 heimbach 1.1 journal = jpo,
520     volume = {27},
521 jmc 1.45 number = 11,
522 heimbach 1.1 pages = {2418--2447},
523     }
524 jmc 1.45
525 heimbach 1.1 @Article{led-tal:86,
526     author = {F.-X. {Le Dimet} and O. Talagrand},
527     year = 1986,
528     title = {Variational algorithms for analysis and
529     assimilation of meteorological observations:
530     theoretical aspects},
531     journal = tel,
532     volume = {38A},
533     pages = {97--110},
534     }
535 cnh 1.6
536     @TechReport{lev:94a,
537     author = {S. Levitus and T.P.Boyer},
538     title = {{World Ocean Atlas 1994 Volume 3: Salinity}},
539     institution = {NOAA Atlas NESDIS 3},
540     year = 1994,
541     OPTkey = {},
542     OPTtype = {},
543     OPTnumber = {},
544     OPTaddress = {U.S. Department of Commerce, Washington D.C.},
545     OPTmonth = {},
546     OPTnote = {},
547     OPTannote = {}
548     }
549    
550    
551     @TechReport{Levitus94,
552     author = {S. Levitus and T.P.Boyer},
553     title = {{World Ocean Atlas 1994 Volume 4: Temperature}},
554     institution = {NOAA Atlas NESDIS 4},
555     year = 1994,
556     OPTkey = {},
557     OPTtype = {},
558     OPTnumber = {},
559     OPTaddress = {U.S. Department of Commerce, Washington D.C.},
560     OPTmonth = {},
561     OPTnote = {},
562     OPTannote = {}
563     }
564    
565 jmc 1.45
566 heimbach 1.1 @Article{lew-der:85,
567     author = {J. Lewis and J. Derber},
568     year = {1985},
569     title = {The use of adjoint equations to solve a variational
570     adjustment problem with advective constraints},
571     journal = {Tellus},
572     volume = {37A},
573     pages = {309--322},
574     }
575 jmc 1.45
576 heimbach 1.1 @techreport{lon:88,
577     author = {R.B. Long},
578     year = 1988,
579     title = {Notes on assimilating observations into
580     numerical models},
581     institution = {Delft Hydraulics},
582     type = {Report},
583     number = {~},
584     pages = {38 pp.},
585     address = {Delft (NL)},
586     }
587 cnh 1.29
588     @ARTICLE{losc-heim:06,
589 mlosch 1.42 author = {Martin Losch and Patrick Heimbach},
590     title = {Adjoint Sensitivity of an Ocean General Circulation
591     Model to Bottom Topography},
592     journal = jpo,
593     year = 2007,
594     volume = 37,
595     doi = {10.1175/JPO3017.1},
596     number = 2,
597     pages = {377--393},
598 cnh 1.29 url = {http://mitgcm.org/pdfs/Los2006a.pdf},
599     }
600    
601 jmc 1.45
602 heimbach 1.1 @Article{maro-wun:93,
603     author = {J. Marotzke and C. Wunsch},
604     year = 1993,
605     title = {Finding the steady state of a general circulation
606     model through data assimilation:
607     Application to the North Atlantic Ocean},
608     journal = jgr,
609     volume = {98, C11},
610     pages = {20,149--20,167},
611     }
612 jmc 1.45
613 heimbach 1.1 @Article{maro-eta:99,
614 jmc 1.45 author = {J. Marotzke and R. Giering and K.Q. Zhang and
615 heimbach 1.1 D. Stammer and C. Hill and T. Lee},
616     year = 1999,
617     title = {Construction of the adjoint MIT ocean general
618     circulation model and application to Atlantic heat
619     transport variability},
620     journal = jgr,
621     volume = {104, C12},
622     pages = {29,529--29,547},
623     }
624 jmc 1.45
625 heimbach 1.1 @Article{mars-eta:97a,
626     author = {J. Marshall and C. Hill and L. Perelman and
627     A. Adcroft},
628     year = {1997a},
629     title = {Hydrostatic, quasi-hydrostatic and
630     nonhydrostatic ocean modeling},
631     journal = jgr,
632     volume = {102, C3},
633     pages = {5,733--5,752},
634     }
635 jmc 1.45
636 heimbach 1.1 @Article{mars-eta:97b,
637 jmc 1.45 author = {J. Marshall and A. Adcroft and C. Hill and
638 heimbach 1.1 L. Perelman and C. Heisey},
639     year = {1997b},
640     title = {Hydrostatic, quasi-hydrostatic and
641     nonhydrostatic ocean modeling},
642     journal = jgr,
643     volume = {102, C3},
644     pages = {5,753--5,766},
645     }
646 jmc 1.45
647 jmc 1.33 @Article{mars-eta:98,
648 heimbach 1.1 author = {J. Marshall and H. Jones and C. Hill},
649     year = 1998,
650     title = {Efficient ocean modeling using
651     non-hydrostatic algorithms},
652     journal = jms,
653     volume = {18},
654     pages = {115--134},
655 cnh 1.29 url = {http://mitgcm.org/pdfs/journal_of_marine_systems_1998.pdf},
656     doi = {10.1016/S0924-7963\%2898\%2900008-6},
657 heimbach 1.1 }
658 jmc 1.45
659 jmc 1.38 @Article{mol:09,
660     author = {Andrea Molod},
661     year = 2009,
662     title = {Running {GCM} physics and dynamics on different grids:
663     algorithm and tests},
664     journal = tel,
665     volume = {61A},
666     pages = {381--393},
667 heimbach 1.1 }
668 edhill 1.13
669     %% Rew, R. K., G. P. Davis, S. Emmerson, and H. Davies
670     %% NetCDF User's Guide for C, An Interface for Data Access, Version 3, April 1997.
671 jmc 1.45 %% (Available from Unidata or in PostScript form by anonymous FTP from
672     %% ftp://ftp.unidata.ucar.edu/pub/netcdf/guidec.ps.Z). There is also
673     %% a hypertext version of the User's Guide available at
674     %% http://www.unidata.ucar.edu/packages/netcdf/guidec. NetCDF User's
675     %% Guide for Fortran 90 and NetCDF User's Guide for Fortran 77 are
676 edhill 1.13 %% also available.
677 jmc 1.45
678 heimbach 1.32 @incollection{naum-etal:06,
679     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},
680     Booktitle = {European Conference on Computational Fluid Dynamics ECCOMAS CFD 2006},
681     Editor = {{P. Wesseling, E. O~nate and J. Periaux}},
682     Pages = {~},
683     Publisher = {TU Delft},
684     Title = {Adjoint code by source transformation with OpenAD/F},
685     Year = {2006}}
686    
687 jmc 1.38 @Article{orl:76,
688     author = {I. Orlanski},
689     year = 1976,
690     title = {A simple boundary condition for unbounded hyperbolic flows},
691     journal = jcp,
692     volume = {21},
693     pages = {251--269},
694     }
695    
696 jmc 1.39 @Article{pal-rom:97,
697     author = {T. Paluszkiewicz and R.D. Romea},
698     year = 1997,
699     title = {A one-dimensional model for the parameterization
700     of deep convection in the ocean},
701     journal = dao,
702     volume = {26},
703     pages = {95--130},
704     }
705    
706 edhill 1.13 @TechReport{rew:97,
707     author = {R. K. Rew and G. P. Davis and S. Emmerson and H. Davies},
708 jmc 1.45 title = {{NetCDF User's Guide for C, FORTRAN 77, and FORTRAN 90},
709 edhill 1.13 An Interface for Data Access, Version 3},
710     institution = {Unidata Program Center},
711     type = {Report},
712     address = {Boulder, Colorado},
713     year = 1997,
714     note = {http://www.unidata.ucar.edu/packages/netcdf/},
715     }
716    
717    
718 heimbach 1.1 @Article{res-eta:98,
719     author = {J.M. Restrepo and G.K. Leaf and A. Griewank},
720     year = 1998,
721 cnh 1.5 title = {Circumventing storage limitations in variational
722 heimbach 1.1 data assimilation studies},
723     journal = {SIAM J. Sci. Comput.},
724     volume = {19},
725     pages = {1586--1605},
726     }
727 jmc 1.45
728 heimbach 1.1 @Article{ros-eta:93,
729     author = {N. Rostaing and S. Dalmas and A. Galligo},
730     year = 1993,
731     title = {Automatic differentiation in Odyss{\'e}e},
732     journal = {Tellus},
733     volume = {45A},
734     pages = {558--568},
735     }
736 jmc 1.45
737 heimbach 1.1 @incollection{she-and:89,
738     author = {J. Sheinbaum and D.L.T. Anderson},
739     year = 1989,
740 jmc 1.45 title = {Assimilation of XBT data using a variational
741 heimbach 1.1 technique},
742     booktitle = {Oceanic circulation models:
743     Combining data and dynamics},
744     pages = {257--285},
745     series = {NATO ASI Series},
746     volume = {C 284},
747     editor = {{D.L.T. Anderson and J. Willebrand}},
748     publisher = {Springer-Verlag},
749     address = {Berlin (Germany)},
750     }
751 cnh 1.6
752 heimbach 1.32 @article{utke-etal:08,
753 mlosch 1.48 Author = {J. Utke and U. Naumann and M. Fagan and N. Tallent
754     and M. Strout and P. Heimbach and C. Hill and
755     D. Ozyurt and C. Wunsch},
756     Date-Modified ={2007-11-19 10:15:08 -0500},
757     Journal = {{ACM} Transactions on Mathematical Software},
758     Pages = {~},
759     Title = {OpenAD/F: A modular open source tool for automatic
760     differentiation of Fortran codes},
761     Volume = {34(4)},
762     Year = 2008
763     }
764 heimbach 1.32
765 cnh 1.6 @Article{DaSilva94,
766     author = {A. da Silva and A. C. Young and S. Levitus},
767     year = 1994,
768     title = {Atlas of Surface Marine Data 1994, Volume 1: Algorithms and Procedures},
769     journal = {NOAA Atlas NESDIS},
770     volume = {6},
771     publisher = {U.S. Department of Commerce},
772     address = {Washington, D.C. (USA)},
773     note = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/},
774 cnh 1.28 url = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/},
775 cnh 1.6 }
776 jmc 1.45
777 heimbach 1.32 @techreport{stam-etal:97,
778 heimbach 1.1 author = {D. Stammer and C. Wunsch and R. Giering and
779 cnh 1.6 Q. Zhang and J. Marotzke and J. Marshall and
780 heimbach 1.1 C. Hill},
781     year = 1997,
782 jmc 1.45 title = {The global ocean circulation estimated from
783 heimbach 1.1 TOPEX/POSEIDON altimetry and a general circulation
784     model},
785     institution = {Center for Global Change Science, Massachusetts
786     Institute of Technology},
787     type = {Technical Report},
788     number = {49},
789     pages = {40 pp.},
790     address = {Cambridge (MA), USA},
791     }
792 jmc 1.45
793 mlosch 1.48 @article{stam-etal:02,
794     author = {D. Stammer and C. Wunsch and R. Giering and
795     C. Eckert and P. Heimbach and J. Marotzke and
796     A. Adcroft and C.N. Hill and J. Marshall},
797     title = {The global ocean circulation and transports during
798     1992 -- 1997, estimated from ocean observations and
799     a general circulation model.},
800     journal = jgr,
801     year = {2002a},
802     volume = {107(C9)},
803     pages = {3118},
804     doi = {10.1029/2001JC000888},
805 cnh 1.29 }
806    
807 cnh 1.6
808     @Article{Stommel66,
809     author = {H. Stommel},
810     year = 1948,
811     title = {The western intensification of wind-driven ocean currents},
812     journal = {Trans. Am. Geophys. Union},
813     volume = {29},
814     pages = {206},
815 heimbach 1.1 }
816    
817     @Article{tal-cou:87,
818     author = {O. Talagrand and P. Courtier},
819     year = 1987,
820 jmc 1.45 title = {Variational assimilation of meteorological
821 heimbach 1.1 observations with the adjoint vorticity equation.
822     I: Theory},
823     journal = qjrms,
824     volume = {113},
825     pages = {1311--1328},
826     }
827 jmc 1.45
828 heimbach 1.1 @Article{tal:97,
829     author = {O. Talagrand},
830     year = 1997,
831     title = {Assimilation of observations, an introduction},
832     journal = {J.~Meteor.~Soc.~Japan},
833     volume = {75},
834     pages = {191--209},
835     }
836 jmc 1.45
837 heimbach 1.1 @book{tar:87,
838     author = {A. Tarantola},
839     title = {Inverse Problem Theory: Methods for data fitting
840     and model parameter estimation},
841     year = 1987,
842     publisher = {Elsevier},
843 jmc 1.45 address = {Amsterdam},
844 heimbach 1.1 pages = {629 pp.},
845     }
846 jmc 1.45
847 heimbach 1.1 @techreport{tha:87,
848     author = {W.C. Thacker},
849     year = 1987,
850     title = {Three lectures on fitting numerical models to
851     observations},
852     institution = {GKSS},
853     type = {Report},
854     number = {87/E/65},
855     pages = {64 pp.},
856     address = {Geesthacht (D)},
857     }
858 jmc 1.45
859 heimbach 1.1 @Article{tha-lon:88,
860     author = {W.C. Thacker and R.B. Long},
861     year = 1988,
862     title = {Fitting dynamics to data},
863     journal = jgr,
864     volume = {93, C2},
865     pages = {1,227--1,240},
866     }
867 jmc 1.45
868 heimbach 1.1 @Article{tha:88,
869     author = {W.C. Thacker},
870     year = 1988,
871     title = {Fitting models to inadequate data by enforcing
872     spatial and temporal smoothness},
873     journal = jgr,
874     volume = {93},
875     pages = {10,655--10,665},
876     }
877 jmc 1.45
878 heimbach 1.1 @Article{tha:89,
879     author = {W.C. Thacker},
880     year = 1989,
881     title = {The role of the Hessian matrix in fitting models
882     to measurements},
883     journal = jgr,
884     volume = {94, C5},
885     pages = {6,177--6,196},
886     }
887 jmc 1.45
888 heimbach 1.1 @Article{tha-rag:94,
889     author = {W.C. Thacker and R. Raghunath},
890     year = 1994,
891     title = {The rigid lid's contribution to the ill-conditioning
892     of oceanic inverse problems},
893     journal = jgr,
894     volume = {99, C5},
895     pages = {10,131--10,141},
896     }
897 jmc 1.45
898 heimbach 1.1 @Article{tzi-tha:89,
899     author = {E. Tziperman and W.C. Thacker},
900     year = {1989},
901     title = {An optimal control / adjoint equation approach
902     to studying the ocean general circulation},
903     journal = jpo,
904     volume = {19},
905     pages = {1471--1485},
906     }
907 jmc 1.45
908 heimbach 1.1 @Article{tzi-eta:92a,
909     author = {E. Tziperman and W.C. Thacker and R.B. Long and
910     S. Hwang},
911     year = {1992a},
912     title = {Oceanic data analysis using a general circulation
913     model. I: Simulations},
914     journal = jpo,
915     volume = {22},
916     pages = {1434--1457},
917     }
918 jmc 1.45
919 heimbach 1.1 @Article{tzi-eta:92b,
920     author = {E. Tziperman and W.C. Thacker and R.B. Long and
921     S. Hwang and S.R. Rintoul},
922     year = {1992b},
923     title = {Oceanic data analysis using a general circulation
924     model. I: A North Atlantic model},
925     journal = jpo,
926     volume = {22},
927     pages = {1458--1485},
928     }
929 jmc 1.45
930 heimbach 1.1 @book{wun:96,
931     author = {C. Wunsch},
932     title = {The ocean circulation inverse problem},
933     year = 1996,
934     publisher = cup,
935 jmc 1.45 address = {Cambridge (UK)},
936 heimbach 1.1 pages = {442 pp.},
937     }
938 jmc 1.45
939 heimbach 1.1 @Article{zha-mar:99,
940     author = {K.Q. Zhang and J. Marotzke},
941     year = 1999,
942     title = {The importance of open-boundary estimation for an
943     Indian Ocean GCM-data synthesis},
944     journal = {J.~Marine Res.},
945     volume = {57},
946     pages = {305--334},
947     }
948 adcroft 1.2
949    
950     @InCollection{hill:95,
951     author = {Hill, C. and J. Marshall},
952     title = {Application of a Parallel Navier-Stokes Model to
953     Ocean Circulation in Parallel Computational Fluid
954     Dynamics},
955     booktitle = {Implementations and Results Using Parallel
956     Computers},
957     pages = {545-552},
958     publisher = {Elsevier Science B.V.: New York},
959     year = 1995,
960     editor = {A. Ecer, J. Periaux, N. Satofuka and S. Taylor}
961     }
962    
963    
964     @Article{marshall:97a,
965 adcroft 1.4 author = {Marshall, J. and C. Hill and L. Perelman and A. Adcroft},
966 adcroft 1.2 title = {Hydrostatic, quasi-hydrostatic, and nonhydrostatic ocean
967     modeling},
968 jmc 1.25 journal = jgr,
969 adcroft 1.2 year = 1997,
970     volume = 102,
971     number = {C3},
972 cnh 1.29 pages = {5733-5752},
973     url = {http://mitgcm.org/pdfs/96JC02775.pdf},
974 adcroft 1.2 }
975    
976     @Article{marshall:97b,
977 cnh 1.10 author = {Marshall, J. and A. Adcroft and C. Hill and L. Perelman and C. Heisey},
978 adcroft 1.2 title = {A finite-volume, incompressible Navier Stokes model for
979     studies of the ocean on parallel computers},
980 jmc 1.25 journal = jgr,
981 adcroft 1.2 year = 1997,
982     volume = 102,
983     number = {C3},
984 cnh 1.29 pages = {5753-5766},
985     url = {http://mitgcm.org/pdfs/96JC02776.pdf},
986 adcroft 1.2 }
987    
988     @Article{adcroft:97,
989 adcroft 1.4 author = {Adcroft, A.J. and Hill, C.N. and J. Marshall},
990 adcroft 1.2 title = {Representation of topography by shaved cells in a height
991     coordinate ocean model},
992 jmc 1.25 journal = mwr,
993 adcroft 1.2 year = 1997,
994     volume = 125,
995 cnh 1.29 pages = {2293-2315},
996     url = {http://mitgcm.org/pdfs/mwr_1997.pdf},
997     doi = {10.1175/1520-0493\%281997\%29125<2293:ROTBSC>2.0.CO;2},
998 adcroft 1.2 }
999    
1000 jmc 1.19 @Article{adcroft:04a,
1001     author = {Adcroft, A. and J.-M. Campin},
1002 jmc 1.14 title = {Re-scaled height coordinates for accurate representation
1003     of free-surface flows in ocean circulation models},
1004     journal = om,
1005     year = 2004,
1006 jmc 1.19 volume = 7,
1007 cnh 1.28 pages = {269-284},
1008     doi = {10.1016/j.ocemod.2003.09.003},
1009 jmc 1.19 }
1010    
1011     @Article{adcroft:04b,
1012     author = {Adcroft, A. and J.-M. Campin and C. Hill and J. Marshall},
1013     title = {Implementation of an Atmosphere-Ocean General Circulation Model
1014     on the Expanded Spherical Cube},
1015     journal = mwr,
1016     year = 2004,
1017     volume = 132,
1018 cnh 1.29 pages = {2845-2863},
1019     url = {http://mitgcm.org/pdfs/mwr_2004.pdf},
1020     doi = {10.1175/MWR2823.1},
1021 jmc 1.19 }
1022    
1023 jmc 1.33 @inproceedings{adcroft:04c,
1024 jmc 1.45 author = {Adcroft, A. and C. Hill and J.-M. Campin and J. Marshall
1025 jmc 1.33 and P. Heimbach},
1026 jmc 1.35 title = {Overview of the Formulation and Numerics of the {MIT}GCM},
1027 jmc 1.33 booktitle = {Proceedings of the ECMWF seminar series on Numerical Methods,
1028 jmc 1.45 Recent developments in numerical methods for atmosphere and
1029 jmc 1.33 ocean modelling},
1030     year = 2004,
1031     pages = {139-149},
1032     url = {http://mitgcm.org/pdfs/ECMWF2004-Adcroft.pdf},
1033     publisher = ecmwf
1034     }
1035    
1036 jmc 1.19 @Article{marshall:04,
1037     author = {Marshall, J. and A. Adcroft and J.-M. Campin and C. Hill and A. White},
1038     title = {Atmosphere-Ocean Modeling Exploiting Fluid Isomorphisms},
1039     journal = mwr,
1040     year = 2004,
1041     volume = 132,
1042 cnh 1.29 pages = {2882-2894},
1043     url = {http://mitgcm.org/pdfs/a_o_iso.pdf},
1044     doi = {10.1175/MWR2835.1},
1045 jmc 1.14 }
1046    
1047 adcroft 1.2 @Article{visbeck:97,
1048 dfer 1.44 author = {M. Visbeck and J. Marshall and T. Haine and M. Spall},
1049     title = {Specification of eddy transfer coefficients in coarse-resolution ocean circulation models},
1050 jmc 1.25 journal = jpo,
1051 adcroft 1.2 year = 1997,
1052     volume = 27,
1053     number = 3,
1054     pages = {381-402}
1055     }
1056    
1057     @Article{shaw:98,
1058     author = {Shaw; A. Arvind, Cho, K.-C., Hill, C., Johnson, R.P.
1059     and Marshall, J.},
1060     title = {A comparison of implicitly parallel multi-threaded and
1061     data-parallel implementations of an ocean model based
1062     on the Navier-Stokes equations},
1063     journal = {J. of Parallel and Distributed Computing},
1064     year = 1998,
1065     volume = 48,
1066     number = 1,
1067     pages = {1-51}
1068     }
1069    
1070     @Article{mjn:99,
1071     author = {Marshall, J., Jamous, D and J. Nilsson},
1072     title = {Reconciling `thermodynamic' and `dynamic' methods of
1073     computation of water-mass transformation rates},
1074     journal = {DSR},
1075     year = 1999,
1076     volume = 46,
1077     pages = {545-572}
1078     }
1079    
1080     @Article{ms:99,
1081     author = {Marshall, J and F. Schott},
1082     title = {Open ocean deep convection: observations, models and theory},
1083     journal = {Rev. Geophys.},
1084     year = 1999,
1085     volume = 37,
1086     number = 1,
1087     pages = {1-64}
1088     }
1089    
1090     @Article{adcroft:99,
1091     author = {Adcroft, A., Hill C. and J. Marshall},
1092     title = {A new treatment of the Coriolis terms in C-grid models
1093     at both high and low resolutions},
1094 jmc 1.25 journal = mwr,
1095 adcroft 1.2 year = 1999,
1096     volume = 127,
1097 cnh 1.29 pages = {1928-1936},
1098     url = {http://mitgcm.org/pdfs/mwr_1999.pdf},
1099     doi = {10.1175/1520-0493\%281999\%29127<1928:ANTOTC>2.0.CO;2},
1100 adcroft 1.2 }
1101    
1102     @InProceedings{hill:99,
1103     author = {Chris Hill, Alistair Adcroft, Daniel Jamous and John Marshall},
1104     title = {A Strategy for Terascale Climate Modeling},
1105 cnh 1.8 booktitle = {In Proceedings of the Eighth ECMWF Workshop on the Use of Parallel Processors in Meteorology},
1106 cnh 1.9 year = 1999,
1107     pages = {406-425},
1108     publisher = {World Scientific},
1109 adcroft 1.2 }
1110    
1111     @Article{wardle:00,
1112     author = {Wardle R. and Marshall J.},
1113     title = {Representation of eddies in primitive equation models by a PV flux},
1114 jmc 1.25 journal = jpo,
1115 adcroft 1.2 year = 2000,
1116     volume = 30,
1117     number = 10,
1118     pages = {2481-2503}
1119     }
1120    
1121     @Article{ac:02,
1122     author = {Adcroft, A. and J.-M. Campin},
1123     title = {Comparison of finite volume schemes and direct-space-time
1124     methods for ocean circulation models},
1125 jmc 1.14 journal = om,
1126 adcroft 1.2 year = 2002,
1127     note = {in preparation}
1128     }
1129    
1130     @Article{adcroft:02,
1131 jmc 1.25 author = {Adcroft, A., et~al.},
1132 adcroft 1.2 title = {Energy conversion in discrete numerical models},
1133 jmc 1.14 journal = om,
1134 adcroft 1.2 year = 2002,
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1485     its Coupling to a Two-Dimensional Atmospheric Model: Uses
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1549     }
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1575 jmc 1.45 institution = {National Aeronautics and Space Administration},
1576     type = {NASA Technical Memorandum},
1577     number = {104606-Vol 3},
1578 molod 1.22 address = {NASA; Goddard Space Flight Center; Greenbelt (MD), 20771; USA},
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2269     title = {Energy-containing scales of turbulence in the ocean thermocline},
2270     journal = jgr,
2271     year = 1996,
2272     volume = {101 (C3)},
2273     pages = {14095--14109}
2274     }
2275    
2276 jmc 1.50 @Article{seimgregg94,
2277     author = {Seim, Harvey E. and Michael C. Gregg},
2278     title = {Detailed observations of a naturally occurring shear instability},
2279     journal = jgr,
2280     year = 1994,
2281     volume = {99 (C5)},
2282     pages = {10049--10073},
2283     }
2284    
2285 jmc 1.49 @Article{thorpe77,
2286     author = {Thorpe, S.A.},
2287     title = {Turbulence and mixing in a Scottish loch},
2288     journal = ptrsl,
2289     year = 1977,
2290     volume = {286},
2291     pages = {125--181}
2292     }
2293    
2294     @Article{wesson94,
2295 jmc 1.50 author = {Wesson, J. C. and Michael C. Gregg},
2296 jmc 1.49 title = {Mixing at Camarinal Sill in the Strait of Gibraltar},
2297     journal = jgr,
2298     year = 1994,
2299     volume = {99 (C5)},
2300     pages = { 9847--9878}
2301 mlosch 1.43 }

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