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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 jmc 1.39 @Article{gas-eta:90,
272 jmc 1.45 author = {P. Gaspar and Y. Gr\'egoris and J.-M. Lefevre},
273 jmc 1.39 year = 1990,
274 jmc 1.45 title = {A Simple Eddy Kinetic Energy Model for Simulations of the
275     Oceanic Vertical Mixing: Tests at Station Papa and Long-Term
276 jmc 1.39 Upper Ocean Study Site},
277     journal = jgr,
278     volume = {95 (C9)},
279     pages = {16,179--16,193},
280     }
281    
282 heimbach 1.1 @Article{gen-mcw:90,
283 dfer 1.44 author = {P. R. Gent and J. C. McWilliams},
284 heimbach 1.1 year = 1990,
285     title = {Isopycnal mixing in ocean circulation models},
286     journal = jpo,
287     volume = {20},
288     pages = {150--155},
289     }
290 jmc 1.45
291 heimbach 1.1 @Article{gen-eta:95,
292 dfer 1.44 author = {P. R. Gent and J. Willebrand and T. J. McDougall and J. C. McWilliams},
293 heimbach 1.1 year = 1995,
294 dfer 1.44 title = {Parameterizing eddy-induced tracer transports in ocean circulation models},
295 heimbach 1.1 journal = jpo,
296     volume = {25},
297     pages = {463--474},
298     }
299 jmc 1.45
300 heimbach 1.1 @Article{gie-kam:98,
301     author = {R. Giering and T. Kaminski},
302     year = 1998,
303     title = {Recipes for adjoint code construction},
304     journal = {ACM Transactions on Mathematical Software},
305     volume = 24,
306     pages = {437--474},
307     }
308    
309     @techreport{gie:99,
310     author = {R. Giering},
311     year = 1999,
312 jmc 1.45 title = {Tangent linear and Adjoint Model Compiler.
313 heimbach 1.1 Users manual 1.4 (TAMC Version 5.2)},
314     institution = {Massachusetts Institute of Technology},
315     type = {Report},
316     number = {~},
317     address = {MIT/EAPS; 77 Massachusetts Ave.; Cambridge (MA)
318     02139; USA},
319     note = {http://puddle.mit.edu/$\sim$ralf/tamc/tamc.html},
320     }
321 jmc 1.45
322 heimbach 1.1 @incollection{gie:00,
323     author = {R. Giering},
324     editor = {P. Kasibhatla and M. Heimann and P. Rayner and
325     N. Mahowald and R.G. Prinn and D.E. Hartley},
326     year = 2000,
327     booktitle = {Inverse methods in global biogeochemical cycles},
328     title = {Tangent linear and adjoint biogeochemical models},
329     publisher = {American Geophysical Union},
330     series = {Geophysical Monograph},
331     volume = {114},
332     address = {Washington, DC},
333     pages = {33--48},
334     }
335    
336     @Article{gil-lem:89,
337     author = {J.C. Gilbert and C. Lemar\'echal},
338     year = 1989,
339     title = {Some numerical experiments with variable-storage
340     quasi-Newton algorithms},
341     journal = {Math. Programming},
342     volume = {45},
343     pages = {407--435},
344     }
345 jmc 1.45
346 heimbach 1.1 @book{gil-eta:81,
347     author = {P.E. Gill and W. Murray and M.H. Wright},
348     title = {Practical optimization},
349     year = 1981,
350     publisher = {Academic Press},
351 jmc 1.45 address = {London},
352 heimbach 1.1 pages = {401 pp.},
353     }
354 jmc 1.45
355 heimbach 1.11 @incollection{gri:89,
356     author = {A. Griewank},
357     year = 1989,
358     title = {On automatic differentiation},
359     booktitle = {Mathematical Programming: Recent Developments and
360     Applications},
361     pages = {83--108},
362     editor = {M. Iri and K. Tanabe},
363     publisher = {Kluwer},
364     address = {Dordrecht, NL},
365     }
366 jmc 1.45
367 heimbach 1.11 @Article{gri:92,
368     author = {A.~Griewank},
369     title = {Achieving logarithmic growth of temporal and spatial
370     complexity in reverse {A}utomatic {D}ifferentiation},
371     journal = {Optimization Methods and Software},
372     year = {1992},
373     volume = {1},
374     pages = {35--54}
375     }
376    
377 heimbach 1.1 @book{gri:00,
378     author = {A. Griewank},
379     title = {Evaluating Derivatives. Principles and Techniques
380     of Algorithmic Differentiation},
381     year = 2000,
382     series = {Frontiers in Applied Mathematics},
383     volume = {19},
384     publisher = {SIAM},
385 jmc 1.45 address = {Philadelphia},
386 heimbach 1.1 pages = {369 pp.},
387     }
388 jmc 1.45
389 heimbach 1.1 @Article{hal-eta:82,
390     author = {M.C.G. Hall and D.G. Caccuci and M.E. Schlesinger},
391     year = 1982,
392     title = {Sensitivity analysis of a radiative-convective
393     model by the adjoint method},
394     journal = jas,
395     volume = {39},
396     pages = {2038--3050},
397     }
398 cnh 1.6
399     @Article{Haney,
400     author = {R.L. Haney},
401     title = {Surface thermal boundary conditions for ocean
402     circulation models},
403     journal = jpo,
404     year = 1971,
405     volume = 1,
406     pages = {241--248}
407     }
408 jmc 1.45
409 cnh 1.16 @Article{held-suar:94,
410     author = {I.M. Held and M.J. Suarez},
411     year = {1994},
412     title = {A proposal for the intercomparison of the dynamical cores of atmospheric general circulation models},
413     journal = {Bulletin of the American Meteorological Society},
414     volume = {75(10)},
415     pages = {1825-1830}
416     }
417 jmc 1.45
418 heimbach 1.1 @Article{hil-eta:01,
419 jmc 1.45 author = {C. Hill and M. Follows and V. Bugnion and
420 heimbach 1.1 J. Marshall},
421 cnh 1.10 year = {2002},
422 jmc 1.45 title = {Spatial and Temporal Impacts of ocean general
423 heimbach 1.1 circulation on carbon sequestration},
424 cnh 1.6 journal = {Global Biogeochemical Cycles},
425 heimbach 1.1 note = {submitted},
426     }
427 cnh 1.6
428 edhill 1.15 @ARTICLE{hib80,
429 mlosch 1.36 author = {Hibler, III, William D.},
430 edhill 1.15 TITLE = "Modeling a Variable Thickness Sea Ice Cover",
431     JOURNAL = mwr,
432     YEAR = 1980,
433     VOLUME = 1,
434     PAGES = "1943-1973"
435     }
436    
437 cnh 1.6 @Article{Holland75,
438     author = {W.R. Holland and L. B. Lin},
439     year = {1975a},
440 jmc 1.45 title = {On the origin of mesoscale eddies and their contribution
441     to the general circulation of the ocean. I. A preliminary
442 cnh 1.6 numerical experiment},
443     journal = jpo,
444     volume = {5},
445     pages = {642-657}
446     }
447    
448     @Article{hol-lin:75b,
449     author = {W.R. Holland and L. B. Lin},
450     year = {1975b},
451 jmc 1.45 title = {On the origin of mesoscale eddies and their contribution
452 cnh 1.6 to the general circulation of the ocean. II. A parameter
453     study},
454     journal = jpo,
455     volume = {5},
456     pages = {658-669}
457     }
458    
459 jmc 1.31 @Article{jam-oze:86,
460 jmc 1.45 author = {B.M. Jamart and J. Ozer},
461 jmc 1.31 year = {1986},
462 jmc 1.45 title = {Numerical boundary layers and spurious residual flows},
463 jmc 1.31 journal = jgr,
464     volume = {91},
465     pages = {10,621-10,631}
466     }
467    
468 heimbach 1.1 @book{kas-eta:00,
469     author = {P. Kasibhatla and M. Heimann and P. Rayner and
470     N. Mahowald and R.G. Prinn and D.E. Hartley},
471     year = 2000,
472     title = {Inverse methods in global biogeochemical cycles},
473     publisher = {American Geophysical Union},
474     series = {Geophysical Monograph},
475     volume = {114},
476     address = {Washington, DC},
477     pages = {324 pp.},
478     }
479    
480     @Article{lar-eta:94,
481     author = {W.G. Large and J.C. McWilliams and S.C. Doney},
482     year = 1994,
483 dfer 1.44 title = {Oceanic vertical mixing: A review and a model with nonlocal boundary layer parameterization},
484 heimbach 1.1 journal = {Rev.~Geophys.},
485     volume = {32},
486     pages = {363--403},
487     }
488 jmc 1.45
489 heimbach 1.1 @Article{lar-eta:97,
490 jmc 1.45 author = {W. G. Large and G. Danabasoglu and S. C. Doney
491     and J. C. McWilliams},
492 heimbach 1.1 year = 1997,
493     title = {Sensitivity to surface forcing and boundary layer
494 jmc 1.45 mixing in a global ocean model: Annual-mean climatology},
495 heimbach 1.1 journal = jpo,
496     volume = {27},
497 jmc 1.45 number = 11,
498 heimbach 1.1 pages = {2418--2447},
499     }
500 jmc 1.45
501 heimbach 1.1 @Article{led-tal:86,
502     author = {F.-X. {Le Dimet} and O. Talagrand},
503     year = 1986,
504     title = {Variational algorithms for analysis and
505     assimilation of meteorological observations:
506     theoretical aspects},
507     journal = tel,
508     volume = {38A},
509     pages = {97--110},
510     }
511 cnh 1.6
512     @TechReport{lev:94a,
513     author = {S. Levitus and T.P.Boyer},
514     title = {{World Ocean Atlas 1994 Volume 3: Salinity}},
515     institution = {NOAA Atlas NESDIS 3},
516     year = 1994,
517     OPTkey = {},
518     OPTtype = {},
519     OPTnumber = {},
520     OPTaddress = {U.S. Department of Commerce, Washington D.C.},
521     OPTmonth = {},
522     OPTnote = {},
523     OPTannote = {}
524     }
525    
526    
527     @TechReport{Levitus94,
528     author = {S. Levitus and T.P.Boyer},
529     title = {{World Ocean Atlas 1994 Volume 4: Temperature}},
530     institution = {NOAA Atlas NESDIS 4},
531     year = 1994,
532     OPTkey = {},
533     OPTtype = {},
534     OPTnumber = {},
535     OPTaddress = {U.S. Department of Commerce, Washington D.C.},
536     OPTmonth = {},
537     OPTnote = {},
538     OPTannote = {}
539     }
540    
541 jmc 1.45
542 heimbach 1.1 @Article{lew-der:85,
543     author = {J. Lewis and J. Derber},
544     year = {1985},
545     title = {The use of adjoint equations to solve a variational
546     adjustment problem with advective constraints},
547     journal = {Tellus},
548     volume = {37A},
549     pages = {309--322},
550     }
551 jmc 1.45
552 heimbach 1.1 @techreport{lon:88,
553     author = {R.B. Long},
554     year = 1988,
555     title = {Notes on assimilating observations into
556     numerical models},
557     institution = {Delft Hydraulics},
558     type = {Report},
559     number = {~},
560     pages = {38 pp.},
561     address = {Delft (NL)},
562     }
563 cnh 1.29
564     @ARTICLE{losc-heim:06,
565 mlosch 1.42 author = {Martin Losch and Patrick Heimbach},
566     title = {Adjoint Sensitivity of an Ocean General Circulation
567     Model to Bottom Topography},
568     journal = jpo,
569     year = 2007,
570     volume = 37,
571     doi = {10.1175/JPO3017.1},
572     number = 2,
573     pages = {377--393},
574 cnh 1.29 url = {http://mitgcm.org/pdfs/Los2006a.pdf},
575     }
576    
577 jmc 1.45
578 heimbach 1.1 @Article{maro-wun:93,
579     author = {J. Marotzke and C. Wunsch},
580     year = 1993,
581     title = {Finding the steady state of a general circulation
582     model through data assimilation:
583     Application to the North Atlantic Ocean},
584     journal = jgr,
585     volume = {98, C11},
586     pages = {20,149--20,167},
587     }
588 jmc 1.45
589 heimbach 1.1 @Article{maro-eta:99,
590 jmc 1.45 author = {J. Marotzke and R. Giering and K.Q. Zhang and
591 heimbach 1.1 D. Stammer and C. Hill and T. Lee},
592     year = 1999,
593     title = {Construction of the adjoint MIT ocean general
594     circulation model and application to Atlantic heat
595     transport variability},
596     journal = jgr,
597     volume = {104, C12},
598     pages = {29,529--29,547},
599     }
600 jmc 1.45
601 heimbach 1.1 @Article{mars-eta:97a,
602     author = {J. Marshall and C. Hill and L. Perelman and
603     A. Adcroft},
604     year = {1997a},
605     title = {Hydrostatic, quasi-hydrostatic and
606     nonhydrostatic ocean modeling},
607     journal = jgr,
608     volume = {102, C3},
609     pages = {5,733--5,752},
610     }
611 jmc 1.45
612 heimbach 1.1 @Article{mars-eta:97b,
613 jmc 1.45 author = {J. Marshall and A. Adcroft and C. Hill and
614 heimbach 1.1 L. Perelman and C. Heisey},
615     year = {1997b},
616     title = {Hydrostatic, quasi-hydrostatic and
617     nonhydrostatic ocean modeling},
618     journal = jgr,
619     volume = {102, C3},
620     pages = {5,753--5,766},
621     }
622 jmc 1.45
623 jmc 1.33 @Article{mars-eta:98,
624 heimbach 1.1 author = {J. Marshall and H. Jones and C. Hill},
625     year = 1998,
626     title = {Efficient ocean modeling using
627     non-hydrostatic algorithms},
628     journal = jms,
629     volume = {18},
630     pages = {115--134},
631 cnh 1.29 url = {http://mitgcm.org/pdfs/journal_of_marine_systems_1998.pdf},
632     doi = {10.1016/S0924-7963\%2898\%2900008-6},
633 heimbach 1.1 }
634 jmc 1.45
635 jmc 1.38 @Article{mol:09,
636     author = {Andrea Molod},
637     year = 2009,
638     title = {Running {GCM} physics and dynamics on different grids:
639     algorithm and tests},
640     journal = tel,
641     volume = {61A},
642     pages = {381--393},
643 heimbach 1.1 }
644 edhill 1.13
645     %% Rew, R. K., G. P. Davis, S. Emmerson, and H. Davies
646     %% NetCDF User's Guide for C, An Interface for Data Access, Version 3, April 1997.
647 jmc 1.45 %% (Available from Unidata or in PostScript form by anonymous FTP from
648     %% ftp://ftp.unidata.ucar.edu/pub/netcdf/guidec.ps.Z). There is also
649     %% a hypertext version of the User's Guide available at
650     %% http://www.unidata.ucar.edu/packages/netcdf/guidec. NetCDF User's
651     %% Guide for Fortran 90 and NetCDF User's Guide for Fortran 77 are
652 edhill 1.13 %% also available.
653 jmc 1.45
654 heimbach 1.32 @incollection{naum-etal:06,
655     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},
656     Booktitle = {European Conference on Computational Fluid Dynamics ECCOMAS CFD 2006},
657     Editor = {{P. Wesseling, E. O~nate and J. Periaux}},
658     Pages = {~},
659     Publisher = {TU Delft},
660     Title = {Adjoint code by source transformation with OpenAD/F},
661     Year = {2006}}
662    
663 jmc 1.38 @Article{orl:76,
664     author = {I. Orlanski},
665     year = 1976,
666     title = {A simple boundary condition for unbounded hyperbolic flows},
667     journal = jcp,
668     volume = {21},
669     pages = {251--269},
670     }
671    
672 jmc 1.39 @Article{pal-rom:97,
673     author = {T. Paluszkiewicz and R.D. Romea},
674     year = 1997,
675     title = {A one-dimensional model for the parameterization
676     of deep convection in the ocean},
677     journal = dao,
678     volume = {26},
679     pages = {95--130},
680     }
681    
682 edhill 1.13 @TechReport{rew:97,
683     author = {R. K. Rew and G. P. Davis and S. Emmerson and H. Davies},
684 jmc 1.45 title = {{NetCDF User's Guide for C, FORTRAN 77, and FORTRAN 90},
685 edhill 1.13 An Interface for Data Access, Version 3},
686     institution = {Unidata Program Center},
687     type = {Report},
688     address = {Boulder, Colorado},
689     year = 1997,
690     note = {http://www.unidata.ucar.edu/packages/netcdf/},
691     }
692    
693    
694 heimbach 1.1 @Article{res-eta:98,
695     author = {J.M. Restrepo and G.K. Leaf and A. Griewank},
696     year = 1998,
697 cnh 1.5 title = {Circumventing storage limitations in variational
698 heimbach 1.1 data assimilation studies},
699     journal = {SIAM J. Sci. Comput.},
700     volume = {19},
701     pages = {1586--1605},
702     }
703 jmc 1.45
704 heimbach 1.1 @Article{ros-eta:93,
705     author = {N. Rostaing and S. Dalmas and A. Galligo},
706     year = 1993,
707     title = {Automatic differentiation in Odyss{\'e}e},
708     journal = {Tellus},
709     volume = {45A},
710     pages = {558--568},
711     }
712 jmc 1.45
713 heimbach 1.1 @incollection{she-and:89,
714     author = {J. Sheinbaum and D.L.T. Anderson},
715     year = 1989,
716 jmc 1.45 title = {Assimilation of XBT data using a variational
717 heimbach 1.1 technique},
718     booktitle = {Oceanic circulation models:
719     Combining data and dynamics},
720     pages = {257--285},
721     series = {NATO ASI Series},
722     volume = {C 284},
723     editor = {{D.L.T. Anderson and J. Willebrand}},
724     publisher = {Springer-Verlag},
725     address = {Berlin (Germany)},
726     }
727 cnh 1.6
728 heimbach 1.32 @article{utke-etal:08,
729 mlosch 1.48 Author = {J. Utke and U. Naumann and M. Fagan and N. Tallent
730     and M. Strout and P. Heimbach and C. Hill and
731     D. Ozyurt and C. Wunsch},
732     Date-Modified ={2007-11-19 10:15:08 -0500},
733     Journal = {{ACM} Transactions on Mathematical Software},
734     Pages = {~},
735     Title = {OpenAD/F: A modular open source tool for automatic
736     differentiation of Fortran codes},
737     Volume = {34(4)},
738     Year = 2008
739     }
740 heimbach 1.32
741 cnh 1.6 @Article{DaSilva94,
742     author = {A. da Silva and A. C. Young and S. Levitus},
743     year = 1994,
744     title = {Atlas of Surface Marine Data 1994, Volume 1: Algorithms and Procedures},
745     journal = {NOAA Atlas NESDIS},
746     volume = {6},
747     publisher = {U.S. Department of Commerce},
748     address = {Washington, D.C. (USA)},
749     note = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/},
750 cnh 1.28 url = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/},
751 cnh 1.6 }
752 jmc 1.45
753 heimbach 1.32 @techreport{stam-etal:97,
754 heimbach 1.1 author = {D. Stammer and C. Wunsch and R. Giering and
755 cnh 1.6 Q. Zhang and J. Marotzke and J. Marshall and
756 heimbach 1.1 C. Hill},
757     year = 1997,
758 jmc 1.45 title = {The global ocean circulation estimated from
759 heimbach 1.1 TOPEX/POSEIDON altimetry and a general circulation
760     model},
761     institution = {Center for Global Change Science, Massachusetts
762     Institute of Technology},
763     type = {Technical Report},
764     number = {49},
765     pages = {40 pp.},
766     address = {Cambridge (MA), USA},
767     }
768 jmc 1.45
769 mlosch 1.48 @article{stam-etal:02,
770     author = {D. Stammer and C. Wunsch and R. Giering and
771     C. Eckert and P. Heimbach and J. Marotzke and
772     A. Adcroft and C.N. Hill and J. Marshall},
773     title = {The global ocean circulation and transports during
774     1992 -- 1997, estimated from ocean observations and
775     a general circulation model.},
776     journal = jgr,
777     year = {2002a},
778     volume = {107(C9)},
779     pages = {3118},
780     doi = {10.1029/2001JC000888},
781 cnh 1.29 }
782    
783 cnh 1.6
784     @Article{Stommel66,
785     author = {H. Stommel},
786     year = 1948,
787     title = {The western intensification of wind-driven ocean currents},
788     journal = {Trans. Am. Geophys. Union},
789     volume = {29},
790     pages = {206},
791 heimbach 1.1 }
792    
793     @Article{tal-cou:87,
794     author = {O. Talagrand and P. Courtier},
795     year = 1987,
796 jmc 1.45 title = {Variational assimilation of meteorological
797 heimbach 1.1 observations with the adjoint vorticity equation.
798     I: Theory},
799     journal = qjrms,
800     volume = {113},
801     pages = {1311--1328},
802     }
803 jmc 1.45
804 heimbach 1.1 @Article{tal:97,
805     author = {O. Talagrand},
806     year = 1997,
807     title = {Assimilation of observations, an introduction},
808     journal = {J.~Meteor.~Soc.~Japan},
809     volume = {75},
810     pages = {191--209},
811     }
812 jmc 1.45
813 heimbach 1.1 @book{tar:87,
814     author = {A. Tarantola},
815     title = {Inverse Problem Theory: Methods for data fitting
816     and model parameter estimation},
817     year = 1987,
818     publisher = {Elsevier},
819 jmc 1.45 address = {Amsterdam},
820 heimbach 1.1 pages = {629 pp.},
821     }
822 jmc 1.45
823 heimbach 1.1 @techreport{tha:87,
824     author = {W.C. Thacker},
825     year = 1987,
826     title = {Three lectures on fitting numerical models to
827     observations},
828     institution = {GKSS},
829     type = {Report},
830     number = {87/E/65},
831     pages = {64 pp.},
832     address = {Geesthacht (D)},
833     }
834 jmc 1.45
835 heimbach 1.1 @Article{tha-lon:88,
836     author = {W.C. Thacker and R.B. Long},
837     year = 1988,
838     title = {Fitting dynamics to data},
839     journal = jgr,
840     volume = {93, C2},
841     pages = {1,227--1,240},
842     }
843 jmc 1.45
844 heimbach 1.1 @Article{tha:88,
845     author = {W.C. Thacker},
846     year = 1988,
847     title = {Fitting models to inadequate data by enforcing
848     spatial and temporal smoothness},
849     journal = jgr,
850     volume = {93},
851     pages = {10,655--10,665},
852     }
853 jmc 1.45
854 heimbach 1.1 @Article{tha:89,
855     author = {W.C. Thacker},
856     year = 1989,
857     title = {The role of the Hessian matrix in fitting models
858     to measurements},
859     journal = jgr,
860     volume = {94, C5},
861     pages = {6,177--6,196},
862     }
863 jmc 1.45
864 heimbach 1.1 @Article{tha-rag:94,
865     author = {W.C. Thacker and R. Raghunath},
866     year = 1994,
867     title = {The rigid lid's contribution to the ill-conditioning
868     of oceanic inverse problems},
869     journal = jgr,
870     volume = {99, C5},
871     pages = {10,131--10,141},
872     }
873 jmc 1.45
874 heimbach 1.1 @Article{tzi-tha:89,
875     author = {E. Tziperman and W.C. Thacker},
876     year = {1989},
877     title = {An optimal control / adjoint equation approach
878     to studying the ocean general circulation},
879     journal = jpo,
880     volume = {19},
881     pages = {1471--1485},
882     }
883 jmc 1.45
884 heimbach 1.1 @Article{tzi-eta:92a,
885     author = {E. Tziperman and W.C. Thacker and R.B. Long and
886     S. Hwang},
887     year = {1992a},
888     title = {Oceanic data analysis using a general circulation
889     model. I: Simulations},
890     journal = jpo,
891     volume = {22},
892     pages = {1434--1457},
893     }
894 jmc 1.45
895 heimbach 1.1 @Article{tzi-eta:92b,
896     author = {E. Tziperman and W.C. Thacker and R.B. Long and
897     S. Hwang and S.R. Rintoul},
898     year = {1992b},
899     title = {Oceanic data analysis using a general circulation
900     model. I: A North Atlantic model},
901     journal = jpo,
902     volume = {22},
903     pages = {1458--1485},
904     }
905 jmc 1.45
906 heimbach 1.1 @book{wun:96,
907     author = {C. Wunsch},
908     title = {The ocean circulation inverse problem},
909     year = 1996,
910     publisher = cup,
911 jmc 1.45 address = {Cambridge (UK)},
912 heimbach 1.1 pages = {442 pp.},
913     }
914 jmc 1.45
915 heimbach 1.1 @Article{zha-mar:99,
916     author = {K.Q. Zhang and J. Marotzke},
917     year = 1999,
918     title = {The importance of open-boundary estimation for an
919     Indian Ocean GCM-data synthesis},
920     journal = {J.~Marine Res.},
921     volume = {57},
922     pages = {305--334},
923     }
924 adcroft 1.2
925    
926     @InCollection{hill:95,
927     author = {Hill, C. and J. Marshall},
928     title = {Application of a Parallel Navier-Stokes Model to
929     Ocean Circulation in Parallel Computational Fluid
930     Dynamics},
931     booktitle = {Implementations and Results Using Parallel
932     Computers},
933     pages = {545-552},
934     publisher = {Elsevier Science B.V.: New York},
935     year = 1995,
936     editor = {A. Ecer, J. Periaux, N. Satofuka and S. Taylor}
937     }
938    
939    
940     @Article{marshall:97a,
941 adcroft 1.4 author = {Marshall, J. and C. Hill and L. Perelman and A. Adcroft},
942 adcroft 1.2 title = {Hydrostatic, quasi-hydrostatic, and nonhydrostatic ocean
943     modeling},
944 jmc 1.25 journal = jgr,
945 adcroft 1.2 year = 1997,
946     volume = 102,
947     number = {C3},
948 cnh 1.29 pages = {5733-5752},
949     url = {http://mitgcm.org/pdfs/96JC02775.pdf},
950 adcroft 1.2 }
951    
952     @Article{marshall:97b,
953 cnh 1.10 author = {Marshall, J. and A. Adcroft and C. Hill and L. Perelman and C. Heisey},
954 adcroft 1.2 title = {A finite-volume, incompressible Navier Stokes model for
955     studies of the ocean on parallel computers},
956 jmc 1.25 journal = jgr,
957 adcroft 1.2 year = 1997,
958     volume = 102,
959     number = {C3},
960 cnh 1.29 pages = {5753-5766},
961     url = {http://mitgcm.org/pdfs/96JC02776.pdf},
962 adcroft 1.2 }
963    
964     @Article{adcroft:97,
965 adcroft 1.4 author = {Adcroft, A.J. and Hill, C.N. and J. Marshall},
966 adcroft 1.2 title = {Representation of topography by shaved cells in a height
967     coordinate ocean model},
968 jmc 1.25 journal = mwr,
969 adcroft 1.2 year = 1997,
970     volume = 125,
971 cnh 1.29 pages = {2293-2315},
972     url = {http://mitgcm.org/pdfs/mwr_1997.pdf},
973     doi = {10.1175/1520-0493\%281997\%29125<2293:ROTBSC>2.0.CO;2},
974 adcroft 1.2 }
975    
976 jmc 1.19 @Article{adcroft:04a,
977     author = {Adcroft, A. and J.-M. Campin},
978 jmc 1.14 title = {Re-scaled height coordinates for accurate representation
979     of free-surface flows in ocean circulation models},
980     journal = om,
981     year = 2004,
982 jmc 1.19 volume = 7,
983 cnh 1.28 pages = {269-284},
984     doi = {10.1016/j.ocemod.2003.09.003},
985 jmc 1.19 }
986    
987     @Article{adcroft:04b,
988     author = {Adcroft, A. and J.-M. Campin and C. Hill and J. Marshall},
989     title = {Implementation of an Atmosphere-Ocean General Circulation Model
990     on the Expanded Spherical Cube},
991     journal = mwr,
992     year = 2004,
993     volume = 132,
994 cnh 1.29 pages = {2845-2863},
995     url = {http://mitgcm.org/pdfs/mwr_2004.pdf},
996     doi = {10.1175/MWR2823.1},
997 jmc 1.19 }
998    
999 jmc 1.33 @inproceedings{adcroft:04c,
1000 jmc 1.45 author = {Adcroft, A. and C. Hill and J.-M. Campin and J. Marshall
1001 jmc 1.33 and P. Heimbach},
1002 jmc 1.35 title = {Overview of the Formulation and Numerics of the {MIT}GCM},
1003 jmc 1.33 booktitle = {Proceedings of the ECMWF seminar series on Numerical Methods,
1004 jmc 1.45 Recent developments in numerical methods for atmosphere and
1005 jmc 1.33 ocean modelling},
1006     year = 2004,
1007     pages = {139-149},
1008     url = {http://mitgcm.org/pdfs/ECMWF2004-Adcroft.pdf},
1009     publisher = ecmwf
1010     }
1011    
1012 jmc 1.19 @Article{marshall:04,
1013     author = {Marshall, J. and A. Adcroft and J.-M. Campin and C. Hill and A. White},
1014     title = {Atmosphere-Ocean Modeling Exploiting Fluid Isomorphisms},
1015     journal = mwr,
1016     year = 2004,
1017     volume = 132,
1018 cnh 1.29 pages = {2882-2894},
1019     url = {http://mitgcm.org/pdfs/a_o_iso.pdf},
1020     doi = {10.1175/MWR2835.1},
1021 jmc 1.14 }
1022    
1023 adcroft 1.2 @Article{visbeck:97,
1024 dfer 1.44 author = {M. Visbeck and J. Marshall and T. Haine and M. Spall},
1025     title = {Specification of eddy transfer coefficients in coarse-resolution ocean circulation models},
1026 jmc 1.25 journal = jpo,
1027 adcroft 1.2 year = 1997,
1028     volume = 27,
1029     number = 3,
1030     pages = {381-402}
1031     }
1032    
1033     @Article{shaw:98,
1034     author = {Shaw; A. Arvind, Cho, K.-C., Hill, C., Johnson, R.P.
1035     and Marshall, J.},
1036     title = {A comparison of implicitly parallel multi-threaded and
1037     data-parallel implementations of an ocean model based
1038     on the Navier-Stokes equations},
1039     journal = {J. of Parallel and Distributed Computing},
1040     year = 1998,
1041     volume = 48,
1042     number = 1,
1043     pages = {1-51}
1044     }
1045    
1046     @Article{mjn:99,
1047     author = {Marshall, J., Jamous, D and J. Nilsson},
1048     title = {Reconciling `thermodynamic' and `dynamic' methods of
1049     computation of water-mass transformation rates},
1050     journal = {DSR},
1051     year = 1999,
1052     volume = 46,
1053     pages = {545-572}
1054     }
1055    
1056     @Article{ms:99,
1057     author = {Marshall, J and F. Schott},
1058     title = {Open ocean deep convection: observations, models and theory},
1059     journal = {Rev. Geophys.},
1060     year = 1999,
1061     volume = 37,
1062     number = 1,
1063     pages = {1-64}
1064     }
1065    
1066     @Article{adcroft:99,
1067     author = {Adcroft, A., Hill C. and J. Marshall},
1068     title = {A new treatment of the Coriolis terms in C-grid models
1069     at both high and low resolutions},
1070 jmc 1.25 journal = mwr,
1071 adcroft 1.2 year = 1999,
1072     volume = 127,
1073 cnh 1.29 pages = {1928-1936},
1074     url = {http://mitgcm.org/pdfs/mwr_1999.pdf},
1075     doi = {10.1175/1520-0493\%281999\%29127<1928:ANTOTC>2.0.CO;2},
1076 adcroft 1.2 }
1077    
1078     @InProceedings{hill:99,
1079     author = {Chris Hill, Alistair Adcroft, Daniel Jamous and John Marshall},
1080     title = {A Strategy for Terascale Climate Modeling},
1081 cnh 1.8 booktitle = {In Proceedings of the Eighth ECMWF Workshop on the Use of Parallel Processors in Meteorology},
1082 cnh 1.9 year = 1999,
1083     pages = {406-425},
1084     publisher = {World Scientific},
1085 adcroft 1.2 }
1086    
1087     @Article{wardle:00,
1088     author = {Wardle R. and Marshall J.},
1089     title = {Representation of eddies in primitive equation models by a PV flux},
1090 jmc 1.25 journal = jpo,
1091 adcroft 1.2 year = 2000,
1092     volume = 30,
1093     number = 10,
1094     pages = {2481-2503}
1095     }
1096    
1097     @Article{ac:02,
1098     author = {Adcroft, A. and J.-M. Campin},
1099     title = {Comparison of finite volume schemes and direct-space-time
1100     methods for ocean circulation models},
1101 jmc 1.14 journal = om,
1102 adcroft 1.2 year = 2002,
1103     note = {in preparation}
1104     }
1105    
1106     @Article{adcroft:02,
1107 jmc 1.25 author = {Adcroft, A., et~al.},
1108 adcroft 1.2 title = {Energy conversion in discrete numerical models},
1109 jmc 1.14 journal = om,
1110 adcroft 1.2 year = 2002,
1111     note = {in preparation}
1112     }
1113    
1114     @InCollection{arakawa:77,
1115     author = {Arakawa, A. and Lamb, V.},
1116     title = {Computational Design of the Basic Dynamical Processes of
1117     the UCLA General Circulation Model},
1118     booktitle = {Methods in Computational Physics},
1119     pages = {174-267},
1120     publisher = {Academic Press},
1121     year = 1977,
1122     volume = 17
1123     }
1124    
1125 jmc 1.24 @Article{miller_white:84,
1126     author = {Miller, M. J. and White, A. A.},
1127     title = {On the non-hydrostatic equations in pressure
1128     and sigma coordiantes},
1129 jmc 1.25 journal = qjrms,
1130 jmc 1.24 year = 1984,
1131     volume = 110,
1132     pages = {515-533}
1133     }
1134    
1135     @Article{white:89,
1136     author = {White, A. A.},
1137     title = {An extended version of a nonhydrostatic, pressure coordiante model},
1138 jmc 1.25 journal = qjrms,
1139 jmc 1.24 year = 1989,
1140     volume = 115,
1141     pages = {1243-1251}
1142     }
1143    
1144 adcroft 1.2 @Article{adcroft:98,
1145     author = {Adcroft, A. and Marshall, D.},
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1529     number = {104606-Vol 3},
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