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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     author = {M. Losch and P. Heimbach},
527     title = {Adjoint sensitivity of an ocean general circulation model
528     to bottom topography},
529     journal = jpo,
530     year = {2006},
531     volume = {{in press}},
532     url = {http://mitgcm.org/pdfs/Los2006a.pdf},
533     }
534    
535 heimbach 1.1
536     @Article{maro-wun:93,
537     author = {J. Marotzke and C. Wunsch},
538     year = 1993,
539     title = {Finding the steady state of a general circulation
540     model through data assimilation:
541     Application to the North Atlantic Ocean},
542     journal = jgr,
543     volume = {98, C11},
544     pages = {20,149--20,167},
545     }
546    
547     @Article{maro-eta:99,
548     author = {J. Marotzke and R. Giering and K.Q. Zhang and
549     D. Stammer and C. Hill and T. Lee},
550     year = 1999,
551     title = {Construction of the adjoint MIT ocean general
552     circulation model and application to Atlantic heat
553     transport variability},
554     journal = jgr,
555     volume = {104, C12},
556     pages = {29,529--29,547},
557     }
558    
559     @Article{mars-eta:97a,
560     author = {J. Marshall and C. Hill and L. Perelman and
561     A. Adcroft},
562     year = {1997a},
563     title = {Hydrostatic, quasi-hydrostatic and
564     nonhydrostatic ocean modeling},
565     journal = jgr,
566     volume = {102, C3},
567     pages = {5,733--5,752},
568     }
569    
570     @Article{mars-eta:97b,
571     author = {J. Marshall and A. Adcroft and C. Hill and
572     L. Perelman and C. Heisey},
573     year = {1997b},
574     title = {Hydrostatic, quasi-hydrostatic and
575     nonhydrostatic ocean modeling},
576     journal = jgr,
577     volume = {102, C3},
578     pages = {5,753--5,766},
579     }
580    
581 jmc 1.33 @Article{mars-eta:98,
582 heimbach 1.1 author = {J. Marshall and H. Jones and C. Hill},
583     year = 1998,
584     title = {Efficient ocean modeling using
585     non-hydrostatic algorithms},
586     journal = jms,
587     volume = {18},
588     pages = {115--134},
589 cnh 1.29 url = {http://mitgcm.org/pdfs/journal_of_marine_systems_1998.pdf},
590     doi = {10.1016/S0924-7963\%2898\%2900008-6},
591 heimbach 1.1 }
592    
593 jmc 1.38 @Article{mol:09,
594     author = {Andrea Molod},
595     year = 2009,
596     title = {Running {GCM} physics and dynamics on different grids:
597     algorithm and tests},
598     journal = tel,
599     volume = {61A},
600     pages = {381--393},
601 heimbach 1.1 }
602 edhill 1.13
603     %% Rew, R. K., G. P. Davis, S. Emmerson, and H. Davies
604     %% NetCDF User's Guide for C, An Interface for Data Access, Version 3, April 1997.
605     %% (Available from Unidata or in PostScript form by anonymous FTP from
606     %% ftp://ftp.unidata.ucar.edu/pub/netcdf/guidec.ps.Z). There is also
607     %% a hypertext version of the User's Guide available at
608     %% http://www.unidata.ucar.edu/packages/netcdf/guidec. NetCDF User's
609     %% Guide for Fortran 90 and NetCDF User's Guide for Fortran 77 are
610     %% also available.
611 jmc 1.38
612 heimbach 1.32 @incollection{naum-etal:06,
613     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},
614     Booktitle = {European Conference on Computational Fluid Dynamics ECCOMAS CFD 2006},
615     Editor = {{P. Wesseling, E. O~nate and J. Periaux}},
616     Pages = {~},
617     Publisher = {TU Delft},
618     Title = {Adjoint code by source transformation with OpenAD/F},
619     Year = {2006}}
620    
621 jmc 1.38 @Article{orl:76,
622     author = {I. Orlanski},
623     year = 1976,
624     title = {A simple boundary condition for unbounded hyperbolic flows},
625     journal = jcp,
626     volume = {21},
627     pages = {251--269},
628     }
629    
630 jmc 1.39 @Article{pal-rom:97,
631     author = {T. Paluszkiewicz and R.D. Romea},
632     year = 1997,
633     title = {A one-dimensional model for the parameterization
634     of deep convection in the ocean},
635     journal = dao,
636     volume = {26},
637     pages = {95--130},
638     }
639    
640 edhill 1.13 @TechReport{rew:97,
641     author = {R. K. Rew and G. P. Davis and S. Emmerson and H. Davies},
642     title = {{NetCDF User's Guide for C, FORTRAN 77, and FORTRAN 90},
643     An Interface for Data Access, Version 3},
644     institution = {Unidata Program Center},
645     type = {Report},
646     address = {Boulder, Colorado},
647     year = 1997,
648     note = {http://www.unidata.ucar.edu/packages/netcdf/},
649     }
650    
651    
652 heimbach 1.1 @Article{res-eta:98,
653     author = {J.M. Restrepo and G.K. Leaf and A. Griewank},
654     year = 1998,
655 cnh 1.5 title = {Circumventing storage limitations in variational
656 heimbach 1.1 data assimilation studies},
657     journal = {SIAM J. Sci. Comput.},
658     volume = {19},
659     pages = {1586--1605},
660     }
661    
662     @Article{ros-eta:93,
663     author = {N. Rostaing and S. Dalmas and A. Galligo},
664     year = 1993,
665     title = {Automatic differentiation in Odyss{\'e}e},
666     journal = {Tellus},
667     volume = {45A},
668     pages = {558--568},
669     }
670    
671     @incollection{she-and:89,
672     author = {J. Sheinbaum and D.L.T. Anderson},
673     year = 1989,
674     title = {Assimilation of XBT data using a variational
675     technique},
676     booktitle = {Oceanic circulation models:
677     Combining data and dynamics},
678     pages = {257--285},
679     series = {NATO ASI Series},
680     volume = {C 284},
681     editor = {{D.L.T. Anderson and J. Willebrand}},
682     publisher = {Springer-Verlag},
683     address = {Berlin (Germany)},
684     }
685 cnh 1.6
686 heimbach 1.32 @article{utke-etal:08,
687     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},
688     Date-Modified = {2007-11-19 10:15:08 -0500},
689     Journal = {{ACM} Transactions on Mathematical Software},
690     Pages = {~},
691     Title = {OpenAD/F: A modular open source tool for automatic differentiation of Fortran codes},
692     Volume = {34(4)},
693     Year = {2008}}
694    
695 cnh 1.6 @Article{DaSilva94,
696     author = {A. da Silva and A. C. Young and S. Levitus},
697     year = 1994,
698     title = {Atlas of Surface Marine Data 1994, Volume 1: Algorithms and Procedures},
699     journal = {NOAA Atlas NESDIS},
700     volume = {6},
701     publisher = {U.S. Department of Commerce},
702     address = {Washington, D.C. (USA)},
703     note = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/},
704 cnh 1.28 url = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/},
705 cnh 1.6 }
706 heimbach 1.1
707 heimbach 1.32 @techreport{stam-etal:97,
708 heimbach 1.1 author = {D. Stammer and C. Wunsch and R. Giering and
709 cnh 1.6 Q. Zhang and J. Marotzke and J. Marshall and
710 heimbach 1.1 C. Hill},
711     year = 1997,
712     title = {The global ocean circulation estimated from
713     TOPEX/POSEIDON altimetry and a general circulation
714     model},
715     institution = {Center for Global Change Science, Massachusetts
716     Institute of Technology},
717     type = {Technical Report},
718     number = {49},
719     pages = {40 pp.},
720     address = {Cambridge (MA), USA},
721     }
722    
723 heimbach 1.32 @ARTICLE{stam-etal:02,
724 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},
725     title = {The global ocean circulation and transports during 1992 -- 1997, estimated from ocean observations and a general circulation model.},
726     journal = jgr,
727     year = {2002a},
728     volume = {107(C9)},
729     pages = {3118},
730     doi = {10.1029/2001JC000888},
731     }
732    
733 cnh 1.6
734     @Article{Stommel66,
735     author = {H. Stommel},
736     year = 1948,
737     title = {The western intensification of wind-driven ocean currents},
738     journal = {Trans. Am. Geophys. Union},
739     volume = {29},
740     pages = {206},
741 heimbach 1.1 }
742    
743     @Article{tal-cou:87,
744     author = {O. Talagrand and P. Courtier},
745     year = 1987,
746     title = {Variational assimilation of meteorological
747     observations with the adjoint vorticity equation.
748     I: Theory},
749     journal = qjrms,
750     volume = {113},
751     pages = {1311--1328},
752     }
753    
754     @Article{tal:97,
755     author = {O. Talagrand},
756     year = 1997,
757     title = {Assimilation of observations, an introduction},
758     journal = {J.~Meteor.~Soc.~Japan},
759     volume = {75},
760     pages = {191--209},
761     }
762    
763     @book{tar:87,
764     author = {A. Tarantola},
765     title = {Inverse Problem Theory: Methods for data fitting
766     and model parameter estimation},
767     year = 1987,
768     publisher = {Elsevier},
769     address = {Amsterdam},
770     pages = {629 pp.},
771     }
772    
773     @techreport{tha:87,
774     author = {W.C. Thacker},
775     year = 1987,
776     title = {Three lectures on fitting numerical models to
777     observations},
778     institution = {GKSS},
779     type = {Report},
780     number = {87/E/65},
781     pages = {64 pp.},
782     address = {Geesthacht (D)},
783     }
784    
785     @Article{tha-lon:88,
786     author = {W.C. Thacker and R.B. Long},
787     year = 1988,
788     title = {Fitting dynamics to data},
789     journal = jgr,
790     volume = {93, C2},
791     pages = {1,227--1,240},
792     }
793    
794     @Article{tha:88,
795     author = {W.C. Thacker},
796     year = 1988,
797     title = {Fitting models to inadequate data by enforcing
798     spatial and temporal smoothness},
799     journal = jgr,
800     volume = {93},
801     pages = {10,655--10,665},
802     }
803    
804     @Article{tha:89,
805     author = {W.C. Thacker},
806     year = 1989,
807     title = {The role of the Hessian matrix in fitting models
808     to measurements},
809     journal = jgr,
810     volume = {94, C5},
811     pages = {6,177--6,196},
812     }
813    
814     @Article{tha-rag:94,
815     author = {W.C. Thacker and R. Raghunath},
816     year = 1994,
817     title = {The rigid lid's contribution to the ill-conditioning
818     of oceanic inverse problems},
819     journal = jgr,
820     volume = {99, C5},
821     pages = {10,131--10,141},
822     }
823    
824     @Article{tzi-tha:89,
825     author = {E. Tziperman and W.C. Thacker},
826     year = {1989},
827     title = {An optimal control / adjoint equation approach
828     to studying the ocean general circulation},
829     journal = jpo,
830     volume = {19},
831     pages = {1471--1485},
832     }
833    
834     @Article{tzi-eta:92a,
835     author = {E. Tziperman and W.C. Thacker and R.B. Long and
836     S. Hwang},
837     year = {1992a},
838     title = {Oceanic data analysis using a general circulation
839     model. I: Simulations},
840     journal = jpo,
841     volume = {22},
842     pages = {1434--1457},
843     }
844    
845     @Article{tzi-eta:92b,
846     author = {E. Tziperman and W.C. Thacker and R.B. Long and
847     S. Hwang and S.R. Rintoul},
848     year = {1992b},
849     title = {Oceanic data analysis using a general circulation
850     model. I: A North Atlantic model},
851     journal = jpo,
852     volume = {22},
853     pages = {1458--1485},
854     }
855    
856     @book{wun:96,
857     author = {C. Wunsch},
858     title = {The ocean circulation inverse problem},
859     year = 1996,
860     publisher = cup,
861     address = {Cambridge (UK)},
862     pages = {442 pp.},
863     }
864    
865     @Article{zha-mar:99,
866     author = {K.Q. Zhang and J. Marotzke},
867     year = 1999,
868     title = {The importance of open-boundary estimation for an
869     Indian Ocean GCM-data synthesis},
870     journal = {J.~Marine Res.},
871     volume = {57},
872     pages = {305--334},
873     }
874 adcroft 1.2
875    
876     @InCollection{hill:95,
877     author = {Hill, C. and J. Marshall},
878     title = {Application of a Parallel Navier-Stokes Model to
879     Ocean Circulation in Parallel Computational Fluid
880     Dynamics},
881     booktitle = {Implementations and Results Using Parallel
882     Computers},
883     pages = {545-552},
884     publisher = {Elsevier Science B.V.: New York},
885     year = 1995,
886     editor = {A. Ecer, J. Periaux, N. Satofuka and S. Taylor}
887     }
888    
889    
890     @Article{marshall:97a,
891 adcroft 1.4 author = {Marshall, J. and C. Hill and L. Perelman and A. Adcroft},
892 adcroft 1.2 title = {Hydrostatic, quasi-hydrostatic, and nonhydrostatic ocean
893     modeling},
894 jmc 1.25 journal = jgr,
895 adcroft 1.2 year = 1997,
896     volume = 102,
897     number = {C3},
898 cnh 1.29 pages = {5733-5752},
899     url = {http://mitgcm.org/pdfs/96JC02775.pdf},
900 adcroft 1.2 }
901    
902     @Article{marshall:97b,
903 cnh 1.10 author = {Marshall, J. and A. Adcroft and C. Hill and L. Perelman and C. Heisey},
904 adcroft 1.2 title = {A finite-volume, incompressible Navier Stokes model for
905     studies of the ocean on parallel computers},
906 jmc 1.25 journal = jgr,
907 adcroft 1.2 year = 1997,
908     volume = 102,
909     number = {C3},
910 cnh 1.29 pages = {5753-5766},
911     url = {http://mitgcm.org/pdfs/96JC02776.pdf},
912 adcroft 1.2 }
913    
914     @Article{adcroft:97,
915 adcroft 1.4 author = {Adcroft, A.J. and Hill, C.N. and J. Marshall},
916 adcroft 1.2 title = {Representation of topography by shaved cells in a height
917     coordinate ocean model},
918 jmc 1.25 journal = mwr,
919 adcroft 1.2 year = 1997,
920     volume = 125,
921 cnh 1.29 pages = {2293-2315},
922     url = {http://mitgcm.org/pdfs/mwr_1997.pdf},
923     doi = {10.1175/1520-0493\%281997\%29125<2293:ROTBSC>2.0.CO;2},
924 adcroft 1.2 }
925    
926 jmc 1.19 @Article{adcroft:04a,
927     author = {Adcroft, A. and J.-M. Campin},
928 jmc 1.14 title = {Re-scaled height coordinates for accurate representation
929     of free-surface flows in ocean circulation models},
930     journal = om,
931     year = 2004,
932 jmc 1.19 volume = 7,
933 cnh 1.28 pages = {269-284},
934     doi = {10.1016/j.ocemod.2003.09.003},
935 jmc 1.19 }
936    
937     @Article{adcroft:04b,
938     author = {Adcroft, A. and J.-M. Campin and C. Hill and J. Marshall},
939     title = {Implementation of an Atmosphere-Ocean General Circulation Model
940     on the Expanded Spherical Cube},
941     journal = mwr,
942     year = 2004,
943     volume = 132,
944 cnh 1.29 pages = {2845-2863},
945     url = {http://mitgcm.org/pdfs/mwr_2004.pdf},
946     doi = {10.1175/MWR2823.1},
947 jmc 1.19 }
948    
949 jmc 1.33 @inproceedings{adcroft:04c,
950     author = {Adcroft, A. and C. Hill and J.-M. Campin and J. Marshall
951     and P. Heimbach},
952 jmc 1.35 title = {Overview of the Formulation and Numerics of the {MIT}GCM},
953 jmc 1.33 booktitle = {Proceedings of the ECMWF seminar series on Numerical Methods,
954     Recent developments in numerical methods for atmosphere and
955     ocean modelling},
956     year = 2004,
957     pages = {139-149},
958     url = {http://mitgcm.org/pdfs/ECMWF2004-Adcroft.pdf},
959     publisher = ecmwf
960     }
961    
962 jmc 1.19 @Article{marshall:04,
963     author = {Marshall, J. and A. Adcroft and J.-M. Campin and C. Hill and A. White},
964     title = {Atmosphere-Ocean Modeling Exploiting Fluid Isomorphisms},
965     journal = mwr,
966     year = 2004,
967     volume = 132,
968 cnh 1.29 pages = {2882-2894},
969     url = {http://mitgcm.org/pdfs/a_o_iso.pdf},
970     doi = {10.1175/MWR2835.1},
971 jmc 1.14 }
972    
973 adcroft 1.2 @Article{visbeck:97,
974     author = {Visbeck, M., J. Marshall, T. Haine, and M. Spall},
975     title = {Specification of eddy transfer coefficients in
976     coarse-resolution ocean circulation models},
977 jmc 1.25 journal = jpo,
978 adcroft 1.2 year = 1997,
979     volume = 27,
980     number = 3,
981     pages = {381-402}
982     }
983    
984     @Article{shaw:98,
985     author = {Shaw; A. Arvind, Cho, K.-C., Hill, C., Johnson, R.P.
986     and Marshall, J.},
987     title = {A comparison of implicitly parallel multi-threaded and
988     data-parallel implementations of an ocean model based
989     on the Navier-Stokes equations},
990     journal = {J. of Parallel and Distributed Computing},
991     year = 1998,
992     volume = 48,
993     number = 1,
994     pages = {1-51}
995     }
996    
997     @Article{mjn:99,
998     author = {Marshall, J., Jamous, D and J. Nilsson},
999     title = {Reconciling `thermodynamic' and `dynamic' methods of
1000     computation of water-mass transformation rates},
1001     journal = {DSR},
1002     year = 1999,
1003     volume = 46,
1004     pages = {545-572}
1005     }
1006    
1007     @Article{ms:99,
1008     author = {Marshall, J and F. Schott},
1009     title = {Open ocean deep convection: observations, models and theory},
1010     journal = {Rev. Geophys.},
1011     year = 1999,
1012     volume = 37,
1013     number = 1,
1014     pages = {1-64}
1015     }
1016    
1017     @Article{adcroft:99,
1018     author = {Adcroft, A., Hill C. and J. Marshall},
1019     title = {A new treatment of the Coriolis terms in C-grid models
1020     at both high and low resolutions},
1021 jmc 1.25 journal = mwr,
1022 adcroft 1.2 year = 1999,
1023     volume = 127,
1024 cnh 1.29 pages = {1928-1936},
1025     url = {http://mitgcm.org/pdfs/mwr_1999.pdf},
1026     doi = {10.1175/1520-0493\%281999\%29127<1928:ANTOTC>2.0.CO;2},
1027 adcroft 1.2 }
1028    
1029     @InProceedings{hill:99,
1030     author = {Chris Hill, Alistair Adcroft, Daniel Jamous and John Marshall},
1031     title = {A Strategy for Terascale Climate Modeling},
1032 cnh 1.8 booktitle = {In Proceedings of the Eighth ECMWF Workshop on the Use of Parallel Processors in Meteorology},
1033 cnh 1.9 year = 1999,
1034     pages = {406-425},
1035     publisher = {World Scientific},
1036 adcroft 1.2 }
1037    
1038     @Article{wardle:00,
1039     author = {Wardle R. and Marshall J.},
1040     title = {Representation of eddies in primitive equation models by a PV flux},
1041 jmc 1.25 journal = jpo,
1042 adcroft 1.2 year = 2000,
1043     volume = 30,
1044     number = 10,
1045     pages = {2481-2503}
1046     }
1047    
1048     @Article{ac:02,
1049     author = {Adcroft, A. and J.-M. Campin},
1050     title = {Comparison of finite volume schemes and direct-space-time
1051     methods for ocean circulation models},
1052 jmc 1.14 journal = om,
1053 adcroft 1.2 year = 2002,
1054     note = {in preparation}
1055     }
1056    
1057     @Article{adcroft:02,
1058 jmc 1.25 author = {Adcroft, A., et~al.},
1059 adcroft 1.2 title = {Energy conversion in discrete numerical models},
1060 jmc 1.14 journal = om,
1061 adcroft 1.2 year = 2002,
1062     note = {in preparation}
1063     }
1064    
1065     @InCollection{arakawa:77,
1066     author = {Arakawa, A. and Lamb, V.},
1067     title = {Computational Design of the Basic Dynamical Processes of
1068     the UCLA General Circulation Model},
1069     booktitle = {Methods in Computational Physics},
1070     pages = {174-267},
1071     publisher = {Academic Press},
1072     year = 1977,
1073     volume = 17
1074     }
1075    
1076 jmc 1.24 @Article{miller_white:84,
1077     author = {Miller, M. J. and White, A. A.},
1078     title = {On the non-hydrostatic equations in pressure
1079     and sigma coordiantes},
1080 jmc 1.25 journal = qjrms,
1081 jmc 1.24 year = 1984,
1082     volume = 110,
1083     pages = {515-533}
1084     }
1085    
1086     @Article{white:89,
1087     author = {White, A. A.},
1088     title = {An extended version of a nonhydrostatic, pressure coordiante model},
1089 jmc 1.25 journal = qjrms,
1090 jmc 1.24 year = 1989,
1091     volume = 115,
1092     pages = {1243-1251}
1093     }
1094    
1095 adcroft 1.2 @Article{adcroft:98,
1096     author = {Adcroft, A. and Marshall, D.},
1097 adcroft 1.3 title = {How slippery are piecewise-constant coastlines in numerical
1098     ocean models?},
1099 adcroft 1.2 journal = {Tellus},
1100 adcroft 1.3 year = 1998,
1101     volume = 50,
1102     number = 1,
1103     pages = {95-108}
1104     }
1105    
1106     @PhdThesis{adcroft:95,
1107     author = {Adcroft, A.},
1108     title = {Numerical Algorithms for use in a Dynamical Model of the
1109     Ocean},
1110     school = {Imperial College, London},
1111     year = 1995
1112     }
1113    
1114     @Article{griffies:00,
1115     author = {Griffies, S.,M. and Hallberg, R.,W.},
1116     title = {Biharmonic friction with a Smagorinsky-like viscosity for
1117     use in large-scale eddy-permitting ocean models},
1118 jmc 1.25 journal = mwr,
1119 adcroft 1.3 year = 2000,
1120     volume = 128,
1121     number = 8,
1122     pages = {2935-2946}
1123     }
1124    
1125     @Article{wajsowicz:93,
1126     author = {Wajsowicz, R.},
1127     title = {A CONSISTENT FORMULATION OF THE ANISOTROPIC STRESS TENSOR
1128     FOR USE IN MODELS OF THE LARGE-SCALE OCEAN CIRCULATION},
1129 jmc 1.25 journal = jcp,
1130 adcroft 1.3 year = 1993,
1131     volume = 105,
1132     number = 2,
1133     pages = {333-338}
1134     }
1135    
1136     @Article{campin:02,
1137 jmc 1.14 author = {Campin, J.-M. and A. Adcroft and C. Hill and J. Marshall},
1138 adcroft 1.3 title = {Conservation of properties in a free-surface model},
1139 jmc 1.14 journal = om,
1140     year = 2004,
1141     volume = 6,
1142     pages = {221-244}
1143 adcroft 1.4 }
1144    
1145     @Article{dm:95,
1146     author = {Danabasoglu, G. and McWilliams J.C.},
1147     title = {Sensitivity of the global ocean circulation to parameterizations of mesoscale tracer transports},
1148 jmc 1.25 journal = jclim,
1149 adcroft 1.4 year = 1995,
1150     volume = 8,
1151     number = 12,
1152     pages = {2967-2987}
1153     }
1154    
1155     @Article{ldd:97,
1156     author = {Large, W.G. and Danabasoglu, G. and Doney, S.C. and McWilliams, J.C.},
1157     title = {Sensitivity to surface forcing and boundary layer mixing in a global ocean model: Annual-mean climatology},
1158 jmc 1.25 journal = jpo,
1159 adcroft 1.4 year = 1997,
1160     volume = 27,
1161     number = 11,
1162     pages = {2418-2447}
1163     }
1164    
1165     @Article{gkw:99,
1166     author = {Gerdes R. and Koberle C. and Beckmann A. and Herrmann P. and Willebrand J.},
1167     title = {Mechanisms for spreading of Mediterranean water in
1168     coarse-resolution numerical models},
1169 jmc 1.25 journal = jpo,
1170 adcroft 1.4 year = 1999,
1171     volume = 29,
1172     number = 8,
1173     pages = {1682-1700}
1174     }
1175    
1176 jmc 1.17 @incollection{roe:85,
1177     author = {P.L. Roe},
1178     year = 1985,
1179     title = {Some contributions to the modelling of discontinuous flows},
1180     booktitle = {Large-Scale Computations in Fluid Mechanics},
1181     series = {Lectures in Applied Mathematics},
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1302 edhill 1.15 TITLE = "A Dynamic Thermodynamic Sea Ice Model",
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1311 edhill 1.15 TITLE = "Modeling pack ice as a cavitating fluid",
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1385     institution = {NCAR},
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1388     OPTtype = {},
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