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A couple of references.

1 heimbach 1.1 @string{arfm = {Annu.~Rev.~Fluid Mech.}}
2     @string{bams = {Bull.~Am.~Met.~Soc.}}
3     @string{blm = {Bound.~Layer~Meteorol.}}
4 jmc 1.14 @string{climd = {Clim.~Dynamics}}
5 heimbach 1.1 @string{jgr = {J.~Geophys.~Res.}}
6     @string{ijrs = {Int.~J.~Remote Sensing}}
7     @string{jas = {J.~Atmos.~Sci.}}
8 jmc 1.25 @string{jam = {J.~Appl.~Meteor.}}
9 heimbach 1.1 @string{jpo = {J.~Phys.~Oceanogr.}}
10     @string{jclim = {J.~Clim.}}
11 jmc 1.25 @string{jcp = {J.~Comput.~Phys.}}
12 heimbach 1.1 @string{ieee = {IEEE Trans.~Geosci. Remote Sensing}}
13     @string{jfm = {J.~Fluid Mech.}}
14     @string{jaot = {J.~Atmos.~Ocean.~Technol.}}
15     @string{jms = {J.~Mar.~Sys.}}
16 jmc 1.14 @string{om = {Ocean Modelling}}
17 heimbach 1.1 @string{gaos = {Global Atmos.~Ocean System}}
18     @string{grl = {Geophys.~Res.~Lett.}}
19     @string{dsr = {Deep Sea Res.}}
20     @string{dao = {Dyn.~Atmos.~Oceans}}
21     @string{mwr = {Mon.~Wea.~Rev.}}
22     @string{qjrms = {{Q.~J.~R.~Meteorol.~Soc.}}}
23     @string{tel = {Tellus}}
24     @string{cup = {Cambridge University Press}}
25     @string{esapub = {ESA Publications Division, ESTEC, Noordwijk (NL)}}
26     @string{ifremer = {IFREMER/CERSAT}}
27     @string{igarss = {IEEE Press, Piscataway, N.J., USA}}
28     @string{dnmi = {The Norwegian Meteorological Institute (DNMI)}}
29     @string{dkrz = {Deutsches Klimarechenzentrum (DKRZ)}}
30     @string{mpi = {MPI f\"ur Meteorologie}}
31     @string{ecmwf = {ECMWF}}
32     @string{estec = {European Space Research and Technology Centre
33     (ESTEC)}}
34     @string{esa = {European Space Agency (ESA)}}
35    
36     @Article{bis-eta:92,
37     author = {C.H. Bishof and G.F. Corliss and L. Green and
38     A. Griewank and K. Haigler and P. Newman},
39     year = 1992,
40     title = {Automatic differentiation of advanced GFD codes
41     for multidisciplinary design},
42     journal = {Journal on Computing Systems in Engineering},
43     volume = {3},
44     pages = {625--638},
45     }
46    
47     @incollection{bis:94,
48     author = {C.H. Bishof},
49     year = 1994,
50     title = {Automatic differentiation, tangent linear models
51     and pseudo-adjoints},
52     booktitle = {High Performance Computing in the Geosciences},
53     series = {Series C: Mathematical and Physical Sciences},
54     pages = {59--80},
55     editor = {F.X. {Le Dimet}},
56     publisher = {Kluwer},
57     address = {Dordrecht, NL},
58     }
59    
60     @techreport{bis-eta:94,
61     author = {C. Bishof and A. Carle and P. Khademi and
62     A. Maurer},
63     year = 1994,
64     title = {The ADIFOR 2.0 system for the automatic
65     differentiation of FORTRAN 77 programs},
66     institution = {Argonne National Laboratory, Mathematics and
67     Computer Science Division},
68     type = {Argonne Preprint},
69     number = {ANL-MCS-P981-1194},
70     address = {ANL; 9700 South Cass Ave.;
71     Argonne (ILL), 90439; USA},
72     note = {http://www.mcs.anl.gov/autodiff/},
73     }
74 cnh 1.29
75     @ARTICLE{bugi-hill:06,
76     author = {V. Bugnion and C. Hill},
77     title = {Equilibration mechanisms in an adjoint ocean general
78     circulation model},
79     journal = {Ocean Dynamics},
80     year = {2006},
81     volume = {56},
82     number = {1},
83     pages = {51-61},
84     doi = {10.1007/s10236-005-0052-z},
85     }
86 heimbach 1.1
87     @techreport{bis-roh:97,
88     author = {C. Bishof and L. Roh},
89     year = 1997,
90     title = {ADIC: An extensible automatic differentiation tool
91     for ANSI-C},
92     institution = {Argonne National Laboratory, Mathematics and
93     Computer Science Division},
94     type = {Argonne Preprint},
95     number = {ANL-MCS-P626-1196},
96     address = {ANL; 9700 South Cass Ave.;
97     Argonne (ILL), 90439; USA},
98     note = {http://www.mcs.anl.gov/autodiff/},
99     }
100    
101     @Article{cou-tal:87,
102     author = {P. Courtier and O. Talagrand},
103     year = 1987,
104     title = {Variational assimilation of meteorological
105     observations with the adjoint vorticity equation.
106     II: Numerical results},
107     journal = qjrms,
108     volume = {113},
109     pages = {1329--1347},
110     }
111    
112     @Article{cou-tal:90,
113     author = {P. Courtier and O. Talagrand},
114     year = 1990,
115     title = {Variational assimilation of meteorological
116     observations with direct and adjoint shallow-water
117     equations},
118     journal = tel,
119     volume = {42A},
120     pages = {531--549},
121     }
122    
123     @Article{cou-eta:94,
124     author = {P. Courtier and J.-N. Th{\'e}paut and
125     A. Hollingsworth},
126     year = 1994,
127     title = {A strategy for operational implementation of
128     4-D-VAR using an incremental approach},
129     journal = qjrms,
130     volume = {120},
131     pages = {1367--1387},
132     }
133 cnh 1.29
134 jmc 1.33 @ARTICLE{durr:91,
135     author = {Dale R. Durran},
136     title = {The Third-Order Adams-Bashforth Method: An Attractive Alternative
137     to Leapfrog Time Differencing},
138     journal = mwr,
139     year = {1991},
140     volume = {119},
141     pages = {702-720},
142     }
143    
144    
145 cnh 1.29 @ARTICLE{dutk-etal:06,
146     author = {S. Dutkiewicz and M.J. Follows and P. Heimbach and J. Marshall},
147     title = {Controls on ocean productivity and air-sea carbon flux:
148     An adjoint model sensitivity study},
149     journal = grl,
150     year = {2006},
151     volume = {33},
152     pages = {L02603},
153     doi = {10.1029/2005GL024987},
154     }
155 heimbach 1.1
156     @Article{err:97,
157     author = {R.M. Errico},
158     year = 1997,
159     title = {What is an adjoint model},
160     journal = bams,
161     volume = {78},
162     pages = {2577--2591},
163     }
164    
165     @Article{far-moo:92,
166     author = {B.F. Farrell and A.M. Moore},
167     year = {1992},
168     title = {An adjoint method for obtaining the most rapidly
169     growing perturbation to oceanic flows},
170     journal = jpo,
171     volume = {22},
172     pages = {338--349},
173     }
174    
175     @Article{far-ioa:96a,
176     author = {B.F. Farrell and P. Ioannou},
177     year = {1996a},
178     title = {Generalized stability theory. Part I:
179     Autonomous operators},
180     journal = jas,
181     volume = {53},
182     pages = {2025--2040},
183     }
184    
185     @Article{far-ioa:96b,
186     author = {B.F. Farrell and P. Ioannou},
187     year = {1996b},
188     title = {Generalized stability theory. Part I:
189     Nonautonomous operators},
190     journal = jas,
191     volume = {53},
192     pages = {2041--2053},
193     }
194    
195     @techreport{fau-pap:98,
196     author = {C. Faure and Y. Papegay},
197     year = 1998,
198     title = {Odyss{\'e}e User's Guide. Version 1.7},
199     institution = {Institut National de Recherche en Informatique
200     et en Automatique},
201     type = {Rapport Technique},
202     number = {0224},
203     address = {INRIA; 2004, route des Luciolis, B.P. 93;
204     06902 Sophia Antipolis Cedex; France},
205     note = {http://www-sop.inria.fr/safir/SAM/Odyssee/odyssee.html},
206     }
207    
208     @Article{fau:00,
209     author = {C. Faure},
210     year = {2000},
211     title = {Adjoining strategies for multi-layered programs},
212     journal = {Optimisation Methods and Software},
213     note = {in press},
214     }
215    
216 dfer 1.34 @Article{fer-eta:05,
217     author = {D. Ferreira and J. Marshall and P. Heimbach},
218     year = 2005,
219     title = {Estimating Eddy Stresses by Fitting Dynamics to Observations
220     using a Residual-Mean Ocean Circulation Model and Its Adjoint},
221     journal = jpo,
222     volume = {35},
223     pages = {1891--1910},
224     }
225    
226 heimbach 1.1 @Article{gen-mcw:90,
227     author = {P.R. Gent and J.C. McWilliams},
228     year = 1990,
229     title = {Isopycnal mixing in ocean circulation models},
230     journal = jpo,
231     volume = {20},
232     pages = {150--155},
233     }
234    
235     @Article{gen-eta:95,
236     author = {P.R. Gent and J. Willebrand and T.J. McDougall
237     and J.C. McWilliams},
238     year = 1995,
239     title = {Parameterizing eddy-induced tracer transports in
240     ocean circulation models},
241     journal = jpo,
242     volume = {25},
243     pages = {463--474},
244     }
245    
246     @Article{gie-kam:98,
247     author = {R. Giering and T. Kaminski},
248     year = 1998,
249     title = {Recipes for adjoint code construction},
250     journal = {ACM Transactions on Mathematical Software},
251     volume = 24,
252     pages = {437--474},
253     }
254    
255     @techreport{gie:99,
256     author = {R. Giering},
257     year = 1999,
258     title = {Tangent linear and Adjoint Model Compiler.
259     Users manual 1.4 (TAMC Version 5.2)},
260     institution = {Massachusetts Institute of Technology},
261     type = {Report},
262     number = {~},
263     address = {MIT/EAPS; 77 Massachusetts Ave.; Cambridge (MA)
264     02139; USA},
265     note = {http://puddle.mit.edu/$\sim$ralf/tamc/tamc.html},
266     }
267    
268     @incollection{gie:00,
269     author = {R. Giering},
270     editor = {P. Kasibhatla and M. Heimann and P. Rayner and
271     N. Mahowald and R.G. Prinn and D.E. Hartley},
272     year = 2000,
273     booktitle = {Inverse methods in global biogeochemical cycles},
274     title = {Tangent linear and adjoint biogeochemical models},
275     publisher = {American Geophysical Union},
276     series = {Geophysical Monograph},
277     volume = {114},
278     address = {Washington, DC},
279     pages = {33--48},
280     }
281    
282     @Article{gil-lem:89,
283     author = {J.C. Gilbert and C. Lemar\'echal},
284     year = 1989,
285     title = {Some numerical experiments with variable-storage
286     quasi-Newton algorithms},
287     journal = {Math. Programming},
288     volume = {45},
289     pages = {407--435},
290     }
291    
292     @book{gil-eta:81,
293     author = {P.E. Gill and W. Murray and M.H. Wright},
294     title = {Practical optimization},
295     year = 1981,
296     publisher = {Academic Press},
297     address = {London},
298     pages = {401 pp.},
299     }
300    
301 heimbach 1.11 @incollection{gri:89,
302     author = {A. Griewank},
303     year = 1989,
304     title = {On automatic differentiation},
305     booktitle = {Mathematical Programming: Recent Developments and
306     Applications},
307     pages = {83--108},
308     editor = {M. Iri and K. Tanabe},
309     publisher = {Kluwer},
310     address = {Dordrecht, NL},
311     }
312    
313     @Article{gri:92,
314     author = {A.~Griewank},
315     title = {Achieving logarithmic growth of temporal and spatial
316     complexity in reverse {A}utomatic {D}ifferentiation},
317     journal = {Optimization Methods and Software},
318     year = {1992},
319     volume = {1},
320     pages = {35--54}
321     }
322    
323 heimbach 1.1 @book{gri:00,
324     author = {A. Griewank},
325     title = {Evaluating Derivatives. Principles and Techniques
326     of Algorithmic Differentiation},
327     year = 2000,
328     series = {Frontiers in Applied Mathematics},
329     volume = {19},
330     publisher = {SIAM},
331     address = {Philadelphia},
332     pages = {369 pp.},
333     }
334    
335     @Article{hal-eta:82,
336     author = {M.C.G. Hall and D.G. Caccuci and M.E. Schlesinger},
337     year = 1982,
338     title = {Sensitivity analysis of a radiative-convective
339     model by the adjoint method},
340     journal = jas,
341     volume = {39},
342     pages = {2038--3050},
343     }
344 cnh 1.6
345     @Article{Haney,
346     author = {R.L. Haney},
347     title = {Surface thermal boundary conditions for ocean
348     circulation models},
349     journal = jpo,
350     year = 1971,
351     volume = 1,
352     pages = {241--248}
353     }
354 heimbach 1.1
355 cnh 1.16 @Article{held-suar:94,
356     author = {I.M. Held and M.J. Suarez},
357     year = {1994},
358     title = {A proposal for the intercomparison of the dynamical cores of atmospheric general circulation models},
359     journal = {Bulletin of the American Meteorological Society},
360     volume = {75(10)},
361     pages = {1825-1830}
362     }
363    
364 heimbach 1.1 @Article{hil-eta:01,
365     author = {C. Hill and M. Follows and V. Bugnion and
366     J. Marshall},
367 cnh 1.10 year = {2002},
368 heimbach 1.1 title = {Spatial and Temporal Impacts of ocean general
369     circulation on carbon sequestration},
370 cnh 1.6 journal = {Global Biogeochemical Cycles},
371 heimbach 1.1 note = {submitted},
372     }
373 cnh 1.6
374 edhill 1.15 @ARTICLE{hib80,
375     AUTHOR = "W. D. {Hibler, III}",
376     TITLE = "Modeling a Variable Thickness Sea Ice Cover",
377     JOURNAL = mwr,
378     YEAR = 1980,
379     VOLUME = 1,
380     PAGES = "1943-1973"
381     }
382    
383 cnh 1.6 @Article{Holland75,
384     author = {W.R. Holland and L. B. Lin},
385     year = {1975a},
386     title = {On the origin of mesoscale eddies and their contribution
387     to the general circulation of the ocean. I. A preliminary
388     numerical experiment},
389     journal = jpo,
390     volume = {5},
391     pages = {642-657}
392     }
393    
394     @Article{hol-lin:75b,
395     author = {W.R. Holland and L. B. Lin},
396     year = {1975b},
397     title = {On the origin of mesoscale eddies and their contribution
398     to the general circulation of the ocean. II. A parameter
399     study},
400     journal = jpo,
401     volume = {5},
402     pages = {658-669}
403     }
404    
405 jmc 1.31 @Article{jam-oze:86,
406     author = {B.M. Jamart and J. Ozer},
407     year = {1986},
408     title = {Numerical boundary layers and spurious residual flows},
409     journal = jgr,
410     volume = {91},
411     pages = {10,621-10,631}
412     }
413    
414 heimbach 1.1 @book{kas-eta:00,
415     author = {P. Kasibhatla and M. Heimann and P. Rayner and
416     N. Mahowald and R.G. Prinn and D.E. Hartley},
417     year = 2000,
418     title = {Inverse methods in global biogeochemical cycles},
419     publisher = {American Geophysical Union},
420     series = {Geophysical Monograph},
421     volume = {114},
422     address = {Washington, DC},
423     pages = {324 pp.},
424     }
425    
426     @Article{lar-eta:94,
427     author = {W.G. Large and J.C. McWilliams and S.C. Doney},
428     year = 1994,
429     title = {Oceanic vertical mixing: A review and a model
430     with nonlocal boundary layer parameterization},
431     journal = {Rev.~Geophys.},
432     volume = {32},
433     pages = {363--403},
434     }
435    
436     @Article{lar-eta:97,
437     author = {W.G. Large and G. Danabasoglu and S.C. Doney
438     and J.C. McWilliams},
439     year = 1997,
440     title = {Sensitivity to surface forcing and boundary layer
441     mixing in a global ocean model: annual-mean
442     climatology},
443     journal = jpo,
444     volume = {27},
445     pages = {2418--2447},
446     }
447    
448     @Article{led-tal:86,
449     author = {F.-X. {Le Dimet} and O. Talagrand},
450     year = 1986,
451     title = {Variational algorithms for analysis and
452     assimilation of meteorological observations:
453     theoretical aspects},
454     journal = tel,
455     volume = {38A},
456     pages = {97--110},
457     }
458 cnh 1.6
459     @TechReport{lev:94a,
460     author = {S. Levitus and T.P.Boyer},
461     title = {{World Ocean Atlas 1994 Volume 3: Salinity}},
462     institution = {NOAA Atlas NESDIS 3},
463     year = 1994,
464     OPTkey = {},
465     OPTtype = {},
466     OPTnumber = {},
467     OPTaddress = {U.S. Department of Commerce, Washington D.C.},
468     OPTmonth = {},
469     OPTnote = {},
470     OPTannote = {}
471     }
472    
473    
474     @TechReport{Levitus94,
475     author = {S. Levitus and T.P.Boyer},
476     title = {{World Ocean Atlas 1994 Volume 4: Temperature}},
477     institution = {NOAA Atlas NESDIS 4},
478     year = 1994,
479     OPTkey = {},
480     OPTtype = {},
481     OPTnumber = {},
482     OPTaddress = {U.S. Department of Commerce, Washington D.C.},
483     OPTmonth = {},
484     OPTnote = {},
485     OPTannote = {}
486     }
487    
488 heimbach 1.1
489     @Article{lew-der:85,
490     author = {J. Lewis and J. Derber},
491     year = {1985},
492     title = {The use of adjoint equations to solve a variational
493     adjustment problem with advective constraints},
494     journal = {Tellus},
495     volume = {37A},
496     pages = {309--322},
497     }
498    
499     @techreport{lon:88,
500     author = {R.B. Long},
501     year = 1988,
502     title = {Notes on assimilating observations into
503     numerical models},
504     institution = {Delft Hydraulics},
505     type = {Report},
506     number = {~},
507     pages = {38 pp.},
508     address = {Delft (NL)},
509     }
510 cnh 1.29
511     @ARTICLE{losc-heim:06,
512     author = {M. Losch and P. Heimbach},
513     title = {Adjoint sensitivity of an ocean general circulation model
514     to bottom topography},
515     journal = jpo,
516     year = {2006},
517     volume = {{in press}},
518     url = {http://mitgcm.org/pdfs/Los2006a.pdf},
519     }
520    
521 heimbach 1.1
522     @Article{maro-wun:93,
523     author = {J. Marotzke and C. Wunsch},
524     year = 1993,
525     title = {Finding the steady state of a general circulation
526     model through data assimilation:
527     Application to the North Atlantic Ocean},
528     journal = jgr,
529     volume = {98, C11},
530     pages = {20,149--20,167},
531     }
532    
533     @Article{maro-eta:99,
534     author = {J. Marotzke and R. Giering and K.Q. Zhang and
535     D. Stammer and C. Hill and T. Lee},
536     year = 1999,
537     title = {Construction of the adjoint MIT ocean general
538     circulation model and application to Atlantic heat
539     transport variability},
540     journal = jgr,
541     volume = {104, C12},
542     pages = {29,529--29,547},
543     }
544    
545     @Article{mars-eta:97a,
546     author = {J. Marshall and C. Hill and L. Perelman and
547     A. Adcroft},
548     year = {1997a},
549     title = {Hydrostatic, quasi-hydrostatic and
550     nonhydrostatic ocean modeling},
551     journal = jgr,
552     volume = {102, C3},
553     pages = {5,733--5,752},
554     }
555    
556     @Article{mars-eta:97b,
557     author = {J. Marshall and A. Adcroft and C. Hill and
558     L. Perelman and C. Heisey},
559     year = {1997b},
560     title = {Hydrostatic, quasi-hydrostatic and
561     nonhydrostatic ocean modeling},
562     journal = jgr,
563     volume = {102, C3},
564     pages = {5,753--5,766},
565     }
566    
567 jmc 1.33 @Article{mars-eta:98,
568 heimbach 1.1 author = {J. Marshall and H. Jones and C. Hill},
569     year = 1998,
570     title = {Efficient ocean modeling using
571     non-hydrostatic algorithms},
572     journal = jms,
573     volume = {18},
574     pages = {115--134},
575 cnh 1.29 url = {http://mitgcm.org/pdfs/journal_of_marine_systems_1998.pdf},
576     doi = {10.1016/S0924-7963\%2898\%2900008-6},
577 heimbach 1.1 }
578    
579     @Article{mcw:96,
580     author = {J. McWilliams},
581     year = 1996,
582     title = {Modeling the oceanic general circulation},
583     journal = arfm,
584     volume = {28},
585     pages = {215--248},
586     }
587 edhill 1.13
588     %% Rew, R. K., G. P. Davis, S. Emmerson, and H. Davies
589     %% NetCDF User's Guide for C, An Interface for Data Access, Version 3, April 1997.
590     %% (Available from Unidata or in PostScript form by anonymous FTP from
591     %% ftp://ftp.unidata.ucar.edu/pub/netcdf/guidec.ps.Z). There is also
592     %% a hypertext version of the User's Guide available at
593     %% http://www.unidata.ucar.edu/packages/netcdf/guidec. NetCDF User's
594     %% Guide for Fortran 90 and NetCDF User's Guide for Fortran 77 are
595     %% also available.
596    
597 heimbach 1.32 @incollection{naum-etal:06,
598     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},
599     Booktitle = {European Conference on Computational Fluid Dynamics ECCOMAS CFD 2006},
600     Editor = {{P. Wesseling, E. O~nate and J. Periaux}},
601     Pages = {~},
602     Publisher = {TU Delft},
603     Title = {Adjoint code by source transformation with OpenAD/F},
604     Year = {2006}}
605    
606 edhill 1.13 @TechReport{rew:97,
607     author = {R. K. Rew and G. P. Davis and S. Emmerson and H. Davies},
608     title = {{NetCDF User's Guide for C, FORTRAN 77, and FORTRAN 90},
609     An Interface for Data Access, Version 3},
610     institution = {Unidata Program Center},
611     type = {Report},
612     address = {Boulder, Colorado},
613     year = 1997,
614     note = {http://www.unidata.ucar.edu/packages/netcdf/},
615     }
616    
617    
618 heimbach 1.1 @Article{res-eta:98,
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620     year = 1998,
621 cnh 1.5 title = {Circumventing storage limitations in variational
622 heimbach 1.1 data assimilation studies},
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624     volume = {19},
625     pages = {1586--1605},
626     }
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633     volume = {45A},
634     pages = {558--568},
635     }
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637     @incollection{she-and:89,
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639     year = 1989,
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642     booktitle = {Oceanic circulation models:
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644     pages = {257--285},
645     series = {NATO ASI Series},
646     volume = {C 284},
647     editor = {{D.L.T. Anderson and J. Willebrand}},
648     publisher = {Springer-Verlag},
649     address = {Berlin (Germany)},
650     }
651 cnh 1.6
652 heimbach 1.32 @article{utke-etal:08,
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654     Date-Modified = {2007-11-19 10:15:08 -0500},
655     Journal = {{ACM} Transactions on Mathematical Software},
656     Pages = {~},
657     Title = {OpenAD/F: A modular open source tool for automatic differentiation of Fortran codes},
658     Volume = {34(4)},
659     Year = {2008}}
660    
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663     year = 1994,
664     title = {Atlas of Surface Marine Data 1994, Volume 1: Algorithms and Procedures},
665     journal = {NOAA Atlas NESDIS},
666     volume = {6},
667     publisher = {U.S. Department of Commerce},
668     address = {Washington, D.C. (USA)},
669     note = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/},
670 cnh 1.28 url = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/},
671 cnh 1.6 }
672 heimbach 1.1
673 heimbach 1.32 @techreport{stam-etal:97,
674 heimbach 1.1 author = {D. Stammer and C. Wunsch and R. Giering and
675 cnh 1.6 Q. Zhang and J. Marotzke and J. Marshall and
676 heimbach 1.1 C. Hill},
677     year = 1997,
678     title = {The global ocean circulation estimated from
679     TOPEX/POSEIDON altimetry and a general circulation
680     model},
681     institution = {Center for Global Change Science, Massachusetts
682     Institute of Technology},
683     type = {Technical Report},
684     number = {49},
685     pages = {40 pp.},
686     address = {Cambridge (MA), USA},
687     }
688    
689 heimbach 1.32 @ARTICLE{stam-etal:02,
690 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},
691     title = {The global ocean circulation and transports during 1992 -- 1997, estimated from ocean observations and a general circulation model.},
692     journal = jgr,
693     year = {2002a},
694     volume = {107(C9)},
695     pages = {3118},
696     doi = {10.1029/2001JC000888},
697     }
698    
699 cnh 1.6
700     @Article{Stommel66,
701     author = {H. Stommel},
702     year = 1948,
703     title = {The western intensification of wind-driven ocean currents},
704     journal = {Trans. Am. Geophys. Union},
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713     observations with the adjoint vorticity equation.
714     I: Theory},
715     journal = qjrms,
716     volume = {113},
717     pages = {1311--1328},
718     }
719    
720     @Article{tal:97,
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722     year = 1997,
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725     volume = {75},
726     pages = {191--209},
727     }
728    
729     @book{tar:87,
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732     and model parameter estimation},
733     year = 1987,
734     publisher = {Elsevier},
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737     }
738    
739     @techreport{tha:87,
740     author = {W.C. Thacker},
741     year = 1987,
742     title = {Three lectures on fitting numerical models to
743     observations},
744     institution = {GKSS},
745     type = {Report},
746     number = {87/E/65},
747     pages = {64 pp.},
748     address = {Geesthacht (D)},
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750    
751     @Article{tha-lon:88,
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753     year = 1988,
754     title = {Fitting dynamics to data},
755     journal = jgr,
756     volume = {93, C2},
757     pages = {1,227--1,240},
758     }
759    
760     @Article{tha:88,
761     author = {W.C. Thacker},
762     year = 1988,
763     title = {Fitting models to inadequate data by enforcing
764     spatial and temporal smoothness},
765     journal = jgr,
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769    
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774     to measurements},
775     journal = jgr,
776     volume = {94, C5},
777     pages = {6,177--6,196},
778     }
779    
780     @Article{tha-rag:94,
781     author = {W.C. Thacker and R. Raghunath},
782     year = 1994,
783     title = {The rigid lid's contribution to the ill-conditioning
784     of oceanic inverse problems},
785     journal = jgr,
786     volume = {99, C5},
787     pages = {10,131--10,141},
788     }
789    
790     @Article{tzi-tha:89,
791     author = {E. Tziperman and W.C. Thacker},
792     year = {1989},
793     title = {An optimal control / adjoint equation approach
794     to studying the ocean general circulation},
795     journal = jpo,
796     volume = {19},
797     pages = {1471--1485},
798     }
799    
800     @Article{tzi-eta:92a,
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802     S. Hwang},
803     year = {1992a},
804     title = {Oceanic data analysis using a general circulation
805     model. I: Simulations},
806     journal = jpo,
807     volume = {22},
808     pages = {1434--1457},
809     }
810    
811     @Article{tzi-eta:92b,
812     author = {E. Tziperman and W.C. Thacker and R.B. Long and
813     S. Hwang and S.R. Rintoul},
814     year = {1992b},
815     title = {Oceanic data analysis using a general circulation
816     model. I: A North Atlantic model},
817     journal = jpo,
818     volume = {22},
819     pages = {1458--1485},
820     }
821    
822     @book{wun:96,
823     author = {C. Wunsch},
824     title = {The ocean circulation inverse problem},
825     year = 1996,
826     publisher = cup,
827     address = {Cambridge (UK)},
828     pages = {442 pp.},
829     }
830    
831     @Article{zha-mar:99,
832     author = {K.Q. Zhang and J. Marotzke},
833     year = 1999,
834     title = {The importance of open-boundary estimation for an
835     Indian Ocean GCM-data synthesis},
836     journal = {J.~Marine Res.},
837     volume = {57},
838     pages = {305--334},
839     }
840 adcroft 1.2
841    
842     @InCollection{hill:95,
843     author = {Hill, C. and J. Marshall},
844     title = {Application of a Parallel Navier-Stokes Model to
845     Ocean Circulation in Parallel Computational Fluid
846     Dynamics},
847     booktitle = {Implementations and Results Using Parallel
848     Computers},
849     pages = {545-552},
850     publisher = {Elsevier Science B.V.: New York},
851     year = 1995,
852     editor = {A. Ecer, J. Periaux, N. Satofuka and S. Taylor}
853     }
854    
855    
856     @Article{marshall:97a,
857 adcroft 1.4 author = {Marshall, J. and C. Hill and L. Perelman and A. Adcroft},
858 adcroft 1.2 title = {Hydrostatic, quasi-hydrostatic, and nonhydrostatic ocean
859     modeling},
860 jmc 1.25 journal = jgr,
861 adcroft 1.2 year = 1997,
862     volume = 102,
863     number = {C3},
864 cnh 1.29 pages = {5733-5752},
865     url = {http://mitgcm.org/pdfs/96JC02775.pdf},
866 adcroft 1.2 }
867    
868     @Article{marshall:97b,
869 cnh 1.10 author = {Marshall, J. and A. Adcroft and C. Hill and L. Perelman and C. Heisey},
870 adcroft 1.2 title = {A finite-volume, incompressible Navier Stokes model for
871     studies of the ocean on parallel computers},
872 jmc 1.25 journal = jgr,
873 adcroft 1.2 year = 1997,
874     volume = 102,
875     number = {C3},
876 cnh 1.29 pages = {5753-5766},
877     url = {http://mitgcm.org/pdfs/96JC02776.pdf},
878 adcroft 1.2 }
879    
880     @Article{adcroft:97,
881 adcroft 1.4 author = {Adcroft, A.J. and Hill, C.N. and J. Marshall},
882 adcroft 1.2 title = {Representation of topography by shaved cells in a height
883     coordinate ocean model},
884 jmc 1.25 journal = mwr,
885 adcroft 1.2 year = 1997,
886     volume = 125,
887 cnh 1.29 pages = {2293-2315},
888     url = {http://mitgcm.org/pdfs/mwr_1997.pdf},
889     doi = {10.1175/1520-0493\%281997\%29125<2293:ROTBSC>2.0.CO;2},
890 adcroft 1.2 }
891    
892 jmc 1.19 @Article{adcroft:04a,
893     author = {Adcroft, A. and J.-M. Campin},
894 jmc 1.14 title = {Re-scaled height coordinates for accurate representation
895     of free-surface flows in ocean circulation models},
896     journal = om,
897     year = 2004,
898 jmc 1.19 volume = 7,
899 cnh 1.28 pages = {269-284},
900     doi = {10.1016/j.ocemod.2003.09.003},
901 jmc 1.19 }
902    
903     @Article{adcroft:04b,
904     author = {Adcroft, A. and J.-M. Campin and C. Hill and J. Marshall},
905     title = {Implementation of an Atmosphere-Ocean General Circulation Model
906     on the Expanded Spherical Cube},
907     journal = mwr,
908     year = 2004,
909     volume = 132,
910 cnh 1.29 pages = {2845-2863},
911     url = {http://mitgcm.org/pdfs/mwr_2004.pdf},
912     doi = {10.1175/MWR2823.1},
913 jmc 1.19 }
914    
915 jmc 1.33 @inproceedings{adcroft:04c,
916     author = {Adcroft, A. and C. Hill and J.-M. Campin and J. Marshall
917     and P. Heimbach},
918     title = {Overview of the Formulation and Numerics of the MIT GCM},
919     booktitle = {Proceedings of the ECMWF seminar series on Numerical Methods,
920     Recent developments in numerical methods for atmosphere and
921     ocean modelling},
922     year = 2004,
923     pages = {139-149},
924     url = {http://mitgcm.org/pdfs/ECMWF2004-Adcroft.pdf},
925     publisher = ecmwf
926     }
927    
928 jmc 1.19 @Article{marshall:04,
929     author = {Marshall, J. and A. Adcroft and J.-M. Campin and C. Hill and A. White},
930     title = {Atmosphere-Ocean Modeling Exploiting Fluid Isomorphisms},
931     journal = mwr,
932     year = 2004,
933     volume = 132,
934 cnh 1.29 pages = {2882-2894},
935     url = {http://mitgcm.org/pdfs/a_o_iso.pdf},
936     doi = {10.1175/MWR2835.1},
937 jmc 1.14 }
938    
939 adcroft 1.2 @Article{visbeck:97,
940     author = {Visbeck, M., J. Marshall, T. Haine, and M. Spall},
941     title = {Specification of eddy transfer coefficients in
942     coarse-resolution ocean circulation models},
943 jmc 1.25 journal = jpo,
944 adcroft 1.2 year = 1997,
945     volume = 27,
946     number = 3,
947     pages = {381-402}
948     }
949    
950     @Article{shaw:98,
951     author = {Shaw; A. Arvind, Cho, K.-C., Hill, C., Johnson, R.P.
952     and Marshall, J.},
953     title = {A comparison of implicitly parallel multi-threaded and
954     data-parallel implementations of an ocean model based
955     on the Navier-Stokes equations},
956     journal = {J. of Parallel and Distributed Computing},
957     year = 1998,
958     volume = 48,
959     number = 1,
960     pages = {1-51}
961     }
962    
963     @Article{mjn:99,
964     author = {Marshall, J., Jamous, D and J. Nilsson},
965     title = {Reconciling `thermodynamic' and `dynamic' methods of
966     computation of water-mass transformation rates},
967     journal = {DSR},
968     year = 1999,
969     volume = 46,
970     pages = {545-572}
971     }
972    
973     @Article{ms:99,
974     author = {Marshall, J and F. Schott},
975     title = {Open ocean deep convection: observations, models and theory},
976     journal = {Rev. Geophys.},
977     year = 1999,
978     volume = 37,
979     number = 1,
980     pages = {1-64}
981     }
982    
983     @Article{adcroft:99,
984     author = {Adcroft, A., Hill C. and J. Marshall},
985     title = {A new treatment of the Coriolis terms in C-grid models
986     at both high and low resolutions},
987 jmc 1.25 journal = mwr,
988 adcroft 1.2 year = 1999,
989     volume = 127,
990 cnh 1.29 pages = {1928-1936},
991     url = {http://mitgcm.org/pdfs/mwr_1999.pdf},
992     doi = {10.1175/1520-0493\%281999\%29127<1928:ANTOTC>2.0.CO;2},
993 adcroft 1.2 }
994    
995     @InProceedings{hill:99,
996     author = {Chris Hill, Alistair Adcroft, Daniel Jamous and John Marshall},
997     title = {A Strategy for Terascale Climate Modeling},
998 cnh 1.8 booktitle = {In Proceedings of the Eighth ECMWF Workshop on the Use of Parallel Processors in Meteorology},
999 cnh 1.9 year = 1999,
1000     pages = {406-425},
1001     publisher = {World Scientific},
1002 adcroft 1.2 }
1003    
1004     @Article{wardle:00,
1005     author = {Wardle R. and Marshall J.},
1006     title = {Representation of eddies in primitive equation models by a PV flux},
1007 jmc 1.25 journal = jpo,
1008 adcroft 1.2 year = 2000,
1009     volume = 30,
1010     number = 10,
1011     pages = {2481-2503}
1012     }
1013    
1014     @Article{ac:02,
1015     author = {Adcroft, A. and J.-M. Campin},
1016     title = {Comparison of finite volume schemes and direct-space-time
1017     methods for ocean circulation models},
1018 jmc 1.14 journal = om,
1019 adcroft 1.2 year = 2002,
1020     note = {in preparation}
1021     }
1022    
1023     @Article{adcroft:02,
1024 jmc 1.25 author = {Adcroft, A., et~al.},
1025 adcroft 1.2 title = {Energy conversion in discrete numerical models},
1026 jmc 1.14 journal = om,
1027 adcroft 1.2 year = 2002,
1028     note = {in preparation}
1029     }
1030    
1031     @InCollection{arakawa:77,
1032     author = {Arakawa, A. and Lamb, V.},
1033     title = {Computational Design of the Basic Dynamical Processes of
1034     the UCLA General Circulation Model},
1035     booktitle = {Methods in Computational Physics},
1036     pages = {174-267},
1037     publisher = {Academic Press},
1038     year = 1977,
1039     volume = 17
1040     }
1041    
1042 jmc 1.24 @Article{miller_white:84,
1043     author = {Miller, M. J. and White, A. A.},
1044     title = {On the non-hydrostatic equations in pressure
1045     and sigma coordiantes},
1046 jmc 1.25 journal = qjrms,
1047 jmc 1.24 year = 1984,
1048     volume = 110,
1049     pages = {515-533}
1050     }
1051    
1052     @Article{white:89,
1053     author = {White, A. A.},
1054     title = {An extended version of a nonhydrostatic, pressure coordiante model},
1055 jmc 1.25 journal = qjrms,
1056 jmc 1.24 year = 1989,
1057     volume = 115,
1058     pages = {1243-1251}
1059     }
1060    
1061 adcroft 1.2 @Article{adcroft:98,
1062     author = {Adcroft, A. and Marshall, D.},
1063 adcroft 1.3 title = {How slippery are piecewise-constant coastlines in numerical
1064     ocean models?},
1065 adcroft 1.2 journal = {Tellus},
1066 adcroft 1.3 year = 1998,
1067     volume = 50,
1068     number = 1,
1069     pages = {95-108}
1070     }
1071    
1072     @PhdThesis{adcroft:95,
1073     author = {Adcroft, A.},
1074     title = {Numerical Algorithms for use in a Dynamical Model of the
1075     Ocean},
1076     school = {Imperial College, London},
1077     year = 1995
1078     }
1079    
1080     @Article{griffies:00,
1081     author = {Griffies, S.,M. and Hallberg, R.,W.},
1082     title = {Biharmonic friction with a Smagorinsky-like viscosity for
1083     use in large-scale eddy-permitting ocean models},
1084 jmc 1.25 journal = mwr,
1085 adcroft 1.3 year = 2000,
1086     volume = 128,
1087     number = 8,
1088     pages = {2935-2946}
1089     }
1090    
1091     @Article{wajsowicz:93,
1092     author = {Wajsowicz, R.},
1093     title = {A CONSISTENT FORMULATION OF THE ANISOTROPIC STRESS TENSOR
1094     FOR USE IN MODELS OF THE LARGE-SCALE OCEAN CIRCULATION},
1095 jmc 1.25 journal = jcp,
1096 adcroft 1.3 year = 1993,
1097     volume = 105,
1098     number = 2,
1099     pages = {333-338}
1100     }
1101    
1102     @Article{campin:02,
1103 jmc 1.14 author = {Campin, J.-M. and A. Adcroft and C. Hill and J. Marshall},
1104 adcroft 1.3 title = {Conservation of properties in a free-surface model},
1105 jmc 1.14 journal = om,
1106     year = 2004,
1107     volume = 6,
1108     pages = {221-244}
1109 adcroft 1.4 }
1110    
1111     @Article{dm:95,
1112     author = {Danabasoglu, G. and McWilliams J.C.},
1113     title = {Sensitivity of the global ocean circulation to parameterizations of mesoscale tracer transports},
1114 jmc 1.25 journal = jclim,
1115 adcroft 1.4 year = 1995,
1116     volume = 8,
1117     number = 12,
1118     pages = {2967-2987}
1119     }
1120    
1121     @Article{ldd:97,
1122     author = {Large, W.G. and Danabasoglu, G. and Doney, S.C. and McWilliams, J.C.},
1123     title = {Sensitivity to surface forcing and boundary layer mixing in a global ocean model: Annual-mean climatology},
1124 jmc 1.25 journal = jpo,
1125 adcroft 1.4 year = 1997,
1126     volume = 27,
1127     number = 11,
1128     pages = {2418-2447}
1129     }
1130    
1131     @Article{gkw:99,
1132     author = {Gerdes R. and Koberle C. and Beckmann A. and Herrmann P. and Willebrand J.},
1133     title = {Mechanisms for spreading of Mediterranean water in
1134     coarse-resolution numerical models},
1135 jmc 1.25 journal = jpo,
1136 adcroft 1.4 year = 1999,
1137     volume = 29,
1138     number = 8,
1139     pages = {1682-1700}
1140     }
1141    
1142 jmc 1.17 @incollection{roe:85,
1143     author = {P.L. Roe},
1144     year = 1985,
1145     title = {Some contributions to the modelling of discontinuous flows},
1146     booktitle = {Large-Scale Computations in Fluid Mechanics},
1147     series = {Lectures in Applied Mathematics},
1148     volume = 22,
1149     pages = {163-193},
1150     editor = {B.E. Engquist and S. Osher and R.C.J. Somerville},
1151     publisher = {American Mathematical Society},
1152     address = {Providence, RI},
1153 adcroft 1.2 }
1154    
1155 mlosch 1.12 @Article{trenberth90,
1156     author = {K. M. Trenberth and J. Olson and W. G. Large},
1157     title = {The Mean Annual Cycle in {G}lobal {O}cean Wind
1158     Stress},
1159     journal = jpo,
1160     year = 1990,
1161     volume = 20,
1162     pages = {1742--1760}
1163 jmc 1.14 }
1164    
1165     @Article{molteni:03,
1166 jmc 1.27 author = {F. Molteni},
1167 edhill 1.30 title = {Atmospheric simulations using a {GCM} with simplified physical
1168     parametrization, {I}: Model climatology and variability in
1169 jmc 1.14 multidecadal experiments},
1170     journal = climd,
1171     year = 2003,
1172     volume = 20,
1173     pages = {175--191}
1174 mlosch 1.12 }
1175    
1176     @Article{jiang99,
1177 edhill 1.21 author = {S. Jiang and P. H. Stone and P. Malanotte-Rizzoli},
1178 mlosch 1.12 title = {An Assessment of the {G}eophysical {F}luid
1179     {D}ynamics {L}aboratory Ocean Model with Coarse
1180     Resolution: Annual-Mean Climatology},
1181     journal = jgr,
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1223     OPTannote = {}
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1229     of Seawater",
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1234     pages = {53 pp.}
1235     }
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1251     JOURNAL = jpo,
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1254     PAGES = "379-389"
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1260     JOURNAL = jaot,
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1262     VOLUME = 17,
1263     PAGES = "525-531"
1264     }
1265    
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1268     TITLE = "A Dynamic Thermodynamic Sea Ice Model",
1269     JOURNAL = jpo,
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1271     VOLUME = 9,
1272     PAGES = "815-846"
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1277     TITLE = "Modeling pack ice as a cavitating fluid",
1278     JOURNAL = jpo,
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1280     VOLUME = 22,
1281     PAGES = "626-651"
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1289     VOLUME = 27,
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1315     its Coupling to a Two-Dimensional Atmospheric Model: Uses
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1317     institution = {MIT Joint Program of the Science and Policy of Global Change},
1318     year = {2005},
1319     OPTnumber = {122},
1320     address = {Cambridge, MA},
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1352     year = {1989},
1353     OPTkey = {},
1354     OPTtype = {},
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1370     }
1371    
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1375     title = {High Resolution Models of the Planetary Boundary Layer.},
1376     booktitle = {Advances in Environmental Science and Engineering, Vol 1 } ,
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1379     }
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1387     pages = {762-772}
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1396     volume = {3},
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1406     type = {NASA Technical Memorandum},
1407     number = {104606-Vol 3},
1408     address = {NASA; Goddard Space Flight Center; Greenbelt (MD), 20771; USA},
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1637     volume = {17},
1638     pages = {777-794}
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1663     year = {1998},
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