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fix few references

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 jmc 1.45
50 heimbach 1.1 @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 jmc 1.45
63 heimbach 1.1 @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 jmc 1.45 address = {ANL; 9700 South Cass Ave.;
74 heimbach 1.1 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 jmc 1.45
90 heimbach 1.1 @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 jmc 1.45 address = {ANL; 9700 South Cass Ave.;
100 heimbach 1.1 Argonne (ILL), 90439; USA},
101     note = {http://www.mcs.anl.gov/autodiff/},
102     }
103 jmc 1.45
104 heimbach 1.1 @Article{cou-tal:87,
105     author = {P. Courtier and O. Talagrand},
106     year = 1987,
107 jmc 1.45 title = {Variational assimilation of meteorological
108 heimbach 1.1 observations with the adjoint vorticity equation.
109     II: Numerical results},
110     journal = qjrms,
111     volume = {113},
112     pages = {1329--1347},
113     }
114 jmc 1.45
115 heimbach 1.1 @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 jmc 1.45
126 heimbach 1.1 @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 jmc 1.45
147 jmc 1.33
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 jmc 1.45
159 heimbach 1.1 @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 jmc 1.45
168 heimbach 1.1 @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 jmc 1.45
178 heimbach 1.1 @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 jmc 1.45
188 heimbach 1.1 @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 jmc 1.45
198 heimbach 1.1 @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 jmc 1.45
211 heimbach 1.1 @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 jmc 1.45
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 jmc 1.45 author = {P. Gaspar and Y. Gr\'egoris and J.-M. Lefevre},
231 jmc 1.39 year = 1990,
232 jmc 1.45 title = {A Simple Eddy Kinetic Energy Model for Simulations of the
233     Oceanic Vertical Mixing: Tests at Station Papa and Long-Term
234 jmc 1.39 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 dfer 1.44 author = {P. R. Gent and J. C. McWilliams},
242 heimbach 1.1 year = 1990,
243     title = {Isopycnal mixing in ocean circulation models},
244     journal = jpo,
245     volume = {20},
246     pages = {150--155},
247     }
248 jmc 1.45
249 heimbach 1.1 @Article{gen-eta:95,
250 dfer 1.44 author = {P. R. Gent and J. Willebrand and T. J. McDougall and J. C. McWilliams},
251 heimbach 1.1 year = 1995,
252 dfer 1.44 title = {Parameterizing eddy-induced tracer transports in ocean circulation models},
253 heimbach 1.1 journal = jpo,
254     volume = {25},
255     pages = {463--474},
256     }
257 jmc 1.45
258 heimbach 1.1 @Article{gie-kam:98,
259     author = {R. Giering and T. Kaminski},
260     year = 1998,
261     title = {Recipes for adjoint code construction},
262     journal = {ACM Transactions on Mathematical Software},
263     volume = 24,
264     pages = {437--474},
265     }
266    
267     @techreport{gie:99,
268     author = {R. Giering},
269     year = 1999,
270 jmc 1.45 title = {Tangent linear and Adjoint Model Compiler.
271 heimbach 1.1 Users manual 1.4 (TAMC Version 5.2)},
272     institution = {Massachusetts Institute of Technology},
273     type = {Report},
274     number = {~},
275     address = {MIT/EAPS; 77 Massachusetts Ave.; Cambridge (MA)
276     02139; USA},
277     note = {http://puddle.mit.edu/$\sim$ralf/tamc/tamc.html},
278     }
279 jmc 1.45
280 heimbach 1.1 @incollection{gie:00,
281     author = {R. Giering},
282     editor = {P. Kasibhatla and M. Heimann and P. Rayner and
283     N. Mahowald and R.G. Prinn and D.E. Hartley},
284     year = 2000,
285     booktitle = {Inverse methods in global biogeochemical cycles},
286     title = {Tangent linear and adjoint biogeochemical models},
287     publisher = {American Geophysical Union},
288     series = {Geophysical Monograph},
289     volume = {114},
290     address = {Washington, DC},
291     pages = {33--48},
292     }
293    
294     @Article{gil-lem:89,
295     author = {J.C. Gilbert and C. Lemar\'echal},
296     year = 1989,
297     title = {Some numerical experiments with variable-storage
298     quasi-Newton algorithms},
299     journal = {Math. Programming},
300     volume = {45},
301     pages = {407--435},
302     }
303 jmc 1.45
304 heimbach 1.1 @book{gil-eta:81,
305     author = {P.E. Gill and W. Murray and M.H. Wright},
306     title = {Practical optimization},
307     year = 1981,
308     publisher = {Academic Press},
309 jmc 1.45 address = {London},
310 heimbach 1.1 pages = {401 pp.},
311     }
312 jmc 1.45
313 heimbach 1.11 @incollection{gri:89,
314     author = {A. Griewank},
315     year = 1989,
316     title = {On automatic differentiation},
317     booktitle = {Mathematical Programming: Recent Developments and
318     Applications},
319     pages = {83--108},
320     editor = {M. Iri and K. Tanabe},
321     publisher = {Kluwer},
322     address = {Dordrecht, NL},
323     }
324 jmc 1.45
325 heimbach 1.11 @Article{gri:92,
326     author = {A.~Griewank},
327     title = {Achieving logarithmic growth of temporal and spatial
328     complexity in reverse {A}utomatic {D}ifferentiation},
329     journal = {Optimization Methods and Software},
330     year = {1992},
331     volume = {1},
332     pages = {35--54}
333     }
334    
335 heimbach 1.1 @book{gri:00,
336     author = {A. Griewank},
337     title = {Evaluating Derivatives. Principles and Techniques
338     of Algorithmic Differentiation},
339     year = 2000,
340     series = {Frontiers in Applied Mathematics},
341     volume = {19},
342     publisher = {SIAM},
343 jmc 1.45 address = {Philadelphia},
344 heimbach 1.1 pages = {369 pp.},
345     }
346 jmc 1.45
347 heimbach 1.1 @Article{hal-eta:82,
348     author = {M.C.G. Hall and D.G. Caccuci and M.E. Schlesinger},
349     year = 1982,
350     title = {Sensitivity analysis of a radiative-convective
351     model by the adjoint method},
352     journal = jas,
353     volume = {39},
354     pages = {2038--3050},
355     }
356 cnh 1.6
357     @Article{Haney,
358     author = {R.L. Haney},
359     title = {Surface thermal boundary conditions for ocean
360     circulation models},
361     journal = jpo,
362     year = 1971,
363     volume = 1,
364     pages = {241--248}
365     }
366 jmc 1.45
367 cnh 1.16 @Article{held-suar:94,
368     author = {I.M. Held and M.J. Suarez},
369     year = {1994},
370     title = {A proposal for the intercomparison of the dynamical cores of atmospheric general circulation models},
371     journal = {Bulletin of the American Meteorological Society},
372     volume = {75(10)},
373     pages = {1825-1830}
374     }
375 jmc 1.45
376 heimbach 1.1 @Article{hil-eta:01,
377 jmc 1.45 author = {C. Hill and M. Follows and V. Bugnion and
378 heimbach 1.1 J. Marshall},
379 cnh 1.10 year = {2002},
380 jmc 1.45 title = {Spatial and Temporal Impacts of ocean general
381 heimbach 1.1 circulation on carbon sequestration},
382 cnh 1.6 journal = {Global Biogeochemical Cycles},
383 heimbach 1.1 note = {submitted},
384     }
385 cnh 1.6
386 edhill 1.15 @ARTICLE{hib80,
387 mlosch 1.36 author = {Hibler, III, William D.},
388 edhill 1.15 TITLE = "Modeling a Variable Thickness Sea Ice Cover",
389     JOURNAL = mwr,
390     YEAR = 1980,
391     VOLUME = 1,
392     PAGES = "1943-1973"
393     }
394    
395 cnh 1.6 @Article{Holland75,
396     author = {W.R. Holland and L. B. Lin},
397     year = {1975a},
398 jmc 1.45 title = {On the origin of mesoscale eddies and their contribution
399     to the general circulation of the ocean. I. A preliminary
400 cnh 1.6 numerical experiment},
401     journal = jpo,
402     volume = {5},
403     pages = {642-657}
404     }
405    
406     @Article{hol-lin:75b,
407     author = {W.R. Holland and L. B. Lin},
408     year = {1975b},
409 jmc 1.45 title = {On the origin of mesoscale eddies and their contribution
410 cnh 1.6 to the general circulation of the ocean. II. A parameter
411     study},
412     journal = jpo,
413     volume = {5},
414     pages = {658-669}
415     }
416    
417 jmc 1.31 @Article{jam-oze:86,
418 jmc 1.45 author = {B.M. Jamart and J. Ozer},
419 jmc 1.31 year = {1986},
420 jmc 1.45 title = {Numerical boundary layers and spurious residual flows},
421 jmc 1.31 journal = jgr,
422     volume = {91},
423     pages = {10,621-10,631}
424     }
425    
426 heimbach 1.1 @book{kas-eta:00,
427     author = {P. Kasibhatla and M. Heimann and P. Rayner and
428     N. Mahowald and R.G. Prinn and D.E. Hartley},
429     year = 2000,
430     title = {Inverse methods in global biogeochemical cycles},
431     publisher = {American Geophysical Union},
432     series = {Geophysical Monograph},
433     volume = {114},
434     address = {Washington, DC},
435     pages = {324 pp.},
436     }
437    
438     @Article{lar-eta:94,
439     author = {W.G. Large and J.C. McWilliams and S.C. Doney},
440     year = 1994,
441 dfer 1.44 title = {Oceanic vertical mixing: A review and a model with nonlocal boundary layer parameterization},
442 heimbach 1.1 journal = {Rev.~Geophys.},
443     volume = {32},
444     pages = {363--403},
445     }
446 jmc 1.45
447 heimbach 1.1 @Article{lar-eta:97,
448 jmc 1.45 author = {W. G. Large and G. Danabasoglu and S. C. Doney
449     and J. C. McWilliams},
450 heimbach 1.1 year = 1997,
451     title = {Sensitivity to surface forcing and boundary layer
452 jmc 1.45 mixing in a global ocean model: Annual-mean climatology},
453 heimbach 1.1 journal = jpo,
454     volume = {27},
455 jmc 1.45 number = 11,
456 heimbach 1.1 pages = {2418--2447},
457     }
458 jmc 1.45
459 heimbach 1.1 @Article{led-tal:86,
460     author = {F.-X. {Le Dimet} and O. Talagrand},
461     year = 1986,
462     title = {Variational algorithms for analysis and
463     assimilation of meteorological observations:
464     theoretical aspects},
465     journal = tel,
466     volume = {38A},
467     pages = {97--110},
468     }
469 cnh 1.6
470     @TechReport{lev:94a,
471     author = {S. Levitus and T.P.Boyer},
472     title = {{World Ocean Atlas 1994 Volume 3: Salinity}},
473     institution = {NOAA Atlas NESDIS 3},
474     year = 1994,
475     OPTkey = {},
476     OPTtype = {},
477     OPTnumber = {},
478     OPTaddress = {U.S. Department of Commerce, Washington D.C.},
479     OPTmonth = {},
480     OPTnote = {},
481     OPTannote = {}
482     }
483    
484    
485     @TechReport{Levitus94,
486     author = {S. Levitus and T.P.Boyer},
487     title = {{World Ocean Atlas 1994 Volume 4: Temperature}},
488     institution = {NOAA Atlas NESDIS 4},
489     year = 1994,
490     OPTkey = {},
491     OPTtype = {},
492     OPTnumber = {},
493     OPTaddress = {U.S. Department of Commerce, Washington D.C.},
494     OPTmonth = {},
495     OPTnote = {},
496     OPTannote = {}
497     }
498    
499 jmc 1.45
500 heimbach 1.1 @Article{lew-der:85,
501     author = {J. Lewis and J. Derber},
502     year = {1985},
503     title = {The use of adjoint equations to solve a variational
504     adjustment problem with advective constraints},
505     journal = {Tellus},
506     volume = {37A},
507     pages = {309--322},
508     }
509 jmc 1.45
510 heimbach 1.1 @techreport{lon:88,
511     author = {R.B. Long},
512     year = 1988,
513     title = {Notes on assimilating observations into
514     numerical models},
515     institution = {Delft Hydraulics},
516     type = {Report},
517     number = {~},
518     pages = {38 pp.},
519     address = {Delft (NL)},
520     }
521 cnh 1.29
522     @ARTICLE{losc-heim:06,
523 mlosch 1.42 author = {Martin Losch and Patrick Heimbach},
524     title = {Adjoint Sensitivity of an Ocean General Circulation
525     Model to Bottom Topography},
526     journal = jpo,
527     year = 2007,
528     volume = 37,
529     doi = {10.1175/JPO3017.1},
530     number = 2,
531     pages = {377--393},
532 cnh 1.29 url = {http://mitgcm.org/pdfs/Los2006a.pdf},
533     }
534    
535 jmc 1.45
536 heimbach 1.1 @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 jmc 1.45
547 heimbach 1.1 @Article{maro-eta:99,
548 jmc 1.45 author = {J. Marotzke and R. Giering and K.Q. Zhang and
549 heimbach 1.1 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 jmc 1.45
559 heimbach 1.1 @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 jmc 1.45
570 heimbach 1.1 @Article{mars-eta:97b,
571 jmc 1.45 author = {J. Marshall and A. Adcroft and C. Hill and
572 heimbach 1.1 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 jmc 1.45
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 jmc 1.45
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 jmc 1.45 %% (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 edhill 1.13 %% also available.
611 jmc 1.45
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 jmc 1.45 title = {{NetCDF User's Guide for C, FORTRAN 77, and FORTRAN 90},
643 edhill 1.13 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 jmc 1.45
662 heimbach 1.1 @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 jmc 1.45
671 heimbach 1.1 @incollection{she-and:89,
672     author = {J. Sheinbaum and D.L.T. Anderson},
673     year = 1989,
674 jmc 1.45 title = {Assimilation of XBT data using a variational
675 heimbach 1.1 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 jmc 1.45
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 jmc 1.45 title = {The global ocean circulation estimated from
713 heimbach 1.1 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 jmc 1.45
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 jmc 1.45 title = {Variational assimilation of meteorological
747 heimbach 1.1 observations with the adjoint vorticity equation.
748     I: Theory},
749     journal = qjrms,
750     volume = {113},
751     pages = {1311--1328},
752     }
753 jmc 1.45
754 heimbach 1.1 @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 jmc 1.45
763 heimbach 1.1 @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 jmc 1.45 address = {Amsterdam},
770 heimbach 1.1 pages = {629 pp.},
771     }
772 jmc 1.45
773 heimbach 1.1 @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 jmc 1.45
785 heimbach 1.1 @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 jmc 1.45
794 heimbach 1.1 @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 jmc 1.45
804 heimbach 1.1 @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 jmc 1.45
814 heimbach 1.1 @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 jmc 1.45
824 heimbach 1.1 @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 jmc 1.45
834 heimbach 1.1 @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 jmc 1.45
845 heimbach 1.1 @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 jmc 1.45
856 heimbach 1.1 @book{wun:96,
857     author = {C. Wunsch},
858     title = {The ocean circulation inverse problem},
859     year = 1996,
860     publisher = cup,
861 jmc 1.45 address = {Cambridge (UK)},
862 heimbach 1.1 pages = {442 pp.},
863     }
864 jmc 1.45
865 heimbach 1.1 @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 jmc 1.45 author = {Adcroft, A. and C. Hill and J.-M. Campin and J. Marshall
951 jmc 1.33 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 jmc 1.45 Recent developments in numerical methods for atmosphere and
955 jmc 1.33 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 dfer 1.44 author = {M. Visbeck and J. Marshall and T. Haine and M. Spall},
975     title = {Specification of eddy transfer coefficients in coarse-resolution ocean circulation models},
976 jmc 1.25 journal = jpo,
977 adcroft 1.2 year = 1997,
978     volume = 27,
979     number = 3,
980     pages = {381-402}
981     }
982    
983     @Article{shaw:98,
984     author = {Shaw; A. Arvind, Cho, K.-C., Hill, C., Johnson, R.P.
985     and Marshall, J.},
986     title = {A comparison of implicitly parallel multi-threaded and
987     data-parallel implementations of an ocean model based
988     on the Navier-Stokes equations},
989     journal = {J. of Parallel and Distributed Computing},
990     year = 1998,
991     volume = 48,
992     number = 1,
993     pages = {1-51}
994     }
995    
996     @Article{mjn:99,
997     author = {Marshall, J., Jamous, D and J. Nilsson},
998     title = {Reconciling `thermodynamic' and `dynamic' methods of
999     computation of water-mass transformation rates},
1000     journal = {DSR},
1001     year = 1999,
1002     volume = 46,
1003     pages = {545-572}
1004     }
1005    
1006     @Article{ms:99,
1007     author = {Marshall, J and F. Schott},
1008     title = {Open ocean deep convection: observations, models and theory},
1009     journal = {Rev. Geophys.},
1010     year = 1999,
1011     volume = 37,
1012     number = 1,
1013     pages = {1-64}
1014     }
1015    
1016     @Article{adcroft:99,
1017     author = {Adcroft, A., Hill C. and J. Marshall},
1018     title = {A new treatment of the Coriolis terms in C-grid models
1019     at both high and low resolutions},
1020 jmc 1.25 journal = mwr,
1021 adcroft 1.2 year = 1999,
1022     volume = 127,
1023 cnh 1.29 pages = {1928-1936},
1024     url = {http://mitgcm.org/pdfs/mwr_1999.pdf},
1025     doi = {10.1175/1520-0493\%281999\%29127<1928:ANTOTC>2.0.CO;2},
1026 adcroft 1.2 }
1027    
1028     @InProceedings{hill:99,
1029     author = {Chris Hill, Alistair Adcroft, Daniel Jamous and John Marshall},
1030     title = {A Strategy for Terascale Climate Modeling},
1031 cnh 1.8 booktitle = {In Proceedings of the Eighth ECMWF Workshop on the Use of Parallel Processors in Meteorology},
1032 cnh 1.9 year = 1999,
1033     pages = {406-425},
1034     publisher = {World Scientific},
1035 adcroft 1.2 }
1036    
1037     @Article{wardle:00,
1038     author = {Wardle R. and Marshall J.},
1039     title = {Representation of eddies in primitive equation models by a PV flux},
1040 jmc 1.25 journal = jpo,
1041 adcroft 1.2 year = 2000,
1042     volume = 30,
1043     number = 10,
1044     pages = {2481-2503}
1045     }
1046    
1047     @Article{ac:02,
1048     author = {Adcroft, A. and J.-M. Campin},
1049     title = {Comparison of finite volume schemes and direct-space-time
1050     methods for ocean circulation models},
1051 jmc 1.14 journal = om,
1052 adcroft 1.2 year = 2002,
1053     note = {in preparation}
1054     }
1055    
1056     @Article{adcroft:02,
1057 jmc 1.25 author = {Adcroft, A., et~al.},
1058 adcroft 1.2 title = {Energy conversion in discrete numerical models},
1059 jmc 1.14 journal = om,
1060 adcroft 1.2 year = 2002,
1061     note = {in preparation}
1062     }
1063    
1064     @InCollection{arakawa:77,
1065     author = {Arakawa, A. and Lamb, V.},
1066     title = {Computational Design of the Basic Dynamical Processes of
1067     the UCLA General Circulation Model},
1068     booktitle = {Methods in Computational Physics},
1069     pages = {174-267},
1070     publisher = {Academic Press},
1071     year = 1977,
1072     volume = 17
1073     }
1074    
1075 jmc 1.24 @Article{miller_white:84,
1076     author = {Miller, M. J. and White, A. A.},
1077     title = {On the non-hydrostatic equations in pressure
1078     and sigma coordiantes},
1079 jmc 1.25 journal = qjrms,
1080 jmc 1.24 year = 1984,
1081     volume = 110,
1082     pages = {515-533}
1083     }
1084    
1085     @Article{white:89,
1086     author = {White, A. A.},
1087     title = {An extended version of a nonhydrostatic, pressure coordiante model},
1088 jmc 1.25 journal = qjrms,
1089 jmc 1.24 year = 1989,
1090     volume = 115,
1091     pages = {1243-1251}
1092     }
1093    
1094 adcroft 1.2 @Article{adcroft:98,
1095     author = {Adcroft, A. and Marshall, D.},
1096 adcroft 1.3 title = {How slippery are piecewise-constant coastlines in numerical
1097     ocean models?},
1098 adcroft 1.2 journal = {Tellus},
1099 adcroft 1.3 year = 1998,
1100     volume = 50,
1101     number = 1,
1102     pages = {95-108}
1103     }
1104    
1105     @PhdThesis{adcroft:95,
1106     author = {Adcroft, A.},
1107     title = {Numerical Algorithms for use in a Dynamical Model of the
1108     Ocean},
1109     school = {Imperial College, London},
1110     year = 1995
1111     }
1112    
1113     @Article{griffies:00,
1114     author = {Griffies, S.,M. and Hallberg, R.,W.},
1115 dfer 1.44 title = {Biharmonic friction with a {Smagorinsky}-like viscosity for
1116 adcroft 1.3 use in large-scale eddy-permitting ocean models},
1117 jmc 1.25 journal = mwr,
1118 adcroft 1.3 year = 2000,
1119     volume = 128,
1120     number = 8,
1121     pages = {2935-2946}
1122     }
1123    
1124     @Article{wajsowicz:93,
1125     author = {Wajsowicz, R.},
1126     title = {A CONSISTENT FORMULATION OF THE ANISOTROPIC STRESS TENSOR
1127     FOR USE IN MODELS OF THE LARGE-SCALE OCEAN CIRCULATION},
1128 jmc 1.25 journal = jcp,
1129 adcroft 1.3 year = 1993,
1130     volume = 105,
1131     number = 2,
1132     pages = {333-338}
1133     }
1134    
1135     @Article{campin:02,
1136 jmc 1.14 author = {Campin, J.-M. and A. Adcroft and C. Hill and J. Marshall},
1137 adcroft 1.3 title = {Conservation of properties in a free-surface model},
1138 jmc 1.14 journal = om,
1139     year = 2004,
1140     volume = 6,
1141     pages = {221-244}
1142 adcroft 1.4 }
1143    
1144 dfer 1.44 @Article{Cox87,
1145     author = {M. D. Cox},
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1329 edhill 1.15 TITLE = "A Dynamic Thermodynamic Sea Ice Model",
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1338 edhill 1.15 TITLE = "Modeling pack ice as a cavitating fluid",
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1386 jmc 1.45 title = {A Three-Dimensional Ocean-Seaice-Carbon Cycle Model and
1387     its Coupling to a Two-Dimensional Atmospheric Model: Uses
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1392     address = {Cambridge, MA},
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1424     year = {1989},
1425     OPTkey = {},
1426     OPTtype = {},
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1448     booktitle = {Advances in Environmental Science and Engineering, Vol 1 } ,
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1450     publisher = {Gordon and Breach, Scientific Publishers}
1451     }
1452 jmc 1.45
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1475     title = {An efficient thermal infrared radiation parameterization
1476     for use in general circulation models},
1477 jmc 1.45 institution = {National Aeronautics and Space Administration},
1478     type = {NASA Technical Memorandum},
1479     number = {104606-Vol 3},
1480 molod 1.22 address = {NASA; Goddard Space Flight Center; Greenbelt (MD), 20771; USA},
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1645 jmc 1.45 institution = {National Aeronautics and Space Administration},
1646     type = {NASA Technical Memorandum},
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1648 molod 1.22 address = {NASA; Goddard Space Flight Center; Greenbelt (MD), 20771; USA},
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1668 molod 1.22 volume = {11},
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1677 molod 1.22 volume = {122},
1678     pages = {903-927}
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1686 molod 1.23 year = 1999,
1687 jmc 1.45 title = {An intercomparison of radiatively driven entrainment and turbulence
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1689 molod 1.23 journal = qjrms,
1690 jmc 1.45 volume = {125},
1691 molod 1.23 pages = {391-423}
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1695 jmc 1.45 author = {A. C. Bushell and G.M. Martin},
1696 molod 1.23 year = 1999,
1697 jmc 1.45 title = {The Impact of Vertical Resolution Upon GCM Simulations of Marine Stratocumulus.},
1698     journal = {Climate Dyn.},
1699     volume = {15},
1700 molod 1.23 pages = {293-318}
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1705 molod 1.23 year = 2001,
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1707     Implications for the Simulation of the Madden-Julian Oscillation.},
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1986     pages = {89-120}
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1996     pages = {1806-1821}
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