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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     @Article{gen-mcw:90,
217     author = {P.R. Gent and J.C. McWilliams},
218     year = 1990,
219     title = {Isopycnal mixing in ocean circulation models},
220     journal = jpo,
221     volume = {20},
222     pages = {150--155},
223     }
224    
225     @Article{gen-eta:95,
226     author = {P.R. Gent and J. Willebrand and T.J. McDougall
227     and J.C. McWilliams},
228     year = 1995,
229     title = {Parameterizing eddy-induced tracer transports in
230     ocean circulation models},
231     journal = jpo,
232     volume = {25},
233     pages = {463--474},
234     }
235    
236     @Article{gie-kam:98,
237     author = {R. Giering and T. Kaminski},
238     year = 1998,
239     title = {Recipes for adjoint code construction},
240     journal = {ACM Transactions on Mathematical Software},
241     volume = 24,
242     pages = {437--474},
243     }
244    
245     @techreport{gie:99,
246     author = {R. Giering},
247     year = 1999,
248     title = {Tangent linear and Adjoint Model Compiler.
249     Users manual 1.4 (TAMC Version 5.2)},
250     institution = {Massachusetts Institute of Technology},
251     type = {Report},
252     number = {~},
253     address = {MIT/EAPS; 77 Massachusetts Ave.; Cambridge (MA)
254     02139; USA},
255     note = {http://puddle.mit.edu/$\sim$ralf/tamc/tamc.html},
256     }
257    
258     @incollection{gie:00,
259     author = {R. Giering},
260     editor = {P. Kasibhatla and M. Heimann and P. Rayner and
261     N. Mahowald and R.G. Prinn and D.E. Hartley},
262     year = 2000,
263     booktitle = {Inverse methods in global biogeochemical cycles},
264     title = {Tangent linear and adjoint biogeochemical models},
265     publisher = {American Geophysical Union},
266     series = {Geophysical Monograph},
267     volume = {114},
268     address = {Washington, DC},
269     pages = {33--48},
270     }
271    
272     @Article{gil-lem:89,
273     author = {J.C. Gilbert and C. Lemar\'echal},
274     year = 1989,
275     title = {Some numerical experiments with variable-storage
276     quasi-Newton algorithms},
277     journal = {Math. Programming},
278     volume = {45},
279     pages = {407--435},
280     }
281    
282     @book{gil-eta:81,
283     author = {P.E. Gill and W. Murray and M.H. Wright},
284     title = {Practical optimization},
285     year = 1981,
286     publisher = {Academic Press},
287     address = {London},
288     pages = {401 pp.},
289     }
290    
291 heimbach 1.11 @incollection{gri:89,
292     author = {A. Griewank},
293     year = 1989,
294     title = {On automatic differentiation},
295     booktitle = {Mathematical Programming: Recent Developments and
296     Applications},
297     pages = {83--108},
298     editor = {M. Iri and K. Tanabe},
299     publisher = {Kluwer},
300     address = {Dordrecht, NL},
301     }
302    
303     @Article{gri:92,
304     author = {A.~Griewank},
305     title = {Achieving logarithmic growth of temporal and spatial
306     complexity in reverse {A}utomatic {D}ifferentiation},
307     journal = {Optimization Methods and Software},
308     year = {1992},
309     volume = {1},
310     pages = {35--54}
311     }
312    
313 heimbach 1.1 @book{gri:00,
314     author = {A. Griewank},
315     title = {Evaluating Derivatives. Principles and Techniques
316     of Algorithmic Differentiation},
317     year = 2000,
318     series = {Frontiers in Applied Mathematics},
319     volume = {19},
320     publisher = {SIAM},
321     address = {Philadelphia},
322     pages = {369 pp.},
323     }
324    
325     @Article{hal-eta:82,
326     author = {M.C.G. Hall and D.G. Caccuci and M.E. Schlesinger},
327     year = 1982,
328     title = {Sensitivity analysis of a radiative-convective
329     model by the adjoint method},
330     journal = jas,
331     volume = {39},
332     pages = {2038--3050},
333     }
334 cnh 1.6
335     @Article{Haney,
336     author = {R.L. Haney},
337     title = {Surface thermal boundary conditions for ocean
338     circulation models},
339     journal = jpo,
340     year = 1971,
341     volume = 1,
342     pages = {241--248}
343     }
344 heimbach 1.1
345 cnh 1.16 @Article{held-suar:94,
346     author = {I.M. Held and M.J. Suarez},
347     year = {1994},
348     title = {A proposal for the intercomparison of the dynamical cores of atmospheric general circulation models},
349     journal = {Bulletin of the American Meteorological Society},
350     volume = {75(10)},
351     pages = {1825-1830}
352     }
353    
354 heimbach 1.1 @Article{hil-eta:01,
355     author = {C. Hill and M. Follows and V. Bugnion and
356     J. Marshall},
357 cnh 1.10 year = {2002},
358 heimbach 1.1 title = {Spatial and Temporal Impacts of ocean general
359     circulation on carbon sequestration},
360 cnh 1.6 journal = {Global Biogeochemical Cycles},
361 heimbach 1.1 note = {submitted},
362     }
363 cnh 1.6
364 edhill 1.15 @ARTICLE{hib80,
365     AUTHOR = "W. D. {Hibler, III}",
366     TITLE = "Modeling a Variable Thickness Sea Ice Cover",
367     JOURNAL = mwr,
368     YEAR = 1980,
369     VOLUME = 1,
370     PAGES = "1943-1973"
371     }
372    
373 cnh 1.6 @Article{Holland75,
374     author = {W.R. Holland and L. B. Lin},
375     year = {1975a},
376     title = {On the origin of mesoscale eddies and their contribution
377     to the general circulation of the ocean. I. A preliminary
378     numerical experiment},
379     journal = jpo,
380     volume = {5},
381     pages = {642-657}
382     }
383    
384     @Article{hol-lin:75b,
385     author = {W.R. Holland and L. B. Lin},
386     year = {1975b},
387     title = {On the origin of mesoscale eddies and their contribution
388     to the general circulation of the ocean. II. A parameter
389     study},
390     journal = jpo,
391     volume = {5},
392     pages = {658-669}
393     }
394    
395 jmc 1.31 @Article{jam-oze:86,
396     author = {B.M. Jamart and J. Ozer},
397     year = {1986},
398     title = {Numerical boundary layers and spurious residual flows},
399     journal = jgr,
400     volume = {91},
401     pages = {10,621-10,631}
402     }
403    
404 heimbach 1.1 @book{kas-eta:00,
405     author = {P. Kasibhatla and M. Heimann and P. Rayner and
406     N. Mahowald and R.G. Prinn and D.E. Hartley},
407     year = 2000,
408     title = {Inverse methods in global biogeochemical cycles},
409     publisher = {American Geophysical Union},
410     series = {Geophysical Monograph},
411     volume = {114},
412     address = {Washington, DC},
413     pages = {324 pp.},
414     }
415    
416     @Article{lar-eta:94,
417     author = {W.G. Large and J.C. McWilliams and S.C. Doney},
418     year = 1994,
419     title = {Oceanic vertical mixing: A review and a model
420     with nonlocal boundary layer parameterization},
421     journal = {Rev.~Geophys.},
422     volume = {32},
423     pages = {363--403},
424     }
425    
426     @Article{lar-eta:97,
427     author = {W.G. Large and G. Danabasoglu and S.C. Doney
428     and J.C. McWilliams},
429     year = 1997,
430     title = {Sensitivity to surface forcing and boundary layer
431     mixing in a global ocean model: annual-mean
432     climatology},
433     journal = jpo,
434     volume = {27},
435     pages = {2418--2447},
436     }
437    
438     @Article{led-tal:86,
439     author = {F.-X. {Le Dimet} and O. Talagrand},
440     year = 1986,
441     title = {Variational algorithms for analysis and
442     assimilation of meteorological observations:
443     theoretical aspects},
444     journal = tel,
445     volume = {38A},
446     pages = {97--110},
447     }
448 cnh 1.6
449     @TechReport{lev:94a,
450     author = {S. Levitus and T.P.Boyer},
451     title = {{World Ocean Atlas 1994 Volume 3: Salinity}},
452     institution = {NOAA Atlas NESDIS 3},
453     year = 1994,
454     OPTkey = {},
455     OPTtype = {},
456     OPTnumber = {},
457     OPTaddress = {U.S. Department of Commerce, Washington D.C.},
458     OPTmonth = {},
459     OPTnote = {},
460     OPTannote = {}
461     }
462    
463    
464     @TechReport{Levitus94,
465     author = {S. Levitus and T.P.Boyer},
466     title = {{World Ocean Atlas 1994 Volume 4: Temperature}},
467     institution = {NOAA Atlas NESDIS 4},
468     year = 1994,
469     OPTkey = {},
470     OPTtype = {},
471     OPTnumber = {},
472     OPTaddress = {U.S. Department of Commerce, Washington D.C.},
473     OPTmonth = {},
474     OPTnote = {},
475     OPTannote = {}
476     }
477    
478 heimbach 1.1
479     @Article{lew-der:85,
480     author = {J. Lewis and J. Derber},
481     year = {1985},
482     title = {The use of adjoint equations to solve a variational
483     adjustment problem with advective constraints},
484     journal = {Tellus},
485     volume = {37A},
486     pages = {309--322},
487     }
488    
489     @techreport{lon:88,
490     author = {R.B. Long},
491     year = 1988,
492     title = {Notes on assimilating observations into
493     numerical models},
494     institution = {Delft Hydraulics},
495     type = {Report},
496     number = {~},
497     pages = {38 pp.},
498     address = {Delft (NL)},
499     }
500 cnh 1.29
501     @ARTICLE{losc-heim:06,
502     author = {M. Losch and P. Heimbach},
503     title = {Adjoint sensitivity of an ocean general circulation model
504     to bottom topography},
505     journal = jpo,
506     year = {2006},
507     volume = {{in press}},
508     url = {http://mitgcm.org/pdfs/Los2006a.pdf},
509     }
510    
511 heimbach 1.1
512     @Article{maro-wun:93,
513     author = {J. Marotzke and C. Wunsch},
514     year = 1993,
515     title = {Finding the steady state of a general circulation
516     model through data assimilation:
517     Application to the North Atlantic Ocean},
518     journal = jgr,
519     volume = {98, C11},
520     pages = {20,149--20,167},
521     }
522    
523     @Article{maro-eta:99,
524     author = {J. Marotzke and R. Giering and K.Q. Zhang and
525     D. Stammer and C. Hill and T. Lee},
526     year = 1999,
527     title = {Construction of the adjoint MIT ocean general
528     circulation model and application to Atlantic heat
529     transport variability},
530     journal = jgr,
531     volume = {104, C12},
532     pages = {29,529--29,547},
533     }
534    
535     @Article{mars-eta:97a,
536     author = {J. Marshall and C. Hill and L. Perelman and
537     A. Adcroft},
538     year = {1997a},
539     title = {Hydrostatic, quasi-hydrostatic and
540     nonhydrostatic ocean modeling},
541     journal = jgr,
542     volume = {102, C3},
543     pages = {5,733--5,752},
544     }
545    
546     @Article{mars-eta:97b,
547     author = {J. Marshall and A. Adcroft and C. Hill and
548     L. Perelman and C. Heisey},
549     year = {1997b},
550     title = {Hydrostatic, quasi-hydrostatic and
551     nonhydrostatic ocean modeling},
552     journal = jgr,
553     volume = {102, C3},
554     pages = {5,753--5,766},
555     }
556    
557 jmc 1.33 @Article{mars-eta:98,
558 heimbach 1.1 author = {J. Marshall and H. Jones and C. Hill},
559     year = 1998,
560     title = {Efficient ocean modeling using
561     non-hydrostatic algorithms},
562     journal = jms,
563     volume = {18},
564     pages = {115--134},
565 cnh 1.29 url = {http://mitgcm.org/pdfs/journal_of_marine_systems_1998.pdf},
566     doi = {10.1016/S0924-7963\%2898\%2900008-6},
567 heimbach 1.1 }
568    
569     @Article{mcw:96,
570     author = {J. McWilliams},
571     year = 1996,
572     title = {Modeling the oceanic general circulation},
573     journal = arfm,
574     volume = {28},
575     pages = {215--248},
576     }
577 edhill 1.13
578     %% Rew, R. K., G. P. Davis, S. Emmerson, and H. Davies
579     %% NetCDF User's Guide for C, An Interface for Data Access, Version 3, April 1997.
580     %% (Available from Unidata or in PostScript form by anonymous FTP from
581     %% ftp://ftp.unidata.ucar.edu/pub/netcdf/guidec.ps.Z). There is also
582     %% a hypertext version of the User's Guide available at
583     %% http://www.unidata.ucar.edu/packages/netcdf/guidec. NetCDF User's
584     %% Guide for Fortran 90 and NetCDF User's Guide for Fortran 77 are
585     %% also available.
586    
587 heimbach 1.32 @incollection{naum-etal:06,
588     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},
589     Booktitle = {European Conference on Computational Fluid Dynamics ECCOMAS CFD 2006},
590     Editor = {{P. Wesseling, E. O~nate and J. Periaux}},
591     Pages = {~},
592     Publisher = {TU Delft},
593     Title = {Adjoint code by source transformation with OpenAD/F},
594     Year = {2006}}
595    
596 edhill 1.13 @TechReport{rew:97,
597     author = {R. K. Rew and G. P. Davis and S. Emmerson and H. Davies},
598     title = {{NetCDF User's Guide for C, FORTRAN 77, and FORTRAN 90},
599     An Interface for Data Access, Version 3},
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606    
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612 heimbach 1.1 data assimilation studies},
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614     volume = {19},
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632     booktitle = {Oceanic circulation models:
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634     pages = {257--285},
635     series = {NATO ASI Series},
636     volume = {C 284},
637     editor = {{D.L.T. Anderson and J. Willebrand}},
638     publisher = {Springer-Verlag},
639     address = {Berlin (Germany)},
640     }
641 cnh 1.6
642 heimbach 1.32 @article{utke-etal:08,
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644     Date-Modified = {2007-11-19 10:15:08 -0500},
645     Journal = {{ACM} Transactions on Mathematical Software},
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648     Volume = {34(4)},
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650    
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656     volume = {6},
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658     address = {Washington, D.C. (USA)},
659     note = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/},
660 cnh 1.28 url = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/},
661 cnh 1.6 }
662 heimbach 1.1
663 heimbach 1.32 @techreport{stam-etal:97,
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665 cnh 1.6 Q. Zhang and J. Marotzke and J. Marshall and
666 heimbach 1.1 C. Hill},
667     year = 1997,
668     title = {The global ocean circulation estimated from
669     TOPEX/POSEIDON altimetry and a general circulation
670     model},
671     institution = {Center for Global Change Science, Massachusetts
672     Institute of Technology},
673     type = {Technical Report},
674     number = {49},
675     pages = {40 pp.},
676     address = {Cambridge (MA), USA},
677     }
678    
679 heimbach 1.32 @ARTICLE{stam-etal:02,
680 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},
681     title = {The global ocean circulation and transports during 1992 -- 1997, estimated from ocean observations and a general circulation model.},
682     journal = jgr,
683     year = {2002a},
684     volume = {107(C9)},
685     pages = {3118},
686     doi = {10.1029/2001JC000888},
687     }
688    
689 cnh 1.6
690     @Article{Stommel66,
691     author = {H. Stommel},
692     year = 1948,
693     title = {The western intensification of wind-driven ocean currents},
694     journal = {Trans. Am. Geophys. Union},
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706     volume = {113},
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708     }
709    
710     @Article{tal:97,
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713     title = {Assimilation of observations, an introduction},
714     journal = {J.~Meteor.~Soc.~Japan},
715     volume = {75},
716     pages = {191--209},
717     }
718    
719     @book{tar:87,
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727     }
728    
729     @techreport{tha:87,
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732     title = {Three lectures on fitting numerical models to
733     observations},
734     institution = {GKSS},
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737     pages = {64 pp.},
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740    
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745     journal = jgr,
746     volume = {93, C2},
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749    
750     @Article{tha:88,
751     author = {W.C. Thacker},
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764     to measurements},
765     journal = jgr,
766     volume = {94, C5},
767     pages = {6,177--6,196},
768     }
769    
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772     year = 1994,
773     title = {The rigid lid's contribution to the ill-conditioning
774     of oceanic inverse problems},
775     journal = jgr,
776     volume = {99, C5},
777     pages = {10,131--10,141},
778     }
779    
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782     year = {1989},
783     title = {An optimal control / adjoint equation approach
784     to studying the ocean general circulation},
785     journal = jpo,
786     volume = {19},
787     pages = {1471--1485},
788     }
789    
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792     S. Hwang},
793     year = {1992a},
794     title = {Oceanic data analysis using a general circulation
795     model. I: Simulations},
796     journal = jpo,
797     volume = {22},
798     pages = {1434--1457},
799     }
800    
801     @Article{tzi-eta:92b,
802     author = {E. Tziperman and W.C. Thacker and R.B. Long and
803     S. Hwang and S.R. Rintoul},
804     year = {1992b},
805     title = {Oceanic data analysis using a general circulation
806     model. I: A North Atlantic model},
807     journal = jpo,
808     volume = {22},
809     pages = {1458--1485},
810     }
811    
812     @book{wun:96,
813     author = {C. Wunsch},
814     title = {The ocean circulation inverse problem},
815     year = 1996,
816     publisher = cup,
817     address = {Cambridge (UK)},
818     pages = {442 pp.},
819     }
820    
821     @Article{zha-mar:99,
822     author = {K.Q. Zhang and J. Marotzke},
823     year = 1999,
824     title = {The importance of open-boundary estimation for an
825     Indian Ocean GCM-data synthesis},
826     journal = {J.~Marine Res.},
827     volume = {57},
828     pages = {305--334},
829     }
830 adcroft 1.2
831    
832     @InCollection{hill:95,
833     author = {Hill, C. and J. Marshall},
834     title = {Application of a Parallel Navier-Stokes Model to
835     Ocean Circulation in Parallel Computational Fluid
836     Dynamics},
837     booktitle = {Implementations and Results Using Parallel
838     Computers},
839     pages = {545-552},
840     publisher = {Elsevier Science B.V.: New York},
841     year = 1995,
842     editor = {A. Ecer, J. Periaux, N. Satofuka and S. Taylor}
843     }
844    
845    
846     @Article{marshall:97a,
847 adcroft 1.4 author = {Marshall, J. and C. Hill and L. Perelman and A. Adcroft},
848 adcroft 1.2 title = {Hydrostatic, quasi-hydrostatic, and nonhydrostatic ocean
849     modeling},
850 jmc 1.25 journal = jgr,
851 adcroft 1.2 year = 1997,
852     volume = 102,
853     number = {C3},
854 cnh 1.29 pages = {5733-5752},
855     url = {http://mitgcm.org/pdfs/96JC02775.pdf},
856 adcroft 1.2 }
857    
858     @Article{marshall:97b,
859 cnh 1.10 author = {Marshall, J. and A. Adcroft and C. Hill and L. Perelman and C. Heisey},
860 adcroft 1.2 title = {A finite-volume, incompressible Navier Stokes model for
861     studies of the ocean on parallel computers},
862 jmc 1.25 journal = jgr,
863 adcroft 1.2 year = 1997,
864     volume = 102,
865     number = {C3},
866 cnh 1.29 pages = {5753-5766},
867     url = {http://mitgcm.org/pdfs/96JC02776.pdf},
868 adcroft 1.2 }
869    
870     @Article{adcroft:97,
871 adcroft 1.4 author = {Adcroft, A.J. and Hill, C.N. and J. Marshall},
872 adcroft 1.2 title = {Representation of topography by shaved cells in a height
873     coordinate ocean model},
874 jmc 1.25 journal = mwr,
875 adcroft 1.2 year = 1997,
876     volume = 125,
877 cnh 1.29 pages = {2293-2315},
878     url = {http://mitgcm.org/pdfs/mwr_1997.pdf},
879     doi = {10.1175/1520-0493\%281997\%29125<2293:ROTBSC>2.0.CO;2},
880 adcroft 1.2 }
881    
882 jmc 1.19 @Article{adcroft:04a,
883     author = {Adcroft, A. and J.-M. Campin},
884 jmc 1.14 title = {Re-scaled height coordinates for accurate representation
885     of free-surface flows in ocean circulation models},
886     journal = om,
887     year = 2004,
888 jmc 1.19 volume = 7,
889 cnh 1.28 pages = {269-284},
890     doi = {10.1016/j.ocemod.2003.09.003},
891 jmc 1.19 }
892    
893     @Article{adcroft:04b,
894     author = {Adcroft, A. and J.-M. Campin and C. Hill and J. Marshall},
895     title = {Implementation of an Atmosphere-Ocean General Circulation Model
896     on the Expanded Spherical Cube},
897     journal = mwr,
898     year = 2004,
899     volume = 132,
900 cnh 1.29 pages = {2845-2863},
901     url = {http://mitgcm.org/pdfs/mwr_2004.pdf},
902     doi = {10.1175/MWR2823.1},
903 jmc 1.19 }
904    
905 jmc 1.33 @inproceedings{adcroft:04c,
906     author = {Adcroft, A. and C. Hill and J.-M. Campin and J. Marshall
907     and P. Heimbach},
908     title = {Overview of the Formulation and Numerics of the MIT GCM},
909     booktitle = {Proceedings of the ECMWF seminar series on Numerical Methods,
910     Recent developments in numerical methods for atmosphere and
911     ocean modelling},
912     year = 2004,
913     pages = {139-149},
914     url = {http://mitgcm.org/pdfs/ECMWF2004-Adcroft.pdf},
915     publisher = ecmwf
916     }
917    
918 jmc 1.19 @Article{marshall:04,
919     author = {Marshall, J. and A. Adcroft and J.-M. Campin and C. Hill and A. White},
920     title = {Atmosphere-Ocean Modeling Exploiting Fluid Isomorphisms},
921     journal = mwr,
922     year = 2004,
923     volume = 132,
924 cnh 1.29 pages = {2882-2894},
925     url = {http://mitgcm.org/pdfs/a_o_iso.pdf},
926     doi = {10.1175/MWR2835.1},
927 jmc 1.14 }
928    
929 adcroft 1.2 @Article{visbeck:97,
930     author = {Visbeck, M., J. Marshall, T. Haine, and M. Spall},
931     title = {Specification of eddy transfer coefficients in
932     coarse-resolution ocean circulation models},
933 jmc 1.25 journal = jpo,
934 adcroft 1.2 year = 1997,
935     volume = 27,
936     number = 3,
937     pages = {381-402}
938     }
939    
940     @Article{shaw:98,
941     author = {Shaw; A. Arvind, Cho, K.-C., Hill, C., Johnson, R.P.
942     and Marshall, J.},
943     title = {A comparison of implicitly parallel multi-threaded and
944     data-parallel implementations of an ocean model based
945     on the Navier-Stokes equations},
946     journal = {J. of Parallel and Distributed Computing},
947     year = 1998,
948     volume = 48,
949     number = 1,
950     pages = {1-51}
951     }
952    
953     @Article{mjn:99,
954     author = {Marshall, J., Jamous, D and J. Nilsson},
955     title = {Reconciling `thermodynamic' and `dynamic' methods of
956     computation of water-mass transformation rates},
957     journal = {DSR},
958     year = 1999,
959     volume = 46,
960     pages = {545-572}
961     }
962    
963     @Article{ms:99,
964     author = {Marshall, J and F. Schott},
965     title = {Open ocean deep convection: observations, models and theory},
966     journal = {Rev. Geophys.},
967     year = 1999,
968     volume = 37,
969     number = 1,
970     pages = {1-64}
971     }
972    
973     @Article{adcroft:99,
974     author = {Adcroft, A., Hill C. and J. Marshall},
975     title = {A new treatment of the Coriolis terms in C-grid models
976     at both high and low resolutions},
977 jmc 1.25 journal = mwr,
978 adcroft 1.2 year = 1999,
979     volume = 127,
980 cnh 1.29 pages = {1928-1936},
981     url = {http://mitgcm.org/pdfs/mwr_1999.pdf},
982     doi = {10.1175/1520-0493\%281999\%29127<1928:ANTOTC>2.0.CO;2},
983 adcroft 1.2 }
984    
985     @InProceedings{hill:99,
986     author = {Chris Hill, Alistair Adcroft, Daniel Jamous and John Marshall},
987     title = {A Strategy for Terascale Climate Modeling},
988 cnh 1.8 booktitle = {In Proceedings of the Eighth ECMWF Workshop on the Use of Parallel Processors in Meteorology},
989 cnh 1.9 year = 1999,
990     pages = {406-425},
991     publisher = {World Scientific},
992 adcroft 1.2 }
993    
994     @Article{wardle:00,
995     author = {Wardle R. and Marshall J.},
996     title = {Representation of eddies in primitive equation models by a PV flux},
997 jmc 1.25 journal = jpo,
998 adcroft 1.2 year = 2000,
999     volume = 30,
1000     number = 10,
1001     pages = {2481-2503}
1002     }
1003    
1004     @Article{ac:02,
1005     author = {Adcroft, A. and J.-M. Campin},
1006     title = {Comparison of finite volume schemes and direct-space-time
1007     methods for ocean circulation models},
1008 jmc 1.14 journal = om,
1009 adcroft 1.2 year = 2002,
1010     note = {in preparation}
1011     }
1012    
1013     @Article{adcroft:02,
1014 jmc 1.25 author = {Adcroft, A., et~al.},
1015 adcroft 1.2 title = {Energy conversion in discrete numerical models},
1016 jmc 1.14 journal = om,
1017 adcroft 1.2 year = 2002,
1018     note = {in preparation}
1019     }
1020    
1021     @InCollection{arakawa:77,
1022     author = {Arakawa, A. and Lamb, V.},
1023     title = {Computational Design of the Basic Dynamical Processes of
1024     the UCLA General Circulation Model},
1025     booktitle = {Methods in Computational Physics},
1026     pages = {174-267},
1027     publisher = {Academic Press},
1028     year = 1977,
1029     volume = 17
1030     }
1031    
1032 jmc 1.24 @Article{miller_white:84,
1033     author = {Miller, M. J. and White, A. A.},
1034     title = {On the non-hydrostatic equations in pressure
1035     and sigma coordiantes},
1036 jmc 1.25 journal = qjrms,
1037 jmc 1.24 year = 1984,
1038     volume = 110,
1039     pages = {515-533}
1040     }
1041    
1042     @Article{white:89,
1043     author = {White, A. A.},
1044     title = {An extended version of a nonhydrostatic, pressure coordiante model},
1045 jmc 1.25 journal = qjrms,
1046 jmc 1.24 year = 1989,
1047     volume = 115,
1048     pages = {1243-1251}
1049     }
1050    
1051 adcroft 1.2 @Article{adcroft:98,
1052     author = {Adcroft, A. and Marshall, D.},
1053 adcroft 1.3 title = {How slippery are piecewise-constant coastlines in numerical
1054     ocean models?},
1055 adcroft 1.2 journal = {Tellus},
1056 adcroft 1.3 year = 1998,
1057     volume = 50,
1058     number = 1,
1059     pages = {95-108}
1060     }
1061    
1062     @PhdThesis{adcroft:95,
1063     author = {Adcroft, A.},
1064     title = {Numerical Algorithms for use in a Dynamical Model of the
1065     Ocean},
1066     school = {Imperial College, London},
1067     year = 1995
1068     }
1069    
1070     @Article{griffies:00,
1071     author = {Griffies, S.,M. and Hallberg, R.,W.},
1072     title = {Biharmonic friction with a Smagorinsky-like viscosity for
1073     use in large-scale eddy-permitting ocean models},
1074 jmc 1.25 journal = mwr,
1075 adcroft 1.3 year = 2000,
1076     volume = 128,
1077     number = 8,
1078     pages = {2935-2946}
1079     }
1080    
1081     @Article{wajsowicz:93,
1082     author = {Wajsowicz, R.},
1083     title = {A CONSISTENT FORMULATION OF THE ANISOTROPIC STRESS TENSOR
1084     FOR USE IN MODELS OF THE LARGE-SCALE OCEAN CIRCULATION},
1085 jmc 1.25 journal = jcp,
1086 adcroft 1.3 year = 1993,
1087     volume = 105,
1088     number = 2,
1089     pages = {333-338}
1090     }
1091    
1092     @Article{campin:02,
1093 jmc 1.14 author = {Campin, J.-M. and A. Adcroft and C. Hill and J. Marshall},
1094 adcroft 1.3 title = {Conservation of properties in a free-surface model},
1095 jmc 1.14 journal = om,
1096     year = 2004,
1097     volume = 6,
1098     pages = {221-244}
1099 adcroft 1.4 }
1100    
1101     @Article{dm:95,
1102     author = {Danabasoglu, G. and McWilliams J.C.},
1103     title = {Sensitivity of the global ocean circulation to parameterizations of mesoscale tracer transports},
1104 jmc 1.25 journal = jclim,
1105 adcroft 1.4 year = 1995,
1106     volume = 8,
1107     number = 12,
1108     pages = {2967-2987}
1109     }
1110    
1111     @Article{ldd:97,
1112     author = {Large, W.G. and Danabasoglu, G. and Doney, S.C. and McWilliams, J.C.},
1113     title = {Sensitivity to surface forcing and boundary layer mixing in a global ocean model: Annual-mean climatology},
1114 jmc 1.25 journal = jpo,
1115 adcroft 1.4 year = 1997,
1116     volume = 27,
1117     number = 11,
1118     pages = {2418-2447}
1119     }
1120    
1121     @Article{gkw:99,
1122     author = {Gerdes R. and Koberle C. and Beckmann A. and Herrmann P. and Willebrand J.},
1123     title = {Mechanisms for spreading of Mediterranean water in
1124     coarse-resolution numerical models},
1125 jmc 1.25 journal = jpo,
1126 adcroft 1.4 year = 1999,
1127     volume = 29,
1128     number = 8,
1129     pages = {1682-1700}
1130     }
1131    
1132 jmc 1.17 @incollection{roe:85,
1133     author = {P.L. Roe},
1134     year = 1985,
1135     title = {Some contributions to the modelling of discontinuous flows},
1136     booktitle = {Large-Scale Computations in Fluid Mechanics},
1137     series = {Lectures in Applied Mathematics},
1138     volume = 22,
1139     pages = {163-193},
1140     editor = {B.E. Engquist and S. Osher and R.C.J. Somerville},
1141     publisher = {American Mathematical Society},
1142     address = {Providence, RI},
1143 adcroft 1.2 }
1144    
1145 mlosch 1.12 @Article{trenberth90,
1146     author = {K. M. Trenberth and J. Olson and W. G. Large},
1147     title = {The Mean Annual Cycle in {G}lobal {O}cean Wind
1148     Stress},
1149     journal = jpo,
1150     year = 1990,
1151     volume = 20,
1152     pages = {1742--1760}
1153 jmc 1.14 }
1154    
1155     @Article{molteni:03,
1156 jmc 1.27 author = {F. Molteni},
1157 edhill 1.30 title = {Atmospheric simulations using a {GCM} with simplified physical
1158     parametrization, {I}: Model climatology and variability in
1159 jmc 1.14 multidecadal experiments},
1160     journal = climd,
1161     year = 2003,
1162     volume = 20,
1163     pages = {175--191}
1164 mlosch 1.12 }
1165    
1166     @Article{jiang99,
1167 edhill 1.21 author = {S. Jiang and P. H. Stone and P. Malanotte-Rizzoli},
1168 mlosch 1.12 title = {An Assessment of the {G}eophysical {F}luid
1169     {D}ynamics {L}aboratory Ocean Model with Coarse
1170     Resolution: Annual-Mean Climatology},
1171     journal = jgr,
1172     year = 1999,
1173     volume = 104,
1174     number = {C11},
1175     pages = {25,623--25,645}
1176     }
1177    
1178     @Article{szoeke02,
1179     author = {de Szoeke, Roland A. and Roger M. Samelson},
1180     title = {The Duality between the {B}oussinesq and
1181     {N}on-{B}oussinesq Hydrostatic Equations of Motion},
1182     journal = jpo,
1183     year = 2002,
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1192     Achieve Static Stability},
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1194     year = 1995,
1195     volume = 12,
1196     number = 4,
1197     pages = {381--389}
1198     }
1199    
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1205     journal = jaot,
1206     year = {2003},
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1208     OPTvolume = {},
1209     OPTnumber = {},
1210     OPTpages = {},
1211     OPTmonth = {},
1212     OPTnote = {{\textup{In press}}},
1213     OPTannote = {}
1214     }
1215    
1216     @TechReport{fofonoff83,
1217     author = "Fofonoff, P. and Millard, Jr., R.C.",
1218     title = "Algorithms for Computation of Fundamental Properties
1219     of Seawater",
1220     institution = "Unesco",
1221     year = 1983,
1222     type = "Unesco Technical Papers in Marine Science",
1223     number = 44,
1224     pages = {53 pp.}
1225     }
1226    
1227 edhill 1.15 @ARTICLE{zha98a,
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1231     JOURNAL = jpo,
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1233     VOLUME = 28,
1234     PAGES = "191-217"
1235     }
1236    
1237     @ARTICLE{sem76,
1238     AUTHOR = "Semtner, Jr., Albert J.",
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1240     numerical investigations of climate",
1241     JOURNAL = jpo,
1242     YEAR = 1976,
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1244     PAGES = "379-389"
1245     }
1246    
1247     @ARTICLE{win00,
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1249     TITLE = "A reformulated three-layer sea ice model",
1250     JOURNAL = jaot,
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1252     VOLUME = 17,
1253     PAGES = "525-531"
1254     }
1255    
1256     @ARTICLE{hib79,
1257     AUTHOR = "W. D. {Hibler, III}",
1258     TITLE = "A Dynamic Thermodynamic Sea Ice Model",
1259     JOURNAL = jpo,
1260     YEAR = 1979,
1261     VOLUME = 9,
1262     PAGES = "815-846"
1263     }
1264    
1265     @ARTICLE{fla92,
1266     AUTHOR = "G. M. Flato and W. D. {Hibler, III}",
1267     TITLE = "Modeling pack ice as a cavitating fluid",
1268     JOURNAL = jpo,
1269     YEAR = 1992,
1270     VOLUME = 22,
1271     PAGES = "626-651"
1272     }
1273    
1274     @ARTICLE{hun97,
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1277     JOURNAL = jpo,
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1279     VOLUME = 27,
1280     PAGES = "1849-1867"
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1282    
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1288     VOLUME = 105,
1289     PAGES = "3325-3338"
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1302 edhill 1.20 @TechReport{Dutkiewicz_etal_05,
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1304     title = {A Three-Dimensional Ocean-Seaice-Carbon Cycle Model and
1305     its Coupling to a Two-Dimensional Atmospheric Model: Uses
1306     in Climate Change Studies, Report 122},
1307     institution = {MIT Joint Program of the Science and Policy of Global Change},
1308     year = {2005},
1309     OPTnumber = {122},
1310     address = {Cambridge, MA},
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1319     year = {{in press}},
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1341     institution = {NCAR},
1342     year = {1989},
1343     OPTkey = {},
1344     OPTtype = {},
1345     number = {NCAR/TN-338+STR},
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1358     pages = {7373--7382},
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1360     }
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1364     year = {1977},
1365     title = {High Resolution Models of the Planetary Boundary Layer.},
1366     booktitle = {Advances in Environmental Science and Engineering, Vol 1 } ,
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1369     }
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1371     @Article{chou:92,
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1377     pages = {762-772}
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1384     by O$_2$ and CO$_2$ with applications to climate studies.},
1385     journal = jclim,
1386     volume = {3},
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1390     @techreport{chsz:94,
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1392     year = {1994},
1393     title = {An efficient thermal infrared radiation parameterization
1394     for use in general circulation models},
1395     institution = {National Aeronautics and Space Administration},
1396     type = {NASA Technical Memorandum},
1397     number = {104606-Vol 3},
1398     address = {NASA; Goddard Space Flight Center; Greenbelt (MD), 20771; USA},
1399     note = {http://www.gmao.nasa.gov/}
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1477     address = {NASA; Goddard Space Flight Center; Greenbelt (MD), 20771; USA},
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1595     volume = {122},
1596     pages = {903-927}
1597     }
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1619     }
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1625     Implications for the Simulation of the Madden-Julian Oscillation.},
1626     journal = {Climate Dyn.},
1627     volume = {17},
1628     pages = {777-794}
1629     }
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1649 edhill 1.26 @TechReport{MPI-std-20,
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1651     title = {{MPI}: A Message-Passing Interface standard (version 2.0)},
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1653     year = {1998},
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