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Revision 1.47 - (hide annotations) (download)
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add a few references for the seaice JFNK-solver

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 mlosch 1.47 @string{siscicom= {SIAM J.\ Sci.\ Comput.}}
39 heimbach 1.1
40     @Article{bis-eta:92,
41     author = {C.H. Bishof and G.F. Corliss and L. Green and
42     A. Griewank and K. Haigler and P. Newman},
43     year = 1992,
44     title = {Automatic differentiation of advanced GFD codes
45     for multidisciplinary design},
46     journal = {Journal on Computing Systems in Engineering},
47     volume = {3},
48     pages = {625--638},
49     }
50 jmc 1.45
51 heimbach 1.1 @incollection{bis:94,
52     author = {C.H. Bishof},
53     year = 1994,
54     title = {Automatic differentiation, tangent linear models
55     and pseudo-adjoints},
56     booktitle = {High Performance Computing in the Geosciences},
57     series = {Series C: Mathematical and Physical Sciences},
58     pages = {59--80},
59     editor = {F.X. {Le Dimet}},
60     publisher = {Kluwer},
61     address = {Dordrecht, NL},
62     }
63 jmc 1.45
64 heimbach 1.1 @techreport{bis-eta:94,
65     author = {C. Bishof and A. Carle and P. Khademi and
66     A. Maurer},
67     year = 1994,
68     title = {The ADIFOR 2.0 system for the automatic
69     differentiation of FORTRAN 77 programs},
70     institution = {Argonne National Laboratory, Mathematics and
71     Computer Science Division},
72     type = {Argonne Preprint},
73     number = {ANL-MCS-P981-1194},
74 jmc 1.45 address = {ANL; 9700 South Cass Ave.;
75 heimbach 1.1 Argonne (ILL), 90439; USA},
76     note = {http://www.mcs.anl.gov/autodiff/},
77     }
78 cnh 1.29
79 jmc 1.46 @ARTICLE{bryan:84,
80     author = {Kirk Bryan},
81     title = {Accelerating the convergence to equilibrium of Ocean-Climate Models},
82     journal = jpo,
83     year = {1984},
84     volume = {14},
85     number = {4},
86     pages = {666-673},
87     }
88    
89 cnh 1.29 @ARTICLE{bugi-hill:06,
90     author = {V. Bugnion and C. Hill},
91     title = {Equilibration mechanisms in an adjoint ocean general
92     circulation model},
93     journal = {Ocean Dynamics},
94     year = {2006},
95     volume = {56},
96     number = {1},
97     pages = {51-61},
98     doi = {10.1007/s10236-005-0052-z},
99     }
100 jmc 1.45
101 heimbach 1.1 @techreport{bis-roh:97,
102     author = {C. Bishof and L. Roh},
103     year = 1997,
104     title = {ADIC: An extensible automatic differentiation tool
105     for ANSI-C},
106     institution = {Argonne National Laboratory, Mathematics and
107     Computer Science Division},
108     type = {Argonne Preprint},
109     number = {ANL-MCS-P626-1196},
110 jmc 1.45 address = {ANL; 9700 South Cass Ave.;
111 heimbach 1.1 Argonne (ILL), 90439; USA},
112     note = {http://www.mcs.anl.gov/autodiff/},
113     }
114 jmc 1.45
115 heimbach 1.1 @Article{cou-tal:87,
116     author = {P. Courtier and O. Talagrand},
117     year = 1987,
118 jmc 1.45 title = {Variational assimilation of meteorological
119 heimbach 1.1 observations with the adjoint vorticity equation.
120     II: Numerical results},
121     journal = qjrms,
122     volume = {113},
123     pages = {1329--1347},
124     }
125 jmc 1.45
126 heimbach 1.1 @Article{cou-tal:90,
127     author = {P. Courtier and O. Talagrand},
128     year = 1990,
129     title = {Variational assimilation of meteorological
130     observations with direct and adjoint shallow-water
131     equations},
132     journal = tel,
133     volume = {42A},
134     pages = {531--549},
135     }
136 jmc 1.45
137 heimbach 1.1 @Article{cou-eta:94,
138     author = {P. Courtier and J.-N. Th{\'e}paut and
139     A. Hollingsworth},
140     year = 1994,
141     title = {A strategy for operational implementation of
142     4-D-VAR using an incremental approach},
143     journal = qjrms,
144     volume = {120},
145     pages = {1367--1387},
146     }
147 cnh 1.29
148 jmc 1.33 @ARTICLE{durr:91,
149     author = {Dale R. Durran},
150     title = {The Third-Order Adams-Bashforth Method: An Attractive Alternative
151     to Leapfrog Time Differencing},
152     journal = mwr,
153     year = {1991},
154     volume = {119},
155     pages = {702-720},
156     }
157 jmc 1.45
158 jmc 1.33
159 cnh 1.29 @ARTICLE{dutk-etal:06,
160     author = {S. Dutkiewicz and M.J. Follows and P. Heimbach and J. Marshall},
161     title = {Controls on ocean productivity and air-sea carbon flux:
162     An adjoint model sensitivity study},
163     journal = grl,
164     year = {2006},
165     volume = {33},
166     pages = {L02603},
167     doi = {10.1029/2005GL024987},
168     }
169 jmc 1.45
170 heimbach 1.1 @Article{err:97,
171     author = {R.M. Errico},
172     year = 1997,
173     title = {What is an adjoint model},
174     journal = bams,
175     volume = {78},
176     pages = {2577--2591},
177     }
178 jmc 1.45
179 heimbach 1.1 @Article{far-moo:92,
180     author = {B.F. Farrell and A.M. Moore},
181     year = {1992},
182     title = {An adjoint method for obtaining the most rapidly
183     growing perturbation to oceanic flows},
184     journal = jpo,
185     volume = {22},
186     pages = {338--349},
187     }
188 jmc 1.45
189 heimbach 1.1 @Article{far-ioa:96a,
190     author = {B.F. Farrell and P. Ioannou},
191     year = {1996a},
192     title = {Generalized stability theory. Part I:
193     Autonomous operators},
194     journal = jas,
195     volume = {53},
196     pages = {2025--2040},
197     }
198 jmc 1.45
199 heimbach 1.1 @Article{far-ioa:96b,
200     author = {B.F. Farrell and P. Ioannou},
201     year = {1996b},
202     title = {Generalized stability theory. Part I:
203     Nonautonomous operators},
204     journal = jas,
205     volume = {53},
206     pages = {2041--2053},
207     }
208 jmc 1.45
209 heimbach 1.1 @techreport{fau-pap:98,
210     author = {C. Faure and Y. Papegay},
211     year = 1998,
212     title = {Odyss{\'e}e User's Guide. Version 1.7},
213     institution = {Institut National de Recherche en Informatique
214     et en Automatique},
215     type = {Rapport Technique},
216     number = {0224},
217     address = {INRIA; 2004, route des Luciolis, B.P. 93;
218     06902 Sophia Antipolis Cedex; France},
219     note = {http://www-sop.inria.fr/safir/SAM/Odyssee/odyssee.html},
220     }
221 jmc 1.45
222 heimbach 1.1 @Article{fau:00,
223     author = {C. Faure},
224     year = {2000},
225     title = {Adjoining strategies for multi-layered programs},
226     journal = {Optimisation Methods and Software},
227     note = {in press},
228     }
229 jmc 1.45
230 dfer 1.34 @Article{fer-eta:05,
231     author = {D. Ferreira and J. Marshall and P. Heimbach},
232     year = 2005,
233     title = {Estimating Eddy Stresses by Fitting Dynamics to Observations
234     using a Residual-Mean Ocean Circulation Model and Its Adjoint},
235     journal = jpo,
236     volume = {35},
237     pages = {1891--1910},
238     }
239    
240 jmc 1.39 @Article{gas-eta:90,
241 jmc 1.45 author = {P. Gaspar and Y. Gr\'egoris and J.-M. Lefevre},
242 jmc 1.39 year = 1990,
243 jmc 1.45 title = {A Simple Eddy Kinetic Energy Model for Simulations of the
244     Oceanic Vertical Mixing: Tests at Station Papa and Long-Term
245 jmc 1.39 Upper Ocean Study Site},
246     journal = jgr,
247     volume = {95 (C9)},
248     pages = {16,179--16,193},
249     }
250    
251 heimbach 1.1 @Article{gen-mcw:90,
252 dfer 1.44 author = {P. R. Gent and J. C. McWilliams},
253 heimbach 1.1 year = 1990,
254     title = {Isopycnal mixing in ocean circulation models},
255     journal = jpo,
256     volume = {20},
257     pages = {150--155},
258     }
259 jmc 1.45
260 heimbach 1.1 @Article{gen-eta:95,
261 dfer 1.44 author = {P. R. Gent and J. Willebrand and T. J. McDougall and J. C. McWilliams},
262 heimbach 1.1 year = 1995,
263 dfer 1.44 title = {Parameterizing eddy-induced tracer transports in ocean circulation models},
264 heimbach 1.1 journal = jpo,
265     volume = {25},
266     pages = {463--474},
267     }
268 jmc 1.45
269 heimbach 1.1 @Article{gie-kam:98,
270     author = {R. Giering and T. Kaminski},
271     year = 1998,
272     title = {Recipes for adjoint code construction},
273     journal = {ACM Transactions on Mathematical Software},
274     volume = 24,
275     pages = {437--474},
276     }
277    
278     @techreport{gie:99,
279     author = {R. Giering},
280     year = 1999,
281 jmc 1.45 title = {Tangent linear and Adjoint Model Compiler.
282 heimbach 1.1 Users manual 1.4 (TAMC Version 5.2)},
283     institution = {Massachusetts Institute of Technology},
284     type = {Report},
285     number = {~},
286     address = {MIT/EAPS; 77 Massachusetts Ave.; Cambridge (MA)
287     02139; USA},
288     note = {http://puddle.mit.edu/$\sim$ralf/tamc/tamc.html},
289     }
290 jmc 1.45
291 heimbach 1.1 @incollection{gie:00,
292     author = {R. Giering},
293     editor = {P. Kasibhatla and M. Heimann and P. Rayner and
294     N. Mahowald and R.G. Prinn and D.E. Hartley},
295     year = 2000,
296     booktitle = {Inverse methods in global biogeochemical cycles},
297     title = {Tangent linear and adjoint biogeochemical models},
298     publisher = {American Geophysical Union},
299     series = {Geophysical Monograph},
300     volume = {114},
301     address = {Washington, DC},
302     pages = {33--48},
303     }
304    
305     @Article{gil-lem:89,
306     author = {J.C. Gilbert and C. Lemar\'echal},
307     year = 1989,
308     title = {Some numerical experiments with variable-storage
309     quasi-Newton algorithms},
310     journal = {Math. Programming},
311     volume = {45},
312     pages = {407--435},
313     }
314 jmc 1.45
315 heimbach 1.1 @book{gil-eta:81,
316     author = {P.E. Gill and W. Murray and M.H. Wright},
317     title = {Practical optimization},
318     year = 1981,
319     publisher = {Academic Press},
320 jmc 1.45 address = {London},
321 heimbach 1.1 pages = {401 pp.},
322     }
323 jmc 1.45
324 heimbach 1.11 @incollection{gri:89,
325     author = {A. Griewank},
326     year = 1989,
327     title = {On automatic differentiation},
328     booktitle = {Mathematical Programming: Recent Developments and
329     Applications},
330     pages = {83--108},
331     editor = {M. Iri and K. Tanabe},
332     publisher = {Kluwer},
333     address = {Dordrecht, NL},
334     }
335 jmc 1.45
336 heimbach 1.11 @Article{gri:92,
337     author = {A.~Griewank},
338     title = {Achieving logarithmic growth of temporal and spatial
339     complexity in reverse {A}utomatic {D}ifferentiation},
340     journal = {Optimization Methods and Software},
341     year = {1992},
342     volume = {1},
343     pages = {35--54}
344     }
345    
346 heimbach 1.1 @book{gri:00,
347     author = {A. Griewank},
348     title = {Evaluating Derivatives. Principles and Techniques
349     of Algorithmic Differentiation},
350     year = 2000,
351     series = {Frontiers in Applied Mathematics},
352     volume = {19},
353     publisher = {SIAM},
354 jmc 1.45 address = {Philadelphia},
355 heimbach 1.1 pages = {369 pp.},
356     }
357 jmc 1.45
358 heimbach 1.1 @Article{hal-eta:82,
359     author = {M.C.G. Hall and D.G. Caccuci and M.E. Schlesinger},
360     year = 1982,
361     title = {Sensitivity analysis of a radiative-convective
362     model by the adjoint method},
363     journal = jas,
364     volume = {39},
365     pages = {2038--3050},
366     }
367 cnh 1.6
368     @Article{Haney,
369     author = {R.L. Haney},
370     title = {Surface thermal boundary conditions for ocean
371     circulation models},
372     journal = jpo,
373     year = 1971,
374     volume = 1,
375     pages = {241--248}
376     }
377 jmc 1.45
378 cnh 1.16 @Article{held-suar:94,
379     author = {I.M. Held and M.J. Suarez},
380     year = {1994},
381     title = {A proposal for the intercomparison of the dynamical cores of atmospheric general circulation models},
382     journal = {Bulletin of the American Meteorological Society},
383     volume = {75(10)},
384     pages = {1825-1830}
385     }
386 jmc 1.45
387 heimbach 1.1 @Article{hil-eta:01,
388 jmc 1.45 author = {C. Hill and M. Follows and V. Bugnion and
389 heimbach 1.1 J. Marshall},
390 cnh 1.10 year = {2002},
391 jmc 1.45 title = {Spatial and Temporal Impacts of ocean general
392 heimbach 1.1 circulation on carbon sequestration},
393 cnh 1.6 journal = {Global Biogeochemical Cycles},
394 heimbach 1.1 note = {submitted},
395     }
396 cnh 1.6
397 edhill 1.15 @ARTICLE{hib80,
398 mlosch 1.36 author = {Hibler, III, William D.},
399 edhill 1.15 TITLE = "Modeling a Variable Thickness Sea Ice Cover",
400     JOURNAL = mwr,
401     YEAR = 1980,
402     VOLUME = 1,
403     PAGES = "1943-1973"
404     }
405    
406 cnh 1.6 @Article{Holland75,
407     author = {W.R. Holland and L. B. Lin},
408     year = {1975a},
409 jmc 1.45 title = {On the origin of mesoscale eddies and their contribution
410     to the general circulation of the ocean. I. A preliminary
411 cnh 1.6 numerical experiment},
412     journal = jpo,
413     volume = {5},
414     pages = {642-657}
415     }
416    
417     @Article{hol-lin:75b,
418     author = {W.R. Holland and L. B. Lin},
419     year = {1975b},
420 jmc 1.45 title = {On the origin of mesoscale eddies and their contribution
421 cnh 1.6 to the general circulation of the ocean. II. A parameter
422     study},
423     journal = jpo,
424     volume = {5},
425     pages = {658-669}
426     }
427    
428 jmc 1.31 @Article{jam-oze:86,
429 jmc 1.45 author = {B.M. Jamart and J. Ozer},
430 jmc 1.31 year = {1986},
431 jmc 1.45 title = {Numerical boundary layers and spurious residual flows},
432 jmc 1.31 journal = jgr,
433     volume = {91},
434     pages = {10,621-10,631}
435     }
436    
437 heimbach 1.1 @book{kas-eta:00,
438     author = {P. Kasibhatla and M. Heimann and P. Rayner and
439     N. Mahowald and R.G. Prinn and D.E. Hartley},
440     year = 2000,
441     title = {Inverse methods in global biogeochemical cycles},
442     publisher = {American Geophysical Union},
443     series = {Geophysical Monograph},
444     volume = {114},
445     address = {Washington, DC},
446     pages = {324 pp.},
447     }
448    
449     @Article{lar-eta:94,
450     author = {W.G. Large and J.C. McWilliams and S.C. Doney},
451     year = 1994,
452 dfer 1.44 title = {Oceanic vertical mixing: A review and a model with nonlocal boundary layer parameterization},
453 heimbach 1.1 journal = {Rev.~Geophys.},
454     volume = {32},
455     pages = {363--403},
456     }
457 jmc 1.45
458 heimbach 1.1 @Article{lar-eta:97,
459 jmc 1.45 author = {W. G. Large and G. Danabasoglu and S. C. Doney
460     and J. C. McWilliams},
461 heimbach 1.1 year = 1997,
462     title = {Sensitivity to surface forcing and boundary layer
463 jmc 1.45 mixing in a global ocean model: Annual-mean climatology},
464 heimbach 1.1 journal = jpo,
465     volume = {27},
466 jmc 1.45 number = 11,
467 heimbach 1.1 pages = {2418--2447},
468     }
469 jmc 1.45
470 heimbach 1.1 @Article{led-tal:86,
471     author = {F.-X. {Le Dimet} and O. Talagrand},
472     year = 1986,
473     title = {Variational algorithms for analysis and
474     assimilation of meteorological observations:
475     theoretical aspects},
476     journal = tel,
477     volume = {38A},
478     pages = {97--110},
479     }
480 cnh 1.6
481     @TechReport{lev:94a,
482     author = {S. Levitus and T.P.Boyer},
483     title = {{World Ocean Atlas 1994 Volume 3: Salinity}},
484     institution = {NOAA Atlas NESDIS 3},
485     year = 1994,
486     OPTkey = {},
487     OPTtype = {},
488     OPTnumber = {},
489     OPTaddress = {U.S. Department of Commerce, Washington D.C.},
490     OPTmonth = {},
491     OPTnote = {},
492     OPTannote = {}
493     }
494    
495    
496     @TechReport{Levitus94,
497     author = {S. Levitus and T.P.Boyer},
498     title = {{World Ocean Atlas 1994 Volume 4: Temperature}},
499     institution = {NOAA Atlas NESDIS 4},
500     year = 1994,
501     OPTkey = {},
502     OPTtype = {},
503     OPTnumber = {},
504     OPTaddress = {U.S. Department of Commerce, Washington D.C.},
505     OPTmonth = {},
506     OPTnote = {},
507     OPTannote = {}
508     }
509    
510 jmc 1.45
511 heimbach 1.1 @Article{lew-der:85,
512     author = {J. Lewis and J. Derber},
513     year = {1985},
514     title = {The use of adjoint equations to solve a variational
515     adjustment problem with advective constraints},
516     journal = {Tellus},
517     volume = {37A},
518     pages = {309--322},
519     }
520 jmc 1.45
521 heimbach 1.1 @techreport{lon:88,
522     author = {R.B. Long},
523     year = 1988,
524     title = {Notes on assimilating observations into
525     numerical models},
526     institution = {Delft Hydraulics},
527     type = {Report},
528     number = {~},
529     pages = {38 pp.},
530     address = {Delft (NL)},
531     }
532 cnh 1.29
533     @ARTICLE{losc-heim:06,
534 mlosch 1.42 author = {Martin Losch and Patrick Heimbach},
535     title = {Adjoint Sensitivity of an Ocean General Circulation
536     Model to Bottom Topography},
537     journal = jpo,
538     year = 2007,
539     volume = 37,
540     doi = {10.1175/JPO3017.1},
541     number = 2,
542     pages = {377--393},
543 cnh 1.29 url = {http://mitgcm.org/pdfs/Los2006a.pdf},
544     }
545    
546 jmc 1.45
547 heimbach 1.1 @Article{maro-wun:93,
548     author = {J. Marotzke and C. Wunsch},
549     year = 1993,
550     title = {Finding the steady state of a general circulation
551     model through data assimilation:
552     Application to the North Atlantic Ocean},
553     journal = jgr,
554     volume = {98, C11},
555     pages = {20,149--20,167},
556     }
557 jmc 1.45
558 heimbach 1.1 @Article{maro-eta:99,
559 jmc 1.45 author = {J. Marotzke and R. Giering and K.Q. Zhang and
560 heimbach 1.1 D. Stammer and C. Hill and T. Lee},
561     year = 1999,
562     title = {Construction of the adjoint MIT ocean general
563     circulation model and application to Atlantic heat
564     transport variability},
565     journal = jgr,
566     volume = {104, C12},
567     pages = {29,529--29,547},
568     }
569 jmc 1.45
570 heimbach 1.1 @Article{mars-eta:97a,
571     author = {J. Marshall and C. Hill and L. Perelman and
572     A. Adcroft},
573     year = {1997a},
574     title = {Hydrostatic, quasi-hydrostatic and
575     nonhydrostatic ocean modeling},
576     journal = jgr,
577     volume = {102, C3},
578     pages = {5,733--5,752},
579     }
580 jmc 1.45
581 heimbach 1.1 @Article{mars-eta:97b,
582 jmc 1.45 author = {J. Marshall and A. Adcroft and C. Hill and
583 heimbach 1.1 L. Perelman and C. Heisey},
584     year = {1997b},
585     title = {Hydrostatic, quasi-hydrostatic and
586     nonhydrostatic ocean modeling},
587     journal = jgr,
588     volume = {102, C3},
589     pages = {5,753--5,766},
590     }
591 jmc 1.45
592 jmc 1.33 @Article{mars-eta:98,
593 heimbach 1.1 author = {J. Marshall and H. Jones and C. Hill},
594     year = 1998,
595     title = {Efficient ocean modeling using
596     non-hydrostatic algorithms},
597     journal = jms,
598     volume = {18},
599     pages = {115--134},
600 cnh 1.29 url = {http://mitgcm.org/pdfs/journal_of_marine_systems_1998.pdf},
601     doi = {10.1016/S0924-7963\%2898\%2900008-6},
602 heimbach 1.1 }
603 jmc 1.45
604 jmc 1.38 @Article{mol:09,
605     author = {Andrea Molod},
606     year = 2009,
607     title = {Running {GCM} physics and dynamics on different grids:
608     algorithm and tests},
609     journal = tel,
610     volume = {61A},
611     pages = {381--393},
612 heimbach 1.1 }
613 edhill 1.13
614     %% Rew, R. K., G. P. Davis, S. Emmerson, and H. Davies
615     %% NetCDF User's Guide for C, An Interface for Data Access, Version 3, April 1997.
616 jmc 1.45 %% (Available from Unidata or in PostScript form by anonymous FTP from
617     %% ftp://ftp.unidata.ucar.edu/pub/netcdf/guidec.ps.Z). There is also
618     %% a hypertext version of the User's Guide available at
619     %% http://www.unidata.ucar.edu/packages/netcdf/guidec. NetCDF User's
620     %% Guide for Fortran 90 and NetCDF User's Guide for Fortran 77 are
621 edhill 1.13 %% also available.
622 jmc 1.45
623 heimbach 1.32 @incollection{naum-etal:06,
624     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},
625     Booktitle = {European Conference on Computational Fluid Dynamics ECCOMAS CFD 2006},
626     Editor = {{P. Wesseling, E. O~nate and J. Periaux}},
627     Pages = {~},
628     Publisher = {TU Delft},
629     Title = {Adjoint code by source transformation with OpenAD/F},
630     Year = {2006}}
631    
632 jmc 1.38 @Article{orl:76,
633     author = {I. Orlanski},
634     year = 1976,
635     title = {A simple boundary condition for unbounded hyperbolic flows},
636     journal = jcp,
637     volume = {21},
638     pages = {251--269},
639     }
640    
641 jmc 1.39 @Article{pal-rom:97,
642     author = {T. Paluszkiewicz and R.D. Romea},
643     year = 1997,
644     title = {A one-dimensional model for the parameterization
645     of deep convection in the ocean},
646     journal = dao,
647     volume = {26},
648     pages = {95--130},
649     }
650    
651 edhill 1.13 @TechReport{rew:97,
652     author = {R. K. Rew and G. P. Davis and S. Emmerson and H. Davies},
653 jmc 1.45 title = {{NetCDF User's Guide for C, FORTRAN 77, and FORTRAN 90},
654 edhill 1.13 An Interface for Data Access, Version 3},
655     institution = {Unidata Program Center},
656     type = {Report},
657     address = {Boulder, Colorado},
658     year = 1997,
659     note = {http://www.unidata.ucar.edu/packages/netcdf/},
660     }
661    
662    
663 heimbach 1.1 @Article{res-eta:98,
664     author = {J.M. Restrepo and G.K. Leaf and A. Griewank},
665     year = 1998,
666 cnh 1.5 title = {Circumventing storage limitations in variational
667 heimbach 1.1 data assimilation studies},
668     journal = {SIAM J. Sci. Comput.},
669     volume = {19},
670     pages = {1586--1605},
671     }
672 jmc 1.45
673 heimbach 1.1 @Article{ros-eta:93,
674     author = {N. Rostaing and S. Dalmas and A. Galligo},
675     year = 1993,
676     title = {Automatic differentiation in Odyss{\'e}e},
677     journal = {Tellus},
678     volume = {45A},
679     pages = {558--568},
680     }
681 jmc 1.45
682 heimbach 1.1 @incollection{she-and:89,
683     author = {J. Sheinbaum and D.L.T. Anderson},
684     year = 1989,
685 jmc 1.45 title = {Assimilation of XBT data using a variational
686 heimbach 1.1 technique},
687     booktitle = {Oceanic circulation models:
688     Combining data and dynamics},
689     pages = {257--285},
690     series = {NATO ASI Series},
691     volume = {C 284},
692     editor = {{D.L.T. Anderson and J. Willebrand}},
693     publisher = {Springer-Verlag},
694     address = {Berlin (Germany)},
695     }
696 cnh 1.6
697 heimbach 1.32 @article{utke-etal:08,
698     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},
699     Date-Modified = {2007-11-19 10:15:08 -0500},
700     Journal = {{ACM} Transactions on Mathematical Software},
701     Pages = {~},
702     Title = {OpenAD/F: A modular open source tool for automatic differentiation of Fortran codes},
703     Volume = {34(4)},
704     Year = {2008}}
705    
706 cnh 1.6 @Article{DaSilva94,
707     author = {A. da Silva and A. C. Young and S. Levitus},
708     year = 1994,
709     title = {Atlas of Surface Marine Data 1994, Volume 1: Algorithms and Procedures},
710     journal = {NOAA Atlas NESDIS},
711     volume = {6},
712     publisher = {U.S. Department of Commerce},
713     address = {Washington, D.C. (USA)},
714     note = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/},
715 cnh 1.28 url = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/},
716 cnh 1.6 }
717 jmc 1.45
718 heimbach 1.32 @techreport{stam-etal:97,
719 heimbach 1.1 author = {D. Stammer and C. Wunsch and R. Giering and
720 cnh 1.6 Q. Zhang and J. Marotzke and J. Marshall and
721 heimbach 1.1 C. Hill},
722     year = 1997,
723 jmc 1.45 title = {The global ocean circulation estimated from
724 heimbach 1.1 TOPEX/POSEIDON altimetry and a general circulation
725     model},
726     institution = {Center for Global Change Science, Massachusetts
727     Institute of Technology},
728     type = {Technical Report},
729     number = {49},
730     pages = {40 pp.},
731     address = {Cambridge (MA), USA},
732     }
733 jmc 1.45
734 heimbach 1.32 @ARTICLE{stam-etal:02,
735 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},
736     title = {The global ocean circulation and transports during 1992 -- 1997, estimated from ocean observations and a general circulation model.},
737     journal = jgr,
738     year = {2002a},
739     volume = {107(C9)},
740     pages = {3118},
741     doi = {10.1029/2001JC000888},
742     }
743    
744 cnh 1.6
745     @Article{Stommel66,
746     author = {H. Stommel},
747     year = 1948,
748     title = {The western intensification of wind-driven ocean currents},
749     journal = {Trans. Am. Geophys. Union},
750     volume = {29},
751     pages = {206},
752 heimbach 1.1 }
753    
754     @Article{tal-cou:87,
755     author = {O. Talagrand and P. Courtier},
756     year = 1987,
757 jmc 1.45 title = {Variational assimilation of meteorological
758 heimbach 1.1 observations with the adjoint vorticity equation.
759     I: Theory},
760     journal = qjrms,
761     volume = {113},
762     pages = {1311--1328},
763     }
764 jmc 1.45
765 heimbach 1.1 @Article{tal:97,
766     author = {O. Talagrand},
767     year = 1997,
768     title = {Assimilation of observations, an introduction},
769     journal = {J.~Meteor.~Soc.~Japan},
770     volume = {75},
771     pages = {191--209},
772     }
773 jmc 1.45
774 heimbach 1.1 @book{tar:87,
775     author = {A. Tarantola},
776     title = {Inverse Problem Theory: Methods for data fitting
777     and model parameter estimation},
778     year = 1987,
779     publisher = {Elsevier},
780 jmc 1.45 address = {Amsterdam},
781 heimbach 1.1 pages = {629 pp.},
782     }
783 jmc 1.45
784 heimbach 1.1 @techreport{tha:87,
785     author = {W.C. Thacker},
786     year = 1987,
787     title = {Three lectures on fitting numerical models to
788     observations},
789     institution = {GKSS},
790     type = {Report},
791     number = {87/E/65},
792     pages = {64 pp.},
793     address = {Geesthacht (D)},
794     }
795 jmc 1.45
796 heimbach 1.1 @Article{tha-lon:88,
797     author = {W.C. Thacker and R.B. Long},
798     year = 1988,
799     title = {Fitting dynamics to data},
800     journal = jgr,
801     volume = {93, C2},
802     pages = {1,227--1,240},
803     }
804 jmc 1.45
805 heimbach 1.1 @Article{tha:88,
806     author = {W.C. Thacker},
807     year = 1988,
808     title = {Fitting models to inadequate data by enforcing
809     spatial and temporal smoothness},
810     journal = jgr,
811     volume = {93},
812     pages = {10,655--10,665},
813     }
814 jmc 1.45
815 heimbach 1.1 @Article{tha:89,
816     author = {W.C. Thacker},
817     year = 1989,
818     title = {The role of the Hessian matrix in fitting models
819     to measurements},
820     journal = jgr,
821     volume = {94, C5},
822     pages = {6,177--6,196},
823     }
824 jmc 1.45
825 heimbach 1.1 @Article{tha-rag:94,
826     author = {W.C. Thacker and R. Raghunath},
827     year = 1994,
828     title = {The rigid lid's contribution to the ill-conditioning
829     of oceanic inverse problems},
830     journal = jgr,
831     volume = {99, C5},
832     pages = {10,131--10,141},
833     }
834 jmc 1.45
835 heimbach 1.1 @Article{tzi-tha:89,
836     author = {E. Tziperman and W.C. Thacker},
837     year = {1989},
838     title = {An optimal control / adjoint equation approach
839     to studying the ocean general circulation},
840     journal = jpo,
841     volume = {19},
842     pages = {1471--1485},
843     }
844 jmc 1.45
845 heimbach 1.1 @Article{tzi-eta:92a,
846     author = {E. Tziperman and W.C. Thacker and R.B. Long and
847     S. Hwang},
848     year = {1992a},
849     title = {Oceanic data analysis using a general circulation
850     model. I: Simulations},
851     journal = jpo,
852     volume = {22},
853     pages = {1434--1457},
854     }
855 jmc 1.45
856 heimbach 1.1 @Article{tzi-eta:92b,
857     author = {E. Tziperman and W.C. Thacker and R.B. Long and
858     S. Hwang and S.R. Rintoul},
859     year = {1992b},
860     title = {Oceanic data analysis using a general circulation
861     model. I: A North Atlantic model},
862     journal = jpo,
863     volume = {22},
864     pages = {1458--1485},
865     }
866 jmc 1.45
867 heimbach 1.1 @book{wun:96,
868     author = {C. Wunsch},
869     title = {The ocean circulation inverse problem},
870     year = 1996,
871     publisher = cup,
872 jmc 1.45 address = {Cambridge (UK)},
873 heimbach 1.1 pages = {442 pp.},
874     }
875 jmc 1.45
876 heimbach 1.1 @Article{zha-mar:99,
877     author = {K.Q. Zhang and J. Marotzke},
878     year = 1999,
879     title = {The importance of open-boundary estimation for an
880     Indian Ocean GCM-data synthesis},
881     journal = {J.~Marine Res.},
882     volume = {57},
883     pages = {305--334},
884     }
885 adcroft 1.2
886    
887     @InCollection{hill:95,
888     author = {Hill, C. and J. Marshall},
889     title = {Application of a Parallel Navier-Stokes Model to
890     Ocean Circulation in Parallel Computational Fluid
891     Dynamics},
892     booktitle = {Implementations and Results Using Parallel
893     Computers},
894     pages = {545-552},
895     publisher = {Elsevier Science B.V.: New York},
896     year = 1995,
897     editor = {A. Ecer, J. Periaux, N. Satofuka and S. Taylor}
898     }
899    
900    
901     @Article{marshall:97a,
902 adcroft 1.4 author = {Marshall, J. and C. Hill and L. Perelman and A. Adcroft},
903 adcroft 1.2 title = {Hydrostatic, quasi-hydrostatic, and nonhydrostatic ocean
904     modeling},
905 jmc 1.25 journal = jgr,
906 adcroft 1.2 year = 1997,
907     volume = 102,
908     number = {C3},
909 cnh 1.29 pages = {5733-5752},
910     url = {http://mitgcm.org/pdfs/96JC02775.pdf},
911 adcroft 1.2 }
912    
913     @Article{marshall:97b,
914 cnh 1.10 author = {Marshall, J. and A. Adcroft and C. Hill and L. Perelman and C. Heisey},
915 adcroft 1.2 title = {A finite-volume, incompressible Navier Stokes model for
916     studies of the ocean on parallel computers},
917 jmc 1.25 journal = jgr,
918 adcroft 1.2 year = 1997,
919     volume = 102,
920     number = {C3},
921 cnh 1.29 pages = {5753-5766},
922     url = {http://mitgcm.org/pdfs/96JC02776.pdf},
923 adcroft 1.2 }
924    
925     @Article{adcroft:97,
926 adcroft 1.4 author = {Adcroft, A.J. and Hill, C.N. and J. Marshall},
927 adcroft 1.2 title = {Representation of topography by shaved cells in a height
928     coordinate ocean model},
929 jmc 1.25 journal = mwr,
930 adcroft 1.2 year = 1997,
931     volume = 125,
932 cnh 1.29 pages = {2293-2315},
933     url = {http://mitgcm.org/pdfs/mwr_1997.pdf},
934     doi = {10.1175/1520-0493\%281997\%29125<2293:ROTBSC>2.0.CO;2},
935 adcroft 1.2 }
936    
937 jmc 1.19 @Article{adcroft:04a,
938     author = {Adcroft, A. and J.-M. Campin},
939 jmc 1.14 title = {Re-scaled height coordinates for accurate representation
940     of free-surface flows in ocean circulation models},
941     journal = om,
942     year = 2004,
943 jmc 1.19 volume = 7,
944 cnh 1.28 pages = {269-284},
945     doi = {10.1016/j.ocemod.2003.09.003},
946 jmc 1.19 }
947    
948     @Article{adcroft:04b,
949     author = {Adcroft, A. and J.-M. Campin and C. Hill and J. Marshall},
950     title = {Implementation of an Atmosphere-Ocean General Circulation Model
951     on the Expanded Spherical Cube},
952     journal = mwr,
953     year = 2004,
954     volume = 132,
955 cnh 1.29 pages = {2845-2863},
956     url = {http://mitgcm.org/pdfs/mwr_2004.pdf},
957     doi = {10.1175/MWR2823.1},
958 jmc 1.19 }
959    
960 jmc 1.33 @inproceedings{adcroft:04c,
961 jmc 1.45 author = {Adcroft, A. and C. Hill and J.-M. Campin and J. Marshall
962 jmc 1.33 and P. Heimbach},
963 jmc 1.35 title = {Overview of the Formulation and Numerics of the {MIT}GCM},
964 jmc 1.33 booktitle = {Proceedings of the ECMWF seminar series on Numerical Methods,
965 jmc 1.45 Recent developments in numerical methods for atmosphere and
966 jmc 1.33 ocean modelling},
967     year = 2004,
968     pages = {139-149},
969     url = {http://mitgcm.org/pdfs/ECMWF2004-Adcroft.pdf},
970     publisher = ecmwf
971     }
972    
973 jmc 1.19 @Article{marshall:04,
974     author = {Marshall, J. and A. Adcroft and J.-M. Campin and C. Hill and A. White},
975     title = {Atmosphere-Ocean Modeling Exploiting Fluid Isomorphisms},
976     journal = mwr,
977     year = 2004,
978     volume = 132,
979 cnh 1.29 pages = {2882-2894},
980     url = {http://mitgcm.org/pdfs/a_o_iso.pdf},
981     doi = {10.1175/MWR2835.1},
982 jmc 1.14 }
983    
984 adcroft 1.2 @Article{visbeck:97,
985 dfer 1.44 author = {M. Visbeck and J. Marshall and T. Haine and M. Spall},
986     title = {Specification of eddy transfer coefficients in coarse-resolution ocean circulation models},
987 jmc 1.25 journal = jpo,
988 adcroft 1.2 year = 1997,
989     volume = 27,
990     number = 3,
991     pages = {381-402}
992     }
993    
994     @Article{shaw:98,
995     author = {Shaw; A. Arvind, Cho, K.-C., Hill, C., Johnson, R.P.
996     and Marshall, J.},
997     title = {A comparison of implicitly parallel multi-threaded and
998     data-parallel implementations of an ocean model based
999     on the Navier-Stokes equations},
1000     journal = {J. of Parallel and Distributed Computing},
1001     year = 1998,
1002     volume = 48,
1003     number = 1,
1004     pages = {1-51}
1005     }
1006    
1007     @Article{mjn:99,
1008     author = {Marshall, J., Jamous, D and J. Nilsson},
1009     title = {Reconciling `thermodynamic' and `dynamic' methods of
1010     computation of water-mass transformation rates},
1011     journal = {DSR},
1012     year = 1999,
1013     volume = 46,
1014     pages = {545-572}
1015     }
1016    
1017     @Article{ms:99,
1018     author = {Marshall, J and F. Schott},
1019     title = {Open ocean deep convection: observations, models and theory},
1020     journal = {Rev. Geophys.},
1021     year = 1999,
1022     volume = 37,
1023     number = 1,
1024     pages = {1-64}
1025     }
1026    
1027     @Article{adcroft:99,
1028     author = {Adcroft, A., Hill C. and J. Marshall},
1029     title = {A new treatment of the Coriolis terms in C-grid models
1030     at both high and low resolutions},
1031 jmc 1.25 journal = mwr,
1032 adcroft 1.2 year = 1999,
1033     volume = 127,
1034 cnh 1.29 pages = {1928-1936},
1035     url = {http://mitgcm.org/pdfs/mwr_1999.pdf},
1036     doi = {10.1175/1520-0493\%281999\%29127<1928:ANTOTC>2.0.CO;2},
1037 adcroft 1.2 }
1038    
1039     @InProceedings{hill:99,
1040     author = {Chris Hill, Alistair Adcroft, Daniel Jamous and John Marshall},
1041     title = {A Strategy for Terascale Climate Modeling},
1042 cnh 1.8 booktitle = {In Proceedings of the Eighth ECMWF Workshop on the Use of Parallel Processors in Meteorology},
1043 cnh 1.9 year = 1999,
1044     pages = {406-425},
1045     publisher = {World Scientific},
1046 adcroft 1.2 }
1047    
1048     @Article{wardle:00,
1049     author = {Wardle R. and Marshall J.},
1050     title = {Representation of eddies in primitive equation models by a PV flux},
1051 jmc 1.25 journal = jpo,
1052 adcroft 1.2 year = 2000,
1053     volume = 30,
1054     number = 10,
1055     pages = {2481-2503}
1056     }
1057    
1058     @Article{ac:02,
1059     author = {Adcroft, A. and J.-M. Campin},
1060     title = {Comparison of finite volume schemes and direct-space-time
1061     methods for ocean circulation models},
1062 jmc 1.14 journal = om,
1063 adcroft 1.2 year = 2002,
1064     note = {in preparation}
1065     }
1066    
1067     @Article{adcroft:02,
1068 jmc 1.25 author = {Adcroft, A., et~al.},
1069 adcroft 1.2 title = {Energy conversion in discrete numerical models},
1070 jmc 1.14 journal = om,
1071 adcroft 1.2 year = 2002,
1072     note = {in preparation}
1073     }
1074    
1075     @InCollection{arakawa:77,
1076     author = {Arakawa, A. and Lamb, V.},
1077     title = {Computational Design of the Basic Dynamical Processes of
1078     the UCLA General Circulation Model},
1079     booktitle = {Methods in Computational Physics},
1080     pages = {174-267},
1081     publisher = {Academic Press},
1082     year = 1977,
1083     volume = 17
1084     }
1085    
1086 jmc 1.24 @Article{miller_white:84,
1087     author = {Miller, M. J. and White, A. A.},
1088     title = {On the non-hydrostatic equations in pressure
1089     and sigma coordiantes},
1090 jmc 1.25 journal = qjrms,
1091 jmc 1.24 year = 1984,
1092     volume = 110,
1093     pages = {515-533}
1094     }
1095    
1096     @Article{white:89,
1097     author = {White, A. A.},
1098     title = {An extended version of a nonhydrostatic, pressure coordiante model},
1099 jmc 1.25 journal = qjrms,
1100 jmc 1.24 year = 1989,
1101     volume = 115,
1102     pages = {1243-1251}
1103     }
1104    
1105 adcroft 1.2 @Article{adcroft:98,
1106     author = {Adcroft, A. and Marshall, D.},
1107 adcroft 1.3 title = {How slippery are piecewise-constant coastlines in numerical
1108     ocean models?},
1109 adcroft 1.2 journal = {Tellus},
1110 adcroft 1.3 year = 1998,
1111     volume = 50,
1112     number = 1,
1113     pages = {95-108}
1114     }
1115    
1116     @PhdThesis{adcroft:95,
1117     author = {Adcroft, A.},
1118     title = {Numerical Algorithms for use in a Dynamical Model of the
1119     Ocean},
1120     school = {Imperial College, London},
1121     year = 1995
1122     }
1123    
1124     @Article{griffies:00,
1125     author = {Griffies, S.,M. and Hallberg, R.,W.},
1126 dfer 1.44 title = {Biharmonic friction with a {Smagorinsky}-like viscosity for
1127 adcroft 1.3 use in large-scale eddy-permitting ocean models},
1128 jmc 1.25 journal = mwr,
1129 adcroft 1.3 year = 2000,
1130     volume = 128,
1131     number = 8,
1132     pages = {2935-2946}
1133     }
1134    
1135     @Article{wajsowicz:93,
1136     author = {Wajsowicz, R.},
1137     title = {A CONSISTENT FORMULATION OF THE ANISOTROPIC STRESS TENSOR
1138     FOR USE IN MODELS OF THE LARGE-SCALE OCEAN CIRCULATION},
1139 jmc 1.25 journal = jcp,
1140 adcroft 1.3 year = 1993,
1141     volume = 105,
1142     number = 2,
1143     pages = {333-338}
1144     }
1145    
1146     @Article{campin:02,
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1488 jmc 1.45 institution = {National Aeronautics and Space Administration},
1489     type = {NASA Technical Memorandum},
1490     number = {104606-Vol 3},
1491 molod 1.22 address = {NASA; Goddard Space Flight Center; Greenbelt (MD), 20771; USA},
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