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1 @string{arfm = {Annu.~Rev.~Fluid Mech.}}
2 @string{bams = {Bull.~Am.~Met.~Soc.}}
3 @string{blm = {Bound.~Layer~Meteorol.}}
4 @string{jgr = {J.~Geophys.~Res.}}
5 @string{ijrs = {Int.~J.~Remote Sensing}}
6 @string{jas = {J.~Atmos.~Sci.}}
7 @string{jpo = {J.~Phys.~Oceanogr.}}
8 @string{jclim = {J.~Clim.}}
9 @string{ieee = {IEEE Trans.~Geosci. Remote Sensing}}
10 @string{jfm = {J.~Fluid Mech.}}
11 @string{jaot = {J.~Atmos.~Ocean.~Technol.}}
12 @string{jms = {J.~Mar.~Sys.}}
13 @string{gaos = {Global Atmos.~Ocean System}}
14 @string{grl = {Geophys.~Res.~Lett.}}
15 @string{dsr = {Deep Sea Res.}}
16 @string{dao = {Dyn.~Atmos.~Oceans}}
17 @string{mwr = {Mon.~Wea.~Rev.}}
18 @string{qjrms = {{Q.~J.~R.~Meteorol.~Soc.}}}
19 @string{tel = {Tellus}}
20 @string{cup = {Cambridge University Press}}
21 @string{esapub = {ESA Publications Division, ESTEC, Noordwijk (NL)}}
22 @string{ifremer = {IFREMER/CERSAT}}
23 @string{igarss = {IEEE Press, Piscataway, N.J., USA}}
24 @string{dnmi = {The Norwegian Meteorological Institute (DNMI)}}
25 @string{dkrz = {Deutsches Klimarechenzentrum (DKRZ)}}
26 @string{mpi = {MPI f\"ur Meteorologie}}
27 @string{ecmwf = {ECMWF}}
28 @string{estec = {European Space Research and Technology Centre
29 (ESTEC)}}
30 @string{esa = {European Space Agency (ESA)}}
31
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34 A. Griewank and K. Haigler and P. Newman},
35 year = 1992,
36 title = {Automatic differentiation of advanced GFD codes
37 for multidisciplinary design},
38 journal = {Journal on Computing Systems in Engineering},
39 volume = {3},
40 pages = {625--638},
41 }
42
43 @incollection{bis:94,
44 author = {C.H. Bishof},
45 year = 1994,
46 title = {Automatic differentiation, tangent linear models
47 and pseudo-adjoints},
48 booktitle = {High Performance Computing in the Geosciences},
49 series = {Series C: Mathematical and Physical Sciences},
50 pages = {59--80},
51 editor = {F.X. {Le Dimet}},
52 publisher = {Kluwer},
53 address = {Dordrecht, NL},
54 }
55
56 @techreport{bis-eta:94,
57 author = {C. Bishof and A. Carle and P. Khademi and
58 A. Maurer},
59 year = 1994,
60 title = {The ADIFOR 2.0 system for the automatic
61 differentiation of FORTRAN 77 programs},
62 institution = {Argonne National Laboratory, Mathematics and
63 Computer Science Division},
64 type = {Argonne Preprint},
65 number = {ANL-MCS-P981-1194},
66 address = {ANL; 9700 South Cass Ave.;
67 Argonne (ILL), 90439; USA},
68 note = {http://www.mcs.anl.gov/autodiff/},
69 }
70
71 @techreport{bis-roh:97,
72 author = {C. Bishof and L. Roh},
73 year = 1997,
74 title = {ADIC: An extensible automatic differentiation tool
75 for ANSI-C},
76 institution = {Argonne National Laboratory, Mathematics and
77 Computer Science Division},
78 type = {Argonne Preprint},
79 number = {ANL-MCS-P626-1196},
80 address = {ANL; 9700 South Cass Ave.;
81 Argonne (ILL), 90439; USA},
82 note = {http://www.mcs.anl.gov/autodiff/},
83 }
84
85 @Article{cou-tal:87,
86 author = {P. Courtier and O. Talagrand},
87 year = 1987,
88 title = {Variational assimilation of meteorological
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91 journal = qjrms,
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94 }
95
96 @Article{cou-tal:90,
97 author = {P. Courtier and O. Talagrand},
98 year = 1990,
99 title = {Variational assimilation of meteorological
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102 journal = tel,
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105 }
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116 }
117
118 @Article{err:97,
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122 journal = bams,
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125 }
126
127 @Article{far-moo:92,
128 author = {B.F. Farrell and A.M. Moore},
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130 title = {An adjoint method for obtaining the most rapidly
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132 journal = jpo,
133 volume = {22},
134 pages = {338--349},
135 }
136
137 @Article{far-ioa:96a,
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139 year = {1996a},
140 title = {Generalized stability theory. Part I:
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143 volume = {53},
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150 title = {Generalized stability theory. Part I:
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153 volume = {53},
154 pages = {2041--2053},
155 }
156
157 @techreport{fau-pap:98,
158 author = {C. Faure and Y. Papegay},
159 year = 1998,
160 title = {Odyss{\'e}e User's Guide. Version 1.7},
161 institution = {Institut National de Recherche en Informatique
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163 type = {Rapport Technique},
164 number = {0224},
165 address = {INRIA; 2004, route des Luciolis, B.P. 93;
166 06902 Sophia Antipolis Cedex; France},
167 note = {http://www-sop.inria.fr/safir/SAM/Odyssee/odyssee.html},
168 }
169
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175 note = {in press},
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181 title = {Isopycnal mixing in ocean circulation models},
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186
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190 year = 1995,
191 title = {Parameterizing eddy-induced tracer transports in
192 ocean circulation models},
193 journal = jpo,
194 volume = {25},
195 pages = {463--474},
196 }
197
198 @Article{gie-kam:98,
199 author = {R. Giering and T. Kaminski},
200 year = 1998,
201 title = {Recipes for adjoint code construction},
202 journal = {ACM Transactions on Mathematical Software},
203 volume = 24,
204 pages = {437--474},
205 }
206
207 @techreport{gie:99,
208 author = {R. Giering},
209 year = 1999,
210 title = {Tangent linear and Adjoint Model Compiler.
211 Users manual 1.4 (TAMC Version 5.2)},
212 institution = {Massachusetts Institute of Technology},
213 type = {Report},
214 number = {~},
215 address = {MIT/EAPS; 77 Massachusetts Ave.; Cambridge (MA)
216 02139; USA},
217 note = {http://puddle.mit.edu/$\sim$ralf/tamc/tamc.html},
218 }
219
220 @incollection{gie:00,
221 author = {R. Giering},
222 editor = {P. Kasibhatla and M. Heimann and P. Rayner and
223 N. Mahowald and R.G. Prinn and D.E. Hartley},
224 year = 2000,
225 booktitle = {Inverse methods in global biogeochemical cycles},
226 title = {Tangent linear and adjoint biogeochemical models},
227 publisher = {American Geophysical Union},
228 series = {Geophysical Monograph},
229 volume = {114},
230 address = {Washington, DC},
231 pages = {33--48},
232 }
233
234 @Article{gil-lem:89,
235 author = {J.C. Gilbert and C. Lemar\'echal},
236 year = 1989,
237 title = {Some numerical experiments with variable-storage
238 quasi-Newton algorithms},
239 journal = {Math. Programming},
240 volume = {45},
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242 }
243
244 @book{gil-eta:81,
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246 title = {Practical optimization},
247 year = 1981,
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256 of Algorithmic Differentiation},
257 year = 2000,
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259 volume = {19},
260 publisher = {SIAM},
261 address = {Philadelphia},
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266 author = {M.C.G. Hall and D.G. Caccuci and M.E. Schlesinger},
267 year = 1982,
268 title = {Sensitivity analysis of a radiative-convective
269 model by the adjoint method},
270 journal = jas,
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275 @Article{hil-eta:01,
276 author = {C. Hill and M. Follows and V. Bugnion and
277 J. Marshall},
278 year = {2001},
279 title = {Spatial and Temporal Impacts of ocean general
280 circulation on carbon sequestration},
281 journal = {journal ???},
282 note = {submitted},
283 }
284
285 @book{kas-eta:00,
286 author = {P. Kasibhatla and M. Heimann and P. Rayner and
287 N. Mahowald and R.G. Prinn and D.E. Hartley},
288 year = 2000,
289 title = {Inverse methods in global biogeochemical cycles},
290 publisher = {American Geophysical Union},
291 series = {Geophysical Monograph},
292 volume = {114},
293 address = {Washington, DC},
294 pages = {324 pp.},
295 }
296
297 @Article{lar-eta:94,
298 author = {W.G. Large and J.C. McWilliams and S.C. Doney},
299 year = 1994,
300 title = {Oceanic vertical mixing: A review and a model
301 with nonlocal boundary layer parameterization},
302 journal = {Rev.~Geophys.},
303 volume = {32},
304 pages = {363--403},
305 }
306
307 @Article{lar-eta:97,
308 author = {W.G. Large and G. Danabasoglu and S.C. Doney
309 and J.C. McWilliams},
310 year = 1997,
311 title = {Sensitivity to surface forcing and boundary layer
312 mixing in a global ocean model: annual-mean
313 climatology},
314 journal = jpo,
315 volume = {27},
316 pages = {2418--2447},
317 }
318
319 @Article{led-tal:86,
320 author = {F.-X. {Le Dimet} and O. Talagrand},
321 year = 1986,
322 title = {Variational algorithms for analysis and
323 assimilation of meteorological observations:
324 theoretical aspects},
325 journal = tel,
326 volume = {38A},
327 pages = {97--110},
328 }
329
330 @Article{lew-der:85,
331 author = {J. Lewis and J. Derber},
332 year = {1985},
333 title = {The use of adjoint equations to solve a variational
334 adjustment problem with advective constraints},
335 journal = {Tellus},
336 volume = {37A},
337 pages = {309--322},
338 }
339
340 @techreport{lon:88,
341 author = {R.B. Long},
342 year = 1988,
343 title = {Notes on assimilating observations into
344 numerical models},
345 institution = {Delft Hydraulics},
346 type = {Report},
347 number = {~},
348 pages = {38 pp.},
349 address = {Delft (NL)},
350 }
351
352 @Article{maro-wun:93,
353 author = {J. Marotzke and C. Wunsch},
354 year = 1993,
355 title = {Finding the steady state of a general circulation
356 model through data assimilation:
357 Application to the North Atlantic Ocean},
358 journal = jgr,
359 volume = {98, C11},
360 pages = {20,149--20,167},
361 }
362
363 @Article{maro-eta:99,
364 author = {J. Marotzke and R. Giering and K.Q. Zhang and
365 D. Stammer and C. Hill and T. Lee},
366 year = 1999,
367 title = {Construction of the adjoint MIT ocean general
368 circulation model and application to Atlantic heat
369 transport variability},
370 journal = jgr,
371 volume = {104, C12},
372 pages = {29,529--29,547},
373 }
374
375 @Article{mars-eta:97a,
376 author = {J. Marshall and C. Hill and L. Perelman and
377 A. Adcroft},
378 year = {1997a},
379 title = {Hydrostatic, quasi-hydrostatic and
380 nonhydrostatic ocean modeling},
381 journal = jgr,
382 volume = {102, C3},
383 pages = {5,733--5,752},
384 }
385
386 @Article{mars-eta:97b,
387 author = {J. Marshall and A. Adcroft and C. Hill and
388 L. Perelman and C. Heisey},
389 year = {1997b},
390 title = {Hydrostatic, quasi-hydrostatic and
391 nonhydrostatic ocean modeling},
392 journal = jgr,
393 volume = {102, C3},
394 pages = {5,753--5,766},
395 }
396
397 @Article{mars-sha:98,
398 author = {J. Marshall and H. Jones and C. Hill},
399 year = 1998,
400 title = {Efficient ocean modeling using
401 non-hydrostatic algorithms},
402 journal = jms,
403 volume = {18},
404 pages = {115--134},
405 }
406
407 @Article{mcw:96,
408 author = {J. McWilliams},
409 year = 1996,
410 title = {Modeling the oceanic general circulation},
411 journal = arfm,
412 volume = {28},
413 pages = {215--248},
414 }
415
416 @Article{res-eta:98,
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418 year = 1998,
419 title = {Circumvening storage limitations in variational
420 data assimilation studies},
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422 volume = {19},
423 pages = {1586--1605},
424 }
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426 @Article{ros-eta:93,
427 author = {N. Rostaing and S. Dalmas and A. Galligo},
428 year = 1993,
429 title = {Automatic differentiation in Odyss{\'e}e},
430 journal = {Tellus},
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433 }
434
435 @incollection{she-and:89,
436 author = {J. Sheinbaum and D.L.T. Anderson},
437 year = 1989,
438 title = {Assimilation of XBT data using a variational
439 technique},
440 booktitle = {Oceanic circulation models:
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442 pages = {257--285},
443 series = {NATO ASI Series},
444 volume = {C 284},
445 editor = {{D.L.T. Anderson and J. Willebrand}},
446 publisher = {Springer-Verlag},
447 address = {Berlin (Germany)},
448 }
449
450 @techreport{sta-eta:97,
451 author = {D. Stammer and C. Wunsch and R. Giering and
452 Q. Zhang and J. Marotzke an J. Marshall and
453 C. Hill},
454 year = 1997,
455 title = {The global ocean circulation estimated from
456 TOPEX/POSEIDON altimetry and a general circulation
457 model},
458 institution = {Center for Global Change Science, Massachusetts
459 Institute of Technology},
460 type = {Technical Report},
461 number = {49},
462 pages = {40 pp.},
463 address = {Cambridge (MA), USA},
464 }
465
466 @Article{sta-eta:01,
467 author = {D. Stammer and C. Wunsch and R. Giering and
468 C. Eckert and P. Heimbach and J. Marotzke and
469 A. Adcroft and C. Hill and J. Marshall},
470 year = 2001,
471 title = {The global ocean circulation during 1992 -- 1997,
472 estimated from ocean observations and a general
473 circulation model},
474 journal = jgr,
475 note = {submitted},
476 }
477
478 @Article{tal-cou:87,
479 author = {O. Talagrand and P. Courtier},
480 year = 1987,
481 title = {Variational assimilation of meteorological
482 observations with the adjoint vorticity equation.
483 I: Theory},
484 journal = qjrms,
485 volume = {113},
486 pages = {1311--1328},
487 }
488
489 @Article{tal:97,
490 author = {O. Talagrand},
491 year = 1997,
492 title = {Assimilation of observations, an introduction},
493 journal = {J.~Meteor.~Soc.~Japan},
494 volume = {75},
495 pages = {191--209},
496 }
497
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499 author = {A. Tarantola},
500 title = {Inverse Problem Theory: Methods for data fitting
501 and model parameter estimation},
502 year = 1987,
503 publisher = {Elsevier},
504 address = {Amsterdam},
505 pages = {629 pp.},
506 }
507
508 @techreport{tha:87,
509 author = {W.C. Thacker},
510 year = 1987,
511 title = {Three lectures on fitting numerical models to
512 observations},
513 institution = {GKSS},
514 type = {Report},
515 number = {87/E/65},
516 pages = {64 pp.},
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518 }
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520 @Article{tha-lon:88,
521 author = {W.C. Thacker and R.B. Long},
522 year = 1988,
523 title = {Fitting dynamics to data},
524 journal = jgr,
525 volume = {93, C2},
526 pages = {1,227--1,240},
527 }
528
529 @Article{tha:88,
530 author = {W.C. Thacker},
531 year = 1988,
532 title = {Fitting models to inadequate data by enforcing
533 spatial and temporal smoothness},
534 journal = jgr,
535 volume = {93},
536 pages = {10,655--10,665},
537 }
538
539 @Article{tha:89,
540 author = {W.C. Thacker},
541 year = 1989,
542 title = {The role of the Hessian matrix in fitting models
543 to measurements},
544 journal = jgr,
545 volume = {94, C5},
546 pages = {6,177--6,196},
547 }
548
549 @Article{tha-rag:94,
550 author = {W.C. Thacker and R. Raghunath},
551 year = 1994,
552 title = {The rigid lid's contribution to the ill-conditioning
553 of oceanic inverse problems},
554 journal = jgr,
555 volume = {99, C5},
556 pages = {10,131--10,141},
557 }
558
559 @Article{tzi-tha:89,
560 author = {E. Tziperman and W.C. Thacker},
561 year = {1989},
562 title = {An optimal control / adjoint equation approach
563 to studying the ocean general circulation},
564 journal = jpo,
565 volume = {19},
566 pages = {1471--1485},
567 }
568
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570 author = {E. Tziperman and W.C. Thacker and R.B. Long and
571 S. Hwang},
572 year = {1992a},
573 title = {Oceanic data analysis using a general circulation
574 model. I: Simulations},
575 journal = jpo,
576 volume = {22},
577 pages = {1434--1457},
578 }
579
580 @Article{tzi-eta:92b,
581 author = {E. Tziperman and W.C. Thacker and R.B. Long and
582 S. Hwang and S.R. Rintoul},
583 year = {1992b},
584 title = {Oceanic data analysis using a general circulation
585 model. I: A North Atlantic model},
586 journal = jpo,
587 volume = {22},
588 pages = {1458--1485},
589 }
590
591 @book{wun:96,
592 author = {C. Wunsch},
593 title = {The ocean circulation inverse problem},
594 year = 1996,
595 publisher = cup,
596 address = {Cambridge (UK)},
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598 }
599
600 @Article{zha-mar:99,
601 author = {K.Q. Zhang and J. Marotzke},
602 year = 1999,
603 title = {The importance of open-boundary estimation for an
604 Indian Ocean GCM-data synthesis},
605 journal = {J.~Marine Res.},
606 volume = {57},
607 pages = {305--334},
608 }
609
610
611 @InCollection{hill:95,
612 author = {Hill, C. and J. Marshall},
613 title = {Application of a Parallel Navier-Stokes Model to
614 Ocean Circulation in Parallel Computational Fluid
615 Dynamics},
616 booktitle = {Implementations and Results Using Parallel
617 Computers},
618 pages = {545-552},
619 publisher = {Elsevier Science B.V.: New York},
620 year = 1995,
621 editor = {A. Ecer, J. Periaux, N. Satofuka and S. Taylor}
622 }
623
624
625 @Article{marshall:97a,
626 author = {Marshall, J. and C. Hill and L. Perelman and A. Adcroft},
627 title = {Hydrostatic, quasi-hydrostatic, and nonhydrostatic ocean
628 modeling},
629 journal = {JGR},
630 year = 1997,
631 volume = 102,
632 number = {C3},
633 pages = {5733-5752}
634 }
635
636 @Article{marshall:97b,
637 author = {Marshall, J., A. Adcroft, C. Hill, L. Perelman, and C. Heise},
638 title = {A finite-volume, incompressible Navier Stokes model for
639 studies of the ocean on parallel computers},
640 journal = {JGR},
641 year = 1997,
642 volume = 102,
643 number = {C3},
644 pages = {5753-5766}
645 }
646
647 @Article{adcroft:97,
648 author = {Adcroft, A.J. and Hill, C.N. and J. Marshall},
649 title = {Representation of topography by shaved cells in a height
650 coordinate ocean model},
651 journal = {MWR},
652 year = 1997,
653 volume = 125,
654 pages = {2293-2315}
655 }
656
657 @Article{visbeck:97,
658 author = {Visbeck, M., J. Marshall, T. Haine, and M. Spall},
659 title = {Specification of eddy transfer coefficients in
660 coarse-resolution ocean circulation models},
661 journal = {JPO},
662 year = 1997,
663 volume = 27,
664 number = 3,
665 pages = {381-402}
666 }
667
668 @Article{shaw:98,
669 author = {Shaw; A. Arvind, Cho, K.-C., Hill, C., Johnson, R.P.
670 and Marshall, J.},
671 title = {A comparison of implicitly parallel multi-threaded and
672 data-parallel implementations of an ocean model based
673 on the Navier-Stokes equations},
674 journal = {J. of Parallel and Distributed Computing},
675 year = 1998,
676 volume = 48,
677 number = 1,
678 pages = {1-51}
679 }
680
681 @Article{marshall:98,
682 author = {Marshall, J., Jones, H. and C. Hill},
683 title = {Efficient ocean modeling using non-hydrostatic algorithms},
684 journal = {JMR},
685 year = 1998,
686 volume = 18,
687 pages = {115-134}
688 }
689
690 @Article{mjn:99,
691 author = {Marshall, J., Jamous, D and J. Nilsson},
692 title = {Reconciling `thermodynamic' and `dynamic' methods of
693 computation of water-mass transformation rates},
694 journal = {DSR},
695 year = 1999,
696 volume = 46,
697 pages = {545-572}
698 }
699
700 @Article{ms:99,
701 author = {Marshall, J and F. Schott},
702 title = {Open ocean deep convection: observations, models and theory},
703 journal = {Rev. Geophys.},
704 year = 1999,
705 volume = 37,
706 number = 1,
707 pages = {1-64}
708 }
709
710 @Article{adcroft:99,
711 author = {Adcroft, A., Hill C. and J. Marshall},
712 title = {A new treatment of the Coriolis terms in C-grid models
713 at both high and low resolutions},
714 journal = {MWR},
715 year = 1999,
716 volume = 127,
717 pages = {1928-1936}
718 }
719
720 @InProceedings{hill:99,
721 author = {Chris Hill, Alistair Adcroft, Daniel Jamous and John Marshall},
722 title = {A Strategy for Terascale Climate Modeling},
723 booktitle = {In Proceedings of the Eight ECMWF Workshop on the Use of Parallel Processors in Meteorology},
724 year = 1999
725 }
726
727 @Article{wardle:00,
728 author = {Wardle R. and Marshall J.},
729 title = {Representation of eddies in primitive equation models by a PV flux},
730 journal = {JPO},
731 year = 2000,
732 volume = 30,
733 number = 10,
734 pages = {2481-2503}
735 }
736
737 @Article{ac:02,
738 author = {Adcroft, A. and J.-M. Campin},
739 title = {Comparison of finite volume schemes and direct-space-time
740 methods for ocean circulation models},
741 journal = {OM},
742 year = 2002,
743 note = {in preparation}
744 }
745
746 @Article{adcroft:02,
747 author = {Adcroft et al.},
748 title = {Energy conversion in discrete numerical models},
749 journal = {OM},
750 year = 2002,
751 note = {in preparation}
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