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revision 1.24 by jmc, Wed Aug 31 18:51:42 2005 UTC revision 1.35 by jmc, Sat Apr 25 13:16:04 2009 UTC
# Line 5  Line 5 
5  @string{jgr     = {J.~Geophys.~Res.}}  @string{jgr     = {J.~Geophys.~Res.}}
6  @string{ijrs    = {Int.~J.~Remote Sensing}}  @string{ijrs    = {Int.~J.~Remote Sensing}}
7  @string{jas     = {J.~Atmos.~Sci.}}  @string{jas     = {J.~Atmos.~Sci.}}
8    @string{jam     = {J.~Appl.~Meteor.}}
9  @string{jpo     = {J.~Phys.~Oceanogr.}}  @string{jpo     = {J.~Phys.~Oceanogr.}}
10  @string{jclim   = {J.~Clim.}}  @string{jclim   = {J.~Clim.}}
11    @string{jcp     = {J.~Comput.~Phys.}}
12  @string{ieee    = {IEEE Trans.~Geosci. Remote Sensing}}  @string{ieee    = {IEEE Trans.~Geosci. Remote Sensing}}
13  @string{jfm     = {J.~Fluid Mech.}}  @string{jfm     = {J.~Fluid Mech.}}
14  @string{jaot    = {J.~Atmos.~Ocean.~Technol.}}  @string{jaot    = {J.~Atmos.~Ocean.~Technol.}}
# Line 69  Line 71 
71                    Argonne (ILL), 90439; USA},                    Argonne (ILL), 90439; USA},
72   note           = {http://www.mcs.anl.gov/autodiff/},   note           = {http://www.mcs.anl.gov/autodiff/},
73                    }                    }
74    
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    
87  @techreport{bis-roh:97,  @techreport{bis-roh:97,
88   author         = {C. Bishof and L. Roh},   author         = {C. Bishof and L. Roh},
# Line 116  Line 130 
130   volume         = {120},   volume         = {120},
131   pages          = {1367--1387},   pages          = {1367--1387},
132                    }                    }
133    
134    @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    @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    
156  @Article{err:97,  @Article{err:97,
157   author         = {R.M. Errico},   author         = {R.M. Errico},
# Line 177  Line 213 
213   note           = {in press},   note           = {in press},
214                    }                    }
215    
216    @Article{fer-eta:05,
217     author         = {D. Ferreira and J. Marshall and P. Heimbach},
218     year           = 2005,
219     title          = {Estimating Eddy Stresses by Fitting Dynamics to Observations
220                       using a Residual-Mean Ocean Circulation Model and Its Adjoint},
221     journal        = jpo,
222     volume         = {35},
223     pages          = {1891--1910},
224                      }
225    
226  @Article{gen-mcw:90,  @Article{gen-mcw:90,
227   author         = {P.R. Gent and J.C. McWilliams},   author         = {P.R. Gent and J.C. McWilliams},
228   year           = 1990,   year           = 1990,
# Line 356  Line 402 
402   pages          = {658-669}   pages          = {658-669}
403                    }                    }
404    
405    @Article{jam-oze:86,
406     author         = {B.M. Jamart and J. Ozer},
407     year           = {1986},
408     title          = {Numerical boundary layers and spurious residual flows},
409     journal        = jgr,
410     volume         = {91},
411     pages          = {10,621-10,631}
412                      }
413    
414  @book{kas-eta:00,  @book{kas-eta:00,
415   author         = {P. Kasibhatla and M. Heimann and P. Rayner and   author         = {P. Kasibhatla and M. Heimann and P. Rayner and
416                    N. Mahowald and R.G. Prinn and D.E. Hartley},                    N. Mahowald and R.G. Prinn and D.E. Hartley},
# Line 452  Line 507 
507   pages          = {38 pp.},   pages          = {38 pp.},
508   address        = {Delft (NL)},   address        = {Delft (NL)},
509                    }                    }
510    
511    @ARTICLE{losc-heim:06,
512      author = {M. Losch and P. Heimbach},
513      title = {Adjoint sensitivity of an ocean general circulation model
514               to bottom topography},
515      journal = jpo,
516      year = {2006},
517      volume = {{in press}},
518      url    = {http://mitgcm.org/pdfs/Los2006a.pdf},
519    }
520    
521    
522  @Article{maro-wun:93,  @Article{maro-wun:93,
523   author         = {J. Marotzke and C. Wunsch},   author         = {J. Marotzke and C. Wunsch},
# Line 498  Line 564 
564   pages          = {5,753--5,766},   pages          = {5,753--5,766},
565                    }                    }
566    
567  @Article{mars-sha:98,  @Article{mars-eta:98,
568   author         = {J. Marshall and H. Jones and C. Hill},   author         = {J. Marshall and H. Jones and C. Hill},
569   year           = 1998,   year           = 1998,
570   title          = {Efficient ocean modeling using   title          = {Efficient ocean modeling using
# Line 506  Line 572 
572   journal        = jms,   journal        = jms,
573   volume         = {18},   volume         = {18},
574   pages          = {115--134},   pages          = {115--134},
575     url            = {http://mitgcm.org/pdfs/journal_of_marine_systems_1998.pdf},
576     doi            = {10.1016/S0924-7963\%2898\%2900008-6},
577                    }                    }
578    
579  @Article{mcw:96,  @Article{mcw:96,
# Line 526  Line 594 
594  %%   Guide for Fortran 90 and NetCDF User's Guide for Fortran 77 are  %%   Guide for Fortran 90 and NetCDF User's Guide for Fortran 77 are
595  %%   also available.  %%   also available.
596    
597    @incollection{naum-etal:06,
598            Author = {U. Naumann and J. Utke and P. Heimbach and C. Hill and D. Ozyurt and C. Wunsch and M. Fagan and N. Tallent and M. Strout},
599            Booktitle = {European Conference on Computational Fluid Dynamics ECCOMAS CFD 2006},
600            Editor = {{P. Wesseling, E. O~nate and J. Periaux}},
601            Pages = {~},
602            Publisher = {TU Delft},
603            Title = {Adjoint code by source transformation with OpenAD/F},
604            Year = {2006}}
605    
606  @TechReport{rew:97,  @TechReport{rew:97,
607    author =       {R. K. Rew and G. P. Davis and S. Emmerson and H. Davies},    author =       {R. K. Rew and G. P. Davis and S. Emmerson and H. Davies},
608    title =        {{NetCDF User's Guide for C, FORTRAN 77, and FORTRAN 90},    title =        {{NetCDF User's Guide for C, FORTRAN 77, and FORTRAN 90},
# Line 572  Line 649 
649   address        = {Berlin (Germany)},   address        = {Berlin (Germany)},
650                    }                    }
651    
652    @article{utke-etal:08,
653            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},
654            Date-Modified = {2007-11-19 10:15:08 -0500},
655            Journal = {{ACM} Transactions on Mathematical Software},
656            Pages = {~},
657            Title = {OpenAD/F: A modular open source tool for automatic differentiation of Fortran codes},
658            Volume = {34(4)},
659            Year = {2008}}
660    
661  @Article{DaSilva94,  @Article{DaSilva94,
662   author         = {A. da Silva and A. C. Young and S. Levitus},   author         = {A. da Silva and A. C. Young and S. Levitus},
663   year           = 1994,   year           = 1994,
# Line 581  Line 667 
667   publisher      = {U.S. Department of Commerce},   publisher      = {U.S. Department of Commerce},
668   address        = {Washington, D.C. (USA)},   address        = {Washington, D.C. (USA)},
669   note           = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/},   note           = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/},
670     url            = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/},
671                    }                    }
672    
673  @techreport{sta-eta:97,  @techreport{stam-etal:97,
674   author         = {D. Stammer and C. Wunsch and R. Giering and   author         = {D. Stammer and C. Wunsch and R. Giering and
675                    Q. Zhang and J. Marotzke and J. Marshall and                    Q. Zhang and J. Marotzke and J. Marshall and
676                    C. Hill},                    C. Hill},
# Line 599  Line 686 
686   address        = {Cambridge (MA), USA},   address        = {Cambridge (MA), USA},
687                    }                    }
688    
689  @Article{sta-eta:01,  @ARTICLE{stam-etal:02,
690   author         = {D. Stammer and C. Wunsch and R. Giering and    author = {D. Stammer and C. Wunsch and R. Giering and C. Eckert and P. Heimbach and J. Marotzke and A. Adcroft and C.N. Hill and J. Marshall},
691                    C. Eckert and P. Heimbach and J. Marotzke and    title = {The global ocean circulation and transports during 1992 -- 1997, estimated from ocean observations and a general circulation model.},
692                    A. Adcroft and C. Hill and J. Marshall},    journal = jgr,
693   year           = 2001,    year = {2002a},
694   title          = {The global ocean circulation during 1992 -- 1997,    volume = {107(C9)},
695                    estimated from ocean observations and a general    pages = {3118},
696                    circulation model},    doi   = {10.1029/2001JC000888},
697   journal        = jgr,  }
698   note           = {in press},  
                   }  
699    
700  @Article{Stommel66,  @Article{Stommel66,
701   author         = {H. Stommel},   author         = {H. Stommel},
# Line 771  Line 857 
857    author =       {Marshall, J. and C. Hill and L. Perelman and A. Adcroft},    author =       {Marshall, J. and C. Hill and L. Perelman and A. Adcroft},
858    title =        {Hydrostatic, quasi-hydrostatic, and nonhydrostatic ocean    title =        {Hydrostatic, quasi-hydrostatic, and nonhydrostatic ocean
859                   modeling},                   modeling},
860    journal =      {JGR},    journal =      jgr,
861    year =         1997,    year =         1997,
862    volume =       102,    volume =       102,
863    number =       {C3},    number =       {C3},
864    pages =        {5733-5752}    pages =        {5733-5752},
865      url      =     {http://mitgcm.org/pdfs/96JC02775.pdf},
866  }  }
867    
868  @Article{marshall:97b,  @Article{marshall:97b,
869    author =       {Marshall, J. and A. Adcroft and C. Hill and L. Perelman and C. Heisey},    author =       {Marshall, J. and A. Adcroft and C. Hill and L. Perelman and C. Heisey},
870    title =        {A finite-volume, incompressible Navier Stokes model for    title =        {A finite-volume, incompressible Navier Stokes model for
871                    studies of the ocean on parallel computers},                    studies of the ocean on parallel computers},
872    journal =      {JGR},    journal =      jgr,
873    year =         1997,    year =         1997,
874    volume =       102,    volume =       102,
875    number =       {C3},    number =       {C3},
876    pages =        {5753-5766}    pages =        {5753-5766},
877      url      =     {http://mitgcm.org/pdfs/96JC02776.pdf},
878  }  }
879    
880  @Article{adcroft:97,  @Article{adcroft:97,
881    author =       {Adcroft, A.J. and Hill, C.N. and J. Marshall},    author =       {Adcroft, A.J. and Hill, C.N. and J. Marshall},
882    title =        {Representation of topography by shaved cells in a height    title =        {Representation of topography by shaved cells in a height
883                    coordinate ocean model},                    coordinate ocean model},
884    journal =      {MWR},    journal =      mwr,
885    year =         1997,    year =         1997,
886    volume =       125,    volume =       125,
887    pages =        {2293-2315}    pages =        {2293-2315},
888      url   =        {http://mitgcm.org/pdfs/mwr_1997.pdf},
889      doi       =    {10.1175/1520-0493\%281997\%29125<2293:ROTBSC>2.0.CO;2},
890  }  }
891    
892  @Article{adcroft:04a,  @Article{adcroft:04a,
# Line 806  Line 896 
896    journal =      om,    journal =      om,
897    year =         2004,    year =         2004,
898    volume =       7,    volume =       7,
899    pages =        {269-284}    pages =        {269-284},
900      doi   =        {10.1016/j.ocemod.2003.09.003},
901  }  }
902    
903  @Article{adcroft:04b,  @Article{adcroft:04b,
# Line 816  Line 907 
907    journal =      mwr,    journal =      mwr,
908    year =         2004,    year =         2004,
909    volume =       132,    volume =       132,
910    pages =        {2845-2863}    pages =        {2845-2863},
911      url   =        {http://mitgcm.org/pdfs/mwr_2004.pdf},
912      doi     =      {10.1175/MWR2823.1},
913    }
914    
915    @inproceedings{adcroft:04c,
916      author =       {Adcroft, A. and C. Hill and J.-M. Campin and J. Marshall
917                      and P. Heimbach},
918      title =        {Overview of the Formulation and Numerics of the {MIT}GCM},
919      booktitle =   {Proceedings of the ECMWF seminar series on Numerical Methods,
920                     Recent developments in numerical methods for atmosphere and
921                     ocean modelling},
922      year =         2004,
923      pages =        {139-149},
924      url   =        {http://mitgcm.org/pdfs/ECMWF2004-Adcroft.pdf},
925     publisher =     ecmwf
926  }  }
927    
928  @Article{marshall:04,  @Article{marshall:04,
# Line 825  Line 931 
931    journal =      mwr,    journal =      mwr,
932    year =         2004,    year =         2004,
933    volume =       132,    volume =       132,
934    pages =        {2882-2894}    pages =        {2882-2894},
935      url   =        {http://mitgcm.org/pdfs/a_o_iso.pdf},
936      doi    =       {10.1175/MWR2835.1},
937  }  }
938    
939  @Article{visbeck:97,  @Article{visbeck:97,
940    author =       {Visbeck, M., J. Marshall, T. Haine, and M. Spall},    author =       {Visbeck, M., J. Marshall, T. Haine, and M. Spall},
941    title =        {Specification of eddy transfer coefficients in    title =        {Specification of eddy transfer coefficients in
942                    coarse-resolution ocean circulation models},                    coarse-resolution ocean circulation models},
943    journal =      {JPO},    journal =      jpo,
944    year =         1997,    year =         1997,
945    volume =       27,    volume =       27,
946    number =       3,    number =       3,
# Line 852  Line 960 
960    pages =        {1-51}    pages =        {1-51}
961  }  }
962    
 @Article{marshall:98,  
   author =       {J. Marshall and H. Jones and C. Hill},  
   title =        {Efficient ocean modeling using non-hydrostatic algorithms},  
   journal =      {JMR},  
   year =         1998,  
   volume =       18,  
   pages =        {115-134}  
 }  
   
963  @Article{mjn:99,  @Article{mjn:99,
964    author =       {Marshall, J., Jamous, D and J. Nilsson},    author =       {Marshall, J., Jamous, D and J. Nilsson},
965    title =        {Reconciling `thermodynamic' and `dynamic' methods of    title =        {Reconciling `thermodynamic' and `dynamic' methods of
# Line 885  Line 984 
984    author =       {Adcroft, A., Hill C. and J. Marshall},    author =       {Adcroft, A., Hill C. and J. Marshall},
985    title =        {A new treatment of the Coriolis terms in C-grid models    title =        {A new treatment of the Coriolis terms in C-grid models
986                    at both high and low resolutions},                    at both high and low resolutions},
987    journal =      {MWR},    journal =      mwr,
988    year =         1999,    year =         1999,
989    volume =       127,    volume =       127,
990    pages =        {1928-1936}    pages =        {1928-1936},
991      url   =        {http://mitgcm.org/pdfs/mwr_1999.pdf},
992      doi   =        {10.1175/1520-0493\%281999\%29127<1928:ANTOTC>2.0.CO;2},
993  }  }
994    
995  @InProceedings{hill:99,  @InProceedings{hill:99,
# Line 903  Line 1004 
1004  @Article{wardle:00,  @Article{wardle:00,
1005    author =       {Wardle R. and Marshall J.},    author =       {Wardle R. and Marshall J.},
1006    title =        {Representation of eddies in primitive equation models by a PV flux},    title =        {Representation of eddies in primitive equation models by a PV flux},
1007    journal =      {JPO},    journal =      jpo,
1008    year =         2000,    year =         2000,
1009    volume =       30,    volume =       30,
1010    number =       10,    number =       10,
# Line 920  Line 1021 
1021  }  }
1022    
1023  @Article{adcroft:02,  @Article{adcroft:02,
1024    author =       {Adcroft et al.},    author =       {Adcroft, A., et~al.},
1025    title =        {Energy conversion in discrete numerical models},    title =        {Energy conversion in discrete numerical models},
1026    journal =      om,    journal =      om,
1027    year =         2002,    year =         2002,
# Line 942  Line 1043 
1043    author =       {Miller, M. J. and White, A. A.},    author =       {Miller, M. J. and White, A. A.},
1044    title =        {On the non-hydrostatic equations in pressure    title =        {On the non-hydrostatic equations in pressure
1045                    and sigma coordiantes},                    and sigma coordiantes},
1046    journal =      {qjrms},    journal =      qjrms,
1047    year =         1984,    year =         1984,
1048    volume =       110,    volume =       110,
1049    pages =        {515-533}    pages =        {515-533}
# Line 951  Line 1052 
1052  @Article{white:89,  @Article{white:89,
1053    author =       {White, A. A.},    author =       {White, A. A.},
1054    title =        {An extended version of a nonhydrostatic, pressure coordiante model},    title =        {An extended version of a nonhydrostatic, pressure coordiante model},
1055    journal =      {qjrms},    journal =      qjrms,
1056    year =         1989,    year =         1989,
1057    volume =       115,    volume =       115,
1058    pages =        {1243-1251}    pages =        {1243-1251}
# Line 980  Line 1081 
1081    author =       {Griffies, S.,M. and Hallberg, R.,W.},    author =       {Griffies, S.,M. and Hallberg, R.,W.},
1082    title =        {Biharmonic friction with a Smagorinsky-like viscosity for    title =        {Biharmonic friction with a Smagorinsky-like viscosity for
1083                    use in large-scale eddy-permitting ocean models},                    use in large-scale eddy-permitting ocean models},
1084    journal =      {MWR},    journal =      mwr,
1085    year =         2000,    year =         2000,
1086    volume =       128,    volume =       128,
1087    number =       8,    number =       8,
# Line 991  Line 1092 
1092    author =       {Wajsowicz, R.},    author =       {Wajsowicz, R.},
1093    title =        {A CONSISTENT FORMULATION OF THE ANISOTROPIC STRESS TENSOR    title =        {A CONSISTENT FORMULATION OF THE ANISOTROPIC STRESS TENSOR
1094                    FOR USE IN MODELS OF THE LARGE-SCALE OCEAN CIRCULATION},                    FOR USE IN MODELS OF THE LARGE-SCALE OCEAN CIRCULATION},
1095    journal =      {JCP},    journal =      jcp,
1096    year =         1993,    year =         1993,
1097    volume =       105,    volume =       105,
1098    number =       2,    number =       2,
# Line 1010  Line 1111 
1111  @Article{dm:95,  @Article{dm:95,
1112    author =       {Danabasoglu, G. and McWilliams J.C.},    author =       {Danabasoglu, G. and McWilliams J.C.},
1113    title =        {Sensitivity of the global ocean circulation to parameterizations of mesoscale tracer transports},    title =        {Sensitivity of the global ocean circulation to parameterizations of mesoscale tracer transports},
1114    journal =      {JC},    journal =      jclim,
1115    year =         1995,    year =         1995,
1116    volume =       8,    volume =       8,
1117    number =       12,    number =       12,
# Line 1020  Line 1121 
1121  @Article{ldd:97,  @Article{ldd:97,
1122    author =       {Large, W.G. and Danabasoglu, G. and Doney, S.C. and McWilliams, J.C.},    author =       {Large, W.G. and Danabasoglu, G. and Doney, S.C. and McWilliams, J.C.},
1123    title =        {Sensitivity to surface forcing and boundary layer mixing in a global ocean model: Annual-mean climatology},    title =        {Sensitivity to surface forcing and boundary layer mixing in a global ocean model: Annual-mean climatology},
1124    journal =      {JPO},    journal =      jpo,
1125    year =         1997,    year =         1997,
1126    volume =       27,    volume =       27,
1127    number =       11,    number =       11,
# Line 1031  Line 1132 
1132    author =       {Gerdes R. and Koberle C. and Beckmann A. and Herrmann P. and Willebrand J.},    author =       {Gerdes R. and Koberle C. and Beckmann A. and Herrmann P. and Willebrand J.},
1133    title =        {Mechanisms for spreading of Mediterranean water in    title =        {Mechanisms for spreading of Mediterranean water in
1134                    coarse-resolution numerical models},                    coarse-resolution numerical models},
1135    journal =      {JPO},    journal =      jpo,
1136    year =         1999,    year =         1999,
1137    volume =       29,    volume =       29,
1138    number =       8,    number =       8,
# Line 1062  Line 1163 
1163  }  }
1164    
1165  @Article{molteni:03,  @Article{molteni:03,
1166    author =       {K. M. Trenberth and J. Olson and W. G. Large},    author =       {F. Molteni},
1167    title =        {Atmospheric simulations using a GCM with simplified physical    title =        {Atmospheric simulations using a {GCM} with simplified physical
1168                    parametrization, I model climatology and variability in                    parametrization, {I}: Model climatology and variability in
1169                    multidecadal experiments},                    multidecadal experiments},
1170    journal =      climd,    journal =      climd,
1171    year =         2003,    year =         2003,
# Line 1237  Line 1338 
1338    title =        {Mechanisms of air-sea CO$_2$ flux variability in the    title =        {Mechanisms of air-sea CO$_2$ flux variability in the
1339                    Equatorial Pacific and the North Atlantic},                    Equatorial Pacific and the North Atlantic},
1340    journal =      {Global Biogeochemical Cycles},    journal =      {Global Biogeochemical Cycles},
1341    year =         {},    year =         {2004},
1342    OPTkey =       {},    OPTkey =       {},
1343    volume =       {18},    volume =       {18},
1344    number =       {doi:10.1029/2003GB002179},    number =       {doi:10.1029/2003GB002179},
# Line 1555  atmospheric boundary layer.}, Line 1656  atmospheric boundary layer.},
1656   volume         = {126},   volume         = {126},
1657   pages          = {991-1000}   pages          = {991-1000}
1658                    }                    }
1659    @TechReport{MPI-std-20,
1660      author =       {{Message Passing Interface Forum}}},
1661      title =        {{MPI}: A Message-Passing Interface standard (version 2.0)},
1662      institution =  {mpi-forum.org},
1663      year =         {1998},
1664    }
1665    
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