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revision 1.24 by jmc, Wed Aug 31 18:51:42 2005 UTC revision 1.33 by jmc, Thu Jan 17 21:28:22 2008 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 356  Line 392 
392   pages          = {658-669}   pages          = {658-669}
393                    }                    }
394    
395    @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  @book{kas-eta:00,  @book{kas-eta:00,
405   author         = {P. Kasibhatla and M. Heimann and P. Rayner and   author         = {P. Kasibhatla and M. Heimann and P. Rayner and
406                    N. Mahowald and R.G. Prinn and D.E. Hartley},                    N. Mahowald and R.G. Prinn and D.E. Hartley},
# Line 452  Line 497 
497   pages          = {38 pp.},   pages          = {38 pp.},
498   address        = {Delft (NL)},   address        = {Delft (NL)},
499                    }                    }
500    
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    
512  @Article{maro-wun:93,  @Article{maro-wun:93,
513   author         = {J. Marotzke and C. Wunsch},   author         = {J. Marotzke and C. Wunsch},
# Line 498  Line 554 
554   pages          = {5,753--5,766},   pages          = {5,753--5,766},
555                    }                    }
556    
557  @Article{mars-sha:98,  @Article{mars-eta:98,
558   author         = {J. Marshall and H. Jones and C. Hill},   author         = {J. Marshall and H. Jones and C. Hill},
559   year           = 1998,   year           = 1998,
560   title          = {Efficient ocean modeling using   title          = {Efficient ocean modeling using
# Line 506  Line 562 
562   journal        = jms,   journal        = jms,
563   volume         = {18},   volume         = {18},
564   pages          = {115--134},   pages          = {115--134},
565     url            = {http://mitgcm.org/pdfs/journal_of_marine_systems_1998.pdf},
566     doi            = {10.1016/S0924-7963\%2898\%2900008-6},
567                    }                    }
568    
569  @Article{mcw:96,  @Article{mcw:96,
# Line 526  Line 584 
584  %%   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
585  %%   also available.  %%   also available.
586    
587    @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  @TechReport{rew:97,  @TechReport{rew:97,
597    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},
598    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 639 
639   address        = {Berlin (Germany)},   address        = {Berlin (Germany)},
640                    }                    }
641    
642    @article{utke-etal:08,
643            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},
644            Date-Modified = {2007-11-19 10:15:08 -0500},
645            Journal = {{ACM} Transactions on Mathematical Software},
646            Pages = {~},
647            Title = {OpenAD/F: A modular open source tool for automatic differentiation of Fortran codes},
648            Volume = {34(4)},
649            Year = {2008}}
650    
651  @Article{DaSilva94,  @Article{DaSilva94,
652   author         = {A. da Silva and A. C. Young and S. Levitus},   author         = {A. da Silva and A. C. Young and S. Levitus},
653   year           = 1994,   year           = 1994,
# Line 581  Line 657 
657   publisher      = {U.S. Department of Commerce},   publisher      = {U.S. Department of Commerce},
658   address        = {Washington, D.C. (USA)},   address        = {Washington, D.C. (USA)},
659   note           = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/},   note           = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/},
660     url            = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/},
661                    }                    }
662    
663  @techreport{sta-eta:97,  @techreport{stam-etal:97,
664   author         = {D. Stammer and C. Wunsch and R. Giering and   author         = {D. Stammer and C. Wunsch and R. Giering and
665                    Q. Zhang and J. Marotzke and J. Marshall and                    Q. Zhang and J. Marotzke and J. Marshall and
666                    C. Hill},                    C. Hill},
# Line 599  Line 676 
676   address        = {Cambridge (MA), USA},   address        = {Cambridge (MA), USA},
677                    }                    }
678    
679  @Article{sta-eta:01,  @ARTICLE{stam-etal:02,
680   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},
681                    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.},
682                    A. Adcroft and C. Hill and J. Marshall},    journal = jgr,
683   year           = 2001,    year = {2002a},
684   title          = {The global ocean circulation during 1992 -- 1997,    volume = {107(C9)},
685                    estimated from ocean observations and a general    pages = {3118},
686                    circulation model},    doi   = {10.1029/2001JC000888},
687   journal        = jgr,  }
688   note           = {in press},  
                   }  
689    
690  @Article{Stommel66,  @Article{Stommel66,
691   author         = {H. Stommel},   author         = {H. Stommel},
# Line 771  Line 847 
847    author =       {Marshall, J. and C. Hill and L. Perelman and A. Adcroft},    author =       {Marshall, J. and C. Hill and L. Perelman and A. Adcroft},
848    title =        {Hydrostatic, quasi-hydrostatic, and nonhydrostatic ocean    title =        {Hydrostatic, quasi-hydrostatic, and nonhydrostatic ocean
849                   modeling},                   modeling},
850    journal =      {JGR},    journal =      jgr,
851    year =         1997,    year =         1997,
852    volume =       102,    volume =       102,
853    number =       {C3},    number =       {C3},
854    pages =        {5733-5752}    pages =        {5733-5752},
855      url      =     {http://mitgcm.org/pdfs/96JC02775.pdf},
856  }  }
857    
858  @Article{marshall:97b,  @Article{marshall:97b,
859    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},
860    title =        {A finite-volume, incompressible Navier Stokes model for    title =        {A finite-volume, incompressible Navier Stokes model for
861                    studies of the ocean on parallel computers},                    studies of the ocean on parallel computers},
862    journal =      {JGR},    journal =      jgr,
863    year =         1997,    year =         1997,
864    volume =       102,    volume =       102,
865    number =       {C3},    number =       {C3},
866    pages =        {5753-5766}    pages =        {5753-5766},
867      url      =     {http://mitgcm.org/pdfs/96JC02776.pdf},
868  }  }
869    
870  @Article{adcroft:97,  @Article{adcroft:97,
871    author =       {Adcroft, A.J. and Hill, C.N. and J. Marshall},    author =       {Adcroft, A.J. and Hill, C.N. and J. Marshall},
872    title =        {Representation of topography by shaved cells in a height    title =        {Representation of topography by shaved cells in a height
873                    coordinate ocean model},                    coordinate ocean model},
874    journal =      {MWR},    journal =      mwr,
875    year =         1997,    year =         1997,
876    volume =       125,    volume =       125,
877    pages =        {2293-2315}    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  }  }
881    
882  @Article{adcroft:04a,  @Article{adcroft:04a,
# Line 806  Line 886 
886    journal =      om,    journal =      om,
887    year =         2004,    year =         2004,
888    volume =       7,    volume =       7,
889    pages =        {269-284}    pages =        {269-284},
890      doi   =        {10.1016/j.ocemod.2003.09.003},
891  }  }
892    
893  @Article{adcroft:04b,  @Article{adcroft:04b,
# Line 816  Line 897 
897    journal =      mwr,    journal =      mwr,
898    year =         2004,    year =         2004,
899    volume =       132,    volume =       132,
900    pages =        {2845-2863}    pages =        {2845-2863},
901      url   =        {http://mitgcm.org/pdfs/mwr_2004.pdf},
902      doi     =      {10.1175/MWR2823.1},
903    }
904    
905    @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  @Article{marshall:04,  @Article{marshall:04,
# Line 825  Line 921 
921    journal =      mwr,    journal =      mwr,
922    year =         2004,    year =         2004,
923    volume =       132,    volume =       132,
924    pages =        {2882-2894}    pages =        {2882-2894},
925      url   =        {http://mitgcm.org/pdfs/a_o_iso.pdf},
926      doi    =       {10.1175/MWR2835.1},
927  }  }
928    
929  @Article{visbeck:97,  @Article{visbeck:97,
930    author =       {Visbeck, M., J. Marshall, T. Haine, and M. Spall},    author =       {Visbeck, M., J. Marshall, T. Haine, and M. Spall},
931    title =        {Specification of eddy transfer coefficients in    title =        {Specification of eddy transfer coefficients in
932                    coarse-resolution ocean circulation models},                    coarse-resolution ocean circulation models},
933    journal =      {JPO},    journal =      jpo,
934    year =         1997,    year =         1997,
935    volume =       27,    volume =       27,
936    number =       3,    number =       3,
# Line 852  Line 950 
950    pages =        {1-51}    pages =        {1-51}
951  }  }
952    
 @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}  
 }  
   
953  @Article{mjn:99,  @Article{mjn:99,
954    author =       {Marshall, J., Jamous, D and J. Nilsson},    author =       {Marshall, J., Jamous, D and J. Nilsson},
955    title =        {Reconciling `thermodynamic' and `dynamic' methods of    title =        {Reconciling `thermodynamic' and `dynamic' methods of
# Line 885  Line 974 
974    author =       {Adcroft, A., Hill C. and J. Marshall},    author =       {Adcroft, A., Hill C. and J. Marshall},
975    title =        {A new treatment of the Coriolis terms in C-grid models    title =        {A new treatment of the Coriolis terms in C-grid models
976                    at both high and low resolutions},                    at both high and low resolutions},
977    journal =      {MWR},    journal =      mwr,
978    year =         1999,    year =         1999,
979    volume =       127,    volume =       127,
980    pages =        {1928-1936}    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  }  }
984    
985  @InProceedings{hill:99,  @InProceedings{hill:99,
# Line 903  Line 994 
994  @Article{wardle:00,  @Article{wardle:00,
995    author =       {Wardle R. and Marshall J.},    author =       {Wardle R. and Marshall J.},
996    title =        {Representation of eddies in primitive equation models by a PV flux},    title =        {Representation of eddies in primitive equation models by a PV flux},
997    journal =      {JPO},    journal =      jpo,
998    year =         2000,    year =         2000,
999    volume =       30,    volume =       30,
1000    number =       10,    number =       10,
# Line 920  Line 1011 
1011  }  }
1012    
1013  @Article{adcroft:02,  @Article{adcroft:02,
1014    author =       {Adcroft et al.},    author =       {Adcroft, A., et~al.},
1015    title =        {Energy conversion in discrete numerical models},    title =        {Energy conversion in discrete numerical models},
1016    journal =      om,    journal =      om,
1017    year =         2002,    year =         2002,
# Line 942  Line 1033 
1033    author =       {Miller, M. J. and White, A. A.},    author =       {Miller, M. J. and White, A. A.},
1034    title =        {On the non-hydrostatic equations in pressure    title =        {On the non-hydrostatic equations in pressure
1035                    and sigma coordiantes},                    and sigma coordiantes},
1036    journal =      {qjrms},    journal =      qjrms,
1037    year =         1984,    year =         1984,
1038    volume =       110,    volume =       110,
1039    pages =        {515-533}    pages =        {515-533}
# Line 951  Line 1042 
1042  @Article{white:89,  @Article{white:89,
1043    author =       {White, A. A.},    author =       {White, A. A.},
1044    title =        {An extended version of a nonhydrostatic, pressure coordiante model},    title =        {An extended version of a nonhydrostatic, pressure coordiante model},
1045    journal =      {qjrms},    journal =      qjrms,
1046    year =         1989,    year =         1989,
1047    volume =       115,    volume =       115,
1048    pages =        {1243-1251}    pages =        {1243-1251}
# Line 980  Line 1071 
1071    author =       {Griffies, S.,M. and Hallberg, R.,W.},    author =       {Griffies, S.,M. and Hallberg, R.,W.},
1072    title =        {Biharmonic friction with a Smagorinsky-like viscosity for    title =        {Biharmonic friction with a Smagorinsky-like viscosity for
1073                    use in large-scale eddy-permitting ocean models},                    use in large-scale eddy-permitting ocean models},
1074    journal =      {MWR},    journal =      mwr,
1075    year =         2000,    year =         2000,
1076    volume =       128,    volume =       128,
1077    number =       8,    number =       8,
# Line 991  Line 1082 
1082    author =       {Wajsowicz, R.},    author =       {Wajsowicz, R.},
1083    title =        {A CONSISTENT FORMULATION OF THE ANISOTROPIC STRESS TENSOR    title =        {A CONSISTENT FORMULATION OF THE ANISOTROPIC STRESS TENSOR
1084                    FOR USE IN MODELS OF THE LARGE-SCALE OCEAN CIRCULATION},                    FOR USE IN MODELS OF THE LARGE-SCALE OCEAN CIRCULATION},
1085    journal =      {JCP},    journal =      jcp,
1086    year =         1993,    year =         1993,
1087    volume =       105,    volume =       105,
1088    number =       2,    number =       2,
# Line 1010  Line 1101 
1101  @Article{dm:95,  @Article{dm:95,
1102    author =       {Danabasoglu, G. and McWilliams J.C.},    author =       {Danabasoglu, G. and McWilliams J.C.},
1103    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},
1104    journal =      {JC},    journal =      jclim,
1105    year =         1995,    year =         1995,
1106    volume =       8,    volume =       8,
1107    number =       12,    number =       12,
# Line 1020  Line 1111 
1111  @Article{ldd:97,  @Article{ldd:97,
1112    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.},
1113    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},
1114    journal =      {JPO},    journal =      jpo,
1115    year =         1997,    year =         1997,
1116    volume =       27,    volume =       27,
1117    number =       11,    number =       11,
# Line 1031  Line 1122 
1122    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.},
1123    title =        {Mechanisms for spreading of Mediterranean water in    title =        {Mechanisms for spreading of Mediterranean water in
1124                    coarse-resolution numerical models},                    coarse-resolution numerical models},
1125    journal =      {JPO},    journal =      jpo,
1126    year =         1999,    year =         1999,
1127    volume =       29,    volume =       29,
1128    number =       8,    number =       8,
# Line 1062  Line 1153 
1153  }  }
1154    
1155  @Article{molteni:03,  @Article{molteni:03,
1156    author =       {K. M. Trenberth and J. Olson and W. G. Large},    author =       {F. Molteni},
1157    title =        {Atmospheric simulations using a GCM with simplified physical    title =        {Atmospheric simulations using a {GCM} with simplified physical
1158                    parametrization, I model climatology and variability in                    parametrization, {I}: Model climatology and variability in
1159                    multidecadal experiments},                    multidecadal experiments},
1160    journal =      climd,    journal =      climd,
1161    year =         2003,    year =         2003,
# Line 1237  Line 1328 
1328    title =        {Mechanisms of air-sea CO$_2$ flux variability in the    title =        {Mechanisms of air-sea CO$_2$ flux variability in the
1329                    Equatorial Pacific and the North Atlantic},                    Equatorial Pacific and the North Atlantic},
1330    journal =      {Global Biogeochemical Cycles},    journal =      {Global Biogeochemical Cycles},
1331    year =         {},    year =         {2004},
1332    OPTkey =       {},    OPTkey =       {},
1333    volume =       {18},    volume =       {18},
1334    number =       {doi:10.1029/2003GB002179},    number =       {doi:10.1029/2003GB002179},
# Line 1555  atmospheric boundary layer.}, Line 1646  atmospheric boundary layer.},
1646   volume         = {126},   volume         = {126},
1647   pages          = {991-1000}   pages          = {991-1000}
1648                    }                    }
1649    @TechReport{MPI-std-20,
1650      author =       {{Message Passing Interface Forum}}},
1651      title =        {{MPI}: A Message-Passing Interface standard (version 2.0)},
1652      institution =  {mpi-forum.org},
1653      year =         {1998},
1654    }
1655    
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