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revision 1.22 by molod, Tue Aug 2 15:42:38 2005 UTC revision 1.32 by heimbach, Thu Jan 17 21:13:04 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{dutk-etal:06,
135      author = {S. Dutkiewicz and M.J. Follows and P. Heimbach and J. Marshall},
136      title = {Controls on ocean productivity and air-sea carbon flux:
137               An adjoint model sensitivity study},
138      journal = grl,
139      year = {2006},
140      volume = {33},
141      pages  = {L02603},
142      doi    = {10.1029/2005GL024987},
143    }
144    
145  @Article{err:97,  @Article{err:97,
146   author         = {R.M. Errico},   author         = {R.M. Errico},
# Line 356  Line 381 
381   pages          = {658-669}   pages          = {658-669}
382                    }                    }
383    
384    @Article{jam-oze:86,
385     author         = {B.M. Jamart and J. Ozer},
386     year           = {1986},
387     title          = {Numerical boundary layers and spurious residual flows},
388     journal        = jgr,
389     volume         = {91},
390     pages          = {10,621-10,631}
391                      }
392    
393  @book{kas-eta:00,  @book{kas-eta:00,
394   author         = {P. Kasibhatla and M. Heimann and P. Rayner and   author         = {P. Kasibhatla and M. Heimann and P. Rayner and
395                    N. Mahowald and R.G. Prinn and D.E. Hartley},                    N. Mahowald and R.G. Prinn and D.E. Hartley},
# Line 452  Line 486 
486   pages          = {38 pp.},   pages          = {38 pp.},
487   address        = {Delft (NL)},   address        = {Delft (NL)},
488                    }                    }
489    
490    @ARTICLE{losc-heim:06,
491      author = {M. Losch and P. Heimbach},
492      title = {Adjoint sensitivity of an ocean general circulation model
493               to bottom topography},
494      journal = jpo,
495      year = {2006},
496      volume = {{in press}},
497      url    = {http://mitgcm.org/pdfs/Los2006a.pdf},
498    }
499    
500    
501  @Article{maro-wun:93,  @Article{maro-wun:93,
502   author         = {J. Marotzke and C. Wunsch},   author         = {J. Marotzke and C. Wunsch},
# Line 506  Line 551 
551   journal        = jms,   journal        = jms,
552   volume         = {18},   volume         = {18},
553   pages          = {115--134},   pages          = {115--134},
554     url            = {http://mitgcm.org/pdfs/journal_of_marine_systems_1998.pdf},
555     doi            = {10.1016/S0924-7963\%2898\%2900008-6},
556                    }                    }
557    
558  @Article{mcw:96,  @Article{mcw:96,
# Line 526  Line 573 
573  %%   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
574  %%   also available.  %%   also available.
575    
576    @incollection{naum-etal:06,
577            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},
578            Booktitle = {European Conference on Computational Fluid Dynamics ECCOMAS CFD 2006},
579            Editor = {{P. Wesseling, E. O~nate and J. Periaux}},
580            Pages = {~},
581            Publisher = {TU Delft},
582            Title = {Adjoint code by source transformation with OpenAD/F},
583            Year = {2006}}
584    
585  @TechReport{rew:97,  @TechReport{rew:97,
586    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},
587    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 628 
628   address        = {Berlin (Germany)},   address        = {Berlin (Germany)},
629                    }                    }
630    
631    @article{utke-etal:08,
632            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},
633            Date-Modified = {2007-11-19 10:15:08 -0500},
634            Journal = {{ACM} Transactions on Mathematical Software},
635            Pages = {~},
636            Title = {OpenAD/F: A modular open source tool for automatic differentiation of Fortran codes},
637            Volume = {34(4)},
638            Year = {2008}}
639    
640  @Article{DaSilva94,  @Article{DaSilva94,
641   author         = {A. da Silva and A. C. Young and S. Levitus},   author         = {A. da Silva and A. C. Young and S. Levitus},
642   year           = 1994,   year           = 1994,
# Line 581  Line 646 
646   publisher      = {U.S. Department of Commerce},   publisher      = {U.S. Department of Commerce},
647   address        = {Washington, D.C. (USA)},   address        = {Washington, D.C. (USA)},
648   note           = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/},   note           = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/},
649     url            = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/},
650                    }                    }
651    
652  @techreport{sta-eta:97,  @techreport{stam-etal:97,
653   author         = {D. Stammer and C. Wunsch and R. Giering and   author         = {D. Stammer and C. Wunsch and R. Giering and
654                    Q. Zhang and J. Marotzke and J. Marshall and                    Q. Zhang and J. Marotzke and J. Marshall and
655                    C. Hill},                    C. Hill},
# Line 599  Line 665 
665   address        = {Cambridge (MA), USA},   address        = {Cambridge (MA), USA},
666                    }                    }
667    
668  @Article{sta-eta:01,  @ARTICLE{stam-etal:02,
669   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},
670                    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.},
671                    A. Adcroft and C. Hill and J. Marshall},    journal = jgr,
672   year           = 2001,    year = {2002a},
673   title          = {The global ocean circulation during 1992 -- 1997,    volume = {107(C9)},
674                    estimated from ocean observations and a general    pages = {3118},
675                    circulation model},    doi   = {10.1029/2001JC000888},
676   journal        = jgr,  }
677   note           = {in press},  
                   }  
678    
679  @Article{Stommel66,  @Article{Stommel66,
680   author         = {H. Stommel},   author         = {H. Stommel},
# Line 771  Line 836 
836    author =       {Marshall, J. and C. Hill and L. Perelman and A. Adcroft},    author =       {Marshall, J. and C. Hill and L. Perelman and A. Adcroft},
837    title =        {Hydrostatic, quasi-hydrostatic, and nonhydrostatic ocean    title =        {Hydrostatic, quasi-hydrostatic, and nonhydrostatic ocean
838                   modeling},                   modeling},
839    journal =      {JGR},    journal =      jgr,
840    year =         1997,    year =         1997,
841    volume =       102,    volume =       102,
842    number =       {C3},    number =       {C3},
843    pages =        {5733-5752}    pages =        {5733-5752},
844      url      =     {http://mitgcm.org/pdfs/96JC02775.pdf},
845  }  }
846    
847  @Article{marshall:97b,  @Article{marshall:97b,
848    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},
849    title =        {A finite-volume, incompressible Navier Stokes model for    title =        {A finite-volume, incompressible Navier Stokes model for
850                    studies of the ocean on parallel computers},                    studies of the ocean on parallel computers},
851    journal =      {JGR},    journal =      jgr,
852    year =         1997,    year =         1997,
853    volume =       102,    volume =       102,
854    number =       {C3},    number =       {C3},
855    pages =        {5753-5766}    pages =        {5753-5766},
856      url      =     {http://mitgcm.org/pdfs/96JC02776.pdf},
857  }  }
858    
859  @Article{adcroft:97,  @Article{adcroft:97,
860    author =       {Adcroft, A.J. and Hill, C.N. and J. Marshall},    author =       {Adcroft, A.J. and Hill, C.N. and J. Marshall},
861    title =        {Representation of topography by shaved cells in a height    title =        {Representation of topography by shaved cells in a height
862                    coordinate ocean model},                    coordinate ocean model},
863    journal =      {MWR},    journal =      mwr,
864    year =         1997,    year =         1997,
865    volume =       125,    volume =       125,
866    pages =        {2293-2315}    pages =        {2293-2315},
867      url   =        {http://mitgcm.org/pdfs/mwr_1997.pdf},
868      doi       =    {10.1175/1520-0493\%281997\%29125<2293:ROTBSC>2.0.CO;2},
869  }  }
870    
871  @Article{adcroft:04a,  @Article{adcroft:04a,
# Line 806  Line 875 
875    journal =      om,    journal =      om,
876    year =         2004,    year =         2004,
877    volume =       7,    volume =       7,
878    pages =        {269-284}    pages =        {269-284},
879      doi   =        {10.1016/j.ocemod.2003.09.003},
880  }  }
881    
882  @Article{adcroft:04b,  @Article{adcroft:04b,
# Line 816  Line 886 
886    journal =      mwr,    journal =      mwr,
887    year =         2004,    year =         2004,
888    volume =       132,    volume =       132,
889    pages =        {2845-2863}    pages =        {2845-2863},
890      url   =        {http://mitgcm.org/pdfs/mwr_2004.pdf},
891      doi     =      {10.1175/MWR2823.1},
892  }  }
893    
894  @Article{marshall:04,  @Article{marshall:04,
# Line 825  Line 897 
897    journal =      mwr,    journal =      mwr,
898    year =         2004,    year =         2004,
899    volume =       132,    volume =       132,
900    pages =        {2882-2894}    pages =        {2882-2894},
901      url   =        {http://mitgcm.org/pdfs/a_o_iso.pdf},
902      doi    =       {10.1175/MWR2835.1},
903  }  }
904    
905  @Article{visbeck:97,  @Article{visbeck:97,
906    author =       {Visbeck, M., J. Marshall, T. Haine, and M. Spall},    author =       {Visbeck, M., J. Marshall, T. Haine, and M. Spall},
907    title =        {Specification of eddy transfer coefficients in    title =        {Specification of eddy transfer coefficients in
908                    coarse-resolution ocean circulation models},                    coarse-resolution ocean circulation models},
909    journal =      {JPO},    journal =      jpo,
910    year =         1997,    year =         1997,
911    volume =       27,    volume =       27,
912    number =       3,    number =       3,
# Line 852  Line 926 
926    pages =        {1-51}    pages =        {1-51}
927  }  }
928    
 @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}  
 }  
   
929  @Article{mjn:99,  @Article{mjn:99,
930    author =       {Marshall, J., Jamous, D and J. Nilsson},    author =       {Marshall, J., Jamous, D and J. Nilsson},
931    title =        {Reconciling `thermodynamic' and `dynamic' methods of    title =        {Reconciling `thermodynamic' and `dynamic' methods of
# Line 885  Line 950 
950    author =       {Adcroft, A., Hill C. and J. Marshall},    author =       {Adcroft, A., Hill C. and J. Marshall},
951    title =        {A new treatment of the Coriolis terms in C-grid models    title =        {A new treatment of the Coriolis terms in C-grid models
952                    at both high and low resolutions},                    at both high and low resolutions},
953    journal =      {MWR},    journal =      mwr,
954    year =         1999,    year =         1999,
955    volume =       127,    volume =       127,
956    pages =        {1928-1936}    pages =        {1928-1936},
957      url   =        {http://mitgcm.org/pdfs/mwr_1999.pdf},
958      doi   =        {10.1175/1520-0493\%281999\%29127<1928:ANTOTC>2.0.CO;2},
959  }  }
960    
961  @InProceedings{hill:99,  @InProceedings{hill:99,
# Line 903  Line 970 
970  @Article{wardle:00,  @Article{wardle:00,
971    author =       {Wardle R. and Marshall J.},    author =       {Wardle R. and Marshall J.},
972    title =        {Representation of eddies in primitive equation models by a PV flux},    title =        {Representation of eddies in primitive equation models by a PV flux},
973    journal =      {JPO},    journal =      jpo,
974    year =         2000,    year =         2000,
975    volume =       30,    volume =       30,
976    number =       10,    number =       10,
# Line 920  Line 987 
987  }  }
988    
989  @Article{adcroft:02,  @Article{adcroft:02,
990    author =       {Adcroft et al.},    author =       {Adcroft, A., et~al.},
991    title =        {Energy conversion in discrete numerical models},    title =        {Energy conversion in discrete numerical models},
992    journal =      om,    journal =      om,
993    year =         2002,    year =         2002,
# Line 938  Line 1005 
1005    volume =       17    volume =       17
1006  }  }
1007    
1008    @Article{miller_white:84,
1009      author =       {Miller, M. J. and White, A. A.},
1010      title =        {On the non-hydrostatic equations in pressure
1011                      and sigma coordiantes},
1012      journal =      qjrms,
1013      year =         1984,
1014      volume =       110,
1015      pages =        {515-533}
1016    }
1017    
1018    @Article{white:89,
1019      author =       {White, A. A.},
1020      title =        {An extended version of a nonhydrostatic, pressure coordiante model},
1021      journal =      qjrms,
1022      year =         1989,
1023      volume =       115,
1024      pages =        {1243-1251}
1025    }
1026    
1027  @Article{adcroft:98,  @Article{adcroft:98,
1028    author =       {Adcroft, A. and Marshall, D.},    author =       {Adcroft, A. and Marshall, D.},
1029    title =        {How slippery are piecewise-constant coastlines in numerical    title =        {How slippery are piecewise-constant coastlines in numerical
# Line 961  Line 1047 
1047    author =       {Griffies, S.,M. and Hallberg, R.,W.},    author =       {Griffies, S.,M. and Hallberg, R.,W.},
1048    title =        {Biharmonic friction with a Smagorinsky-like viscosity for    title =        {Biharmonic friction with a Smagorinsky-like viscosity for
1049                    use in large-scale eddy-permitting ocean models},                    use in large-scale eddy-permitting ocean models},
1050    journal =      {MWR},    journal =      mwr,
1051    year =         2000,    year =         2000,
1052    volume =       128,    volume =       128,
1053    number =       8,    number =       8,
# Line 972  Line 1058 
1058    author =       {Wajsowicz, R.},    author =       {Wajsowicz, R.},
1059    title =        {A CONSISTENT FORMULATION OF THE ANISOTROPIC STRESS TENSOR    title =        {A CONSISTENT FORMULATION OF THE ANISOTROPIC STRESS TENSOR
1060                    FOR USE IN MODELS OF THE LARGE-SCALE OCEAN CIRCULATION},                    FOR USE IN MODELS OF THE LARGE-SCALE OCEAN CIRCULATION},
1061    journal =      {JCP},    journal =      jcp,
1062    year =         1993,    year =         1993,
1063    volume =       105,    volume =       105,
1064    number =       2,    number =       2,
# Line 991  Line 1077 
1077  @Article{dm:95,  @Article{dm:95,
1078    author =       {Danabasoglu, G. and McWilliams J.C.},    author =       {Danabasoglu, G. and McWilliams J.C.},
1079    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},
1080    journal =      {JC},    journal =      jclim,
1081    year =         1995,    year =         1995,
1082    volume =       8,    volume =       8,
1083    number =       12,    number =       12,
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1087  @Article{ldd:97,  @Article{ldd:97,
1088    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.},
1089    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},
1090    journal =      {JPO},    journal =      jpo,
1091    year =         1997,    year =         1997,
1092    volume =       27,    volume =       27,
1093    number =       11,    number =       11,
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1098    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.},
1099    title =        {Mechanisms for spreading of Mediterranean water in    title =        {Mechanisms for spreading of Mediterranean water in
1100                    coarse-resolution numerical models},                    coarse-resolution numerical models},
1101    journal =      {JPO},    journal =      jpo,
1102    year =         1999,    year =         1999,
1103    volume =       29,    volume =       29,
1104    number =       8,    number =       8,
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1129  }  }
1130    
1131  @Article{molteni:03,  @Article{molteni:03,
1132    author =       {K. M. Trenberth and J. Olson and W. G. Large},    author =       {F. Molteni},
1133    title =        {Atmospheric simulations using a GCM with simplified physical    title =        {Atmospheric simulations using a {GCM} with simplified physical
1134                    parametrization, I model climatology and variability in                    parametrization, {I}: Model climatology and variability in
1135                    multidecadal experiments},                    multidecadal experiments},
1136    journal =      climd,    journal =      climd,
1137    year =         2003,    year =         2003,
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1304    title =        {Mechanisms of air-sea CO$_2$ flux variability in the    title =        {Mechanisms of air-sea CO$_2$ flux variability in the
1305                    Equatorial Pacific and the North Atlantic},                    Equatorial Pacific and the North Atlantic},
1306    journal =      {Global Biogeochemical Cycles},    journal =      {Global Biogeochemical Cycles},
1307    year =         {},    year =         {2004},
1308    OPTkey =       {},    OPTkey =       {},
1309    volume =       {18},    volume =       {18},
1310    number =       {doi:10.1029/2003GB002179},    number =       {doi:10.1029/2003GB002179},
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1571   volume       = {122},   volume       = {122},
1572   pages        = {903-927}   pages        = {903-927}
1573  }  }
1574    
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1577                       and W.R. Cotton and J. Cuxart and H. Cuijpers and M. Khairoutdinov
1578                       and B. Kosovic and D. Lewellen and C-H. Moeng and P. Siebesma and
1579                       B. Stevens and D.E. Stevens and I. Sykes and M.C. Wyant},
1580     year           = 1999,
1581     title          = {An intercomparison of radiatively driven entrainment and turbulence
1582                      in a smoke cloud, as simulated by different numerical models.},
1583     journal        = qjrms,
1584     volume         = {125},
1585     pages          = {391-423}
1586                      }
1587    
1588    @Article{bm:99,
1589     author         = {A. C. Bushell and G.M. Martin},
1590     year           = 1999,
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1592     journal        = {Climate Dyn.},
1593     volume         = {15},
1594     pages          = {293-318}
1595                      }
1596    
1597    @Article{Inn:01,
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1599     year           = 2001,
1600     title          = {Organization of Tropical Convection in a GCM with Verying Vertical Resolution;
1601                      Implications for the Simulation of the Madden-Julian Oscillation.},
1602     journal        = {Climate Dyn.},
1603     volume         = {17},
1604     pages          = {777-794}
1605                      }
1606    
1607    @Article{kal:89,
1608     author         = {E. Kalnay and M. Kanamitsu and J. Pfaendtner and J. Sela and M. Suarez and
1609                       J. Stackpole and J. Tucillo and L. Umscheid and and D. Williamson},
1610     year           = 1989,
1611     title          = {Rules for Interchange of Physical Parameterizations.},
1612     journal        = bams,
1613     volume         = {70},
1614     pages          = {620-622}
1615                      }
1616    
1617    @Article{wo:98,
1618     author         = {D. Williamson and J.G. Olsen},
1619     year           = 1998,
1620     title          = {A Comparison of Semi-Langrangian and Eulerian Polar Climate Simulations.},
1621     journal        = mwr,
1622     volume         = {126},
1623     pages          = {991-1000}
1624                      }
1625    @TechReport{MPI-std-20,
1626      author =       {{Message Passing Interface Forum}}},
1627      title =        {{MPI}: A Message-Passing Interface standard (version 2.0)},
1628      institution =  {mpi-forum.org},
1629      year =         {1998},
1630    }
1631    
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