| 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.}} | 
| 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}, | 
| 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}, | 
| 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}, | 
| 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}, | 
| 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, | 
| 628 | publisher      = {U.S. Department of Commerce}, | publisher      = {U.S. Department of Commerce}, | 
| 629 | address        = {Washington, D.C. (USA)}, | address        = {Washington, D.C. (USA)}, | 
| 630 | note           = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/}, | note           = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/}, | 
| 631 |  | url            = {http:////ingrid.ldeo.columbia.edu/SOURCES/.DASILVA/.SMD94/}, | 
| 632 | } | } | 
| 633 |  |  | 
| 634 | @techreport{sta-eta:97, | @techreport{sta-eta:97, | 
| 647 | address        = {Cambridge (MA), USA}, | address        = {Cambridge (MA), USA}, | 
| 648 | } | } | 
| 649 |  |  | 
| 650 | @Article{sta-eta:01, | @ARTICLE{stam-eta:01, | 
| 651 | 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}, | 
| 652 | 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.}, | 
| 653 | A. Adcroft and C. Hill and J. Marshall}, | journal = jgr, | 
| 654 | year           = 2001, | year = {2002a}, | 
| 655 | title          = {The global ocean circulation during 1992 -- 1997, | volume = {107(C9)}, | 
| 656 | estimated from ocean observations and a general | pages = {3118}, | 
| 657 | circulation model}, | doi   = {10.1029/2001JC000888}, | 
| 658 | journal        = jgr, | } | 
| 659 | note           = {in press}, |  | 
|  | } |  | 
| 660 |  |  | 
| 661 | @Article{Stommel66, | @Article{Stommel66, | 
| 662 | author         = {H. Stommel}, | author         = {H. Stommel}, | 
| 818 | author =       {Marshall, J. and C. Hill and L. Perelman and A. Adcroft}, | author =       {Marshall, J. and C. Hill and L. Perelman and A. Adcroft}, | 
| 819 | title =        {Hydrostatic, quasi-hydrostatic, and nonhydrostatic ocean | title =        {Hydrostatic, quasi-hydrostatic, and nonhydrostatic ocean | 
| 820 | modeling}, | modeling}, | 
| 821 | journal =      {JGR}, | journal =      jgr, | 
| 822 | year =         1997, | year =         1997, | 
| 823 | volume =       102, | volume =       102, | 
| 824 | number =       {C3}, | number =       {C3}, | 
| 825 | pages =        {5733-5752} | pages =        {5733-5752}, | 
| 826 |  | url      =     {http://mitgcm.org/pdfs/96JC02775.pdf}, | 
| 827 | } | } | 
| 828 |  |  | 
| 829 | @Article{marshall:97b, | @Article{marshall:97b, | 
| 830 | 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}, | 
| 831 | title =        {A finite-volume, incompressible Navier Stokes model for | title =        {A finite-volume, incompressible Navier Stokes model for | 
| 832 | studies of the ocean on parallel computers}, | studies of the ocean on parallel computers}, | 
| 833 | journal =      {JGR}, | journal =      jgr, | 
| 834 | year =         1997, | year =         1997, | 
| 835 | volume =       102, | volume =       102, | 
| 836 | number =       {C3}, | number =       {C3}, | 
| 837 | pages =        {5753-5766} | pages =        {5753-5766}, | 
| 838 |  | url      =     {http://mitgcm.org/pdfs/96JC02776.pdf}, | 
| 839 | } | } | 
| 840 |  |  | 
| 841 | @Article{adcroft:97, | @Article{adcroft:97, | 
| 842 | author =       {Adcroft, A.J. and Hill, C.N. and J. Marshall}, | author =       {Adcroft, A.J. and Hill, C.N. and J. Marshall}, | 
| 843 | title =        {Representation of topography by shaved cells in a height | title =        {Representation of topography by shaved cells in a height | 
| 844 | coordinate ocean model}, | coordinate ocean model}, | 
| 845 | journal =      {MWR}, | journal =      mwr, | 
| 846 | year =         1997, | year =         1997, | 
| 847 | volume =       125, | volume =       125, | 
| 848 | pages =        {2293-2315} | pages =        {2293-2315}, | 
| 849 |  | url   =        {http://mitgcm.org/pdfs/mwr_1997.pdf}, | 
| 850 |  | doi       =    {10.1175/1520-0493\%281997\%29125<2293:ROTBSC>2.0.CO;2}, | 
| 851 | } | } | 
| 852 |  |  | 
| 853 | @Article{adcroft:04a, | @Article{adcroft:04a, | 
| 857 | journal =      om, | journal =      om, | 
| 858 | year =         2004, | year =         2004, | 
| 859 | volume =       7, | volume =       7, | 
| 860 | pages =        {269-284} | pages =        {269-284}, | 
| 861 |  | doi   =        {10.1016/j.ocemod.2003.09.003}, | 
| 862 | } | } | 
| 863 |  |  | 
| 864 | @Article{adcroft:04b, | @Article{adcroft:04b, | 
| 868 | journal =      mwr, | journal =      mwr, | 
| 869 | year =         2004, | year =         2004, | 
| 870 | volume =       132, | volume =       132, | 
| 871 | pages =        {2845-2863} | pages =        {2845-2863}, | 
| 872 |  | url   =        {http://mitgcm.org/pdfs/mwr_2004.pdf}, | 
| 873 |  | doi     =      {10.1175/MWR2823.1}, | 
| 874 | } | } | 
| 875 |  |  | 
| 876 | @Article{marshall:04, | @Article{marshall:04, | 
| 879 | journal =      mwr, | journal =      mwr, | 
| 880 | year =         2004, | year =         2004, | 
| 881 | volume =       132, | volume =       132, | 
| 882 | pages =        {2882-2894} | pages =        {2882-2894}, | 
| 883 |  | url   =        {http://mitgcm.org/pdfs/a_o_iso.pdf}, | 
| 884 |  | doi    =       {10.1175/MWR2835.1}, | 
| 885 | } | } | 
| 886 |  |  | 
| 887 | @Article{visbeck:97, | @Article{visbeck:97, | 
| 888 | author =       {Visbeck, M., J. Marshall, T. Haine, and M. Spall}, | author =       {Visbeck, M., J. Marshall, T. Haine, and M. Spall}, | 
| 889 | title =        {Specification of eddy transfer coefficients in | title =        {Specification of eddy transfer coefficients in | 
| 890 | coarse-resolution ocean circulation models}, | coarse-resolution ocean circulation models}, | 
| 891 | journal =      {JPO}, | journal =      jpo, | 
| 892 | year =         1997, | year =         1997, | 
| 893 | volume =       27, | volume =       27, | 
| 894 | number =       3, | number =       3, | 
| 908 | pages =        {1-51} | pages =        {1-51} | 
| 909 | } | } | 
| 910 |  |  | 
|  | @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} |  | 
|  | } |  | 
|  |  |  | 
| 911 | @Article{mjn:99, | @Article{mjn:99, | 
| 912 | author =       {Marshall, J., Jamous, D and J. Nilsson}, | author =       {Marshall, J., Jamous, D and J. Nilsson}, | 
| 913 | title =        {Reconciling `thermodynamic' and `dynamic' methods of | title =        {Reconciling `thermodynamic' and `dynamic' methods of | 
| 932 | author =       {Adcroft, A., Hill C. and J. Marshall}, | author =       {Adcroft, A., Hill C. and J. Marshall}, | 
| 933 | title =        {A new treatment of the Coriolis terms in C-grid models | title =        {A new treatment of the Coriolis terms in C-grid models | 
| 934 | at both high and low resolutions}, | at both high and low resolutions}, | 
| 935 | journal =      {MWR}, | journal =      mwr, | 
| 936 | year =         1999, | year =         1999, | 
| 937 | volume =       127, | volume =       127, | 
| 938 | pages =        {1928-1936} | pages =        {1928-1936}, | 
| 939 |  | url   =        {http://mitgcm.org/pdfs/mwr_1999.pdf}, | 
| 940 |  | doi   =        {10.1175/1520-0493\%281999\%29127<1928:ANTOTC>2.0.CO;2}, | 
| 941 | } | } | 
| 942 |  |  | 
| 943 | @InProceedings{hill:99, | @InProceedings{hill:99, | 
| 952 | @Article{wardle:00, | @Article{wardle:00, | 
| 953 | author =       {Wardle R. and Marshall J.}, | author =       {Wardle R. and Marshall J.}, | 
| 954 | title =        {Representation of eddies in primitive equation models by a PV flux}, | title =        {Representation of eddies in primitive equation models by a PV flux}, | 
| 955 | journal =      {JPO}, | journal =      jpo, | 
| 956 | year =         2000, | year =         2000, | 
| 957 | volume =       30, | volume =       30, | 
| 958 | number =       10, | number =       10, | 
| 969 | } | } | 
| 970 |  |  | 
| 971 | @Article{adcroft:02, | @Article{adcroft:02, | 
| 972 | author =       {Adcroft et al.}, | author =       {Adcroft, A., et~al.}, | 
| 973 | title =        {Energy conversion in discrete numerical models}, | title =        {Energy conversion in discrete numerical models}, | 
| 974 | journal =      om, | journal =      om, | 
| 975 | year =         2002, | year =         2002, | 
| 987 | volume =       17 | volume =       17 | 
| 988 | } | } | 
| 989 |  |  | 
| 990 |  | @Article{miller_white:84, | 
| 991 |  | author =       {Miller, M. J. and White, A. A.}, | 
| 992 |  | title =        {On the non-hydrostatic equations in pressure | 
| 993 |  | and sigma coordiantes}, | 
| 994 |  | journal =      qjrms, | 
| 995 |  | year =         1984, | 
| 996 |  | volume =       110, | 
| 997 |  | pages =        {515-533} | 
| 998 |  | } | 
| 999 |  |  | 
| 1000 |  | @Article{white:89, | 
| 1001 |  | author =       {White, A. A.}, | 
| 1002 |  | title =        {An extended version of a nonhydrostatic, pressure coordiante model}, | 
| 1003 |  | journal =      qjrms, | 
| 1004 |  | year =         1989, | 
| 1005 |  | volume =       115, | 
| 1006 |  | pages =        {1243-1251} | 
| 1007 |  | } | 
| 1008 |  |  | 
| 1009 | @Article{adcroft:98, | @Article{adcroft:98, | 
| 1010 | author =       {Adcroft, A. and Marshall, D.}, | author =       {Adcroft, A. and Marshall, D.}, | 
| 1011 | title =        {How slippery are piecewise-constant coastlines in numerical | title =        {How slippery are piecewise-constant coastlines in numerical | 
| 1029 | author =       {Griffies, S.,M. and Hallberg, R.,W.}, | author =       {Griffies, S.,M. and Hallberg, R.,W.}, | 
| 1030 | title =        {Biharmonic friction with a Smagorinsky-like viscosity for | title =        {Biharmonic friction with a Smagorinsky-like viscosity for | 
| 1031 | use in large-scale eddy-permitting ocean models}, | use in large-scale eddy-permitting ocean models}, | 
| 1032 | journal =      {MWR}, | journal =      mwr, | 
| 1033 | year =         2000, | year =         2000, | 
| 1034 | volume =       128, | volume =       128, | 
| 1035 | number =       8, | number =       8, | 
| 1040 | author =       {Wajsowicz, R.}, | author =       {Wajsowicz, R.}, | 
| 1041 | title =        {A CONSISTENT FORMULATION OF THE ANISOTROPIC STRESS TENSOR | title =        {A CONSISTENT FORMULATION OF THE ANISOTROPIC STRESS TENSOR | 
| 1042 | FOR USE IN MODELS OF THE LARGE-SCALE OCEAN CIRCULATION}, | FOR USE IN MODELS OF THE LARGE-SCALE OCEAN CIRCULATION}, | 
| 1043 | journal =      {JCP}, | journal =      jcp, | 
| 1044 | year =         1993, | year =         1993, | 
| 1045 | volume =       105, | volume =       105, | 
| 1046 | number =       2, | number =       2, | 
| 1059 | @Article{dm:95, | @Article{dm:95, | 
| 1060 | author =       {Danabasoglu, G. and McWilliams J.C.}, | author =       {Danabasoglu, G. and McWilliams J.C.}, | 
| 1061 | 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}, | 
| 1062 | journal =      {JC}, | journal =      jclim, | 
| 1063 | year =         1995, | year =         1995, | 
| 1064 | volume =       8, | volume =       8, | 
| 1065 | number =       12, | number =       12, | 
| 1069 | @Article{ldd:97, | @Article{ldd:97, | 
| 1070 | 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.}, | 
| 1071 | 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}, | 
| 1072 | journal =      {JPO}, | journal =      jpo, | 
| 1073 | year =         1997, | year =         1997, | 
| 1074 | volume =       27, | volume =       27, | 
| 1075 | number =       11, | number =       11, | 
| 1080 | 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.}, | 
| 1081 | title =        {Mechanisms for spreading of Mediterranean water in | title =        {Mechanisms for spreading of Mediterranean water in | 
| 1082 | coarse-resolution numerical models}, | coarse-resolution numerical models}, | 
| 1083 | journal =      {JPO}, | journal =      jpo, | 
| 1084 | year =         1999, | year =         1999, | 
| 1085 | volume =       29, | volume =       29, | 
| 1086 | number =       8, | number =       8, | 
| 1111 | } | } | 
| 1112 |  |  | 
| 1113 | @Article{molteni:03, | @Article{molteni:03, | 
| 1114 | author =       {K. M. Trenberth and J. Olson and W. G. Large}, | author =       {F. Molteni}, | 
| 1115 | title =        {Atmospheric simulations using a GCM with simplified physical | title =        {Atmospheric simulations using a {GCM} with simplified physical | 
| 1116 | parametrization, I model climatology and variability in | parametrization, {I}: Model climatology and variability in | 
| 1117 | multidecadal experiments}, | multidecadal experiments}, | 
| 1118 | journal =      climd, | journal =      climd, | 
| 1119 | year =         2003, | year =         2003, | 
| 1286 | title =        {Mechanisms of air-sea CO$_2$ flux variability in the | title =        {Mechanisms of air-sea CO$_2$ flux variability in the | 
| 1287 | Equatorial Pacific and the North Atlantic}, | Equatorial Pacific and the North Atlantic}, | 
| 1288 | journal =      {Global Biogeochemical Cycles}, | journal =      {Global Biogeochemical Cycles}, | 
| 1289 | year =         {}, | year =         {2004}, | 
| 1290 | OPTkey =       {}, | OPTkey =       {}, | 
| 1291 | volume =       {18}, | volume =       {18}, | 
| 1292 | number =       {doi:10.1029/2003GB002179}, | number =       {doi:10.1029/2003GB002179}, | 
| 1604 | volume         = {126}, | volume         = {126}, | 
| 1605 | pages          = {991-1000} | pages          = {991-1000} | 
| 1606 | } | } | 
| 1607 |  | @TechReport{MPI-std-20, | 
| 1608 |  | author =       {{Message Passing Interface Forum}}}, | 
| 1609 |  | title =        {{MPI}: A Message-Passing Interface standard (version 2.0)}, | 
| 1610 |  | institution =  {mpi-forum.org}, | 
| 1611 |  | year =         {1998}, | 
| 1612 |  | } | 
| 1613 |  |  |