| 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{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}, | 
| 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, | 
| 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}, | 
| 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}, | 
| 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 | 
| 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, | 
| 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}, | 
| 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, | 
| 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}, | 
| 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}, | 
| 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, | 
| 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, | 
| 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, | 
| 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, | 
| 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 | 
| 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, | 
| 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, | 
| 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, | 
| 1039 | volume =       17 | volume =       17 | 
| 1040 | } | } | 
| 1041 |  |  | 
| 1042 |  | @Article{miller_white:84, | 
| 1043 |  | author =       {Miller, M. J. and White, A. A.}, | 
| 1044 |  | title =        {On the non-hydrostatic equations in pressure | 
| 1045 |  | and sigma coordiantes}, | 
| 1046 |  | journal =      qjrms, | 
| 1047 |  | year =         1984, | 
| 1048 |  | volume =       110, | 
| 1049 |  | pages =        {515-533} | 
| 1050 |  | } | 
| 1051 |  |  | 
| 1052 |  | @Article{white:89, | 
| 1053 |  | author =       {White, A. A.}, | 
| 1054 |  | title =        {An extended version of a nonhydrostatic, pressure coordiante model}, | 
| 1055 |  | journal =      qjrms, | 
| 1056 |  | year =         1989, | 
| 1057 |  | volume =       115, | 
| 1058 |  | pages =        {1243-1251} | 
| 1059 |  | } | 
| 1060 |  |  | 
| 1061 | @Article{adcroft:98, | @Article{adcroft:98, | 
| 1062 | author =       {Adcroft, A. and Marshall, D.}, | author =       {Adcroft, A. and Marshall, D.}, | 
| 1063 | title =        {How slippery are piecewise-constant coastlines in numerical | title =        {How slippery are piecewise-constant coastlines in numerical | 
| 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 | 
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