Bibliography

From WikiROMS
Jump to navigationJump to search
Bibliography

The following references list follows the the American Meteorological Society (AMS) guidelines for citation style (PDF).

Contents

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

Allen, S. E., M. S. Dinniman, J. M. Klinck, B. M. Hickey, D. D. Gorby, A. J. Hewett, 2003: On vertical advection truncation errors in terrain following numerical models: Comparison to a laboratory model for upwelling over submarine canyons, J. Geophys. Res., 108 (C1), 1-16, doi:10.1029/2001JC000978. (PDF)

Arakawa, A. and V. R. Lamb, 1977: Methods of computational physics, Academic Press, 174-265.

Arango, H. G., A. M. Moore, A. J. Miller, B. D. Cornuelle, E. Di Lorenzo, and D. J. Neilson, 2003: The ROMS Tangent Linear and Adjoint Models: A comprehensive ocean prediction and analysis system, IMCS Technical Reports, Rutgers Univeristy, 69pp. (PDF)

B

Batchelor, G. K., 1967: An introduction to fluid dynamics, Cambridge University Press.

Bissett, W.P., J.J. Walsh, D.A. Dieterle, K.L. Carder, 1999a: Carbon cycling in the upper waters of the Sargasso Sea: I. Numerical simulation of differential carbon and nitrogen fluxes, Deep-Sea Res., 46, 205-269.

Bissett, W. P., K. L. Carder, J. J. Walsh, D. A. Dieterle, 1999b: Carbon cycling in the upper waters of the Sargasso Sea: II. Numerical simulation of apparent and inherent optical properties, Deep-Sea Res., 46, 271-317.

Bissett, W., Arnone, R., DeBra, S., Dieterle, D., Dye, D., Kirkpatrick, G., Schofield, O. and Vargo, G., 2005. Predicting the optical properties of the West Florida Shelf: Resolving the potential impacts of a terrestrial boundary condition on the distribution of colored dissolved and particulate matter. Marine Chemistry, 95(3-4), 199-233.

Booij, N., R. C. Ris, and L. H. Holthuijsen, 1999: A third-generation wave model for coastal regions. Part I - Model description and validation. Journal of Geophysical Research, 104, 7649-7666.

Budgell, W.P., 2005: Numerical simulation of ice-ocean variability in the Barents Sea region, Ocean Dynamics, DOI 10.1007/s10236-005-0008-3. (PDF)

Burchard, H., 2001: Simulating the wave-enhanced layer under breaking surface waves with two-equation turbulence models, J. Phys. Oceanogr., 31, 3133-3145.

C

Canuto, V. M., A. Howard, Y. Cheng, M. S. Dubovikov, 2001: Ocean turbulence I: one-point closure model. Momentum and heat vertical diffusivities, J. Phys. Oceanogr., 31, 1413-1426.

Chapman, S. J., 2004: Fortan 90/95 for Scientists and Engineers. Second Edition. McGraw-Hill. 814 pp.

Chassignet, E. P., H. G. Arango, D. Dietrich, T. Ezer, M. Ghil, D. B. Haidvogel C.-C. Ma, A. Mehra, A. M. Paiva, Z. Sirkes, 2000: DAMEE-NAB: The Base Experiments, Dyn. Atmos. Oceans, 32, 155-183. (PDF)

Choi, B.-J., and J. L. Wilkin, 2006a: The effect of wind on the dispersal of the Hudson River plume, J. Phys. Oceanogr., 37, 1878-1897. (PDF)

Chua, B. S. and A. F. Bennett, 2001: An inverse ocean modeling system, Ocean Modelling, 3, 137-165. (PDF)

D

Daley, R., 1991: Atmospheric Data Analysis, Cambridge Atmospheric and Space Science Series, Cambridge University Press, 457 pages.

Dean, R. G., and R. A. Dalrymple, 1991: Water Wave Mechanics for Engineers and Scientists. World Scientific, 353 pp.

Di Lorenzo, E., 2003: Seasonal dynamics of the surface circulation in the southern California Current System, Deep-Sea Res., Part II, 50, 2371-2388.

Di Lorenzo, E., A.M. Moore, H.G. Arango, B.D. Cornuelle, A.J. Miller, B. Powell, B.S. Chua, and A.F. Bennett, 2006: Weak and Strong Constraint Data Assimilation in the inverse Regional Ocean Modeling System (ROMS): development and applications for a baroclinic costal upwelling system, Ocean Modelling, in press.

Dinniman, M. S. and J. M. Klinck, 2002: The influence of open versus periodic alongshore boundaries on circulations near submarine canyons, J. Atmos. Oceanic Tech., 19, 1722-1737 (PDF)

Dinniman, M. S., J. M. Klinck, and W. O. Smith Jr., 2003: Cross shelf exchange in a model of the Ross Sea circulation and biogeochemistry, Deep-Sea Res., Part II, 50, 3103-3120. (PDF)

Dinniman, M. S. and J. M. Klinck, 2004: A model study of circulation and cross shelf exchange on the west Antarctic Peninsula continental shelf, Deep-Sea Res., Part II, 51, 2003-2022. (PDF)

Durski, S. M., S. M. Glenn, D. B. Haidvogel, 2004: Vertical mixing schemes in the coastal ocean: Comparison of the Level 2.5 Mellor-Yamada scheme with an enhanced version of the K-profile parameterization, J. Geophys. Res., 109, C01015, doi:10.1029/2002JC001702. (PDF)

E

Ezer, T., H. G. Arango and A. F. Shchepetkin, 2002: Developments in terrain-following ocean models: intercomparisons of numerical aspects, Ocean Modelling, 4, 249-267. (PDF)

F

Fairall, C. W., E. F. Bradley, D. P. Rogers, J. B. Edson and G. S. Young, 1996: Bulk parameterization of air-sea fluxes for tropical ocean-global atmosphere Coupled-Ocean Atmosphere Response Experiment, J. Geophys. Res., 101, 3747-3764.

Fasham, M. J. R., H. W. Ducklow, and S. M. McKelvie, 1990: A nitrogen-based model of plankton dynamics in the oceanic mixed layer, J. Mar. Res., 48, 591-639.

Fennel, K., J. Wilkin, M. Previdi, R. Najjar, 2008: Denitrification effects on air-sea CO2 flux in the coastal ocean: Simulations for the Northwest North Atlantic, Geophys. Res. Let., 35, L24608. (PDF)

Fennel, K., J. Wilkin, J. Levin, J. Moisan, J. O'Reilly, and D. Haidvogel, 2006: Nitrogen cycling in the Middle Atlantic Bight: Results from a three-dimensional model and implications for the North Atlantic nitrogen budget, Global Biogeochem. Cycles, 20, GB3007, doi:10.1029/2005GB002456. (PDF)

Fiechter, J., A.M. Moore, C.A. Edwards, K.W. Bruland, E. Di Lorenzo, C.V.W. Lewis, T.M. Powell, E. Curchitser, and K. Hedstrom, 2009: Modeling iron limitation of primary production in the coastal Gulf of Alaska, Deep_Sea Res. II, 56(24), 2503-2519. (PDF)

Fisher, M., 1997: Efficient minimization of quadratic penalty functions. Unpublished manuscript.

Fisher, M., 1998: Minimization algorithms for variational data assimilation. Recent Developments in Numerical Methods for Atmospheric Modelling, ECMWF publication, 364-385.

Franks, P. J. S., J. S. Wroblewski, and G. R. Flierl, 1986: Behavior of simple plankton model with food-level acclimation by herbivores, Mar. Biol., 91, 121-129.

Freeman, N. G., A. M. Hale, and M. B. Danard, 1972: A modified sigma equations' approach to the numerical modeling of great lake hydrodynamics, J. Geophys. Res., 77, 1050-1060.

G

Galperin, B., L. H. Kantha, S. Hassid, and A. Rosati, 1988: A quasi-equilibrium turbulent energy model for geophysical flows, J. Atmos. Sci., 45, 55-62.

Golub, G. H. and C. Van Loan, 1989: Matrix Computations, Johns Hopkins University Press, 2nd edition, Baltimore, Maryland.

Griffies, S.M., A. Gnanadesikan, R.C. Pacanowski, V. Larichev, J.K. Dukowicz, and R.D. Smith, 1998: Isoneutral diffusion in a z-coordinate ocean model, J. Phys. Oceanogr., 28, 805--830.

Griffies, S.M. and R.W. Hallberg, 2000: Biharmonic friction with a Smagorinsky-like viscosity for use in large-scale eddy-permitting ocean models, Monthly Weather Rev., 128, 8, 2935--2946.

H

Haidvogel, D. B. and A. Beckmann, 1999: Numerical Ocean Circulation Modeling. Series on Environmental Science and Management, Vol. 2, Imperial College Press, 319 pp.

Haidvogel, D. B., H. G. Arango, K. Hedstrom, A. Beckmann, P. Malanotte-Rizzoli, and A. F. Shchepetkin, 2000: Model evaluation experiments in the North Atlantic Basin: Simulations in nonlinear terrain-following coordinates, Dyn. Atmos. Oceans, 32, 239-281. (PDF)

Hakkinen, S. and G. L. Mellor, 1992: Modeling the seasonal variability of a coupled arctic ice-ocean system, J. Geophys. Res., 97, 20285-20304.

He, R., and J. L. Wilkin, 2006a: Barotropic tides on the southeast New England shelf: A view from a hybrid data assimilative modeling approach, J. Geophys. Res., 111, C08002, doi:10.1029/2005JC003254. (PDF)

Hibler, III, W. D., 1979: A dynamic thermodynamic sea ice model, J. Phys. Oceanogr., 9, 815-846.

Hunke, E. C., 2001: Viscous-plastic sea ice dynamics with the EVP model: linearization issues, J. Comp. Phys., 170, 18-38.

Hunke, E. C. and J. K. Dukowicz, 1997: An elastic-viscous-plastic model for sea ice dynamics, J. Phys. Oceanogr., 27, 1849-1868.

I

J

Jackett, D. R. and T. J. McDougall, 1995: Minimal Adjustment of Hydrostatic Profiles to Achieve Static Stability, J. Atmos. Oceanic Techn., 12, 381-389.

K

Kantha, L.H., C.A. Clayson, 1994: Nermerical Models of Oceans and Oceanic Processes. In: International Geophysics Series, Vol. 66. Academic Press, San Diego. 940 pp.

Keeling, R. F., B. B. Stephens, R. G. Najjar, S. C. Doney, D. Archer, and M. Heimann, 1998: Seasonal variations in the atmospheric O2/N2 ratio in relation to the kinetics of air-sea gas exchange, Global Biogeochem. Cycles, 12(1), 141-163.

Kishi, M. J., et al., 2007: Nemuro - a lower trophic level model for the North Pacific marine ecosystem, Ecological Modelling, 202, 12-25.

Kosters, F., 2004: Denmark Strait overflow: Comparing model results and hydraulic transport estimates, J. Geophys. Res., 109, C10011, doi:10.1029/2004JC002297. (PDF)

L

Laevastu, T., 1960: Factors affecting the temperature od the surface layer of the sea, Comments Phys. Math., 25, 1.

Large, W. G., J. C. McWilliams, and S. C. Doney, 1994: Oceanic vertical mixing: a review and a model with a nonlocal boundary layer parameterization, Rev. Geophys., 32, 363-403.

Leonard, B. P., 1979: A stable and accurate convective modelling procedure based on quadratic upstream interpolation. Comput. Methods Appl. Mech. Eng., 19, 59-98.

Lesser, G. R., J. A. Roelvink, J. A. T. M. van Kester, and G. S. Stelling, 2004: Development and validation of a three-dimensional morphological model. Coastal Engineering, 51, 883-915.

M

MacCready, P. and W. R. Geyer, 2001: Estuarine salt flux through an isohaline surface, J. Geophys. Res., 106 (C6), 11629-11637. (PDF)

Malanotte-Rizzoli, P., K. Hedstrom, H.G. Arango, and D.B. Haidvogel, 2000: Water mass pathways between the subtropical and tropical ocean in a climatological simulation of the North Atlantic ocean circulation, Dyn. Atmos. Oceans, 32, 331-371. (PDF)

Marchesiello, P., J. C. McWilliams, A. F. Shchepetkin, 2001: Open boundary conditions for long-term integration of regional ocean models, Ocean Modelling, 3, 1-20. (PDF)

Marchesiello, P., J. C. McWilliams, and A. Shchepetkin, 2003: Equilibrium structure and dynamics of the California Current System, J. Phys. Oceanogr., 33, 753-783. (PDF)

Mellor, G. L. and T. Yamada, 1982: Developement of a turbulence closure model for geophysical fluid problems, Rev. Geophys. Space Phys., 20, 851-875.

Mellor, G. L. and L. Kantha, 1989: An ice-ocean coupled model, J. Geophys. Res., 94, 10,937-10,954.

Meyer-Peter, E., and R. Mueller, 1948: Formulas for bedload transport. In: Report on the Second Meeting of the International Association Hydraulic Structure Research, Stockholm, Sweden, 39-64.

Moore, A. M., H. G. Arango, A. J. Miller, B. D. Cornuelle, E. Di Lorenzo and D. J. Neilson, 2004: A Comprehensive Ocean Prediction and Analysis System Based on the Tangent Linear and Adjoint Components of a Regional Ocean Model, Ocean Modelling, 7, 227-258. (PDF)

Moore, A.M., H.G. Arango, E. Di Lorenzo, A.J. Miller and B.D. Cornuelle, 2006: An adjoint sensitivity analysis of the southern portion of the California Current circulation and ecosystem, Part I: The physical circulation, J. Phys. Oceanogr., submitted.

Muccino, J. C., H. G. Arango, A. B. Bennett, B. S. chua, B. D. Cornuelle, E. Di Lorenzo, G. D. Egbert, D. B. Haidvogel, L. Hao, J. C. Levin, A. J. Miller, A. M. Moore, and E. D. Zaron, 2006: The Inverse Ocean Modeling System. II: Applications, J. Atmos. Oceanic Tech., submitted.

N

O

P

Parkinson, C. L. and W. M. Washington, 1979: A large-scale numerical model of sea ice, J. Geophys. Res., 84, 311-337.

Peliz, A., J. Dubert, D. B. Haidvogel, 2003: Subinertial Response of a Density-Driven Eastern Boundary Poleward Current to Wind Forcing, J. Phys. Oceanogr., 33, 1633-1650. (PDF)

Peliz, A., J. Dubert, D. B. Haidvogel, and B. Le Cann, 2003: Generation and unstable evolution of a density-driven Eastern Poleward Current: The Iberian Poleward Current, J. Geophys. Res., 108 (C8), 3268, doi:10.1029/2002JC001443. (PDF)

Penven, P., C. Roy, A. Colin de Verdiere and J. Largier, 2000: Simulation of a coastal jet retention process using a barotropic model, Oceanology Acta, 23(5), 615-634. (PDF)

Penven, P., C. Roy, J.R.E. Lutjeharms, A. Colin de Verdiere, A. Johnson, F. Shillington, P. Freon and G. Brundrit, 2001: A regional hydrodynamic model of the Southern Benguela, S. Afr. J. Sci. Res. Letters, 97, 1-4. (PDF)

Penven, P., J. R. E. Lutjeharms, P. Marchesiello, C. Roy and S. J. Weeks, 2001: Generation of cyclonic eddies by the Agulhas Current in the lee of the Agulhas Bank, Geophys. Res. Letters, 27, 1055-1058. (PDF)

Phillips, N. A., 1957: A coordinate system having some special advantages for numerical forecasting, J. Meteorology, 14, 184-185.

Powell, B.S., H.G. Arango, A.M. Moore, E. DiLorenzo, R.F. Milliff and D. Foley, 2008: 4DVAR Data Assimilation in the Intra-Americas Sea with the Regional Ocean Modeling System (ROMS). Ocean Modelling, 25, 173-188.

Powell T. P., C. V. W. Lewis, E. N. Curchitser, D. B. Haidvogel, A. J. Hermann, E. L. Dobbins (2006), Results from a three-dimensional, nested biological-physical model of the California Current System and comparisons with statistics from satellite imagery, J. Geophys. Res., 111, C07018, doi:10.1029/2004JC002506.

Q

R

Rasch, P.J., 1994: Conservative shape-preserving two-dimensional transport on a spherical reduced grid, Mon. Wea. Rev, 122, 1337-1350.

Robertson, R., 2006: Modeling internal tides over Fieberling Guyot: resolution, parameterization, performance, Ocean Dynamics, doi:10.1007/s10236-006-0062-5. (PDF)

S

Sadourny, R. and K. Maynard, 1997: Formulations of lateral diffusion in geophysical fluid dynamics models, In Numerical Methods of Atmospheric and Oceanic Modelling, C.A. Lin, R. Laprise, and H. Ritchie, Eds., NRC Research Press, 547--556.

Semtner, Jr., A. J., 1976: A model for the thermodynamic growth of sea ice in numerical investigations of climate, J. Phys. Oceanogr., 6, 379-389.

Shchepetkin, A. F., and J. C. McWilliams, 1998: Quasi-monotone advection schemes based on explicit locally adaptive dissipation, Monthly Weather Rev., 126, 1541-1580. (PDF)

Shchepetkin, A. F., and J. C. McWilliams, 2003: A method for computing horizontal pressure-gradient force in an oceanic model with a nonaligned vertical coordinate, J. Geophys. Res., 108 (C3), 3090, doi:10.1029/2001JC001047. (PDF)

Shchepetkin, A. F., and J. C. McWilliams, 2005: The Regional Ocean Modeling System: A split-explicit, free-surface, topography following coordinates ocean model, Ocean Modelling, 9, 347-404. (PDF)

Shchepetkin, A. F., and J. C. McWilliams, 2009: Correction and Commentary for "Ocean forecasting in terrain-following coordinates: formulation and skill assessment of the Regional Ocean Modeling System" by Haidvogel et al., J. Comp. Phys., 227, 3595-3624.

Shchepetkin, A. F., and J. C. McWilliams, 2009: Computational kernel algorithms for fine-scale, multi-process, long-time oceanic simulations. In: Handbook of Numerical Analysis: Computational Methods for the Ocean and the Atmosphere, eds. R. Temam & J. Tribbia, Elsevier Science, in press.

Shchepetkin, A. F., and J. C. McWilliams, 2008: An Accurate Boussinesq oceanic model with a practical, "Stiffened" equation of state, submitted to Elsevier Science.

She, J. and J. M. Klinck, 2000: Flow near submarine canyons driven by constant winds, J. Geophys. Res., 105(C12), 28671-28694. (PDF)

Signell, R. P., R. C. Beardsley, H. C. Graber, and A. Capotondi, 1990: Effect of Wave-Current Interaction on Steady Wind-Driven Circulation in Narrow, Shallow Embayments, J. Geophys. Res., 95(C6), 9671-9678.

Signell, R. P., W. R. Geyer, 1991: Transient Eddy Formation Around Headlands, J. Geophys. Res., 96(C2), 2561-2575.

Smith, W.O., Jr., M.S. Dinniman, J.M. Klinck and E.E. Hofmann, 2003: Biogeochemical Climatologies of the Ross Sea, Antarctica: Seasonal Patterns of Nutrients and Biomass, Deep-Sea Res., Part II, 50, 3083-3101. (PDF)

Soulsby, R. L. and Damgaard, J. S. 2005: Bedload sediment transport in coastal waters. Coastal Engineering, 52, 673-689.

Soulsby, R. L. and Whitehouse, R. J. S., 2005: Prediction of Ripple Properties in Shelf Seas; Mark 2 Predictor for Time Evolution. Report TR 154, HR Wallingford, Wallingford, UK.

Soulsby, R. L., 2006: Simplified calculation of wave-orbital velocities. Report TR 155, HR Wallingford, Wallingford, UK.

Song, Y. and D. B. Haidvogel, 1994: A semi-implicit ocean circulation model using a generalized topography-following coordinate system, J. Comp. Phys., 115 (1), 228-244. (PDF)

Steele, M., G. L. Mellor and M. G. McPhee, 1989: Role of the molecular sublayer in the melting or freezing of sea ice, J. Phys. Oceanogr., 19, 139-147.

Styles, R. and S. M. Glenn, 2000: Modeling stratified wave and current bottom boundary layers in the continental shelf, J. Geophys. Res., 105, 24119-24139. (PDF)

T

Thuburn, J., 1995: Dissipation and cascade to small scales in numerical models using a shape-preserving advection scheme. Mon. Wea. Rev., 123, 1888-1903.

Tshimanga, J., 2007: On a class of limited memory preconditioners for large-scale nonlinear least-squares problems. PhD thesis, Facultes Universitaires Notre-Dame de la Paix, Namur, Belgium.

Tshimanga, J., S. Gratton, A.T. Weaver and A. Sartenaer, 2008: Limited-memory preconditioners with application to incremental variational data assimilation. Q. J. R. Meteorol. Soc., 134, 751-769.

U

Umlauf, L., H. Burchard, 2003: A generic length-scale equation for geophysical turbulence models, J. Marine Res., 61, 235-265.

V

W

Wajsowicz, R.C, 1993: A consistent formulation of the anisotropic stress tensor for use in models of the large-scale ocean circulation, J. Comput. Phys., 105, 333-338.

Wanninkhof, R., 1992: Relationship between wind speed and gas exchange over the ocean, J. Geophys. Res., 97(C5), 7373-7382.

Warner, J. C., C. R. Sherwood, H. G. Arango, and R. P. Signell, 2005a: Performance of four turbulence closure methods implemented using a generic length scale method, Ocean Modelling, 8, 81-113. (PDF)

Warner, J. C., W. R. Geyer, and J. A. Lerczak, 2005b: Numerical modeling of an estuary: a comprehensive skill assessment, J. Geophys. Res., 110, C05001, doi:10.1029/2004JC002691. (PDF)

Warner, J. C., C. R. Sherwood, R. P. Signell, C. K. Harris, and H. G. Arango, 2008: Development of a three-dimensional, regional, coupled wave, current, and sediment-transport model, Computers & Geosciences, 34, 1284-1306.

Warner, J. C., N. Perlin, E. D. Skyllingstad, 2008: Using the Model Coupling Toolkit to couple earth system models, Environmental Modelling & Software, 23, 1240-1249.

Wiberg, P. L. and C. K. Harris, 1994: Ripple geometry in wave-dominated environments. Journal of Geophysical Research, 99(C1), 775-789.

Wiberg, P. L. and C. R. Sherwood, 2008: Calculating wave-generated bottom orbital velocity from surfacewave parameters. Computers & Geosciences, 34, 1243-1262.

Weaver, A.T., J. Vialard and D.L.T. Anderson, 2003: Three and four-dimensional variational data assimilation with a general circulation model of the tropical Pacific Ocean. Part I: Formulation, internal diagnostics, and consistency checks. Mon. Wea. Rev., 131, 1360-1378.

Wilkin, J. L., H. G. Arango, D. B. Haidvogel, C. S. Lichtenwalner, S. M. Durski, and K. S. Hedstrom, 2005: A regional Ocean Modeling System for the Long-term Ecosystem Observatory, J. Geophys. Res., 110, C06S91, doi:10.1029/2003JC002218. (PDF)

Wilkin, J. L., and L. Lanerolle, 2005: Ocean Forecast and Analysis Models for Coastal Observatories, in: Ocean Weather Forecasting, An Integrated View of Oceanography, Springer, 577p., ISBN: 978-1-4020-3981-2. (Publisher)

Wilkin, J. L., 2006: The summer time heat budget and circulation of southeast New England shelf, J. Phys. Oceanog., 36, 1997-2011. (PDF)

Wilkin, J. L., and W. Zhang, 2006: Modes of mesoscale sea surface height and temperature variability in the East Australian Current, J. Geophys. Res., 112, C01013, doi:10.1029/2006JC003590. (PDF)

Winsor, P. and D. C. Chapman, 2004: Pathways of Pacific water across the Chukchi Sea: A numerical model study, J. Geophys. Res., 109, C03002, doi: 10.1029/2003JC001962. (PDF)

X

Y

Z

Zillman, J. W., 1972: A study of some aspects of radiation and heat budgets of southern hemisphere oceans, Meteorological Studies, 26, 562-575.

Zhu, Y. and R. Gelaro, 2008: Observation Sensitivity Calculations Using the Adjoint of the Gridpoint Statistical Interpolation (GSI) Analysis System, Monthly Weather Review, 136, 335-351.