Changeset 14073

Timestamp:

2020-12-04T10:19:21+01:00 (3 years ago)

Author:

nicolasmartin

Message:

#2414 Updating and formatting the BibTeX files
Still 2 undefined references in the NEMO manual: fairall.ea_19 on chap_ZDF.tex and
grant+etal18 on chap_ZDF.tex

Location:

NEMO/branches/2020/dev_r13787_doc_latex_recovery

Files:

• doc/latex/NEMO/main/bibliography.bib (modified) (31 diffs)
• doc/rst/source/cfgs.bib (modified) (1 diff)
• doc/rst/source/refs.bib (moved) (moved from NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/rst/source/ref.bib)
• doc/rst/source/zooms.bib (modified) (1 diff)
• src/NST/zooms.bib (moved) (moved from NEMO/branches/2020/dev_r13787_doc_latex_recovery/cfgs/AGRIF_DEMO/zooms.bib) (1 diff)
• tests/test_cases.bib (modified) (1 diff)

NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/latex/NEMO/main/bibliography.bib

@@ -188 +188 @@
 }
 
-@article{ beljaars_QJRMS95,
-title = "The parametrization of surface fluxes in large-scale models under free convection",
-pages = "255--270",
-journal = "Quarterly Journal of the Royal Meteorological Society",
-volume = "121",
-number = "522",
-author = "Beljaars, Anton C. M.",
-year = "1995",
-month = "jan",
- publisher     = "Wiley",
-issn = "00359009",
-doi = "10.1002/qj.49712152203"
+@article{         beljaars_QJRMS95,
+  title         = "The parametrization of surface fluxes in large-scale
+                  models under free convection",
+  pages         = "255--270",
+  journal       = "Quarterly Journal of the Royal Meteorological Society",
+  volume        = "121",
+  number        = "522",
+  author        = "Beljaars, Anton C. M.",
+  year          = "1995",
+  month         = "jan",
+  publisher     = "Wiley",
+  issn          = "00359009",
+  doi           = "10.1002/qj.49712152203"
 }
 
@@ -384 +385 @@
 }
 
+@article{         brodeau.barnier.ea_JPO16,
+  title         = "Climatologically Significant Effects of Some
+                  Approximations in the Bulk Parameterizations of Turbulent
+                  Air–Sea Fluxes",
+  pages         = "5--28",
+  journal       = "Journal of Physical Oceanography",
+  volume        = "47",
+  number        = "1",
+  author        = "Brodeau, Laurent and Barnier, Bernard and Gulev, Sergey K.
+                  and Woods, Cian",
+  year          = "2016",
+  month         = "jan",
+  publisher     = "American Meteorological Society",
+  issn          = "0022-3670",
+  doi           = "10.1175/jpo-d-16-0169.1"
+}
+
 @article{         brodeau.barnier.ea_OM10,
   title         = "An {ERA40}-based atmospheric forcing for global ocean
@@ -398 +416 @@
   issn          = "1463-5003",
   doi           = "10.1016/j.ocemod.2009.10.005"
-}
-
-@article{         brodeau.barnier.ea_JPO16,
-  title         = "Climatologically Significant Effects of Some Approximations in the Bulk Parameterizations of Turbulent Air–Sea Fluxes",
-  pages         = "5--28",
-  journal       = "Journal of Physical Oceanography",
-  volume        = "47",
-  number        = "1",
-  author        = "Brodeau, Laurent and Barnier, Bernard and Gulev, Sergey K. and Woods, Cian",
-  year          = "2016",
-  month         = "jan",
-  publisher     = "American Meteorological Society",
-  issn          = "0022-3670",
-  doi           = "10.1175/jpo-d-16-0169.1",
 }
 
@@ -519 +523 @@
 }
 
-@article{         carrere.lyard_GRL03,
-  title         = "Modeling the barotropic response of the global ocean to
-                  atmospheric wind and pressure forcing - comparisons with
-                  observations",
-  journal       = "Geophysical Research Letters",
-  volume        = "30",
-  number        = "6",
-  author        = "L. Carr\`{e}re and F. Lyard",
-  year          = "2003",
-  month         = "mar",
-  publisher     = "American Geophysical Union (AGU)",
-  issn          = "0094-8276",
-  doi           = "10.1029/2002gl016473"
-}
-
-@techreport{      chanut_rpt05,
+@techreport{      chanut_trpt05,
   title         = "Nesting code for {NEMO}",
   pages         = "25",
@@ -773 +762 @@
 }
 
-@article{ edson.jampana.ea_JPO13,
-title = "On the Exchange of Momentum over the Open Ocean",
-pages = "1589--1610",
-journal = "Journal of Physical Oceanography",
-volume = "43",
-number = "8",
-author = "Edson, James B. and Jampana, Venkata and Weller, Robert A. and Bigorre, Sebastien P. and Plueddemann, Albert J. and Fairall, Christopher W. and Miller, Scott D. and Mahrt, Larry and Vickers, Dean and Hersbach, Hans",
-year = "2013",
-month = "aug",
-publisher = "American Meteorological Society",
-issn = "0022-3670",
-doi = "10.1175/JPO-D-12-0173.1"
-}
-
-@article{         egbert.ray_JGR01,
-  title         = "Estimates of {M2} tidal energy dissipation from
-                  {TOPEX}/Poseidon altimeter data",
-  pages         = "22475--22502",
-  journal       = "Journal of Geophysical Research",
-  volume        = "106",
-  number        = "C10",
-  author        = "G. D. Egbert and R. D. Ray",
-  year          = "2001",
-  month         = "oct",
-  publisher     = "American Geophysical Union (AGU)",
-  issn          = "0148-0227",
-  doi           = "10.1029/2000jc000699"
-}
-
-@article{         egbert.ray_N00,
-  title         = "Significant dissipation of tidal energy in the deep ocean
-                  inferred from satellite altimeter data",
-  pages         = "775--778",
-  journal       = "Nature",
-  volume        = "405",
-  number        = "6788",
-  author        = "G. D. Egbert and R. D. Ray",
-  year          = "2000",
-  month         = "jun",
-  publisher     = "Springer Nature",
-  issn          = "1476-4687",
-  doi           = "10.1038/35015531"
+@article{         edson.jampana.ea_JPO13,
+  title         = "On the Exchange of Momentum over the Open Ocean",
+  pages         = "1589--1610",
+  journal       = "Journal of Physical Oceanography",
+  volume        = "43",
+  number        = "8",
+  author        = "Edson, James B. and Jampana, Venkata and Weller, Robert A.
+                  and Bigorre, Sebastien P. and Plueddemann, Albert J. and
+                  Fairall, Christopher W. and Miller, Scott D. and Mahrt,
+                  Larry and Vickers, Dean and Hersbach, Hans",
+  year          = "2013",
+  month         = "aug",
+  publisher     = "American Meteorological Society",
+  issn          = "0022-3670",
+  doi           = "10.1175/JPO-D-12-0173.1"
 }
 
@@ -861 +823 @@
 }
 
-@article{ fairall.bradley.ea_JC03,
-title = "Bulk parameterization of air-sea fluxes: Updates and verification for the COARE algorithm",
-pages = "571--591",
-journal = "Journal of Climate",
-volume = "16",
-number = "4",
-author = "Fairall, C. W. and Bradley, E. F. and Hare, J. E. and Grachev, A. A. and Edson, J. B.",
-year = "2003",
-publisher = "American Meteorological Society",
-issn = "08948755",
-doi = "10.1175/1520-0442(2003)016<0571:BPOASF>2.0.CO;2"
+@article{         fairall.bradley.ea_JC03,
+  title         = "Bulk parameterization of air-sea fluxes: Updates and
+                  verification for the COARE algorithm",
+  pages         = "571--591",
+  journal       = "Journal of Climate",
+  volume        = "16",
+  number        = "4",
+  author        = "Fairall, C. W. and Bradley, E. F. and Hare, J. E. and
+                  Grachev, A. A. and Edson, J. B.",
+  year          = "2003",
+  publisher     = "American Meteorological Society",
+  issn          = "08948755",
+  doi           = "10.1175/1520-0442(2003)016<0571:BPOASF>2.0.CO;2"
+}
+
+@article{         fairall.bradley.ea_JGRO96,
+  title         = "Cool-skin and warm-layer effects on sea surface
+                  temperature",
+  pages         = "1295--1308",
+  journal       = "Journal of Geophysical Research: Oceans",
+  volume        = "101",
+  number        = "C1",
+  author        = "C. W. Fairall and E. F. Bradley and J. S. Godfrey and G.
+                  A. Wick and J. B. Edson and G. S. Young",
+  year          = "1996",
+  month         = "jan",
+  publisher     = "American Geophysical Union",
+  doi           = "10.1029/95jc03190"
 }
 
@@ -928 +907 @@
 }
 
-@article{         foxkemper.ferrari_JPO08,
-  title         = "Parameterization of Mixed Layer Eddies. Part I: Theory and Diagnosis",
+@article{         fox-kemper.ferrari.ea_JPO08,
+  title         = "Parameterization of Mixed Layer Eddies. Part I: Theory and
+                  Diagnosis",
   pages         = "1145--1165",
   journal       = "Journal of Physical Oceanography",
@@ -1030 +1010 @@
 }
 
-@article{         gerdes_JGR93*a,
+@article{         gerdes_JGR93,
   title         = "A primitive equation ocean circulation model using a
                   general vertical coordinate transformation: 1. Description
@@ -1045 +1025 @@
 }
 
-@article{         gerdes_JGR93*b,
+@article{         gerdes_JGR93*a,
   title         = "A primitive equation ocean circulation model using a
                   general vertical coordinate transformation: 2. Application
@@ -1060 +1040 @@
 }
 
-@techreport{      gibson_rpt86,
+@techreport{      gibson_trpt86,
   title         = "Standards for software development and maintenance",
   pages         = "21",
@@ -1099 +1079 @@
   issn          = "0148-0227",
   doi           = "10.1029/2010jb007867"
-}
-
-@article{         goosse.deleersnijder.ea_JGR99,
-  title         = "Sensitivity of a global coupled ocean-sea ice model to the
-                  parameterization of vertical mixing",
-  pages         = "13681--13695",
-  journal       = "Journal of Geophysical Research",
-  volume        = "104",
-  number        = "C6",
-  author        = "H. Goosse and E. Deleersnijder and T. Fichefet and M. H.
-                  England",
-  year          = "1999",
-  month         = "jun",
-  publisher     = "American Geophysical Union (AGU)",
-  issn          = "0148-0227",
-  doi           = "10.1029/1999jc900099"
 }
 
@@ -1369 +1333 @@
 }
 
-@techreport{      hunter_rpt06,
+@techreport{      hunter_trpt06,
   title         = "Specification for Test Models of Ice Shelf Cavities",
   pages         = "17",
@@ -1410 +1374 @@
 }
 
-@techreport{      janssen.breivik.ea_rpt13,
+@techreport{      janssen.breivik.ea_trpt13,
   title         = "Air-sea interaction and surface waves",
   pages         = "36",
@@ -1450 +1414 @@
   issn          = "0148-0227",
   doi           = "10.1029/91jc01842"
+}
+
+@article{         josey.gulev.ea_OCC13,
+  title         = "Exchanges Through the Ocean Surface",
+  pages         = "115--140",
+  journal       = "Ocean Circulation and Climate",
+  author        = "Josey, Simon A. and Gulev, Serge and Yu, Lisan",
+  year          = "2013",
+  publisher     = "Elsevier",
+  issn          = "0074-6142",
+  isbn          = "9780123918512",
+  doi           = "10.1016/b978-0-12-391851-2.00005-2"
 }
 
@@ -1541 +1517 @@
 }
 
-@article{         koch-larrouy.lengaigne.ea_CD10,
-  title         = "Tidal mixing in the Indonesian Seas and its effect on the
-                  tropical climate system",
-  pages         = "891--904",
-  journal       = "Climate Dynamics",
-  volume        = "34",
-  number        = "6",
-  author        = "A. Koch-Larrouy and M. Lengaigne and P. Terray and G.
-                  Madec and S. Masson",
-  year          = "2010",
-  month         = "aug",
-  publisher     = "Springer Nature",
-  issn          = "1432-0894",
-  doi           = "10.1007/s00382-009-0642-4"
-}
-
 @article{         koch-larrouy.madec.ea_GRL07,
   title         = "On the transformation of Pacific water into Indonesian
@@ -1573 +1533 @@
 }
 
-@article{         koch-larrouy.madec.ea_OD08*a,
-  title         = "Water mass transformation along the Indonesian ThroughFlow
-                  in an {OGCM}",
-  pages         = "289--309",
-  journal       = "Ocean Dynamics",
-  volume        = "58",
-  number        = "3-4",
-  author        = "A. Koch-Larrouy and G. Madec and B. Blanke and R. Molcard",
-  year          = "2008",
-  month         = "oct",
-  publisher     = "Springer Nature",
-  issn          = "1616-7228",
-  doi           = "10.1007/s10236-008-0155-4"
-}
-
-@article{         koch-larrouy.madec.ea_OD08*b,
-  title         = "Physical processes contributing to the water mass
-                  transformation of the Indonesian ThroughFlow",
-  pages         = "275--288",
-  journal       = "Ocean Dynamics",
-  volume        = "58",
-  number        = "3-4",
-  author        = "A. Koch-Larrouy and G. Madec and D. Iudicone and A.
-                  Atmadipoera and R. Molcard",
-  year          = "2008",
-  month         = "oct",
-  publisher     = "Springer Nature",
-  issn          = "1616-7228",
-  doi           = "10.1007/s10236-008-0154-5"
-}
-
 @article{         kolmogorov_IANS42,
   title         = "Equations of turbulent motion in an incompressible fluid",
@@ -1614 +1543 @@
 }
 
-@article{         kraus.turner_tellus67,
-  author = {Kraus, E.B. and Turner, J.},
-  journal = {Tellus},
-  pages = {98--106},
-  title = {A one dimensional model of the seasonal thermocline {II}. {T}he general theory and its consequences},
-  volume = {19},
-  year = {1967}
-}
-
-@article{        large.ea_RG97,
+@article{         kraus.businger_QJRMS96,
+  title         = "Atmosphere-ocean interaction.",
+  pages         = "324--325",
+  journal       = "Quarterly Journal of the Royal Meteorological Society",
+  volume        = "122",
+  number        = "529",
+  author        = "E. B. Kraus and J. A. Businger",
+  year          = "1996",
+  publisher     = "John Wiley & Sons, Ltd",
+  issn          = "1477-870X",
+  doi           = "10.1002/qj.49712252914"
+}
+
+@article{         kraus.turner_T67,
+  title         = "A one-dimensional model of the seasonal thermocline II.
+                  The general theory and its consequences",
+  pages         = "98--106",
+  journal       = "Tellus",
+  volume        = "19",
+  number        = "1",
+  author        = "Kraus, E. B. and Turner, J. S.",
+  year          = "1967",
+  month         = "Jan",
+  publisher     = "Informa UK Limited",
+  issn          = "2153-3490",
+  doi           = "10.3402/tellusa.v19i1.9753"
+}
+
+@article{         large.mcwilliams.ea_RG94,
+  title         = "Oceanic vertical mixing: {A} review and a model with a
+                  nonlocal boundary layer parameterization",
+  pages         = "363--403",
+  journal       = "Reviews of Geophysics",
+  number        = "4",
   author        = "Large, W. G. and McWilliams, J. C. and Doney, S. C.",
-  doi           = "10.1029/94RG01872",
-  journal       = "Reviews of Geophysics",
-  number        = {4},
-  pages         = {363--403},
-  publisher     = {AGU},
-  title         = "Oceanic vertical mixing: {A} review and a model with a nonlocal boundary layer parameterization",
-  year          = "1994"
-}
-
-@techreport{      large.yeager_rpt04,
+  year          = "1994",
+  publisher     = "AGU",
+  doi           = "10.1029/94RG01872"
+}
+
+@article{         large.yeager_CD09,
+  title         = "The Global Climatology of an Interannually Varying Air-Sea
+                  Flux Data Set",
+  pages         = "341--364",
+  journal       = "Climate Dynamics",
+  volume        = "33",
+  number        = "2-3",
+  author        = "Large, W. G. and Yeager, S. G.",
+  year          = "2009",
+  month         = "aug",
+  publisher     = "Springer Science and Business Media LLC",
+  doi           = "10.1007/s00382-008-0441-3"
+}
+
+@techreport{      large.yeager_trpt04,
   title         = "Diurnal to decadal global forcing for ocean and sea-ice
                   models: the data sets and flux climatologies",
@@ -1849 +1812 @@
 }
 
-@techreport{      levier.treguier.ea_rpt07,
+@techreport{      levier.treguier.ea_trpt07,
   title         = "Free surface and variable volume in the {NEMO} code",
   pages         = "47",
@@ -1930 +1893 @@
 }
 
-@article{     lupkes.gryanik.ea_JGR12,
-  author    = "L{\"{u}}pkes, Christof and Gryanik, Vladimir M. and Hartmann, J{\"{o}}rg and Andreas, Edgar L.",
-  doi       = "10.1029/2012JD017630",
-  issn      = "01480227",
-  journal   = "Journal of Geophysical Research Atmospheres",
-  number    = "13",
-  pages  = "1--18",
-  title  = "A parametrization, based on sea ice morphology, of the neutral atmospheric drag coefficients for weather prediction and climate models",
-  volume    = "117",
-  year      = "2012"
-}
-
-@article{     lupkes.gryanik_JGR15,
-  author    = "L{\"{u}}pkes, Christof and Gryanik, Vladimir M.",
-  doi       = "10.1002/2014JD022418",
-  issn      = "21562202",
-  journal   = "Journal of Geophysical Research",
-  number    = "2",
-  pages  = "552--581",
-  title  = "A stability-dependent parametrization of transfer coefficients formomentum and heat over polar sea ice to be used in climate models",
-  volume    = "120",
-  year      = "2015"
+@article{         lupkes.gryanik.ea_JGRA12,
+  title         = "A parametrization, based on sea ice morphology, of the
+                  neutral atmospheric drag coefficients for weather
+                  prediction and climate models",
+  pages         = "1--18",
+  journal       = "Journal of Geophysical Research Atmospheres",
+  volume        = "117",
+  number        = "13",
+  author        = "L{\"{u}}pkes, Christof and Gryanik, Vladimir M. and
+                  Hartmann, J{\"{o}}rg and Andreas, Edgar L.",
+  year          = "2012",
+  issn          = "01480227",
+  doi           = "10.1029/2012JD017630"
+}
+
+@article{         lupkes.gryanik_JGR15,
+  title         = "A stability-dependent parametrization of transfer
+                  coefficients formomentum and heat over polar sea ice to be
+                  used in climate models",
+  pages         = "552--581",
+  journal       = "Journal of Geophysical Research",
+  volume        = "120",
+  number        = "2",
+  author        = "L{\"{u}}pkes, Christof and Gryanik, Vladimir M.",
+  year          = "2015",
+  issn          = "21562202",
+  doi           = "10.1002/2014JD022418"
 }
 
@@ -2204 +2172 @@
 }
 
-@article{mcwilliams.ea_JFM97,
-   author = {McWilliams, James C. and Sullivan, Peter P. and Moeng, Chin-Hoh},
-   doi = {10.1017/S0022112096004375},
-   journal = {Journal of Fluid Mechanics},
-   pages = {1--30},
-   title = {Langmuir turbulence in the ocean},
-   volume = {334},
-   year = {1997},
-}
+@article{         mcwilliams.sullivan.ea_JFM97,
+  title         = "Langmuir turbulence in the ocean",
+  pages         = "1--30",
+  journal       = "Journal of Fluid Mechanics",
+  volume        = "334",
+  author        = "McWilliams, James C. and Sullivan, Peter P. and Moeng,
+                  Chin-Hoh",
+  year          = "1997",
+  doi           = "10.1017/S0022112096004375"
+}
+
 @article{         mellor.blumberg_JPO04,
   title         = "Wave Breaking and Ocean Surface Layer Thermal Response",
@@ -2429 +2399 @@
 
 @article{         qiao.yuan.ea_OD10,
-  title         = "A three-dimensional surface wave–ocean circulation coupled 
-                  model and its initial testing",
+  title         = "A three-dimensional surface wave–ocean circulation
+                  coupled model and its initial testing",
   pages         = "1339--1335",
   journal       = "Ocean Dynamics",
   volume        = "60",
   number        = "5",
-  author        = "F. Qiao and Y. Yuan and T. Ezer and C. Xia and 
-                   Y. Yang and X. Lu and Z. Song ",
+  author        = "F. Qiao and Y. Yuan and T. Ezer and C. Xia and Y. Yang and
+                  X. Lu and Z. Song ",
   year          = "2010",
   month         = "oct",
@@ -2458 +2428 @@
 }
 
-@article{         reffray.guillaume.ea_GMD15,
-  title         = "Modelling turbulent vertical mixing sensitivity using
-                   a 1-D version of NEMO",
+@article{         reffray.bourdalle-badie.ea_GMD15,
+  title         = "Modelling turbulent vertical mixing sensitivity using a
+                  1-D version of NEMO",
   pages         = "69--86",
   journal       = "Geoscientific Model Development",
@@ -2638 +2608 @@
 
 @article{         shchepetkin_OM15,
-  title         = "An Adaptive, Courant-number-dependent implicit
-       scheme for vertical advection in oceanic modeling",
+  title         = "An Adaptive, Courant-number-dependent implicit scheme for
+                  vertical advection in oceanic modeling",
   pages         = "38--69",
   journal       = "Ocean Modelling",
@@ -2666 +2636 @@
 }
 
-@article{         simmons.jayne.ea_OM04,
-  title         = "Tidally driven mixing in a numerical model of the ocean
-                  general circulation",
-  pages         = "245--263",
-  journal       = "Ocean Modelling",
-  volume        = "6",
-  number        = "3-4",
-  author        = "H. L. Simmons and S. R. Jayne and L. C. {St Laurent} and
-                  A. J. Weaver",
-  year          = "2004",
-  month         = "jan",
-  publisher     = "Elsevier BV",
-  issn          = "1463-5003",
-  doi           = "10.1016/s1463-5003(03)00011-8"
-}
-
-@article{         smagorinsky_MW63,
-  title         = "General circulation experiments with the primitive equations: I. The basic experiment ",
+@article{         smagorinsky_MWR63,
+  title         = "General circulation experiments with the primitive
+                  equations: I. The basic experiment ",
   pages         = "99--164",
   journal       = "Monthly Weather Review",
@@ -2724 +2679 @@
   issn          = "1520-0493",
   doi           = "10.1175/1520-0493(1998)126<3213:agpgff>2.0.co;2"
-}
-
-@article{         st-laurent.nash_DSR04,
-  title         = "An examination of the radiative and dissipative properties
-                  of deep ocean internal tides",
-  pages         = "3029--3042",
-  journal       = "Deep Sea Research",
-  volume        = "51",
-  number        = "25-26",
-  author        = "L. C. {St Laurent} and J. D. Nash",
-  year          = "2004",
-  month         = "dec",
-  publisher     = "Elsevier BV",
-  issn          = "0967-0645",
-  doi           = "10.1016/j.dsr2.2004.09.008"
 }
 
@@ -2812 +2752 @@
   isbn          = "9780511702242",
   doi           = "10.1017/cbo9780511702242.013"
+}
+
+@book{            sverdrup.johnson.ea_bk42,
+  title         = "The Oceans, Their Physics, Chemistry, and General Biology",
+  pages         = "1087",
+  author        = "H. U. Sverdrup and Martin W. Johnson and Richard H.
+                  Fleming",
+  year          = "1942",
+  publisher     = "Prentice-Hall",
+  address       = "New York"
 }
 
@@ -2942 +2892 @@
 }
 
-@article{         vancoppenolle.fichefet.ea_OM09*a,
-  title         = "Simulating the mass balance and salinity of Arctic and
-                  Antarctic sea ice. 1. Model description and validation",
-  pages         = "33--53",
-  journal       = "Ocean Modelling",
-  volume        = "27",
-  number        = "1-2",
-  author        = "M. Vancoppenolle and T. Fichefet and H. Goosse and S.
-                  Bouillon and G. Madec and M. A. Morales Maqueda",
-  year          = "2009",
-  month         = "jan",
-  publisher     = "Elsevier BV",
-  issn          = "1463-5003",
-  doi           = "10.1016/j.ocemod.2008.10.005"
-}
-
-@article{         vancoppenolle.fichefet.ea_OM09*b,
-  title         = "Simulating the mass balance and salinity of Arctic and
-                  Antarctic sea ice. 2. Importance of sea ice salinity
-                  variations",
-  pages         = "54--69",
-  journal       = "Ocean Modelling",
-  volume        = "27",
-  number        = "1-2",
-  author        = "M. Vancoppenolle and T. Fichefet and H. Goosse",
-  year          = "2009",
-  month         = "jan",
-  publisher     = "Elsevier BV",
-  issn          = "1463-5003",
-  doi           = "10.1016/j.ocemod.2008.11.003"
-}
-
 @article{         warner.defne.ea_CG13,
   title         = "A wetting and drying scheme for {ROMS}",
@@ -3048 +2966 @@
 }
 
-@article{         white.hoskins.ea_QJRMS05,
-  title         = "Consistent approximate models of the global atmosphere: shallow, deep,
-                  hydrostatic, quasi-hydrostatic and non-hydrostatic",
-  pages         = "2081--2107",
-  journal       = "Quarterly Journal of the Royal Meteorological Society",
-  volume        = "131",
-  author        = "A. A. White and B. J. Hoskins and I. Roulstone and A. Staniforth",
-  year          = "2005",
-  doi           = "10.1256/qj.04.49"
-}
-
 @article{         white.adcroft.ea_JCP09,
   title         = "High-order regridding-remapping schemes for continuous
@@ -3072 +2979 @@
   issn          = "0021-9991",
   doi           = "10.1016/j.jcp.2009.08.016"
+}
+
+@article{         white.hoskins.ea_QJRMS05,
+  title         = "Consistent approximate models of the global atmosphere:
+                  shallow, deep, hydrostatic, quasi-hydrostatic and
+                  non-hydrostatic",
+  pages         = "2081--2107",
+  journal       = "Quarterly Journal of the Royal Meteorological Society",
+  volume        = "131",
+  author        = "A. A. White and B. J. Hoskins and I. Roulstone and A.
+                  Staniforth",
+  year          = "2005",
+  doi           = "10.1256/qj.04.49"
 }
 
@@ -3121 +3041 @@
 }
 
+@article{         zeng.beljaars_GRL05,
+  title         = "A prognostic scheme of sea surface skin temperature for
+                  modeling and data assimilation",
+  journal       = "Geophysical Research Letters",
+  volume        = "32",
+  number        = "14",
+  author        = "Xubin Zeng and Anton Beljaars",
+  year          = "2005",
+  month         = "jul",
+  publisher     = "American Geophysical Union",
+  doi           = "10.1029/2005gl023030"
+}
+
 @article{         zhang.endoh_JGR92,
   title         = "A free surface General Circulation Model for the tropical
@@ -3134 +3067 @@
   doi           = "10.1029/92jc00911"
 }
-
-@article{large.yeager_CD09,
-author="Large, W. G. and Yeager, S. G.",
-title="The Global Climatology of an Interannually Varying Air-Sea Flux Data Set",
-pages = "341--364",
-journal="Climate Dynamics",
-volume = "33",
-number = "2-3",
-year="2009",
-month = "aug",
-publisher = "Springer Science and Business Media LLC",
-doi="10.1007/s00382-008-0441-3"
-}
-
-@book{sverdrup.johnson.ea_1942,
-author = {H. U. Sverdrup and Martin W. Johnson and Richard H. Fleming},
-title = {The Oceans, Their Physics, Chemistry, and General Biology},
-publisher = {Prentice-Hall},
-address = {New York},
-year = {1942},
-pages = {1087},
-}
-
-@article{kraus.businger_QJRMS96,
-author = "E. B. Kraus and J. A. Businger",
-title = "Atmosphere-ocean interaction.",
-journal="Quarterly Journal of the Royal Meteorological Society",
-year = "1996",
-volume = "122",
-number = "529",
-pages = "324-325",
-publisher = "John Wiley & Sons, Ltd",
-issn = "1477-870X",
-doi = "10.1002/qj.49712252914"
-}
-
-@article{josey.gulev.ea_2013,
-title = "Exchanges through the ocean surface",
-journal = "Ocean Circulation and Climate - A 21st Century Perspective, Int. Geophys. Ser.",
-year = "2013",
-author = "S. A. Josey and S. Gulev and L. Yu",
-pages = "115-140, edited by G. Siedler et al., Academic Press, Oxford",
-volume = "103",
-doi = "10.1016/B978-0-12-391851-2.00005-2"
-}
-
-@article{fairall.bradley.ea_JGR96,
-  year = "1996",
- journal = "Journal of Geophysical Research: Oceans",
-  month = "jan",
-  publisher = "American Geophysical Union",
-  volume = "101",
-  number = "C1",
-  pages = "1295-1308",
-  author = "C. W. Fairall and E. F. Bradley and J. S. Godfrey and G. A. Wick and J. B. Edson and G. S. Young",
-  title = "Cool-skin and warm-layer effects on sea surface temperature",
-  doi = "10.1029/95jc03190"
-}
-
-@article{zeng.beljaars_GRL05,
-  year = "2005",
-  month = "jul",
-  publisher = "American Geophysical Union",
-  volume = "32",
-  number = "14",
-  author = "Xubin Zeng and Anton Beljaars",
-  title = "A prognostic scheme of sea surface skin temperature for modeling and data assimilation",
-  journal = "Geophysical Research Letters",
-  doi = "10.1029/2005gl023030"
-}

NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/rst/source/cfgs.bib

@@ -1 @@
-@article{ODEA2012,
-author = {E J O’Dea and A K Arnold and K P Edwards and R Furner and P Hyder and M J Martin and J R Siddorn and D Storkey and J While and J T Holt and H Liu},
-title = {An operational ocean forecast system incorporating NEMO and SST data assimilation for the tidally driven European North-West shelf},
-journal = {Journal of Operational Oceanography},
-volume = {5},
-number = {1},
-pages = {3-17},
-year  = {2012},
-publisher = {Taylor & Francis},
-doi = {10.1080/1755876X.2012.11020128},
-URL = {https://doi.org/10.1080/1755876X.2012.11020128},
-eprint = {https://doi.org/10.1080/1755876X.2012.11020128}
+
+@article{         aumont.ethé.ea_GMD15,
+  title         = "PISCES-v2: an ocean biogeochemical model for carbon and
+                  ecosystem studies",
+  pages         = "2465--2513",
+  journal       = "Geoscientific Model Development",
+  volume        = "8",
+  number        = "8",
+  author        = "Aumont, O. and Ethé, C. and Tagliabue, A. and Bopp, L.
+                  and Gehlen, M.",
+  year          = "2015",
+  month         = "Aug",
+  publisher     = "Copernicus GmbH",
+  issn          = "1991-9603",
+  doi           = "10.5194/gmd-8-2465-2015"
 }
 
-@Article{gmd-8-2465-2015,
-AUTHOR = {Aumont, O. and Eth\'e, C. and Tagliabue, A. and Bopp, L. and Gehlen, M.},
-TITLE = {PISCES-v2: an ocean biogeochemical model for carbon and ecosystem studies},
-JOURNAL = {Geoscientific Model Development},
-VOLUME = {8},
-YEAR = {2015},
-NUMBER = {8},
-PAGES = {2465--2513},
-URL = {https://www.geosci-model-dev.net/8/2465/2015/},
-DOI = {10.5194/gmd-8-2465-2015}
+@article{         o’dea.arnold.ea_JOO12,
+  title         = "An operational ocean forecast system incorporating NEMO
+                  and SST data assimilation for the tidally driven European
+                  North-West shelf",
+  pages         = "3--17",
+  journal       = "Journal of Operational Oceanography",
+  volume        = "5",
+  number        = "1",
+  author        = "O’Dea, E J and Arnold, A K and Edwards, K P and Furner,
+                  R and Hyder, P and Martin, M J and Siddorn, J R and
+                  Storkey, D and While, J and Holt, J T and et al.",
+  year          = "2012",
+  month         = "Feb",
+  publisher     = "Informa UK Limited",
+  issn          = "1755-8778",
+  doi           = "10.1080/1755876x.2012.11020128"
 }

NEMO/branches/2020/dev_r13787_doc_latex_recovery/doc/rst/source/zooms.bib

@@ -1 @@
-link ../../../cfgs/AGRIF_DEMO/zooms.bib
+link ../../../src/NST/zooms.bib

NEMO/branches/2020/dev_r13787_doc_latex_recovery/src/NST/zooms.bib

@@ -1 @@
-@article{DEBREU2012,
-   title = "Two-way nesting in split-explicit ocean models: Algorithms, implementation and validation",
-   journal = "Ocean Modelling",
-   volume = "49-50",
-   pages = "1 - 21",
-   year = "2012",
-   issn = "1463-5003",
-   doi = "10.1016/j.ocemod.2012.03.003",
-   author = "Laurent Debreu and Patrick Marchesiello and Pierrick Penven and Gildas Cambon",
-   keywords = "Two-way nesting, Finite difference method, Modeling, Boundary conditions, Coastal upwelling"
+
+@article{         debreu.marchesiello.ea_OM12,
+  title         = "Two-way nesting in split-explicit ocean models:
+                  Algorithms, implementation and validation",
+  pages         = "1--21",
+  journal       = "Ocean Modelling",
+  volume        = "49-50",
+  author        = "Debreu, Laurent and Marchesiello, Patrick and Penven,
+                  Pierrick and Cambon, Gildas",
+  year          = "2012",
+  month         = "Jun",
+  publisher     = "Elsevier BV",
+  issn          = "1463-5003",
+  doi           = "10.1016/j.ocemod.2012.03.003"
 }
 
-@article{PENVEN2006,
-   title = "Evaluation and application of the {ROMS} 1-way embedding procedure to the central california upwelling system",
-   journal = "Ocean Modelling",
-   volume = "12",
-   number = "1",
-   pages = "157 - 187",
-   year = "2006",
-   issn = "1463-5003",
-   doi = "10.1016/j.ocemod.2005.05.002",
-   author = "Pierrick Penven and Laurent Debreu and Patrick Marchesiello and James C. McWilliams",
-   keywords = "Ocean models, Boundary conditions, Embedding, Coastal upwelling, Mesoscale eddies, Eddy kinetic energy, North America, West Coast, Central upwelling system, Monterey Bay, 35–41°N, 128–121°W"
+@article{         penven.debreu.ea_OM06,
+  title         = "Evaluation and application of the ROMS 1-way embedding
+                  procedure to the central california upwelling system",
+  pages         = "157--187",
+  journal       = "Ocean Modelling",
+  volume        = "12",
+  number        = "1-2",
+  author        = "Penven, Pierrick and Debreu, Laurent and Marchesiello,
+                  Patrick and McWilliams, James C.",
+  year          = "2006",
+  month         = "Jan",
+  publisher     = "Elsevier BV",
+  issn          = "1463-5003",
+  doi           = "10.1016/j.ocemod.2005.05.002"
 }
 
-@article{SPALL1991,
-   author = {Spall, Michael A. and Holland, William R.},
-   title = {A Nested Primitive Equation Model for Oceanic Applications},
-   journal = {Journal of Physical Oceanography},
-   volume = {21},
-   number = {2},
-   pages = {205-220},
-   year = {1991},
-   doi = {10.1175/1520-0485(1991)021<0205:ANPEMF>2.0.CO;2},
+@article{         spall.holland_JPO91,
+  title         = "A Nested Primitive Equation Model for Oceanic
+                  Applications",
+  pages         = "205--220",
+  journal       = "Journal of Physical Oceanography",
+  volume        = "21",
+  number        = "2",
+  author        = "Spall, Michael A. and Holland, William R.",
+  year          = "1991",
+  month         = "Feb",
+  publisher     = "American Meteorological Society",
+  issn          = "1520-0485",
+  doi           = "10.1175/1520-0485(1991)021<0205:anpemf>2.0.co;2"
 }

NEMO/branches/2020/dev_r13787_doc_latex_recovery/tests/test_cases.bib

@@ -1 @@
-@book{HAIDVOGEL1999,
-   author = {D. B. Haidvogel and A. Beckmann},
-   publisher = {Imperial College Press, London},
-   year = {1999},
-   title = {Numerical ocean circulation modeling}
+
+@article{         brodeau.barnier.ea_JPO16,
+  title         = "Climatologically Significant Effects of Some
+                  Approximations in the Bulk Parameterizations of Turbulent
+                  Air–Sea Fluxes",
+  pages         = "5--28",
+  journal       = "Journal of Physical Oceanography",
+  volume        = "47",
+  number        = "1",
+  author        = "Brodeau, Laurent and Barnier, Bernard and Gulev, Sergey K.
+                  and Woods, Cian",
+  year          = "2016",
+  month         = "Dec",
+  publisher     = "American Meteorological Society",
+  issn          = "1520-0485",
+  doi           = "10.1175/jpo-d-16-0169.1"
 }
 
-@book{BURCHARD2002,
-   title={GETM: A General Estuarine Transport Model; Scientific Documentation},
-   author={Burchard, Hans and Bolding, Karsten},
-   year={2002},
-   publisher={European Commission, Joint Research Centre, Institute for Environment and Sustainability}
+@techreport{      burchard.bolding_trpt02,
+  title         = "GETM, A General Estuarine Transport Model: Scientific
+                  Documentation",
+  pages         = "",
+  series        = "Tech. Rep. EUR 20253 EN",
+  author        = "Burchard, Hans and Bolding, Karsten",
+  institution   = "European Commission",
+  year          = "2002",
+  month         = "01"
 }
 
-@article{ILICAK2012,
-   title = "Spurious dianeutral mixing and the role of momentum closure",
-   journal = "Ocean Modelling",
-   volume = "45-46",
-   pages = "37 - 58",
-   year = "2012",
-   issn = "1463-5003",
-   doi = "10.1016/j.ocemod.2011.10.003",
-   author = "Mehmet Ilicak and Alistair J. Adcroft and Stephen M. Griffies and Robert W. Hallberg",
-   keywords = "Spurious dianeutral transport, Cabbeling, Overflows, Exchange-flow, Ocean models, Momentum transport, Tracer advection, Reference potential energy"
+@article{         haidvogel.beckmann_SESM99,
+  title         = "Numerical Ocean Circulation Modeling",
+  journal       = "Series on Environmental Science and Management",
+  author        = "Haidvogel, Dale B and Beckmann, Aike",
+  year          = "1999",
+  month         = "Apr",
+  publisher     = "IMPERIAL COLLEGE PRESS",
+  issn          = "0219-9793",
+  isbn          = "9781860943935",
+  doi           = "10.1142/p097"
 }
 
-@article{DEBREU2012,
-   title = "Two-way nesting in split-explicit ocean models: Algorithms, implementation and validation",
-   journal = "Ocean Modelling",
-   volume = "49-50",
-   pages = "1 - 21",
-   year = "2012",
-   issn = "1463-5003",
-   doi = "10.1016/j.ocemod.2012.03.003",
-   author = "Laurent Debreu and Patrick Marchesiello and Pierrick Penven and Gildas Cambon",
-   keywords = "Two-way nesting, Finite difference method, Modeling, Boundary conditions, Coastal upwelling"
+@article{         ilıcak.adcroft.ea_OM12,
+  title         = "Spurious dianeutral mixing and the role of momentum
+                  closure",
+  pages         = "37--58",
+  journal       = "Ocean Modelling",
+  volume        = "45-46",
+  author        = "Ilıcak, Mehmet and Adcroft, Alistair J. and Griffies,
+                  Stephen M. and Hallberg, Robert W.",
+  year          = "2012",
+  month         = "Jan",
+  publisher     = "Elsevier BV",
+  issn          = "1463-5003",
+  doi           = "10.1016/j.ocemod.2011.10.003"
 }
 
-@article{PENVEN2006,
-   title = "Evaluation and application of the ROMS 1-way embedding procedure to the central california upwelling system",
-   journal = "Ocean Modelling",
-   volume = "12",
-   number = "1",
-   pages = "157 - 187",
-   year = "2006",
-   issn = "1463-5003",
-   doi = "10.1016/j.ocemod.2005.05.002",
-   author = "Pierrick Penven and Laurent Debreu and Patrick Marchesiello and James C. McWilliams",
-   keywords = "Ocean models, Boundary conditions, Embedding, Coastal upwelling, Mesoscale eddies, Eddy kinetic energy, North America, West Coast, Central upwelling system, Monterey Bay, 35–41°N, 128–121°W"
+@article{         lipscomb.hunke_MWR04,
+  title         = "Modeling Sea Ice Transport Using Incremental Remapping",
+  pages         = "1341--1354",
+  journal       = "Monthly Weather Review",
+  volume        = "132",
+  number        = "6",
+  author        = "Lipscomb, William H. and Hunke, Elizabeth C.",
+  year          = "2004",
+  month         = "Jun",
+  publisher     = "American Meteorological Society",
+  issn          = "1520-0493",
+  doi           = "10.1175/1520-0493(2004)132<1341:msitui>2.0.co;2"
 }
 
-@article{SPALL1991,
-   author = {Spall, M. A. and Holland, W. R.},
-   title = {A Nested Primitive Equation Model for Oceanic Applications},
-   journal = {Journal of Physical Oceanography},
-   volume = {21},
-   number = {2},
-   pages = {205-220},
-   year = {1991},
-   doi = {10.1175/1520-0485(1991)021<0205:ANPEMF>2.0.CO;2},
+@article{         losch_JGR08,
+  title         = "Modeling ice shelf cavities in a z coordinate ocean
+                  general circulation model",
+  journal       = "Journal of Geophysical Research",
+  volume        = "113",
+  number        = "C8",
+  author        = "Losch, M.",
+  year          = "2008",
+  month         = "Aug",
+  publisher     = "American Geophysical Union (AGU)",
+  issn          = "0148-0227",
+  doi           = "10.1029/2007jc004368"
 }
 
-@article{MATHIOT2017,
-   author = {Mathiot, P. and Jenkins, A. and Harris, C. and Madec, G.},
-   title = {Explicit representation and parametrised impacts of under ice shelf seas in the ${z}^{\ast}$ coordinate ocean model NEMO 3.6},
-   journal = {Geoscientific Model Development},
-   volume = {10},
-   year = {2017},
-   number = {7},
-   pages = {2849--2874},
-   url = {https://www.geosci-model-dev.net/10/2849/2017/},
-   doi = {10.5194/gmd-10-2849-2017}
+@article{         mathiot.jenkins.ea_GMD17,
+  title         = "Explicit representation and parametrised impacts of under
+                  ice shelf seas in the ${z}^{\ast}$ coordinate ocean model
+                  NEMO 3.6",
+  pages         = "2849--2874",
+  journal       = "Geoscientific Model Development",
+  volume        = "10",
+  number        = "7",
+  author        = "Mathiot, Pierre and Jenkins, Adrian and Harris,
+                  Christopher and Madec, Gurvan",
+  year          = "2017",
+  month         = "Jul",
+  publisher     = "Copernicus GmbH",
+  issn          = "1991-9603",
+  doi           = "10.5194/gmd-10-2849-2017"
 }
 
-@article{LOSCH2008,
-   author = {Losch, M.},
-   title = {Modeling ice shelf cavities in a z coordinate ocean general circulation model},
-   journal = {Journal of Geophysical Research: Oceans},
-   volume = {113},
-   year = {2008},
-   number = {C8},
-   pages = {},
-   keywords = {Ice shelf cavities, numerical ocean modeling, z coordinates},
-   doi = {10.1029/2007JC004368},
-   url = {https://agupubs.onlinelibrary.wiley.com/doi/abs/10.1029/2007JC004368},
-   eprint = {https://agupubs.onlinelibrary.wiley.com/doi/pdf/10.1029/2007JC004368},
-   abstract = {Processes at the ice shelf-ocean interface and in particular in ice shelf cavities around Antarctica have an observable effect on the solutions of basin scale to global coupled ice-ocean models. Despite this, these processes are not routinely represented in global ocean and climate models. It is shown that a new ice shelf cavity model for z coordinate models can reproduce results from an intercomparison project of earlier approaches with vertical ?~C or isopycnic coordinates. As a proof of concept, ice shelves are incorporated in a 100-year global integration of a z coordinate model. In this simulation, glacial meltwater can be traced as far as north as 15??S. The observed effects of processes in the ice shelf cavities agree with previous results from a ?~C coordinate model, notably the increase in sea ice thickness. However, melt rates are overestimated probably because the parameterization of basal melting does not suit the low resolution of this configuration.}
+@article{         schär.smolarkiewicz_JCP96,
+  title         = "A Synchronous and Iterative Flux-Correction Formalism for
+                  Coupled Transport Equations",
+  pages         = "101--120",
+  journal       = "Journal of Computational Physics",
+  volume        = "128",
+  number        = "1",
+  author        = "Schär, Christoph and Smolarkiewicz, Piotr K.",
+  year          = "1996",
+  month         = "Oct",
+  publisher     = "Elsevier BV",
+  issn          = "0021-9991",
+  doi           = "10.1006/jcph.1996.0198"
 }
-
-@article{LIPSCOMB2004,
-   author = {Lipscomb, William H. and Hunke, Elizabeth C.},
-   title = {Modeling Sea Ice Transport Using Incremental Remapping},
-   journal = {Monthly Weather Review},
-   volume = {132},
-   number = {6},
-   pages = {1341-1354},
-   year = {2004},
-   doi = {10.1175/1520-0493(2004)132<1341:MSITUI>2.0.CO;2},
-   URL = {https://doi.org/10.1175/1520-0493(2004)132<1341:MSITUI>2.0.CO;2},
-   eprint = {https://doi.org/10.1175/1520-0493(2004)132<1341:MSITUI>2.0.CO;2},
-   abstract = { Abstract Sea ice models contain transport equations for the area, volume, and energy of ice and snow in various thickness categories. These equations typically are solved with first-order-accurate upwind schemes, which are very diffusive; with second-order-accurate centered schemes, which are highly oscillatory; or with more sophisticated second-order schemes that are computationally costly if many quantities must be transported [e.g., multidimensional positive-definite advection transport algorithm (MPDATA)]. Here an incremental remapping scheme, originally designed for horizontal transport in ocean models, is adapted for sea ice transport. This scheme has several desirable features: it preserves the monotonicity of both conserved quantities and tracers; it is second-order accurate except where the accuracy is reduced locally to preserve monotonicity; and it efficiently solves the large number of equations in sea ice models with multiple thickness categories and tracers. Remapping outperforms the first-order upwind scheme and basic MPDATA scheme in several simple test problems. In realistic model runs, remapping is less diffusive than the upwind scheme and about twice as fast as MPDATA. }
-}
-
-@article{SCHAR1996,
-   author = {Christoph Schär and Piotr K. Smolarkiewicz},
-   title = {A Synchronous and Iterative Flux-Correction Formalism for Coupled Transport Equations},
-   journal = {Journal of Computational Physics},
-   volume = {128},
-   number = {1},
-   pages = {101 - 120},
-   year = {1996},
-   issn = {0021-9991},
-   doi = {https://doi.org/10.1006/jcph.1996.0198},
-   url = {http://www.sciencedirect.com/science/article/pii/S0021999196901989},
-   abstract = {Many problems of fluid dynamics involve the coupled transport of several, density-like, dependent variables (for instance, densities of mass and momenta in elastic flows). In this paper, a conservative and synchronous flux-corrected transport (FCT) formalism is developed which aims at a consistent transport of such variables. The technique differs from traditional FCT algorithms in two respects. First, the limiting of transportive fluxes of the primary variables (e.g., mass and momentum) does not derive from smooth estimates of the variables, but it derives from analytic constraints implied by the Lagrangian form of the governing continuity equations, which are imposed on the specific mixing ratios of the variables (e.g., velocity components). Second, the traditional FCT limiting based on sufficiency conditions is augmented by an iterative procedure which approaches the necessity requirements. This procedure can also be used in the framework of traditional FCT schemes, and a demonstration is provided that it can significantly reduce some of the pathological behaviors of FCT algorithms. Although the approach derived is applicable to the transport of arbitrary conserved quantities, it is particularly useful for the synchronous transport of mass and momenta in elastic flows, where it assures intrinsic stability of the algorithm regardless of the magnitude of the mass-density variable. This latter property becomes especially important in fluids with large density variations, or in models with a material “vertical” coordinate (e.g., geophysical hydrostatic stratified flows in isopycnic/isentropic coordinates), where material surfaces can collapse to zero-mass layers admitting, therefore, arbitrarily large local Courant numbers.}
-}
-
-@article{Brodeau_al_2017,
-author={Laurent Brodeau and Bernard Barnier and Sergey Gulev and Cian Woods},
-title={Climatologically significant effects of some approximations in the bulk parameterizations of turbulent air-sea fluxes},
-journal={J. Phys. Oceanogr.},
-doi={10.1175/JPO-D-16-0169.1},
-year={2017},
-pages = {5-28},
-volume={47},
-number={1}
-}