Commit b1811168 authored by Knut's avatar Knut
Browse files

Merge branch 'hvel' into save_fluxes

parents 99925192 863ab048
......@@ -105,15 +105,13 @@ gradient from vertically integrated equations with explicit vertical resolution
of these processes. These slow terms which are updated every macro
time step only (that is why we call them slow terms) need to be considered
for the external mode included in module {\tt 2d}.
Those slow terms are calculated here in the {\tt 3d} module in the routines
{\tt slow\_bottom\_friction}, {\tt slow\_advection}
and {\tt slow\_diffusion}, and they are added together in {\tt slow\_terms},
see the descriptions in sections \ref{sec-slow-bottom-friction},
\ref{sec-slow-advection},\ref{sec-slow-diffusion} and \ref{sec-slow-terms}
on pages \pageref{sec-slow-bottom-friction},
\pageref{sec-slow-advection},\pageref{sec-slow-diffusion} and
\pageref{sec-slow-terms},
respectively.
Those slow terms are calculated here in the {\tt 3d} module at the end
of {\tt integrate\_3d} and in the routine {\tt slow\_bottom\_friction},
and they are added together in {\tt slow\_terms},
see the descriptions in sections \ref{sec-integrate-3d},
\ref{sec-slow-bottom-friction} and \ref{sec-slow-terms}
on pages \pageref{sec-integrate-3d}, \pageref{sec-slow-bottom-friction},
and \pageref{sec-slow-terms}, respectively.
One other important measure of coupling the two modes is to
add to all calculated $u$- and $v$-velocity profiles the difference
......
......@@ -60,7 +60,7 @@ a4.dvi: a4.tex $(TEXSRC) $(PROTEXSRC)
latex a4.tex
latex a4.tex
html: a4.tex $(TEXSRC) $(PROTEXSRC)
html: a4.dvi
mkdir -p html
latex2html -dir html a4.tex
......
......@@ -15,13 +15,31 @@
@String{OMOD = "Ocean Modelling"}
@String{OSCI = "Ocean Science"}
@article{buchmann_and_soderkvist_2016,
author = {Bjarne B\"uchmann and Johan S\"oderkvist},
title = {{Internal variability of a 3-D ocean model}},
journal = {Tellus A},
volume = {68},
year = {2016},
url = {http://dx.doi.org/10.3402/tellusa.v68.30417},
doi = {10.3402/tellusa.v68.30417}
}
@Article{graewe_etal_2016,
Title = {{A numerical model for the entire Wadden Sea: Skill assessment and analysis of hydrodynamics}},
Author = {Gr\"awe, Ulf and Fl\"oser, G\"otz and Gerkema, Theo and Duran-Matute, Matias and Badewien, Thomas H. and Schulz, Elisabeth and Burchard, Hans},
Journal = {Journal of Geophysical Research: Oceans},
Year = {2016},
Pages = {5231--5251},
Volume = {121},
Doi = {10.1002/2016JC011655},
}
@Article{liquete_etal_2016,
author = {Liquete, Camino and Piroddi, Chiara and Mac{\'i}as, Diego and Druon, Jean-No{\"e}l and Zulian, Grazia},
title = {Ecosystem services sustainability in the Mediterranean Sea: assessment of status and trends using multiple modelling approaches},
journal = {Scientific Reports},
year = {2016},
month = {Sep},
day = {30},
publisher = {The Author(s)},
volume = {6},
pages = {34162},
......@@ -40,6 +58,16 @@
Doi = {10.1007/s10236-015-0914-y},
}
@Article{purkiani2016wiv,
Title = {{Wind-induced variability of estuarine circulation in a tidally energetic inlet with curvature}},
Author = {Purkiani, Kaveh and Becherer, Johannes and Klingbeil, Knut and Burchard, Hans},
Journal = {Journal of Geophysical Research: Oceans},
Year = {2016},
Pages = {1--17},
Volume = {121},
Doi = {10.1002/2015JC010945},
}
@Article{schwemmer_etal_2016,
Author = {Schwemmer, P. and G\"upner, F. and Adler, S. and Klingbeil, K. and Garthe, S.},
Title = {{Modelling small-scale foraging habitat use in breeding Eurasian oystercatchers (\textit{Haematopus ostralegus}) in relation to prey distribution and environmental predictors}},
......@@ -52,6 +80,39 @@
Url = {http://dx.doi.org/10.1016/j.ecolmodel.2015.10.023},
}
@Article{stanev_etal_2016,
author = {Stanev, E. V. and Schulz-Stellenfleth, J. and Staneva, J. and Grayek, S. and Grashorn, S. and Behrens, A. and Koch, W. and Pein, J.},
title = {{Ocean forecasting for the German Bight: from regional to coastal scales}},
journal = {Ocean Science},
volume = {12},
year = {2016},
number = {5},
pages = {1105--1136},
doi = {10.5194/os-12-1105-2016}
}
@Article{staneva_etal_2016a,
AUTHOR = {Staneva, J. and Wahle, K. and G\"unther, H. and Stanev, E.},
TITLE = {Coupling of wave and circulation models in coastal--ocean predicting systems: a case study for the {G}erman {B}ight},
JOURNAL = {Ocean Science},
VOLUME = {12},
YEAR = {2016},
NUMBER = {3},
PAGES = {797--806},
DOI = {10.5194/os-12-797-2016}
}
@Article{staneva_etal_2016b,
AUTHOR = {Staneva, J. and Wahle, K. and Koch, W. and Behrens, A. and Fenoglio-Marc, L. and Stanev, E. V.},
TITLE = {Coastal flooding: impact of waves on storm surge during extremes -- a case study for the {G}erman {B}ight},
JOURNAL = {Natural Hazards and Earth System Sciences},
VOLUME = {16},
YEAR = {2016},
NUMBER = {11},
PAGES = {2373--2389},
DOI = {10.5194/nhess-16-2373-2016}
}
@article{burchard_and_badewien_2015,
author = {Burchard, Hans and Badewien, T. H.},
title = {{Thermohaline residual circulation of the Wadden Sea}},
......@@ -103,6 +164,17 @@
Doi = {10.1002/2015JC010733},
}
@article{kourafalou_etal_2015,
author = {V.H. Kourafalou and P. De Mey and J. Staneva and N. Ayoub and A. Barth and Y. Chao and M. Cirano and J. Fiechter and M. Herzfeld and A. Kurapov and A.M. Moore and P. Oddo and J. Pullen and A. van der Westhuysen and R.H. Weisberg},
title = {Coastal Ocean Forecasting: science foundation and user benefits},
journal = {Journal of Operational Oceanography},
volume = {8},
number = {sup1},
pages = {s147-s167},
year = {2015},
doi = {10.1080/1755876X.2015.1022348},
}
@article{macias_etal_2015,
author = {Diego Macias and Elisa Garcia-Gorriz and Adolf Stips},
title = {Productivity changes in the Mediterranean Sea for the twenty-first
......@@ -164,6 +236,18 @@
doi = {10.1175/JPO-D-14-0084.1},
}
@Article{stanev_etal_2015,
author = "Stanev, Emil V. and Al-Nadhairi, Rahma and Valle-Levinson, Arnoldo",
title = "The role of density gradients on tidal asymmetries in the German Bight",
journal = "Ocean Dynamics",
year = "2015",
volume = "65",
number = "1",
pages = "77--92",
issn = "1616-7228",
doi = "10.1007/s10236-014-0784-8",
}
@article{tett_etal_2013,
author = {Tett, Paul and Gowen, R. J. and Painting, S. J. and Elliott, Mike and Forster, Rodney and Mills, D. K. and Bresnan, Eileen and Capuzzo, Elisa and Fernandes, Teresa and Foden, J. and others},
title = {Framework for understanding marine ecosystem health},
......@@ -176,7 +260,7 @@
@article{leeuwen_etal_2013,
author = {van Leeuwen, Sonja M. and van der Molen, Johan and Ruardij, Piet and Fernand, Liam and Jickells, Tim},
title = {Modelling the contribution of deep chlorophyll maxima to annual primary production in the North Sea},
title = {Modelling the contribution of deep chlorophyll maxima to annual primary production in the {N}orth {S}ea},
journal = {Biogeochemistry},
volume = {113},
pages = {137--152},
......@@ -266,6 +350,28 @@
doi = {10.1016/j.ocemod.2014.06.001},
}
@Article{stanev_etal_2014a,
author = "Stanev, Emil V. and Al-Nadhairi, Rahma and Staneva, Joanna and Schulz-Stellenfleth, Johannes and Valle-Levinson, Arnoldo",
title = "Tidal wave transformations in the {G}erman {B}ight",
journal = "Ocean Dynamics",
year = "2014",
volume = "64",
number = "7",
pages = "951--968",
doi = "10.1007/s10236-014-0733-6",
}
@Article{stanev_etal_2014b,
AUTHOR = {Stanev, E. V. and He, Y. and Staneva, J. and Yakushev, E.},
TITLE = {Mixing in the Black Sea detected from the temporal and spatial variability of oxygen and sulfide – Argo float observations and numerical modelling},
JOURNAL = {Biogeosciences},
VOLUME = {11},
YEAR = {2014},
NUMBER = {20},
PAGES = {5707--5732},
DOI = {10.5194/bg-11-5707-2014}
}
@article{hofmeister_etal_2013,
author = {Richard Hofmeister and Karsten Bolding and Robert D. Hetland and Gerald Schernewski and Hans Burchard},
title = {The dynamics of cooling water discharge in a shallow, non-tidal embayment},
......@@ -356,41 +462,16 @@
doi = {10.1016/j.ocemod.2012.10.002},
}
@article{vanleeuwen_et_all_2012,
author = {S. M. van Leeuwen and J. van der Molen and P. Ruardij and
L. Fernand and T. Jickells},
title = {Modelling the contribution of deep chlorophyll maxima to
annual primary production in the {N}orth {S}ea},
journal = {Biogeochemistry},
year = {2012},
doi = {doi:10.1007/s10533-012-9704-5},
}
@article{lenhart_et_all_2010,
author = {H. J. Lenhart and D. K. Mills and H. Baretta-Bekker and
S. M. van Leeuwen and J. van der Molen and J. W. Baretta and
M. Blaas and X. Desmit and W. K<FC>hn and G. Lacroix and
H. J. Los and A. M<E9>nesguen and R. Neves and R. Proctor and
P. Ruardij and M. D. Skogen and A. Vanhoutte-Grunier and
M. T. Villars and S. L. Wakelin},
title = {Predicting the consequences of nutrient reduction on the
eutrophication status of the {N}orth {S}ea},
year = {2010},
journal = JMS,
volume = {81},
pages = {148--170},
}
@article{schernewski_etal_submitted,
@article{schernewski_etal_2012,
author = {G. Schernewski and E. Fischer and T. Huttula and G. Jost
and M. Ras},
title = {Model tools to support bathing water quality management:
title = {Simulation tools to support bathing water quality management:
{E}scherichia coli bacteria in a {B}altic lagoon},
journal = {Journal of Coastal Conservation},
volume = {},
pages = {},
year = {2011},
note = {submitted},
volume = {16},
pages = {473--488},
year = {2012},
doi = {10.1007/s11852-012-0202-7}
}
@article{burchard_schuttelaars_jpo_2012,
......@@ -539,6 +620,7 @@
volume = {59},
pages = {629-641},
year = {2009},
doi = {10.1007/s10236-009-0187-4}
}
@article{graewe_wolff_efm_2009,
......@@ -550,7 +632,7 @@
pages = "21-39",
year = "2009",
issn = "1567-7419",
doi = "doi: 110.1007/s10652-009-9141-8",
doi = "10.1007/s10652-009-9141-8",
}
@article{hofmeister_etal_csr_2009,
......@@ -630,6 +712,7 @@
volume = {38},
pages = {566-587},
year = {2008},
doi = {10.1175/2007JPO3796.1}
}
@article{burchard_hofmeister_eccs_2008,
......@@ -758,6 +841,7 @@
volume = 54,
pages = {266-283},
year = {2004},
doi = {10.1007/s10236-003-0077-0},
}
@article{stanev_etal_od_2003a,
......
......@@ -77,10 +77,10 @@
<element name="gamma_surf" type="bool" label="layer thickness constant at surface (else at the bottom)">
<condition type="eq" variable="./vert_cord" value="3"/>
</element>
<element name="il" type="int" label="lower bound of used i-indices (mandatory for dynamic compilation; default -1 indicates full domain for static compilation)"/>
<element name="ih" type="int" label="upper bound of used i-indices (mandatory for dynamic compilation; default -1 indicates full domain for static compilation)"/>
<element name="jl" type="int" label="lower bound of used j-indices (mandatory for dynamic compilation; default -1 indicates full domain for static compilation)"/>
<element name="jh" type="int" label="upper bound of used j-indices (mandatory for dynamic compilation; default -1 indicates full domain for static compilation)"/>
<element name="il" type="int" label="lower bound of used i-indices (mandatory for dynamic compilation; default -1 indicates full domain for static compilation, i.e. il=1)"/>
<element name="ih" type="int" label="upper bound of used i-indices (mandatory for dynamic compilation; default -1 indicates full domain for static compilation, i.e. ih=iextr)"/>
<element name="jl" type="int" label="lower bound of used j-indices (mandatory for dynamic compilation; default -1 indicates full domain for static compilation, i.e. jl=1)"/>
<element name="jh" type="int" label="upper bound of used j-indices (mandatory for dynamic compilation; default -1 indicates full domain for static compilation, i.e. jh=jextr)"/>
<element name="z0_method" type="int" label="bottom roughness specification">
<options>
<option value="0" label="constant - using z0_const"/>
......
......@@ -496,10 +496,6 @@
! {\tt do\_getm\_bio} & call to GOTM-BIO (not yet released) & \\
! {\tt slow\_bottom\_friction} & slow bottom friction & see page
! \pageref{sec-slow-bottom-friction} \\
! {\tt slow\_advection} & slow advection terms & see page
! \pageref{sec-slow-advection} \\
! {\tt slow\_diffusion} & slow diffusion terms & see page
! \pageref{sec-slow-diffusion} \\
! {\tt slow\_terms} & sum of slow terms & see page
! \pageref{sec-slow-terms} \\
! {\tt stop\_macro} & finishing a 3d step & see page
......
......@@ -15,8 +15,7 @@
! equations (\ref{Slowfirst}) - (\ref{Slowlast}), see section
! \ref{SectionVerticalIntegrated}.
! These calculations have been prepared in the routines
! {\tt slow\_bottom\_friction}, {\tt slow\_advection} and
! {\tt slow\_diffusion}.
! {\tt integrate\_3d} and {\tt slow\_bottom\_friction}.
!
! !USES:
use domain, only: imin,imax,jmin,jmax,kmax,HU,HV,au,av
......
......@@ -79,8 +79,7 @@ if(GETM_USE_FABM)
endif(GETM_USE_FABM)
include(CMakeDependentOption)
CMAKE_DEPENDENT_OPTION(GETM_USE_FLEXIBLE_OUTPUT "Use new output manager" ON "GETM_USE_FABM" OFF)
option(GETM_USE_FLEXIBLE_OUTPUT "Use new output manager" ON)
if(GETM_USE_FLEXIBLE_OUTPUT)
add_definitions(-D_FLEXIBLE_OUTPUT_)
endif()
......
......@@ -95,7 +95,7 @@
integer, parameter :: INNER = 1
REALTYPE, private, parameter :: pi = 3.141592654
REALTYPE, private, parameter :: deg2rad = pi/180.
REALTYPE, private, parameter :: omega = 2.*pi/86400.
REALTYPE, private, parameter :: omega = 2.*pi/86164.
!
! !REVISION HISTORY:
! Original author(s): Karsten Bolding & Hans Burchard
......@@ -363,6 +363,9 @@
! Compute Coriolis parameter
if (f_plane) then
if (have_lonlat) then
LEVEL2 "WARNING: f_plane despite available lat data from topo!"
end if
LEVEL2 "Assuming constant Coriolis parameter - lat = ",latitude
cori = 2.*omega*sin(deg2rad*latitude)
coru = cori
......
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