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<article xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:oasis="http://docs.oasis-open.org/ns/oasis-exchange/table" dtd-version="3.0"><?xmltex \makeatother\@nolinetrue\makeatletter?>
  <front>
    <journal-meta>
<journal-id journal-id-type="publisher">GMD</journal-id>
<journal-title-group>
<journal-title>Geoscientific Model Development</journal-title>
<abbrev-journal-title abbrev-type="publisher">GMD</abbrev-journal-title>
<abbrev-journal-title abbrev-type="nlm-ta">Geosci. Model Dev.</abbrev-journal-title>
</journal-title-group>
<issn pub-type="epub">1991-9603</issn>
<publisher><publisher-name>Copernicus Publications</publisher-name>
<publisher-loc>Göttingen, Germany</publisher-loc>
</publisher>
</journal-meta>

    <article-meta>
      <article-id pub-id-type="doi">10.5194/gmd-10-2947-2017</article-id><title-group><article-title>The CO5 configuration of the 7 km Atlantic Margin Model: <?xmltex \hack{\newline}?> large-scale biases and sensitivity to forcing, physics options <?xmltex \hack{\newline}?>and vertical resolution</article-title>
      </title-group><?xmltex \runningtitle{CO5 standard configuration }?><?xmltex \runningauthor{E. O'Dea et al.}?>
      <contrib-group>
        <contrib contrib-type="author" corresp="yes" rid="aff1">
          <name><surname>O'Dea</surname><given-names>Enda</given-names></name>
          <email>enda.odea@metoffice.gov.uk</email>
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Furner</surname><given-names>Rachel</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff2">
          <name><surname>Wakelin</surname><given-names>Sarah</given-names></name>
          
        <ext-link>https://orcid.org/0000-0002-2081-2693</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Siddorn</surname><given-names>John</given-names></name>
          
        <ext-link>https://orcid.org/0000-0003-3848-8868</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>While</surname><given-names>James</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Sykes</surname><given-names>Peter</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>King</surname><given-names>Robert</given-names></name>
          
        <ext-link>https://orcid.org/0000-0002-9573-2567</ext-link></contrib>
        <contrib contrib-type="author" corresp="no" rid="aff2">
          <name><surname>Holt</surname><given-names>Jason</given-names></name>
          
        </contrib>
        <contrib contrib-type="author" corresp="no" rid="aff1">
          <name><surname>Hewitt</surname><given-names>Helene</given-names></name>
          
        <ext-link>https://orcid.org/0000-0001-7432-6001</ext-link></contrib>
        <aff id="aff1"><label>1</label><institution>Met Office, Exeter, UK</institution>
        </aff>
        <aff id="aff2"><label>2</label><institution>National Oceanography Centre, Liverpool, UK</institution>
        </aff>
      </contrib-group>
      <author-notes><corresp id="corr1">Enda O'Dea (enda.odea@metoffice.gov.uk)</corresp></author-notes><pub-date><day>4</day><month>August</month><year>2017</year></pub-date>
      
      <volume>10</volume>
      <issue>8</issue>
      <fpage>2947</fpage><lpage>2969</lpage>
      <history>
        <date date-type="received"><day>20</day><month>January</month><year>2017</year></date>
           <date date-type="rev-request"><day>26</day><month>January</month><year>2017</year></date>
           <date date-type="rev-recd"><day>18</day><month>May</month><year>2017</year></date>
           <date date-type="accepted"><day>14</day><month>June</month><year>2017</year></date>
      </history>
      <permissions>
<license license-type="open-access">
<license-p>This work is licensed under the Creative Commons Attribution 3.0 Unported License. To view a copy of this licence, visit <ext-link ext-link-type="uri" xlink:href="https://creativecommons.org/licenses/by/3.0/">https://creativecommons.org/licenses/by/3.0/</ext-link></license-p>
</license>
</permissions><self-uri xlink:href="https://gmd.copernicus.org/articles/10/2947/2017/gmd-10-2947-2017.html">This article is available from https://gmd.copernicus.org/articles/10/2947/2017/gmd-10-2947-2017.html</self-uri>
<self-uri xlink:href="https://gmd.copernicus.org/articles/10/2947/2017/gmd-10-2947-2017.pdf">The full text article is available as a PDF file from https://gmd.copernicus.org/articles/10/2947/2017/gmd-10-2947-2017.pdf</self-uri>


      <abstract>
    <p>We describe the physical model component of the standard Coastal
Ocean version 5 configuration (CO5) of the European north-west shelf (NWS).
CO5 was developed jointly between the Met Office and the National
Oceanography Centre. CO5 is designed with the seamless approach in mind,
which allows for modelling of multiple timescales for a variety of
applications from short-range ocean forecasting to climate
projections. The configuration constitutes the basis of the latest update to
the ocean and data assimilation components of the Met Office's operational
Forecast Ocean Assimilation Model (FOAM) for the NWS. A 30.5-year
non-assimilating control hindcast of CO5 was integrated from January 1981 to
June 2012. Sensitivity simulations were conducted with reference to the
control run. The control run is compared against a previous non-assimilating
Proudman Oceanographic Laboratory Coastal Ocean Modelling System (POLCOMS)
hindcast of the NWS. The CO5 control hindcast is shown to have much reduced
biases compared to POLCOMS. Emphasis in the system description is weighted to
updates in CO5 over previous versions. Updates include an increase in
vertical resolution, a new vertical coordinate stretching function, the
replacement of climatological riverine sources with the pan-European
hydrological model E-HYPE, a new Baltic boundary condition and switching from
directly imposed atmospheric model boundary fluxes to calculating the fluxes
within the model using a bulk formula. Sensitivity tests of the updates are
detailed with a view toward attributing observed changes in the new system from
the previous system and suggesting future directions of research to further
improve the system.</p>
  </abstract>
    </article-meta>
  <notes notes-type="copyrightstatement">
  
      <p>The works published in this journal are distributed under
the Creative Commons Attribution 3.0 License. This license does not affect
the Crown copyright work, which is reusable under the Open Government
Licence (OGL). The Creative Commons Attribution 3.0 License and the OGL are
interoperable and do not conflict with, reduce or limit each
other.<?xmltex \hack{\newline}?><?xmltex \hack{\newline}?> © Crown copyright 2017</p>
</notes></front>
<body>
      


<sec id="Ch1.S1" sec-type="intro">
  <title>Introduction</title>
      <p>The European north-west shelf (NWS) is an area of intense socioeconomic
interest with a wide variety of dynamical regimes. It is a region that has
been the subject of numerous research models over many years both domain-wide
and focusing on smaller subregions. Research models and associated
assimilation schemes for the region have matured into a number of operational
systems. As part of the Copernicus Marine Environment Monitoring Service
(CMEMS), an operational forecast system based on the Atlantic Margin Model
(AMM) domain <xref ref-type="bibr" rid="bib1.bibx28" id="paren.1"/> has been developed to provide products for
coastal modelling downstream users. The AMM term refers to the model domain
rather than the full configuration
for the NWS as implemented at the Met Office.
It is the model domain of previous Met Office NWS configurations up to and
including CO5, and it is shown in Fig. <xref ref-type="fig" rid="Ch1.F1"/>.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F1"><caption><p>NOOS bathymetry for the AMM domain. </p></caption>
        <?xmltex \igopts{width=236.157874pt}?><graphic xlink:href="https://gmd.copernicus.org/articles/10/2947/2017/gmd-10-2947-2017-f01.png"/>

      </fig>

      <p>Complimentary to the forecast systems, CMEMS also make reanalysis products
available to the end users. The reanalysis products not only provide end
users with data from past decades but also provide a way to assess and
validate the operational systems over longer periods against historical data.
The presentation of systematic biases and drifts allows the users to
understand the limitations and appropriateness of a particular product to
their interest or application. Furthermore, as systems are upgraded, the
associated reanalyses provide a means to intercompare and evaluate the
effectiveness of system updates.</p>
      <p>Here, we describe the non-assimilating standard Coastal Ocean configuration
version 5 (CO5) control hindcast. This CO5 hindcast provides a reference to
understand underlying biases and drifts attributable to changes in the
physics updates alone. CO5 includes all input parameters, ancillary files,
model code and compilation keys required to run the model. CO5 forms the
physics component of the Copernicus reanalysis product replacing the
preexisting POLCOMS-derived hindcast
product.
In support of the full reanalysis, a non-assimilative control hindcast was
integrated from January 1981 to June 2012. CO5 was jointly developed by the
Met Office and the National Oceanography Centre. Standard configurations such
as CO5 are subsequently incorporated as constituent parts of broader modelling
systems such as climate projections <xref ref-type="bibr" rid="bib1.bibx35" id="paren.2"/> or coupled systems
<xref ref-type="bibr" rid="bib1.bibx33" id="paren.3"/>.</p>
      <p>CO5 is an update of the Nucleus for European Modelling of the Ocean (NEMO)
<xref ref-type="bibr" rid="bib1.bibx23" id="paren.4"/> configuration used to model the NWS in <xref ref-type="bibr" rid="bib1.bibx28" id="normal.5"/>.
For convenience, we reference the configuration in <xref ref-type="bibr" rid="bib1.bibx28" id="normal.6"/> as CO4.
CO4 was also based on the operational AMM domain at the Met Office. Changes
include new riverine forcing, updated Baltic boundary conditions, increased
vertical resolution, different surface forcing, as well as an updated base
NEMO from version 3.2 to 3.4. The CO5 reanalysis product is an update to the
12 <inline-formula><mml:math id="M1" display="inline"><mml:mi mathvariant="normal">km</mml:mi></mml:math></inline-formula> POLCOMS hindcast <xref ref-type="bibr" rid="bib1.bibx13" id="paren.7"/> for 1965–2004
of the same AMM region.
We compare the CO5 non-assimilative control hindcast with the POLCOMS
hindcast over common years of integration for the period 1985–2004 and exclude the CO5
spin-up years 1981–1984. Both are compared against standard climatologies
and observations. Individual updates incorporated into CO5 are also
investigated systematically by a series of 30-year sensitivity experiments,
looking at the changes in isolation. The surface and boundary forcing
datasets used in CO4 only start from 2006, so it is not possible to do a full
30-year like-for-like CO4 and CO5 comparison. However, shorter 5-year
experiments looking at the effects of the forcing are also investigated.</p>
      <p>The structure of the paper is as follows. Section 2 gives an overview of the
standard configuration CO5. Configuration updates are detailed in Sect. 3.
The experimental design including the specifics of the sensitivity
experiments are outlined in Sect. 4. Section 5 has three main subsections:
<list list-type="bullet"><list-item>
      <p>Section 5.1 is concerned with tidal analysis of CO5.</p></list-item><list-item>
      <p>Section 5.2 isolates long-term biases compared to climatology, observations and the POLCOMS hindcast.</p></list-item><list-item>
      <p>Section 5.3 presents results from sensitivity experiments that look in isolation
at changes brought into CO5.</p></list-item></list>
Section 6 summarises and discusses the results before commenting on future
system upgrades which are informed by the analysis of this paper.</p>
</sec>
<sec id="Ch1.S2">
  <title>Core model description</title>
      <p>CO5 builds upon and thus shares many of the core features of the previous Met
Office shelf seas model configuration CO4, as described in
<xref ref-type="bibr" rid="bib1.bibx28" id="normal.8"/>. Elaboration of the key features particular to CO5 that
are distinct from CO4 is deferred to Sect. 3.</p>
      <p>CO5 is based on version 3.4 of NEMO <xref ref-type="bibr" rid="bib1.bibx23" id="paren.9"/>. The model domain
extends from 20<inline-formula><mml:math id="M2" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> W, 40<inline-formula><mml:math id="M3" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N to 13<inline-formula><mml:math id="M4" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> E,
65<inline-formula><mml:math id="M5" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N on a regular latitude–longitude grid. The domain covers the
entirety of the European NWS and includes a sufficient portion
of the deep waters of the eastern North Atlantic to encapsulate cross-shelf
break exchange. The bathymetry for CO5 is derived from the North West European Shelf
Operational Oceanographic System (NOOS) bathymetry. The NOOS bathymetry is a
combination of GEBCO 1 arcmin data
and a variety of local data sources from the
NOOS partners. The meridional grid resolution is <inline-formula><mml:math id="M6" display="inline"><mml:mrow><mml:mn mathvariant="normal">1</mml:mn><mml:mo>/</mml:mo><mml:msup><mml:mn mathvariant="normal">15</mml:mn><mml:mo>∘</mml:mo></mml:msup></mml:mrow></mml:math></inline-formula> or
7.4 <inline-formula><mml:math id="M7" display="inline"><mml:mi mathvariant="normal">km</mml:mi></mml:math></inline-formula>. The zonal resolution of <inline-formula><mml:math id="M8" display="inline"><mml:mrow><mml:mn mathvariant="normal">1</mml:mn><mml:mo>/</mml:mo><mml:msup><mml:mn mathvariant="normal">9</mml:mn><mml:mo>∘</mml:mo></mml:msup></mml:mrow></mml:math></inline-formula> varies from
9.4 <inline-formula><mml:math id="M9" display="inline"><mml:mi mathvariant="normal">km</mml:mi></mml:math></inline-formula> along the southern boundary to 5.2 <inline-formula><mml:math id="M10" display="inline"><mml:mi mathvariant="normal">km</mml:mi></mml:math></inline-formula> along the
northern boundary with a mean of 7.4 <inline-formula><mml:math id="M11" display="inline"><mml:mi mathvariant="normal">km</mml:mi></mml:math></inline-formula> at <inline-formula><mml:math id="M12" display="inline"><mml:mrow><mml:msup><mml:mn mathvariant="normal">52.5</mml:mn><mml:mo>∘</mml:mo></mml:msup></mml:mrow></mml:math></inline-formula> N.
Although the grid horizontal resolution readily resolves the external Rossby
radius (200 <inline-formula><mml:math id="M13" display="inline"><mml:mi mathvariant="normal">km</mml:mi></mml:math></inline-formula>), it is not sufficient to resolve the internal Rossby
radius on the shelf which is of the order 4 <inline-formula><mml:math id="M14" display="inline"><mml:mi mathvariant="normal">km</mml:mi></mml:math></inline-formula> <xref ref-type="bibr" rid="bib1.bibx12" id="paren.10"/>.
However, at the time of integration of the reanalysis, it was not
computationally feasible to conduct multiple 30-year hindcasts of the CO5
domain with a resolution approaching the 1.5 <inline-formula><mml:math id="M15" display="inline"><mml:mi mathvariant="normal">km</mml:mi></mml:math></inline-formula> required to resolve
the internal radius.</p>
      <p>As tides and surges play such important roles on the European NWS,
a non-linear free surface is implemented using the variable volume
layer <xref ref-type="bibr" rid="bib1.bibx20" id="paren.11"/> and time-splitting approaches in NEMO. The baroclinic time
step used in the 30-year hindcasts of CO5 is 300 s with a barotropic time step of 10 s.
The advection of momentum is both energy and enstrophy conserving
<xref ref-type="bibr" rid="bib1.bibx1" id="paren.12"/>. Both bi-Laplacian and Laplacian horizontal
viscosities are applied. The Laplacian viscosity is applied along
geopotential levels with a coefficient of <inline-formula><mml:math id="M16" display="inline"><mml:mn mathvariant="normal">30.0</mml:mn></mml:math></inline-formula> <inline-formula><mml:math id="M17" display="inline"><mml:mrow><mml:msup><mml:mi mathvariant="normal">m</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">s</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>. The
bi-Laplacian viscosity is used to retain model stability and is applied on
model levels with a coefficient of <inline-formula><mml:math id="M18" display="inline"><mml:mrow><mml:mn mathvariant="normal">1.0</mml:mn><mml:mo>×</mml:mo><mml:msup><mml:mn mathvariant="normal">10</mml:mn><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">10</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula> <inline-formula><mml:math id="M19" display="inline"><mml:mrow><mml:msup><mml:mi mathvariant="normal">m</mml:mi><mml:mn mathvariant="normal">4</mml:mn></mml:msup><mml:mspace width="0.125em" linebreak="nobreak"/><mml:msup><mml:mi mathvariant="normal">s</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>.
The lateral momentum boundary condition is free slip. Tracer advection is
implemented using the total variation diminishing (TVD) scheme
<xref ref-type="bibr" rid="bib1.bibx39" id="paren.13"/>. Unlike CO4, Laplacian tracer diffusion operates
only along geopotential levels with a coefficient of
<inline-formula><mml:math id="M20" display="inline"><mml:mn mathvariant="normal">50</mml:mn></mml:math></inline-formula> <inline-formula><mml:math id="M21" display="inline"><mml:mrow><mml:msup><mml:mi mathvariant="normal">m</mml:mi><mml:mn mathvariant="normal">2</mml:mn></mml:msup><mml:mspace linebreak="nobreak" width="0.125em"/><mml:msup><mml:mi mathvariant="normal">s</mml:mi><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">1</mml:mn></mml:mrow></mml:msup></mml:mrow></mml:math></inline-formula>.</p>
      <p>The generic length scale (GLS) turbulence scheme calculates the turbulent
viscosities and diffusivities <xref ref-type="bibr" rid="bib1.bibx36" id="paren.14"/>.
The second-moment algebraic closure of <xref ref-type="bibr" rid="bib1.bibx3" id="normal.15"/>
is solved with two dynamical equations <xref ref-type="bibr" rid="bib1.bibx31" id="paren.16"/>
for the turbulence kinetic energy (TKE), <inline-formula><mml:math id="M22" display="inline"><mml:mi>k</mml:mi></mml:math></inline-formula> and TKE dissipation,
<inline-formula><mml:math id="M23" display="inline"><mml:mi mathvariant="italic">ϵ</mml:mi></mml:math></inline-formula> <xref ref-type="bibr" rid="bib1.bibx37" id="paren.17"/>.
At the surface and bed, Neumann boundary conditions on <inline-formula><mml:math id="M24" display="inline"><mml:mi>k</mml:mi></mml:math></inline-formula> and <inline-formula><mml:math id="M25" display="inline"><mml:mi mathvariant="italic">ϵ</mml:mi></mml:math></inline-formula> are
applied. Surface wave mixing is parameterised as in <xref ref-type="bibr" rid="bib1.bibx5" id="normal.18"/>.
Dissipation under stable stratification is limited using the Galperin limit
<xref ref-type="bibr" rid="bib1.bibx8" id="paren.19"/> of 0.267. A spatially varying log-layer-derived
drag coefficient
with a minimum set at 0.0025 controls the bottom friction.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F2"><caption><p>Thickness of surface model levels in CO4 <bold>(a)</bold> and
CO5 <bold>(b)</bold>.</p></caption>
        <?xmltex \igopts{width=193.47874pt}?><graphic xlink:href="https://gmd.copernicus.org/articles/10/2947/2017/gmd-10-2947-2017-f02.png"/>

      </fig>

</sec>
<sec id="Ch1.S3">
  <title>Summary of main model updates</title>
      <p>CO5 has four configuration updates from CO4. These updates involve the
vertical levels,
the source riverine input,
the treatment of the exchange with the Baltic through the Kattegat and the base version of NEMO.
Furthermore, the inputs at the oceanic lateral boundary conditions
and the surface boundary condition (SBC)
for the 30-year hindcast are substantially different from the shorter runs
detailed for the forecast implementation of CO4 in <xref ref-type="bibr" rid="bib1.bibx28" id="normal.20"/>. Here,
we describe in detail each of the changes, and in Sect. 4 a set of sensitivity
experiments explores the impacts of these changes.</p>
<sec id="Ch1.S3.SS1">
  <title>Vertical coordinate</title>
      <p>The vertical coordinate in CO5 is inherited from CO4
and is a <inline-formula><mml:math id="M26" display="inline"><mml:mrow><mml:msup><mml:mi>z</mml:mi><mml:mo>*</mml:mo></mml:msup><mml:mo>-</mml:mo><mml:mi mathvariant="italic">σ</mml:mi></mml:mrow></mml:math></inline-formula>  coordinate.
It is terrain following and is fitted to a smoothed envelope bathymetry.
Where the actual bathymetry is too steep, it intersects the bed and levels
are lost analogously to a <inline-formula><mml:math id="M27" display="inline"><mml:mi>z</mml:mi></mml:math></inline-formula>-level model. Relative to CO4, which uses the
stretching function in <xref ref-type="bibr" rid="bib1.bibx34" id="normal.21"/>, CO5 both features more model
levels (increased from 33 to 51) and uses the stretching function as detailed
in <xref ref-type="bibr" rid="bib1.bibx32" id="normal.22"/> for the terrain-following coordinate system. We
refer to the stretching function in CO4 as SH and that in CO5 as SF. The new
stretching function maintains near-uniform vertical resolution at the
surface. Keeping the surface vertical resolution almost the same across most
of the domain implies a more consistent air–sea exchange domain-wide. The
stretching function also aims to minimise horizontal pressure gradient errors
induced by sloping horizontal model levels. A comparison of the thickness of
the surface model level in CO4 and CO5 is shown in
Fig. <xref ref-type="fig" rid="Ch1.F2"/>. It is only in the shallowest regions
(bathymetry of less than 50 <inline-formula><mml:math id="M28" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula>) where the surface level thickness in CO5 is
not set equal to 1 <inline-formula><mml:math id="M29" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula>, whereas in CO4 the surface model level varies
considerably over the domain from deep water to shelf. Thus, any change in
CO5 that impacts upon air–sea exchange will be applied equally across most of
the domain allowing cause and effect to be more readily parsed. Furthermore,
follow-on configurations of CO5 will feature ocean–atmosphere coupling where
again consistent air–sea exchange will be important.</p>
</sec>
<sec id="Ch1.S3.SS2">
  <title>Riverine input</title>
      <p>The second significant change between CO4 and CO5 is the data source for
riverine input. In CO4, an annual climatology of some 320 European rivers
mapped to 165 outflow points on the CO4 grid constitutes the riverine input
regardless of the model year <xref ref-type="bibr" rid="bib1.bibx38" id="paren.23"/>. As a step towards
temporal variation and higher resolution of riverine sources, the old
climatology is replaced with data from a pan-European implementation of the
hydrological model HYdrological Predictions for the Environment (HYPE)
<xref ref-type="bibr" rid="bib1.bibx21" id="paren.24"/>. The European implementation of HYPE is
known as E-HYPE <xref ref-type="bibr" rid="bib1.bibx7" id="paren.25"/> and has a sub-basin resolution of
120 <inline-formula><mml:math id="M30" display="inline"><mml:mi mathvariant="normal">km</mml:mi></mml:math></inline-formula><inline-formula><mml:math id="M31" display="inline"><mml:msup><mml:mi/><mml:mn mathvariant="normal">2</mml:mn></mml:msup></mml:math></inline-formula>. There is both an operational forecast and hindcast of
E-HYPE, and the data are freely available at
<uri>http://hypeweb.smhi.se/europehype/long-term-means</uri>. Daily river outflow
data are mapped to 476 outflow points on the CO5 grid from version 2.1 of
E-HYPE. Data were provided by the Swedish Meteorological and Hydrological
Institute (SMHI) for the entire period of the hindcast. The E-HYPE data
provide a greater number of river sources along the coastline of continental
Europe. Figure <xref ref-type="fig" rid="Ch1.F3"/> compares the total riverine input
from all rivers in the domain for both the CO4 river climatology and the
1980–2012 mean of the E-HYPE data. Two individual years of E-HYPE data are
also included to show the day-to-day and year-to-year variability that E-HYPE
daily data contain compared to the climatological means. The difference in
subregions along subsections of coast is shown in
Fig. <xref ref-type="fig" rid="Ch1.F4"/>. The increase in continental river
outflow leads to the mean E-HYPE outflow being considerably larger than the
CO4 river climatology. However, as presented in
Fig. <xref ref-type="fig" rid="Ch1.F4"/>, the increase is not uniform and
indeed the mean outflow from regions of the UK is actually slightly reduced
in E-HYPE. In some areas, such as the German Bight and the Norwegian coast,
E-HYPE outflow is substantially increased.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F3"><caption><p>Comparison of total river flow rate between E-HYPE individual years,
30-year mean and CO4 climatological rivers.</p></caption>
          <?xmltex \igopts{width=199.169291pt}?><graphic xlink:href="https://gmd.copernicus.org/articles/10/2947/2017/gmd-10-2947-2017-f03.png"/>

        </fig>

</sec>
<sec id="Ch1.S3.SS3">
  <title>Baltic exchange</title>
      <p>The third update to CO5 concerns the exchange between the North Sea and the
Baltic through the Danish straits and the Kattegat. At 7 <inline-formula><mml:math id="M32" display="inline"><mml:mi mathvariant="normal">km</mml:mi></mml:math></inline-formula>
resolution, it is not possible to resolve the Danish straits, given that
Öresund is 4 <inline-formula><mml:math id="M33" display="inline"><mml:mi mathvariant="normal">km</mml:mi></mml:math></inline-formula> wide at its narrowest.
Thus, alternative approaches are required.
The approach in CO4 was to apply a daily climatological flux through two
additional river points at roughly where the Great Belt and the Öresund
open to the Kattegat. If the flux is negative, i.e. water leaves the
Kattegat and enters the Baltic,
ocean water is removed at the river point according to the magnitude of the flux.
If the flux is positive, a flux of water of specified salinity and
temperature is added at the river point. In CO5, a different approach is taken
and involves the specification of a new lateral boundary condition with a
relaxation zone spread across the Kattegat. No attempt is made to model the
Danish straits and they are removed from the domain as seen in the hashed-out
region of Fig. <xref ref-type="fig" rid="Ch1.F2"/>. Data for the lateral boundary
condition come from a general estuarine transport model (GETM) of the North
Sea and the Baltic Sea. The North Sea–Baltic Sea (NSBS) model was run at the
Leibniz Institut für Ostseeforschung Warnemünde (IOW) <xref ref-type="bibr" rid="bib1.bibx10" id="paren.26"/>.
The horizontal resolution was 1 nautical mile, and there are 50 vertical
levels. The version of GETM was v2.3.1. Daily NSBS data are only available
from 2001 to 2012, and a climatology of this daily boundary dataset is created
to cover 1981–2001. Temperature and salinity data are relaxed over the
relaxation zone. Barotropic velocity and sea surface elevation boundaries
from the NSBS model can also
be prescribed by the Flather radiation boundary condition.
However, the reference elevation in the NSBS model and the data from the
models of the Atlantic into which CO5 is nested are not the same. Such a
difference could lead to a persistent flux in or out of the Baltic that is
not physically based. An anomaly of elevation about a mean value at the
boundary could provide a suitable solution. For the hindcast, we describe
here, only relaxation of the temperature and salinity is used,
though a sensitivity run including elevation was conducted.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F4"><caption><p>Comparison of coastal subsections of total river flow rate between
E-HYPE and CO4 climatological rivers.</p></caption>
          <?xmltex \igopts{width=236.157874pt}?><graphic xlink:href="https://gmd.copernicus.org/articles/10/2947/2017/gmd-10-2947-2017-f04.png"/>

        </fig>

<?xmltex \hack{\newpage}?>
</sec>
<sec id="Ch1.S3.SS4">
  <title>Surface boundary condition</title>
      <p>The surface boundary condition in CO5 has also changed from CO4. In CO4, the
surface boundary conditions are directly prescribed fluxes from the Met
Office's numerical weather prediction (NWP) model. Directly prescribed fluxes
are replaced by calculating momentum, heat and freshwater fluxes using the
Common Ocean-ice Reference Experiment (CORE) bulk formulae
<xref ref-type="bibr" rid="bib1.bibx17" id="paren.27"/>. The NWP data are only available from November 2006,
and so a different surface boundary condition must be used for the 30-year
CO5 hindcasts starting in 1981. The atmospheric forcing dataset used to force
the 30-year hindcast is the ERA-Interim dataset of the European Centre for
Medium-Range Weather Forecasts (ECMWF) <xref ref-type="bibr" rid="bib1.bibx6" id="paren.28"/>. In addition to
switching to bulk formulae, the light attenuation scheme used in CO5 is also
changed to the standard NEMO tri-band red–blue–green (RGB) scheme of
<xref ref-type="bibr" rid="bib1.bibx19" id="normal.29"/>. The RGB scheme replaces the single-band scheme presented in
<xref ref-type="bibr" rid="bib1.bibx14" id="normal.30"/> which is used in CO4. We refer to this single-band
scheme as PDWL in this paper. One consequence of this change in the light scheme
in CO5 is that the extinction depths do not vary across the domain in
proportion to the bathymetry as in CO4 and POLCOMS. The variance in
extinction depth was a first-order attempt to mimic the change in water
clarity from deep waters to shallow.</p><?xmltex \hack{\newpage}?>
</sec>
</sec>
<sec id="Ch1.S4">
  <title>Experimental design</title>
      <p>The CO5 control run forms the baseline experiment for this paper. This
baseline control run and the older POLCOMS hindcast are compared to evaluate
how the two modelling systems perform irrespective of assimilation. The
relevant configuration differences between CO5, CO4 and POLCOMS are shown in
Table <xref ref-type="table" rid="Ch1.T1"/>.</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T1" specific-use="star"><caption><p>Key configuration differences.</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="5">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="left"/>
     <oasis:colspec colnum="3" colname="col3" align="left"/>
     <oasis:colspec colnum="4" colname="col4" align="left"/>
     <oasis:colspec colnum="5" colname="col5" align="left"/>
     <oasis:thead>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1">Configuration</oasis:entry>  
         <oasis:entry colname="col2">POLCOMS</oasis:entry>  
         <oasis:entry colname="col3">CO4</oasis:entry>  
         <oasis:entry colname="col4">CO5</oasis:entry>  
         <oasis:entry colname="col5"/>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>  
         <oasis:entry colname="col1">Code base</oasis:entry>  
         <oasis:entry colname="col2">POLCOMS</oasis:entry>  
         <oasis:entry colname="col3">NEMO 3.4</oasis:entry>  
         <oasis:entry colname="col4">NEMO3.6</oasis:entry>  
         <oasis:entry colname="col5"/>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Horizontal resolution</oasis:entry>  
         <oasis:entry colname="col2">12 <inline-formula><mml:math id="M34" display="inline"><mml:mi mathvariant="normal">km</mml:mi></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col3">7 <inline-formula><mml:math id="M35" display="inline"><mml:mi mathvariant="normal">km</mml:mi></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4">7 <inline-formula><mml:math id="M36" display="inline"><mml:mi mathvariant="normal">km</mml:mi></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col5"/>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Vertical levels</oasis:entry>  
         <oasis:entry colname="col2">40 SH levels</oasis:entry>  
         <oasis:entry colname="col3">33 SH levels</oasis:entry>  
         <oasis:entry colname="col4">51 SF levels</oasis:entry>  
         <oasis:entry colname="col5"/>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Surface forcing</oasis:entry>  
         <oasis:entry colname="col2">ERA40</oasis:entry>  
         <oasis:entry colname="col3">NWP</oasis:entry>  
         <oasis:entry colname="col4">ERAI</oasis:entry>  
         <oasis:entry colname="col5"/>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Lateral boundary</oasis:entry>  
         <oasis:entry colname="col2">1 <inline-formula><mml:math id="M37" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula>global</oasis:entry>  
         <oasis:entry colname="col3">North Atlantic 12 <inline-formula><mml:math id="M38" display="inline"><mml:mi mathvariant="normal">km</mml:mi></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col4"><inline-formula><mml:math id="M39" display="inline"><mml:mrow><mml:mn mathvariant="normal">1</mml:mn><mml:mo>/</mml:mo><mml:msup><mml:mn mathvariant="normal">4</mml:mn><mml:mo>∘</mml:mo></mml:msup></mml:mrow></mml:math></inline-formula> global GO5.0 and GLOSEA5</oasis:entry>  
         <oasis:entry colname="col5"/>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">River source</oasis:entry>  
         <oasis:entry colname="col2">Climatology</oasis:entry>  
         <oasis:entry colname="col3">Climatology</oasis:entry>  
         <oasis:entry colname="col4">E-HYPE</oasis:entry>  
         <oasis:entry colname="col5"/>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Baltic boundary</oasis:entry>  
         <oasis:entry colname="col2">Climatology at two points</oasis:entry>  
         <oasis:entry colname="col3">Climatology at two points</oasis:entry>  
         <oasis:entry colname="col4">IoW  boundary condition</oasis:entry>  
         <oasis:entry colname="col5"/>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Light penetration</oasis:entry>  
         <oasis:entry colname="col2">PDWL</oasis:entry>  
         <oasis:entry colname="col3">PDWL</oasis:entry>  
         <oasis:entry colname="col4">RGB</oasis:entry>  
         <oasis:entry colname="col5"/>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Integration period</oasis:entry>  
         <oasis:entry colname="col2">1960–2004</oasis:entry>  
         <oasis:entry colname="col3">2007–2012</oasis:entry>  
         <oasis:entry colname="col4">1981–2012</oasis:entry>  
         <oasis:entry colname="col5"/>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table><table-wrap-foot><p>
NWP refers to Met Office numerical weather prediction (NWP) fluxes directly prescribed.
IoW refers to data from the IoW NSBS GETM model of the Baltic <xref ref-type="bibr" rid="bib1.bibx10" id="paren.31"/>.
RGB is the default tri-band light attenuation scheme in NEMO <xref ref-type="bibr" rid="bib1.bibx19" id="paren.32"/>.
PDWL refers to the single-band scheme that varies attenuation in proportion to sea bed depth <xref ref-type="bibr" rid="bib1.bibx14" id="paren.33"/>.   </p></table-wrap-foot></table-wrap>

      <p>The configurations are compared with respect to satellite-derived sea surface
temperature (SST), in situ subsurface observations, as well as both global
and regional climatologies. To establish the effect of the key changes from
CO4 to CO5, a set
of sensitivity experiments are integrated over the full 30-year period.
The key differences of the 30-year experiments are listed in
Table <xref ref-type="table" rid="Ch1.T2"/>.</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T2"><caption><p>The 30-year sensitivity experiments.</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="5">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="left"/>
     <oasis:colspec colnum="3" colname="col3" align="left"/>
     <oasis:colspec colnum="4" colname="col4" align="left"/>
     <oasis:colspec colnum="5" colname="col5" align="left"/>
     <oasis:thead>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1">EXP</oasis:entry>  
         <oasis:entry colname="col2">Levels</oasis:entry>  
         <oasis:entry colname="col3">River</oasis:entry>  
         <oasis:entry colname="col4">Baltic</oasis:entry>  
         <oasis:entry colname="col5">Light</oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>  
         <oasis:entry colname="col1">CNTL</oasis:entry>  
         <oasis:entry colname="col2">SF51</oasis:entry>  
         <oasis:entry colname="col3">E-HYPE</oasis:entry>  
         <oasis:entry colname="col4">IoW</oasis:entry>  
         <oasis:entry colname="col5">RGB</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">S30_1</oasis:entry>  
         <oasis:entry colname="col2">SH33</oasis:entry>  
         <oasis:entry colname="col3">E-HYPE</oasis:entry>  
         <oasis:entry colname="col4">IoW</oasis:entry>  
         <oasis:entry colname="col5">RGB</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">S30_2</oasis:entry>  
         <oasis:entry colname="col2">SH33</oasis:entry>  
         <oasis:entry colname="col3">Climatology</oasis:entry>  
         <oasis:entry colname="col4">Climatology</oasis:entry>  
         <oasis:entry colname="col5">RGB</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">S30_3</oasis:entry>  
         <oasis:entry colname="col2">SH33</oasis:entry>  
         <oasis:entry colname="col3">Climatology</oasis:entry>  
         <oasis:entry colname="col4">IoW</oasis:entry>  
         <oasis:entry colname="col5">RGB</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">S30_4</oasis:entry>  
         <oasis:entry colname="col2">SH33</oasis:entry>  
         <oasis:entry colname="col3">E-HYPE</oasis:entry>  
         <oasis:entry colname="col4">Climatology</oasis:entry>  
         <oasis:entry colname="col5">RGB</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">S30_5</oasis:entry>  
         <oasis:entry colname="col2">SF51</oasis:entry>  
         <oasis:entry colname="col3">E-HYPE</oasis:entry>  
         <oasis:entry colname="col4">IoW</oasis:entry>  
         <oasis:entry colname="col5">PDWL</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table><table-wrap-foot><p>CNTL is the CO5 control. SF51 refers to 51 SF levels.
SH33 refers to 33 SH levels.
IoW refers to data from the IoW NSBS GETM model of the Baltic <xref ref-type="bibr" rid="bib1.bibx10" id="paren.34"/>.
RGB is the default tri-band light attenuation scheme in NEMO <xref ref-type="bibr" rid="bib1.bibx19" id="paren.35"/>.
PDWL refers to the single-band scheme that varies attenuation in proportion to sea bed depth <xref ref-type="bibr" rid="bib1.bibx14" id="paren.36"/>.   </p></table-wrap-foot></table-wrap>

      <p>The shorter CO4 experiments in <xref ref-type="bibr" rid="bib1.bibx28" id="normal.37"/> used direct fluxes from
NWP atmospheric forcing at v3.2 of NEMO. The Met Office NWP forcing dataset
only covers November 2006–2012. Thus, to investigate the effect of the
different surface forcing,
a second set of experiments was integrated.  The key differences are shown in Table <xref ref-type="table" rid="Ch1.T3"/>.</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T3"><caption><p>The 5-year sensitivity experiments.</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="5">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="left"/>
     <oasis:colspec colnum="3" colname="col3" align="left"/>
     <oasis:colspec colnum="4" colname="col4" align="left"/>
     <oasis:colspec colnum="5" colname="col5" align="left"/>
     <oasis:thead>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1">EXP</oasis:entry>  
         <oasis:entry colname="col2">NEMO</oasis:entry>  
         <oasis:entry colname="col3">Invbar</oasis:entry>  
         <oasis:entry colname="col4">Boundary data</oasis:entry>  
         <oasis:entry colname="col5">SBC</oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>  
         <oasis:entry colname="col1">S5_1</oasis:entry>  
         <oasis:entry colname="col2">v3.4</oasis:entry>  
         <oasis:entry colname="col3">No</oasis:entry>  
         <oasis:entry colname="col4">ORCA025</oasis:entry>  
         <oasis:entry colname="col5">NWP</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">S5_2</oasis:entry>  
         <oasis:entry colname="col2">v3.4</oasis:entry>  
         <oasis:entry colname="col3">Yes</oasis:entry>  
         <oasis:entry colname="col4">ORCA025</oasis:entry>  
         <oasis:entry colname="col5">NWP</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">S5_3</oasis:entry>  
         <oasis:entry colname="col2">v3.2</oasis:entry>  
         <oasis:entry colname="col3">No</oasis:entry>  
         <oasis:entry colname="col4">ORCA025</oasis:entry>  
         <oasis:entry colname="col5">NWP</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">S5_4</oasis:entry>  
         <oasis:entry colname="col2">v3.4</oasis:entry>  
         <oasis:entry colname="col3">No</oasis:entry>  
         <oasis:entry colname="col4">NATL12</oasis:entry>  
         <oasis:entry colname="col5">NWP</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">S5_5</oasis:entry>  
         <oasis:entry colname="col2">v3.4</oasis:entry>  
         <oasis:entry colname="col3">No</oasis:entry>  
         <oasis:entry colname="col4">ORCA025</oasis:entry>  
         <oasis:entry colname="col5">ERAI</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table><table-wrap-foot><p>
All 5-year experiments use the single-band light attenuation of <xref ref-type="bibr" rid="bib1.bibx14" id="normal.38"/>.
S5_1–S5_4 use directly specified fluxes
from the Met Office NWP model.
S5_5 uses ERA-Interim (ERAI) derived fluxes as in the CO5 control.
Versions v3.2 and v3.4 refer to the base version of NEMO.
Invbar  specifies whether the inverse barometer effect is
added at the boundary or not. ORCA025 and NATL12 refer to
the source model data used for the open lateral boundary conditions.
</p></table-wrap-foot></table-wrap>

      <p>This second set of experiments also determines the difference between
upgrading the NEMO code and keeping all other parameters as similar as is
feasible. In the CO4 experiments, there was also a bug involving the
application of the inverse barometer at the lateral boundaries, and its effect
is explored in the 5-year experiments by re-inclusion in one v3.4
experiment.</p>
<sec id="Ch1.S4.SS1">
  <title>Model initialisation and forcing</title>
      <p>CO5 was initialised in January 1981 by interpolating temperature and salinity
fields from the <inline-formula><mml:math id="M40" display="inline"><mml:mrow><mml:mn mathvariant="normal">1</mml:mn><mml:mo>/</mml:mo><mml:msup><mml:mn mathvariant="normal">4</mml:mn><mml:mo>∘</mml:mo></mml:msup></mml:mrow></mml:math></inline-formula> ORCA025 hindcast of the standard global ocean
configuration GO5.0 <xref ref-type="bibr" rid="bib1.bibx24" id="paren.39"/>. GO5.0 was itself initialised from a mean of
the EN3 monthly objective analysis <xref ref-type="bibr" rid="bib1.bibx16" id="paren.40"/> and integrated from 1976 to
2005. The lateral open ocean boundary conditions for 1981 to 1989
were also taken from the GO5.0 hindcast. However, the boundary conditions
from 1989 onwards were taken from the Global Seasonal Forecast system version
5 (GLOSEA5) <xref ref-type="bibr" rid="bib1.bibx22" id="paren.41"/>. GLOSEA5 was chosen for this period as it includes
data assimilation. Unfortunately, there was no continuous run of GLOSEA5 that
covered all of 1989–2012. Instead there were only two separate runs of
GLOSEA5 available. The first GLOSEA5 run covered 1989–2003 and the second
covered 2003–2012. The different global models all had different mean sea
surface height (SSH) which needed to be matched as close as feasible to limit
jumps at the cross-over dates. Furthermore, both the GO5.0 hindcast and the
first 4 years of the GLOSEA5 integration have substantial
drifts that needed to be removed.
Details on the drift removal are given in Appendix <xref ref-type="sec" rid="App1.Ch1.S2"/>.
From 1993 onwards, GLOSEA5 is constrained by assimilation of altimeter data,
and no SSH drift removal is required over this period. NSBS GETM data at 1
nautical mile resolution were made available from IoW for the years
2000–2012. For years prior to this, an annual climatology was created based
on the 2000–2012 NSBS GETM data. In the control run, river forcings from
E-HYPE data are utilised for the full 30-year hindcast. The sensitivity
experiments include hindcasts with the climatological rivers and
climatological Baltic boundary
to understand the impacts of the newer inputs.</p><?xmltex \hack{\newpage}?>
</sec>
</sec>
<sec id="Ch1.S5">
  <title>Results</title>
<sec id="Ch1.S5.SS1">
  <title>Tidal harmonics</title>
      <p>The co-tidal charts of the M2 SSH tidal harmonic, as analysed from CO4 and
CO5,
are given in Fig. <xref ref-type="fig" rid="Ch1.F5"/>. Overall, the general representation is
fairly similar. CO4 and CO5 broadly agree with amphidrome positions derived
from observations such as in <xref ref-type="bibr" rid="bib1.bibx15" id="normal.42"/>. Whilst the position of
degenerate amphidrome in southern Norway in CO5 may appear to align more
closely with the observations, it must be noted that the data sparsity in
this region is significant, and thus there is large uncertainty in the
location of the degenerate amphidrome. In any case, it is found that the
change in the land–sea mask from CO4 to CO5 due to the new Baltic boundary
condition is the main driver behind the shift in the amphidrome rather than a
targeted model improvement for the amphidrome's position. Two almost
identical integrations of CO5 with and without
the Baltic boundary masking were integrated.
In the integration with the CO4 mask, the amphidrome
returns to the position calculated in CO4.</p>
      <p>Harmonic analysis of CO5 surface elevation is compared against
tide gauge and bottom pressure data from the British Oceanographic Data Centre (BODC).
Root mean square errors (RMSEs) of model SSH amplitude and phase are shown in
Tables <xref ref-type="table" rid="Ch1.T4"/> and <xref ref-type="table" rid="Ch1.T5"/>.</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T4"><caption><p>Elevation RMSE of amplitude in centimetres as compared to observations.
</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="6">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="right"/>
     <oasis:colspec colnum="3" colname="col3" align="right"/>
     <oasis:colspec colnum="4" colname="col4" align="right"/>
     <oasis:colspec colnum="5" colname="col5" align="right"/>
     <oasis:colspec colnum="6" colname="col6" align="right"/>
     <oasis:thead>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">M2</oasis:entry>  
         <oasis:entry colname="col3">S2</oasis:entry>  
         <oasis:entry colname="col4">K1</oasis:entry>  
         <oasis:entry colname="col5">O1</oasis:entry>  
         <oasis:entry colname="col6">N2</oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>  
         <oasis:entry colname="col1">CO4</oasis:entry>  
         <oasis:entry colname="col2">10.3</oasis:entry>  
         <oasis:entry colname="col3">3.7</oasis:entry>  
         <oasis:entry colname="col4">1.8</oasis:entry>  
         <oasis:entry colname="col5">1.9</oasis:entry>  
         <oasis:entry colname="col6">2.9</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">CO5</oasis:entry>  
         <oasis:entry colname="col2">11.4</oasis:entry>  
         <oasis:entry colname="col3">4.5</oasis:entry>  
         <oasis:entry colname="col4">2.0</oasis:entry>  
         <oasis:entry colname="col5">1.9</oasis:entry>  
         <oasis:entry colname="col6">3.4</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">CO5*</oasis:entry>  
         <oasis:entry colname="col2">9.5</oasis:entry>  
         <oasis:entry colname="col3">4.0</oasis:entry>  
         <oasis:entry colname="col4">1.8</oasis:entry>  
         <oasis:entry colname="col5">1.6</oasis:entry>  
         <oasis:entry colname="col6">3.3</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table><table-wrap-foot><p>CO5* refers to CO5 with lower reference density and time-splitting bug fix.</p></table-wrap-foot></table-wrap>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T5"><caption><p>Elevation RMSE of phase in degrees as compared to observations.</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="6">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="right"/>
     <oasis:colspec colnum="3" colname="col3" align="right"/>
     <oasis:colspec colnum="4" colname="col4" align="right"/>
     <oasis:colspec colnum="5" colname="col5" align="right"/>
     <oasis:colspec colnum="6" colname="col6" align="right"/>
     <oasis:thead>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1"/>  
         <oasis:entry colname="col2">M2</oasis:entry>  
         <oasis:entry colname="col3">S2</oasis:entry>  
         <oasis:entry colname="col4">K1</oasis:entry>  
         <oasis:entry colname="col5">O1</oasis:entry>  
         <oasis:entry colname="col6">N2</oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>  
         <oasis:entry colname="col1">CO4</oasis:entry>  
         <oasis:entry colname="col2">14.7</oasis:entry>  
         <oasis:entry colname="col3">12.8</oasis:entry>  
         <oasis:entry colname="col4">17.1</oasis:entry>  
         <oasis:entry colname="col5">15.7</oasis:entry>  
         <oasis:entry colname="col6">21.6</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">CO5</oasis:entry>  
         <oasis:entry colname="col2">15.5</oasis:entry>  
         <oasis:entry colname="col3">15.1</oasis:entry>  
         <oasis:entry colname="col4">18.7</oasis:entry>  
         <oasis:entry colname="col5">14.7</oasis:entry>  
         <oasis:entry colname="col6">20.6</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">CO5*</oasis:entry>  
         <oasis:entry colname="col2">12.6</oasis:entry>  
         <oasis:entry colname="col3">11.8</oasis:entry>  
         <oasis:entry colname="col4">15.4</oasis:entry>  
         <oasis:entry colname="col5">14.8</oasis:entry>  
         <oasis:entry colname="col6">19.2</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table><table-wrap-foot><p>CO5* refers to CO5 with lower reference density and time-splitting bug fix.</p></table-wrap-foot></table-wrap>

      <p>The CO5 configuration, as used in all sensitivity experiments in this paper,
has a slightly larger RMSE in both amplitude and phase compared to CO4.
Two issues behind this increase in error were found. One was due to an order
of calculation bug in the time splitting in CO5. This resulted in a small
error in the surface pressure gradient term. The second was in relation to
the reference density within NEMO. In the CO4 configuration, the reference
density was 1027 <inline-formula><mml:math id="M41" display="inline"><mml:mi mathvariant="normal">kg</mml:mi></mml:math></inline-formula> <inline-formula><mml:math id="M42" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula><inline-formula><mml:math id="M43" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula>. However, in CO5, the NEMO v3.4
default of 1035 <inline-formula><mml:math id="M44" display="inline"><mml:mi mathvariant="normal">kg</mml:mi></mml:math></inline-formula> <inline-formula><mml:math id="M45" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula><inline-formula><mml:math id="M46" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> was used. When these were
corrected for, CO5 slightly improves upon CO4 when compared to the standard
observations. To understand if these changes have any significant impact on
the control and reanalysis, a further experiment with the changes was
integrated. No significant difference in mean temperature or salinity fields
was found.</p>

      <fig id="Ch1.F5" specific-use="star"><caption><p>M2 co-tidal charts. <bold>(a)</bold> CO4, NEMO v3.2. <bold>(b)</bold> CO5,
NEMO v3.4. </p></caption>
          <?xmltex \igopts{width=472.315748pt}?><graphic xlink:href="https://gmd.copernicus.org/articles/10/2947/2017/gmd-10-2947-2017-f05.png"/>

        </fig>

</sec>
<sec id="Ch1.S5.SS2">
  <title>Surface biases</title>
<sec id="Ch1.S5.SS2.SSS1">
  <title>Seasonal SST biases</title>
      <p>The mean seasonal model SST from 1985 to 2004 is compared with remotely sensed
products. These include the National Oceanic and Atmospheric Administration
(NOAA) Advanced Very High Resolution Radiometer (AVHRR) product
<xref ref-type="bibr" rid="bib1.bibx4" id="paren.43"/> and the European Space Agency (ESA) Climate Change
Initiative (CCI) product <xref ref-type="bibr" rid="bib1.bibx25" id="paren.44"/>. The period 1985–2004 is chosen for
two reasons. First, it allows for the CO5 hindcast to be spun up from rest in
1981. Secondly, it presents a common period with which to compare the POLCOMS
hindcast that ends in 2005.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F6" specific-use="star"><caption><p>The difference between the mean seasonal model SST and the mean
satellite SST for 1985–2004. <bold>(a)</bold> CO5 December–January–February
(DJF) bias, <bold>(b)</bold> CO5 spring March–April–May (MAM) bias,
<bold>(c)</bold> CO5 summer June–July–August (JJA) bias, <bold>(d)</bold> CO5
autumn bias September–October–November (SON), <bold>(e)</bold> POLCOMS (POLC)
winter (DJF) bias, <bold>(f)</bold> POLC spring (MAM) bias, <bold>(g)</bold> POLC
summer (JJA) bias and <bold>(h)</bold> POLC autumn bias (SON). </p></caption>
            <?xmltex \igopts{width=472.315748pt}?><graphic xlink:href="https://gmd.copernicus.org/articles/10/2947/2017/gmd-10-2947-2017-f06.png"/>

          </fig>

      <p>Figure <xref ref-type="fig" rid="Ch1.F6"/> compares the CO5 control and POLCOMS hindcast SST bias
against the AVHRR data. The largest bias in CO5 SST is the cold bias
extending from eastern Iceland south-eastwards to the Faroe–Shetland Channel
(FSC) and from the FSC north-westwards to the northern boundary of the domain.
This SST bias is less apparent in summer as seen in Fig. <xref ref-type="fig" rid="Ch1.F6"/>c. The
reduction in the bias might be caused by over-stratification in summer. The
regions immediately surrounding the cold bias area appear to be warm biased
in summer. This suggests the cold bias may be of a remote origin such as the
boundary condition. Elsewhere off shelf there is a smaller cold bias in
winter, spring and autumn. Along the Celtic shelf break, there is a slight
warm bias. The model is probably underestimating the cold water surface
signal associated
with enhanced vertical mixing at the shelf break.  In summer, off shelf southward of 50<inline-formula><mml:math id="M47" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N, CO5 appears to be too warm.
On shelf, CO5 SST is slightly cold biased in most regions for most seasons.</p>
      <p>However, there are some warm biases, particularly in summer. The Southern
Bight, the Western Isles of Scotland and the western Irish Sea all have
summertime warm biases. The English Channel also has a warm SST bias in
autumn.</p>
      <p>Figure <xref ref-type="fig" rid="Ch1.F6"/>e–h show the equivalent seasonal SST bias for the
POLCOMS hindcast. POLCOMS also has a large cold bias from Iceland to the FSC
and from the FSC to the northern boundary in winter,
spring and to some extent in autumn.
However, the POLCOMS SST cold bias appears to be more extensive. It also
extends south-westwards from the FSC to roughly the Porcupine Bank. Near the
western boundary, there is also a significant warm SST bias in POLCOMS north
of 55<inline-formula><mml:math id="M48" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N in winter. Off shelf in summer, there is a large warm
bias in POLCOMS across much of the domain. However, there is also a large
summertime SST cold bias in the Norwegian Trench, the Skagerrak and the
Kattegat.</p>
      <p>In summary, the CO5 control hindcast appears to have a much smaller SST bias
than the preceding POLCOMS hindcast. One particularly large bias in CO5 is
the large cold bias in the northern part of the domain
which is also present in POLCOMS.
This bias is explored further with comparisons against temperature and
salinity profiles, as well as climatology. CO5 does appear to be too warm off
shelf in summer but much less so than POLCOMS. On shelf, CO5 is generally
slightly cold biased, whereas POLCOMS alternates from a large wintertime cold
bias to a large summertime warm bias. POLCOMS is too cold in the Norwegian
Trench during summer, while CO5 appears to do reasonably well there.</p>
</sec>
<sec id="Ch1.S5.SS2.SSS2">
  <title>Surface salinity biases</title>

      <?xmltex \floatpos{t}?><fig id="Ch1.F7" specific-use="star"><caption><p>Mean model sea surface salinity (SSS) differences 1985–2004 from
WOA13, KLIWAS and EN4: <bold>(a)</bold> CO5 – WOA13 climatology, <bold>(b)</bold>
POLCOMS – WOA13 climatology, <bold>(c)</bold> O5 – EN4, <bold>(d)</bold> POLCOMS –
EN4, <bold>(e)</bold> CO5 – KLIWAS North Sea climatology, <bold>(f)</bold> POLCOMS
– KLIWAS North Sea climatology, <bold>(g)</bold> CO5 – EN4 in the North Sea and
<bold>(h)</bold> POLCOMS – EN4 in the North Sea. </p></caption>
            <?xmltex \igopts{width=472.315748pt}?><graphic xlink:href="https://gmd.copernicus.org/articles/10/2947/2017/gmd-10-2947-2017-f07.png"/>

          </fig>

      <p>The mean sea surface salinity (SSS) of CO5 for 1985–2004 and the POLCOMS
hindcast are compared against the World Ocean Atlas 2013 (WOA13) global
climatology <xref ref-type="bibr" rid="bib1.bibx40" id="paren.45"/>, the KLIWAS North Sea climatology (KLIWAS)
<xref ref-type="bibr" rid="bib1.bibx2" id="paren.46"/> and EN4 <xref ref-type="bibr" rid="bib1.bibx9" id="paren.47"/> profile data in Fig. <xref ref-type="fig" rid="Ch1.F7"/>. A
similar pattern in negative SSS bias as SST bias from Iceland to the FSC and
to the northern boundary is present in CO5. With the exception of this
northern region, CO5 off shelf is in reasonably good agreement with both the
climatology and the mean profiles. However, POLCOMS appears too fresh off
shelf except along the western French coast, indicating an offset in surface
salinity between CO5 and POLCOMS. On the shelf, CO5 is in general slightly too
saline. In particular, the Irish Sea is saline biased in CO5 and indicates
the E-HYPE freshwater flux may be too small there.</p>
      <p>Both CO5 and POLCOMS have large SSS biases compared to the climatologies and
profiles in the Norwegian Trench. POLCOMS is too saline in the Norwegian
Trench, while the salinity bias in CO5 is a dipole:
near the Norwegian coast it is too fresh and near
the western limb of the Norwegian Trench it is too saline. In POLCOMS, not
only are there fewer vertical levels but the vertical resolution near the
surface is proportional to the ocean depth as in CO4. Consequently, compared
to CO5, the surface resolution in POLCOMS in the Norwegian Trench is much
reduced. The surface resolution in POLCOMS over the Norwegian Trench is
typically 4 to 5 m compared to the uniform 1 m resolution for CO5. This may
account for the much more saline SSS in POLCOMS there. The Baltic boundary in
POLCOMS is also more similar to CO4 than CO5 when using climatological river
points to represent the exchange with the Baltic. The sensitivity experiments
below investigate the effect of both these changes within the NEMO framework.
With regards to the dipole in CO5, the resolution at 7 <inline-formula><mml:math id="M49" display="inline"><mml:mi mathvariant="normal">km</mml:mi></mml:math></inline-formula> is not
sufficient to resolve the intense mixing processes in the trench where
northward-flowing freshwater of Baltic origin along the Norwegian coast
mixes laterally with adjacent incoming southward-flowing saline Atlantic
water. It is anticipated that with increased horizontal resolution, better
representation of eddy-induced mixing may reduce the dipole there.</p>
      <p>POLCOMS and CO5 have biases of opposite signs in the German Bight;
CO5 is too fresh and POLCOMS is too saline.
POLCOMS uses the climatological rivers as in CO4 in contrast to the E-HYPE
rivers used in CO5. Thus, the sensitivity experiments S30_1, S30_2 and
S30_3 that compare the different river sources should help to understand the
difference in this bias. POLCOMS also appears to be too fresh in the Southern
Bight, and this may be contributing to the saline bias in the German Bight.
POLCOMS may not be advecting the Rhine outflow to the east close enough to
the coast. CO5 in contrast appears to be too fresh in the vicinity of the
Rhine outflow.</p>
</sec>
<sec id="Ch1.S5.SS2.SSS3">
  <title>Off-shelf temperature and salinity biases through depth against WOA13 climatology</title>

      <?xmltex \floatpos{t}?><fig id="Ch1.F8" specific-use="star"><caption><p>CO5 and POLCOMS temperature bias compared to WOA13 1985–2005.
Panels <bold>(a)</bold>, <bold>(e)</bold>, <bold>(i)</bold> and <bold>(m)</bold> are
CO5 – WOA13 temperature bias transects along 42, 45, 58 and 63<inline-formula><mml:math id="M50" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N.
Panels <bold>(b)</bold>, <bold>(f)</bold>, <bold>(j)</bold> and <bold>(n)</bold> are
POLCOMS – WOA13 temperature bias transects along 42, 45, 58 and
63<inline-formula><mml:math id="M51" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N. Panels <bold>(c)</bold>, <bold>(g)</bold>, <bold>(k)</bold> and
<bold>(o)</bold> are the CO5 – WOA13 temperature bias at depths 0, 100, 1000 and
2000 <inline-formula><mml:math id="M52" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula>. Panels <bold>(d)</bold>, <bold>(h)</bold>, <bold>(l)</bold> and
<bold>(p)</bold> are the POLCOMS – WOA13 temperature bias at depths 0, 100, 1000
and 2000 <inline-formula><mml:math id="M53" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula>. </p></caption>
            <?xmltex \igopts{width=472.315748pt}?><graphic xlink:href="https://gmd.copernicus.org/articles/10/2947/2017/gmd-10-2947-2017-f08.png"/>

          </fig>

      <p>To assess how CO5 and POLCOMS behave throughout the water column off shelf,
they are compared against WOA13 data.
Figure <xref ref-type="fig" rid="Ch1.F8"/> displays both zonal transects and
depth level temperature biases for 1985–2004
compared  to WOA13.
Both CO5 and POLCOMS temperature biases are included in
Fig. <xref ref-type="fig" rid="Ch1.F8"/>.
Figure <xref ref-type="fig" rid="Ch1.F9"/> is the equivalent salinity plot. As
the mean is for the entire period, seasonal biases such as in the SST plots of
Fig. <xref ref-type="fig" rid="Ch1.F6"/> are not discernible. The location of the transects are
chosen to intersect regions of particularly large bias. Note that these
comparisons use the CMEMS POLCOMS dataset, which was interpolated onto
standard depth levels from the native POLCOMS grid which uses 40 s levels in
the vertical <xref ref-type="bibr" rid="bib1.bibx13" id="paren.48"/>. The interpolated POLCOMS data are
particularly coarse at depth which is reflected in the step-like
nature of the POLCOMS bias plots at depth.
This accounts for some of the differences seen towards the bottom of profiles
in Fig. <xref ref-type="fig" rid="Ch1.F8"/>.</p>
      <p>In Fig. <xref ref-type="fig" rid="Ch1.F8"/>, the first two columns are zonal
transects of difference in the mean temperature from the WOA13 climatology
over the period 1985–2005. The first column is for CO5 and the second
POLCOMS. The geographical extent of the biases highlighted in the transects
is shown for four depths in the last two columns of
Fig. <xref ref-type="fig" rid="Ch1.F8"/>. Both CO5 and POLCOMS have a cold
water bias centred around roughly 1000 <inline-formula><mml:math id="M54" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula> that originates near the
southern boundary away from the relaxation zone. A warm temperature bias
surrounds the cold temperature bias away from the coast. A similar pattern in
salinity bias is shown in Fig. <xref ref-type="fig" rid="Ch1.F9"/>. It appears
the models are diffusing both horizontally and vertically the warm and saline
waters of Mediterranean origin entering the domain from the southern
boundary. The extra diffusion in the relaxation zone and the relatively
coarse vertical resolution of about 100 <inline-formula><mml:math id="M55" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula> at a depth of
1000 <inline-formula><mml:math id="M56" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula> may be contributing to the loss in identity of the
Mediterranean waters. The anomaly is also present in the Bay of Biscay but is
much reduced in CO5 further north.</p>
      <p>In the seasonal SST anomalies, a large cold bias was shown in both CO5 and
POLCOMS in winter. This cold bias is also present with respect to the WOA13
climatology. In CO5 and POLCOMS, it extends down to around 500 <inline-formula><mml:math id="M57" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula>.
There is a warm bias in CO5 along the sea bed of the Iceland–Faroe ridge at
around 500 <inline-formula><mml:math id="M58" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula> and at a similar depth on the Shetland side of the FSC.
The vertical resolution of POLCOMS is quite coarse at this depth. However, it
suggests that at depths greater than 500 <inline-formula><mml:math id="M59" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula> POLCOMS is warm biased in
the FSC and Norwegian Sea, and CO5 appears to be close to the climatology below
500 <inline-formula><mml:math id="M60" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula>. There is a similar pattern in the salinity bias with both CO5
and POLCOMS relatively fresh near the surface in this region. On the other hand,
POLCOMS appears to be slightly fresher than WOA13 off shelf right through
depth for most of the domain. Off shelf, away from Biscay and the northern
boundary, CO5 salinity is quite similar to WOA13.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F9" specific-use="star"><caption><p>CO5 and POLCOMS salinity bias compared to WOA13 for 1985–2005. Panels
<bold>(a)</bold>, <bold>(e)</bold>, <bold>(i)</bold> and <bold>(m)</bold> are CO5 – WOA13
salinity bias transects along 42, 45, 58 and 63<inline-formula><mml:math id="M61" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N. Panels
<bold>(b)</bold>, <bold>(f)</bold>, <bold>(j)</bold> and <bold>(n)</bold> are POLCOMS – WOA13
salinity bias transects along 42, 45, 58 and 63<inline-formula><mml:math id="M62" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N. Panels
<bold>(c)</bold>, <bold>(g)</bold>, <bold>(k)</bold> and <bold>(o)</bold> are the CO5 – WOA13
salinity bias at depths 0, 100, 1000 and 2000 <inline-formula><mml:math id="M63" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula>. Panels <bold>(d)</bold>,
<bold>(h)</bold>, <bold>(l)</bold> and <bold>(p)</bold> are the POLCOMS – WOA13 salinity
bias at depths 0, 100, 1000 and 2000 <inline-formula><mml:math id="M64" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula>. </p></caption>
            <?xmltex \igopts{width=472.315748pt}?><graphic xlink:href="https://gmd.copernicus.org/articles/10/2947/2017/gmd-10-2947-2017-f09.png"/>

          </fig>

</sec>
<sec id="Ch1.S5.SS2.SSS4">
  <title>North Sea temperature and salinity biases through depth</title>

      <?xmltex \floatpos{t}?><fig id="Ch1.F10" specific-use="star"><caption><p>North Sea temperature bias compared to EN4 and the KLIWAS
climatology for summer (JJA). Panels <bold>(a)</bold>–<bold>(d)</bold> compare CO5
and EN4 at 10, 30 and 40 <inline-formula><mml:math id="M65" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula> and along a transect at 56<inline-formula><mml:math id="M66" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N.
Panels <bold>(e)</bold>–<bold>(h)</bold> compare CO5 and KLIWAS climatology at 10,
30 and 40 <inline-formula><mml:math id="M67" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula> and along a transect at 56<inline-formula><mml:math id="M68" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N. Panels
<bold>(e)</bold>–<bold>(h)</bold> compare POLCOMS and KLIWAS climatology at
10, 30 and 40 <inline-formula><mml:math id="M69" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula> and along a transect at
56<inline-formula><mml:math id="M70" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N. Panels <bold>(m)</bold>–<bold>(o)</bold> are transects through
depth for each case along longitude 2.8<inline-formula><mml:math id="M71" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> E. </p></caption>
            <?xmltex \igopts{width=472.315748pt}?><graphic xlink:href="https://gmd.copernicus.org/articles/10/2947/2017/gmd-10-2947-2017-f10.png"/>

          </fig>

      <p>The KLIWAS climatology for the NWS in combination with EN4 provides an
alternative to WOA13 for evaluation of the models on the shelf itself.
Figures <xref ref-type="fig" rid="Ch1.F10"/> and
<xref ref-type="fig" rid="Ch1.F11"/> compare CO5 with both the KLIWAS
climatology and the EN4 data over the period 1985–2004. A comparison of
POLCOMS against KLIWAS is also included as a reference.
Figure <xref ref-type="fig" rid="Ch1.F10"/> focuses on the summer months
when there is seasonal thermal stratification, while
Fig. <xref ref-type="fig" rid="Ch1.F11"/> is the salinity mean for all seasons.
Including all seasons allows for a larger number of in situ profiles to
compare against. In addition to biases at depth levels of 10, 30 and
40 <inline-formula><mml:math id="M72" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula>, transects are taken through areas of significant bias to give
an overview of the vertical structure in the model bias.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F11" specific-use="star"><caption><p>North Sea salinity bias compared to annual EN4 and KLIWAS
climatology. Panels <bold>(a)</bold>–<bold>(d)</bold> compare CO5 and EN4 at 6, 20
and 30 <inline-formula><mml:math id="M73" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula> and along a transect at 58<inline-formula><mml:math id="M74" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N.
Panels <bold>(e)</bold>–<bold>(h)</bold> compare CO5 and KLIWAS climatology at 6,
20 and 30 <inline-formula><mml:math id="M75" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula> and along a transect at 58<inline-formula><mml:math id="M76" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N.
Panels <bold>(e)</bold>–<bold>(h)</bold> compare POLCOMS and KLIWAS climatology at
6, 20 and 30 <inline-formula><mml:math id="M77" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula> and along a transect at 58<inline-formula><mml:math id="M78" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N.
Panels <bold>(m)</bold>–<bold>(o)</bold> are transects through depth for each case
along longitude 4.8<inline-formula><mml:math id="M79" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> E. </p></caption>
            <?xmltex \igopts{width=472.315748pt}?><graphic xlink:href="https://gmd.copernicus.org/articles/10/2947/2017/gmd-10-2947-2017-f11.png"/>

          </fig>

      <p>Generally, the structure of the temperature bias between CO5 and EN4 is in
reasonable agreement with the structure of the bias between CO5 and the
KLIWAS climatology. In the seasonally stratified areas of the North Sea, CO5
compares favourably near the surface compared to POLCOMS. POLCOMS there is
significantly warm biased. Immediately below the thermocline, both CO5 and
POLCOMS are cold biased with the cold bias in POLCOMS being somewhat larger
than CO5. In CO5, the cold bias does not extend to the bed and in fact
reverses sign to be warm biased near the bed, whilst in POLCOMS the cold bias
reduces towards the bed with only a small bias remaining at the sea floor.
The light attenuation schemes in CO5 and POLCOMS are quite different and may
partially explain why POLCOMS is more warm biased at the surface and more
cold biased at depth. The light scheme used in POLCOMS (PDWL) is also
implemented in CO4 and is included in the sensitivity experiments to enable
its impact to be assessed.</p>
      <p>The CO5 salinity bias against EN4 is also broadly in agreement with the bias
against the KLIWAS climatology. As in the surface plots of
Fig. <xref ref-type="fig" rid="Ch1.F7"/>, over most of the North Sea, CO5 is slightly too saline
through depth. Along the coasts of Holland, Germany and Denmark, CO5 is
clearly too fresh, suggesting too much riverine input as discussed earlier.
Away from the coasts, POLCOMS is in fairly good agreement with EN4 and KLIWAS
while just slightly fresher at depth. The transects in
Fig. <xref ref-type="fig" rid="Ch1.F11"/> are taken to go through the Norwegian
Trench and the Rhine plume. CO5 is shown to be roughly 0.5 too fresh above
20 <inline-formula><mml:math id="M80" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula> in the Norwegian Trench near the coast of Norway, while below
20 <inline-formula><mml:math id="M81" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula> CO5 is slightly too saline. The warmer and more saline water
from the Atlantic appears to make CO5 too saline along the rim of the
Norwegian Trench. In contrast, POLCOMS is shown to be typically greater than
1.1 too saline above 20 <inline-formula><mml:math id="M82" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula> in the Norwegian Trench, while below
40 <inline-formula><mml:math id="M83" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula>, POLCOMS switches from the large saline bias to a significantly
fresh bias. It appears that CO5 is representing the haline stratification in
the Norwegian Trench with greater fidelity than POLCOMS. Both the vertical
resolution and the Baltic boundary condition may play some role in this and
are included in the sensitivity experiments that follow.</p>
</sec>
</sec>
<sec id="Ch1.S5.SS3">
  <title>The 30-year sensitivity runs</title>
<sec id="Ch1.S5.SS3.SSS1">
  <title>Vertical levels and stretching function</title>

      <?xmltex \floatpos{t}?><fig id="Ch1.F12"><caption><p>Comparison of mean salinity at 5 <inline-formula><mml:math id="M84" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula> between CO5 with 51
vertical levels using the Siddorn and Furner
stretching function (CNTL) and 33 vertical levels using the Song and Haidvogel stretching function (S30_1).
The hashed area in the Kattegat indicates the interface to Baltic NSBS model data.
</p></caption>
            <?xmltex \igopts{width=227.622047pt}?><graphic xlink:href="https://gmd.copernicus.org/articles/10/2947/2017/gmd-10-2947-2017-f12.png"/>

          </fig>

      <p>The effect of the changes of surface vertical resolution between CO4 and CO5
is shown in Fig. <xref ref-type="fig" rid="Ch1.F2"/>. Sensitivity experiment S30_1 is
exactly the same as the control (CNTL) except it uses 33 SH vertical levels
instead of 51 SF levels. Although there are some small changes in summertime
stratification off the shelf,
the most dramatic change concerns the surface
salinity in the Norwegian Trench. Figure <xref ref-type="fig" rid="Ch1.F12"/> is the
difference in salinity at 5 <inline-formula><mml:math id="M85" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula> between the control experiment CNTL
(SF51) and sensitivity experiment S30_1 (SH33). The extra vertical
resolution in the control run results in less diffusion of the surface fresh
layer with depth. The POLCOMS hindcast also has much less vertical resolution
at the surface than CO5, which may be one factor underlying its saline bias
in the surface waters of the Norwegian Trench.</p>
</sec>
<sec id="Ch1.S5.SS3.SSS2">
  <title>Baltic and rivers</title>

      <?xmltex \floatpos{t}?><fig id="Ch1.F13"><caption><p>Comparing SSS using climatological river and Baltic inputs against
E-HYPE rivers and IoW Baltic. Panel <bold>(a)</bold> shows 33 SH levels with E-HYPE
rivers and IoW Baltic (S30_1) vs. EN4. Panel <bold>(b)</bold> shows 33 SH levels with
climatological rivers and climatological Baltic (S30_2) vs. EN4. Panel
<bold>(c)</bold> shows climatological rivers minus E-HYPE rivers (S30_3–S30_1). Panel
<bold>(d)</bold> shows climatological Baltic – IoW Baltic (S30_4–S30_1). </p></caption>
            <?xmltex \igopts{width=236.157874pt}?><graphic xlink:href="https://gmd.copernicus.org/articles/10/2947/2017/gmd-10-2947-2017-f13.png"/>

          </fig>

      <?xmltex \floatpos{t}?><fig id="Ch1.F14"><caption><p>CO5 mean transport across selected NOOS transects surrounding the
North Sea and
the CO5 transport field shown  only every fourth grid point for clarity.</p></caption>
            <?xmltex \igopts{width=236.157874pt}?><graphic xlink:href="https://gmd.copernicus.org/articles/10/2947/2017/gmd-10-2947-2017-f14.png"/>

          </fig>

      <p>Both the river forcing and Baltic boundary condition are changed in CO5 from
climatological inputs to E-HYPE riverine inputs and IoW Baltic boundary data.
The 30-year sensitivity experiments S30_2 and S30_1
are compared
in Fig. <xref ref-type="fig" rid="Ch1.F13"/>.
S30_1 is a 33-level version of the CO5 control but with exactly the same
E-HYPE rivers and IoW Baltic boundary. S30_2 is exactly the same as S30_1
except that it uses the older climatological inputs for rivers and Baltic
boundary as used in CO4. Figure <xref ref-type="fig" rid="Ch1.F13"/>a shows the
surface salinity bias against EN4 data for S30_1.
Figure <xref ref-type="fig" rid="Ch1.F13"/>b is the same but for S30_2 and shows a
large reduction in the freshwater bias in the German Bight.
Figure <xref ref-type="fig" rid="Ch1.F13"/>c compares experiment S30_3 with S30_1
to show differences created by the change in rivers alone. For most of
continental Europe, the E-HYPE rivers clearly have a greater discharge as
shown in Fig. <xref ref-type="fig" rid="Ch1.F4"/>. The difference is
pronounced in the German Bight and along the Norwegian coast and is likely
contributing to the fresh bias in CO5 compared to EN4 data there. Another
possible source of salinity bias could be incorrect transports and
representation of the North Sea circulation. Figure
<xref ref-type="fig" rid="Ch1.F14"/> shows a background field of mean transport
in the North Sea and also the mean transport across selected NOOS transects
into and out of the North Sea. The calculated transports are similar to
reported values from observational estimates as shown in
Table <xref ref-type="table" rid="Ch1.T6"/>.</p>

<?xmltex \floatpos{t}?><table-wrap id="Ch1.T6" specific-use="star"><caption><p>Net transports across NOOS sections.</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="5">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="right"/>
     <oasis:colspec colnum="3" colname="col3" align="left"/>
     <oasis:colspec colnum="4" colname="col4" align="right"/>
     <oasis:colspec colnum="5" colname="col5" align="right"/>
     <oasis:thead>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1">Name</oasis:entry>  
         <oasis:entry colname="col2">NOOS ID</oasis:entry>  
         <oasis:entry colname="col3">Paper reference</oasis:entry>  
         <oasis:entry colname="col4">Observational value</oasis:entry>  
         <oasis:entry colname="col5">CO5 value</oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>  
         <oasis:entry colname="col1">Feie–Shetland west</oasis:entry>  
         <oasis:entry colname="col2">1</oasis:entry>  
         <oasis:entry colname="col3">
                      <xref ref-type="bibr" rid="bib1.bibx29" id="normal.49"/>
                    </oasis:entry>  
         <oasis:entry colname="col4">0.6 <inline-formula><mml:math id="M86" display="inline"><mml:mi mathvariant="normal">Sv</mml:mi></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col5">0.54 <inline-formula><mml:math id="M87" display="inline"><mml:mi mathvariant="normal">Sv</mml:mi></mml:math></inline-formula></oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Feie–Shetland east</oasis:entry>  
         <oasis:entry colname="col2">2</oasis:entry>  
         <oasis:entry colname="col3">
                      <xref ref-type="bibr" rid="bib1.bibx29" id="normal.50"/>
                    </oasis:entry>  
         <oasis:entry colname="col4">0.7–1.1 <inline-formula><mml:math id="M88" display="inline"><mml:mi mathvariant="normal">Sv</mml:mi></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col5">1.11 <inline-formula><mml:math id="M89" display="inline"><mml:mi mathvariant="normal">Sv</mml:mi></mml:math></inline-formula></oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Orkney–Shetland</oasis:entry>  
         <oasis:entry colname="col2">3</oasis:entry>  
         <oasis:entry colname="col3">
                      <xref ref-type="bibr" rid="bib1.bibx29" id="normal.51"/>
                    </oasis:entry>  
         <oasis:entry colname="col4">0.3 <inline-formula><mml:math id="M90" display="inline"><mml:mi mathvariant="normal">Sv</mml:mi></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col5">0.4 <inline-formula><mml:math id="M91" display="inline"><mml:mi mathvariant="normal">Sv</mml:mi></mml:math></inline-formula></oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">Dover Strait</oasis:entry>  
         <oasis:entry colname="col2">13</oasis:entry>  
         <oasis:entry colname="col3">
                      <xref ref-type="bibr" rid="bib1.bibx30" id="normal.52"/>
                    </oasis:entry>  
         <oasis:entry colname="col4">0.09 <inline-formula><mml:math id="M92" display="inline"><mml:mi mathvariant="normal">Sv</mml:mi></mml:math></inline-formula></oasis:entry>  
         <oasis:entry colname="col5">0.091 <inline-formula><mml:math id="M93" display="inline"><mml:mi mathvariant="normal">Sv</mml:mi></mml:math></inline-formula></oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table></table-wrap>

      <p>Around parts of the coast of the UK, the E-HYPE river discharge in some
regions is actually slightly less than the climatology or only slightly
greater in others. This is also reflected in the difference of salinity
shown in Fig. <xref ref-type="fig" rid="Ch1.F13"/>c. Combining the correlation
between areas of larger E-HYPE river discharge than climatological rivers and
the larger salinity biases in CO5 with what appears
reasonable transports in CO5, it seems likely that the E-HYPE rivers
are the first-order source of the salinity biases observed in CO5.</p>
      <p>Figure <xref ref-type="fig" rid="Ch1.F13"/>d compares experiment S30_4 with S30_1
to show the impact resulting from the different Baltic boundaries. The
IoW boundary results in a slightly more saline SSS over in the Norwegian
Trench. The effect of the Baltic boundary condition is much smaller than the
freshening due to the E-HYPE rivers resulting in an overall freshening
compared to the climatologies.</p>
</sec>
<sec id="Ch1.S5.SS3.SSS3">
  <title>Light attenuation</title>

      <?xmltex \floatpos{t}?><fig id="Ch1.F15" specific-use="star"><caption><p>Comparison of summertime profiles compared to NEMO's three-band
light attenuation scheme (RGB) and POLCOMS single-band scheme (PDWL). Panel
<bold>(a)</bold> compares CNTL and S30_5 against the mean of profiles in the
seasonally stratified part of the domain on shelf. Panel <bold>(b)</bold>
compares CNTL and S30_5 against the mean of profiles off shelf south of
60<inline-formula><mml:math id="M94" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N. </p></caption>
            <?xmltex \igopts{width=472.315748pt}?><graphic xlink:href="https://gmd.copernicus.org/articles/10/2947/2017/gmd-10-2947-2017-f15.png"/>

          </fig>

      <p>The summertime biases in temperature were shown to be significantly
different between POLCOMS and CO5. Sensitivity experiment S30_5 explores
replacing the light attenuation scheme in CO5 with the PDWL scheme.
Figure <xref ref-type="fig" rid="Ch1.F15"/> compares the control experiment and
experiment S30_5
over the summer.
Figure <xref ref-type="fig" rid="Ch1.F15"/>a compares each run on shelf in regions of
seasonal stratification. Using the PDWL light scheme has three effects: it
increases the warm surface temperature bias, it increases the mid-depth cold
bias and it reduces the bias from 40 <inline-formula><mml:math id="M95" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula> to the bed. The partition of
solar radiation into a penetrating part and a non-penetrating part is dealt
with differently in each scheme and influences the degree of bias at the
surface. In the PDWL scheme, all of the non-penetrating part is added to the
surface layer, while in the RGB scheme there is still a slight penetration of
the quickly attenuating light. The cold bias in both models indicates that
the depth of the thermocline is too shallow, which could be either be due to
the light not penetrating far enough in both schemes or insufficient vertical
mixing. At depth, the PDWL scheme results in less heat being mixed down,
resulting
in a better agreement with the bed temperature as the RGB scheme is biased warm there.
However, in mixed areas on shelf, both models appear to be too warm, which may indicate
a bias in the surface flux forcing.</p>
      <p>Figure <xref ref-type="fig" rid="Ch1.F15"/>b compares each scheme against the mean of
the profiles off shelf south of 60<inline-formula><mml:math id="M96" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N.
Figure <xref ref-type="fig" rid="Ch1.F15"/>b does not show depths below 140 <inline-formula><mml:math id="M97" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula>
as the differences due to light below this depth are negligible.
The large cold bias in the upper layers of the ocean north of
60<inline-formula><mml:math id="M98" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N biases the whole field cold. Thus, to obtain a better
representation of the effect of the light scheme in the absence of large
underlying biases, we restrict the mean to south of 60<inline-formula><mml:math id="M99" display="inline"><mml:msup><mml:mi/><mml:mo>∘</mml:mo></mml:msup></mml:math></inline-formula> N. As the
light penetrates more deeply off shelf in the PDWL light scheme, the warm
bias at the surface is less than the RGB scheme and the cold bias below
20 <inline-formula><mml:math id="M100" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula> is also reduced. Both schemes are similarly cold biased below
60 <inline-formula><mml:math id="M101" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula> where the direct effect of light penetration is small.</p><?xmltex \hack{\newpage}?>
</sec>
</sec>
<sec id="Ch1.S5.SS4">
  <title>The 5-year sensitivity runs</title>
      <p>The shorter CO4 experiments of <xref ref-type="bibr" rid="bib1.bibx28" id="normal.53"/> used different open ocean
boundary conditions and surface boundary conditions relative to the CO5 control
run. To further explore CO4 and CO5 differences whilst using the same forcing
conditions of CO4,
a set of sensitivity experiments for 5 years were undertaken starting in November 2006.
The constraint on the start date is the availability of Met Office NWP flux
data and the open boundary conditions used in CO4 which start from November
2006. All the 5-year experiments as detailed in Table <xref ref-type="table" rid="Ch1.T3"/> have
33
vertical levels with the Song and Haidvogel stretching function <xref ref-type="bibr" rid="bib1.bibx34" id="paren.54"/>.
They also use climatological rivers, climatological Baltic
and the single-band light attenuation scheme implemented in CO4.
The sensitivity of the model to
the vertical coordinate, rivers, the Baltic boundary and the light attenuation
scheme is explored in the 30-year experiments in Sect. <xref ref-type="sec" rid="Ch1.S5.SS3"/>.
They are not shown to have significant impact on the large SST bias from
Iceland to the Faroe Islands. In the following sections, the effects of changed
boundaries and fluxes with an emphasis on the sensitivity of the SST bias to
these changes is detailed.</p>
<sec id="Ch1.S5.SS4.SSS1">
  <title>Inverse barometer and open ocean boundary condition</title>

      <?xmltex \floatpos{t}?><fig id="Ch1.F16" specific-use="star"><caption><p>Isolating the difference in northern SST bias between CO4 and CO5.
Panel <bold>(a)</bold> shows the mean SST difference between the NEMO v3.4 with the inverse barometer
applied to the boundary and without (S5_2–S5_1). Panel <bold>(b)</bold> shows the mean SST
difference between NEMO v3.4 with the inverse barometer applied to the boundary
and NEMO v3.2 (S5_2–S5_3). Panel <bold>(c)</bold> shows the mean SST difference between NEMO
v3.4 with ORCA025 and NATL12 boundary data (S5_4–S5_1). Panel <bold>(d)</bold>
shows the difference between SST RMSE between NEMO v3.4 with the inverse barometer applied to
the boundary and without (S5_2–S5_1). Panel <bold>(e)</bold> shows the difference between SST RMSE
between the NEMO v3.4 with the inverse barometer applied to the boundary and NEMO v3.2
(S5_2–S5_3). Panel <bold>(f)</bold> shows the difference of SST RMSE between NEMO v3.4
with ORCA025 and NATL12 boundary data (S5_4–S5_1). </p></caption>
            <?xmltex \igopts{width=472.315748pt}?><graphic xlink:href="https://gmd.copernicus.org/articles/10/2947/2017/gmd-10-2947-2017-f16.png"/>

          </fig>

      <p>The 5-year sensitivity experiments show that the most significant differences
between CO4 and CO5 are related to the lateral boundary conditions. A bug in
NEMO v3.2 prevented the application of the inverse barometer effect on the
open ocean lateral boundaries. Thus, two sensitivity experiments with NEMO
v3.4 were conducted: S5_1 with this bug deliberately included and S5_2
without. An additional experiment, S5_3, is an equivalent experiment with
exactly the same forcing
but with NEMO v3.2 as the base model.</p>
      <p>The resulting 5-year mean SST difference between S5_1 and S5_2 is shown in
Fig. <xref ref-type="fig" rid="Ch1.F16"/>a. Clearly the switching on or off of the inverse
barometer on the open boundary has a large impact on the SST in the north of
the domain. The difference between the SST RMSE of S5_1 and S5_2 shown in
Fig. <xref ref-type="fig" rid="Ch1.F16"/>d. The much larger RMSE of S5_1 indicates that
the inclusion of the inverse barometer
effect on the boundary considerably reduces the SST skill there.
However, if the inverse barometer is not included on the boundaries, anomalous
northward-flowing boundary jet currents result.
Figure <xref ref-type="fig" rid="Ch1.F16"/>b and e are the equivalent mean and RMSE
differences between S5_2 and S5_3,
which are very similar to that of Fig. <xref ref-type="fig" rid="Ch1.F16"/>a and d.
The difference (not shown) between S5_1 and S5_3 is much smaller. Thus, a
large component of the difference between CO4 and CO5 is the difference in
the application of the inverse barometer effect on the lateral boundary.</p>
      <p><?xmltex \hack{\newpage}?>Another significant difference was the open ocean source data
interpolated onto the open boundaries of CO5 and CO4.
The 30-year sensitivity experiments of CO5 used data from the <inline-formula><mml:math id="M102" display="inline"><mml:mrow><mml:mn mathvariant="normal">1</mml:mn><mml:mo>/</mml:mo><mml:msup><mml:mn mathvariant="normal">4</mml:mn><mml:mo>∘</mml:mo></mml:msup></mml:mrow></mml:math></inline-formula>
global ocean domain (ORCA025). However, CO4 was forced using a
<inline-formula><mml:math id="M103" display="inline"><mml:mrow><mml:mn mathvariant="normal">1</mml:mn><mml:mo>/</mml:mo><mml:msup><mml:mn mathvariant="normal">12</mml:mn><mml:mo>∘</mml:mo></mml:msup></mml:mrow></mml:math></inline-formula> model of the North Atlantic (NATL12). In operational
implementation of CO5, the higher resolution NATL12 model is also used to
derive open boundaries. Sensitivity experiment S5_4 is exactly the same as
S5_1 but replaces the ORCA025-derived boundaries
with boundaries derived from the NATL12 model.
The mean and RMSE SST differences between S5_1 and S5_4 are shown in
Fig. <xref ref-type="fig" rid="Ch1.F16"/>c and f. The NATL12 data result in a warmer SST from
Iceland to the Faroe Islands and a reduced RMSE compared to the ORCA025 data.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F17"><caption><p>GLOSEA5 minus WOA13. Panel <bold>(a)</bold> is mean surface salinity.
Panel <bold>(b)</bold> is the mean surface temperature. </p></caption>
            <?xmltex \igopts{width=236.157874pt}?><graphic xlink:href="https://gmd.copernicus.org/articles/10/2947/2017/gmd-10-2947-2017-f17.png"/>

          </fig>

      <p>The GLOSEA5 surface data are compared against WOA13 in
Fig. <xref ref-type="fig" rid="Ch1.F17"/>. Compared to WOA13, GLOSEA5 is anomalously cold
and fresh along the CO5 boundary of <inline-formula><mml:math id="M104" display="inline"><mml:mrow><mml:msup><mml:mn mathvariant="normal">65</mml:mn><mml:mo>∘</mml:mo></mml:msup></mml:mrow></mml:math></inline-formula> N. This suggests that a
significant component of the northern bias in CO5 originates in the global
model that provides its northern boundary condition.</p>
</sec>
<sec id="Ch1.S5.SS4.SSS2">
  <title>Surface fluxes</title>

      <?xmltex \floatpos{t}?><fig id="Ch1.F18"><caption><p>Comparison of mean SST <bold>(a)</bold> and SSS <bold>(b)</bold> differences
between ERAI fluxes and NWP fluxes (S5_1 vs. S5_5). </p></caption>
            <?xmltex \igopts{width=236.157874pt}?><graphic xlink:href="https://gmd.copernicus.org/articles/10/2947/2017/gmd-10-2947-2017-f18.png"/>

          </fig>

      <p>Another important difference between CO4 and CO5 is the surface fluxes. In
operational implementation, the surface fluxes are taken from the Met Office
NWP model. The experiments in <xref ref-type="bibr" rid="bib1.bibx28" id="normal.55"/> were also forced with NWP
directly prescribed fluxes. However, comparable NWP model data were not
available from before 2006, and thus the longer runs, as in the CO5 control, use
ERAI surface fluxes. Furthermore, the NWP fluxes are directly prescribed in
contrast to the CORE bulk formulae used with ERAI. A Haney correction
<xref ref-type="bibr" rid="bib1.bibx11" id="paren.56"/> must also be applied when using direct fluxes with a
prescribed reference SST as used by the NWP model itself.</p>
      <p>Sensitivity experiment S5_5 is exactly as S5_1 but with ERAI-derived fluxes
instead of NWP fluxes. Figure <xref ref-type="fig" rid="Ch1.F18"/>a and b compare the mean
SST and SSS between S5_5 and S5_1. The SST is almost uniformly warmer with
NWP fluxes than ERAI-derived fluxes, particularly
in the Bay of Biscay, around the coast of the UK and
into the Skagerrak and southern Norwegian Trench.</p>
      <p>However, it should also be noted that because direct fluxes use the Haney
correction, the resulting model SST is indirectly relaxed to the prescribed
SST in a hindcast simulation. Furthermore, in NEMO version 3.2, the surface stress
from direct fluxes was based on absolute wind velocity rather than wind
velocity relative to the moving ocean surface. This has important localised
effects in the vicinity of persistently strong surface currents, such as the
Skagerrak. This sensitivity of the model to relative winds versus absolute
winds using ERAI-derived forcing is also investigated.
Figure <xref ref-type="fig" rid="Ch1.F19"/> is the difference in the mean for 1 year
of surface stress, salinity, current and temperature between using the
relative wind velocity to the ocean surface and the absolute wind
velocity.</p>

      <?xmltex \floatpos{t}?><fig id="Ch1.F19"><caption><p>Comparison between using wind velocity relative to
ocean surface and absolute wind velocity for the 2011 annual mean.
Panel <bold>(a)</bold> shows the difference in surface shear stress in <inline-formula><mml:math id="M105" display="inline"><mml:mi mathvariant="normal">Pa</mml:mi></mml:math></inline-formula>. Panel
<bold>(b)</bold> shows the difference in surface salinity. Panel <bold>(c)</bold> shows the difference in
surface current. Panel <bold>(d)</bold> shows the difference in surface temperature. </p></caption>
            <?xmltex \igopts{width=236.157874pt}?><graphic xlink:href="https://gmd.copernicus.org/articles/10/2947/2017/gmd-10-2947-2017-f19.png"/>

          </fig>

      <p>Furthermore, the  details of the fluxes near coastlines, and particularly the wind stress
in the Skagerrak and southern Norwegian Trench,
are quite different between the lower-resolution ERAI and higher-resolution
NWP fluxes. The differing resolution of the surface forcing and the use of
absolute instead of relative wind stress is thus likely to play a role in the
different sensitivity experiments.</p>
      <p>In Fig. <xref ref-type="fig" rid="Ch1.F18"/>b, it is shown that the experiment with ERAI-derived
forcing is slightly more saline on shelf but significantly fresher in
the Skagerrak and the Norwegian Trench mirroring the SST differences there.
The difference in the shear stress modifies
both the transport of the surface fresh layer out of the Skagerrak
and the transport of relatively saline water from the North Sea into the Skagerrak.
The difference in relative and absolute winds is significant also along the
shelf break from the Shetland Islands northwards. In this case, the effect of using
the absolute wind velocity is to reduce the transport of North Atlantic water
northwards, which results in locally lower mean SST. With respect to the
difference between ERAI-derived forcing and NWP-forced experiments, the
difference in the SST in this local region is reduced. The reduction in the mean
difference of SST is due to the countervailing effects of general domain-wide
cold bias between ERAI-derived forcing and NWP fluxes, and the local cooling
due to using absolute winds with the direct NWP fluxes.</p>
</sec>
</sec>
</sec>
<sec id="Ch1.S6" sec-type="conclusions">
  <title>Summary and discussion</title>
      <p>The details of the standard coastal
ocean model CO5 for the NWS were presented. CO5 was jointly developed by the
Met Office and the National Oceanography Centre. This standard model forms
the basis of the physics component of the current
CMEMS reanalysis of the NWS, which also includes data assimilation.
CO5 is a regional tidal implementation of NEMO version 3.4, building
upon CO4 <xref ref-type="bibr" rid="bib1.bibx28" id="paren.57"/> which used NEMO version 3.2 as the base code. In
this paper, a 30-year physics-only control of CO5 using ERAI-derived surface
forcing and ORCA025 lateral boundary conditions has been assessed against
standard climatologies and observations to understand the impact of model
physics on biases. The assessment compares CO5 to a POLCOMS-based hindcast
over the period 1985–2004, which is a period covered by both hindcasts. A
set of 30-year sensitivity hindcasts has also been assessed to understand
several changes, relative to CO4, introduced into CO5. A further set of
5-year sensitivity experiments focusing on different surface and lateral
boundary conditions has also been investigated.</p>
      <p>Overall the CO5 tides are of comparable quality to CO4. The reference density
of 1035 <inline-formula><mml:math id="M106" display="inline"><mml:mi mathvariant="normal">kg</mml:mi></mml:math></inline-formula> <inline-formula><mml:math id="M107" display="inline"><mml:mi mathvariant="normal">m</mml:mi></mml:math></inline-formula><inline-formula><mml:math id="M108" display="inline"><mml:msup><mml:mi/><mml:mrow><mml:mo>-</mml:mo><mml:mn mathvariant="normal">3</mml:mn></mml:mrow></mml:msup></mml:math></inline-formula> used in the control run slightly degraded
the tidal predictions. The position of the degenerate amphidrome in southern
Norway is slightly changed in CO5 mainly due to a small modification the land–sea
mask originating from a change in the Baltic boundary condition.</p>
      <p>Compared to AVHRR data, CO5 has a large SST bias extending
from Iceland to the FSC.
It is particularly pronounced in winter and partially obscured in summer due
to surface heating. POLCOMS also has a large seasonal cold SST bias in the
region but also a significant warm SST bias domain-wide in summer. In
comparison to the AVHRR observations, CO5 appears to significantly improve
upon the simulation of SST in the POLCOMS hindcast.</p>
      <p>As in the SST, CO5 has a similar pattern of fresh bias in the near-surface
salinity from Iceland to the FSC as well as a large fresh bias in the German
Bight due to E-HYPE rivers and a dipole of surface salinity bias along the
Norwegian Trench that suggests insufficient lateral mixing. POLCOMS, in
contrast, is slightly too saline in the German Bight and uniformly too saline
at the surface along the Norwegian Trench.</p>
      <p>Both CO5 and POLCOMS appear to lose the identity of relatively warm saline
Mediterranean water near the southern boundary of the domain. In CO5, there is
a sponge layer in the boundary relaxation zone where the diffusion is
increased for model stability. Furthermore, the vertical resolution is
focused on the surface and bed and is particularly coarse mid-water in the
deeper parts of the domain. Both of these may be contributing to the apparent
overestimation of
diffusion of this water mass both laterally and vertically.</p>
      <p>In the North Sea, there is a marked difference in the vertical summer
temperature profile between POLCOMS and CO5 in seasonally stratified regions.
Compared to climatology and observations, POLCOMS is much too warm at the
surface, while both POLCOMS and CO5 are too cold mid-water, and CO5 is too
warm towards the bed.</p>
      <p>The single-band light scheme (PDWL) used in POLCOMS and CO4 was seen to
significantly alter the temperature profile in seasonally stratified regions
in CO5. Introducing the PDWL scheme into CO5 leads to a larger warm bias at
the surface and a larger colder
mid-water cold bias  than the CO5 control.
From 40 m to the bed, the PDWL light attenuation scheme resulted in closer
agreement with climatology than the CO5 control run. Both models appear to be
over-stratifying with a very abrupt thermocline. Whilst the light attenuation
scheme may be a component of this error, the vertical mixing will also be an
important contributor and should be a subject of further refinement.</p>
      <p>The sensitivity experiments also explored the significance of changing the
riverine inputs and the Baltic boundary condition. The older climatological
rivers greatly reduce the freshwater bias in the German Bight and also near
the Norwegian coast. It appears that the version of E-HYPE used in CO5 has
too much freshwater discharge from continental Europe. The Baltic boundary
condition used in CO5 results in
slightly more saline surface waters
in the Norwegian Trench. The added variability introduced by the CO5 Baltic
boundary relative to the CO4 climatological boundary
cannot be  assessed by the long-term climatological means used in this paper.
Further site-specific studies in the Kattegat and Skagerrak are required
to evaluate the variability.</p>
      <p>The impact of the change in vertical levels has a significant impact on the
mean surface salinity in the Norwegian Trench. The increase in surface
resolution allows retention of the relatively fresh layer of Baltic origin
more than the coarser vertical levels used in CO4.</p>
      <p>The 5-year sensitivity experiments revealed that a bug fix in CO5 related to
the application of the inverse barometer effect on the lateral boundaries
results in a colder SST from Iceland to the FSC. This is the region where CO5
has a particularly large SST cold bias and partially explains why CO5 has
larger SST errors here than CO4. The inclusion of the inverse barometer
effect on the boundaries results in a greater transport of water southwards
from the northern boundary and with it colder fresher water. The source data
for the boundaries themselves also have a significant impact in this region.
The higher resolution <inline-formula><mml:math id="M109" display="inline"><mml:mrow><mml:mn mathvariant="normal">1</mml:mn><mml:mo>/</mml:mo><mml:msup><mml:mn mathvariant="normal">12</mml:mn><mml:mo>∘</mml:mo></mml:msup></mml:mrow></mml:math></inline-formula> NATL12 model results in smaller cold
bias there also. It is likely that <inline-formula><mml:math id="M110" display="inline"><mml:mrow><mml:mn mathvariant="normal">1</mml:mn><mml:mo>/</mml:mo><mml:msup><mml:mn mathvariant="normal">4</mml:mn><mml:mo>∘</mml:mo></mml:msup></mml:mrow></mml:math></inline-formula> ORCA025 global model lacks
sufficient resolution
to model the Icelandic shelf in the vicinity of the northern CO5 boundary.
The increased southwards transport of water from the northern boundary condition
due to the inclusion of the inverse barometer effect amplifies the
cold and fresh anomaly of the ORCA025 boundary data.</p>
      <p>The impact of changing the surface boundary conditions from ERAI and CORE
bulk forcing and directly specified fluxes from the Met Office NWP model was
also investigated. The NWP fluxes as used in CO4 resulted in a warmer mean
SST, further offsetting the generally cold bias in the CO5 control off shelf.
However, it also led to a slight mean warm bias on shelf, with the exception
of the Skagerrak where the fluxes have a fairly large cold bias. The direct
fluxes as applied in CO4 used the absolute wind velocity rather than the
relative wind velocity compared to the moving ocean surface. The effect of
using relative versus absolute wind velocities has important impacts in
localised regions with persistent strong surface currents such as the
Skagerrak. The ERAI-derived forcing is also of a relatively coarse resolution
and the details of near-coastal fluxes are quiet different from the NWP
fluxes. The combined difference of absolute versus relative winds and
differing details in the fluxes combine to have significant impacts on
surface transport and hence surface salinity in
local regions such as the Skagerrak.</p>
      <p>In summary, CO5 has been shown to produce a significantly improved hindcast
of the NWS compared to POLCOMS against climatologies and observations.
However, there are a number of notable biases in CO5 that need addressing in
future configurations. Particular issues relate to freshwater inputs from
rivers, surface boundary conditions as well as seasonal stratification in the
North Sea.</p>
      <p>The next standard configuration CO6 will be an incremental update for the physics
based on some of the lessons learned from CO5.
The relative stability of physics developments between CO5 and CO6 allows for
significant updates to both data assimilation and biology components for the
NWS forecast system. Physics changes will include updating the base version
of NEMO to 3.6, updating the light attenuation to use satellite-observed
climatology of ocean colour instead of a domain-wide coefficient. The river
inputs will be from an updated climatology with reduced biases compared to
the E-HYPE rivers used in CO5. However, a step change in the physics will
occur in CO7 when the resolution will be increased from 7 to 1.5 <inline-formula><mml:math id="M111" display="inline"><mml:mi mathvariant="normal">km</mml:mi></mml:math></inline-formula>.
CO7 will be of a sufficient resolution to resolve the internal Rossby radius
on the shelf. Possible improvements include capturing to first order the
generation of internal tides at the shelf break, resolving mesoscale eddies
and consequently enhanced mixing in the Norwegian Trench and greatly
improving bathymetry and coastline to name but a few. Furthermore, CO7 is being
developed in anticipation of the longer-term goals of coupling to wave,
atmosphere and land system models. The aspiration is to drive towards
eventual operational coupled implementation for which CO7 will form the basis
of the ocean model component.</p><?xmltex \hack{\newpage}?>
</sec>

      
      </body>
    <back><notes notes-type="codedataavailability">

      <p>The model code for NEMO v3.4 is freely available from
the NEMO website (<uri>www.nemo-ocean.eu</uri>). After registration, the FORTRAN
code is readily available using the open-source subversion software
(<uri>http:/subervsion.apache.org</uri>). Additional modifications to the NEMO3.4
trunk are required for CO5.0 and are merged into the CO5 package branch. The
CO5 package branch is freely available from the NEMO repository under
branches/UKMO/CO5_package_branch.</p>

      <p>The NEMO namelist used for CO5 is publicly available at
<ext-link xlink:href="https://doi.org/10.13140/RG.2.2.17410.89286" ext-link-type="DOI">10.13140/RG.2.2.17410.89286</ext-link> <xref ref-type="bibr" rid="bib1.bibx27" id="paren.58"/>.</p>

      <p>The nature of the 4-D data generated require a large tape storage facility.
The data that comprise the CO5 control experiment are of the order of 6 TB,
and the data for each 30-year sensitivity experiment are of the same order.
However, the data can be made available upon contacting the authors.</p>
  </notes><?xmltex \hack{\clearpage}?><app-group>

<app id="App1.Ch1.S1">
  <title>FPP keys used in CO5</title>

<?xmltex \floatpos{h}?><table-wrap id="App1.Ch1.T1"><caption><p>FPP keys used with the CO5 control experiment.</p></caption><oasis:table frame="topbot"><oasis:tgroup cols="2">
     <oasis:colspec colnum="1" colname="col1" align="left"/>
     <oasis:colspec colnum="2" colname="col2" align="left"/>
     <oasis:thead>
       <oasis:row rowsep="1">  
         <oasis:entry colname="col1">key_tide</oasis:entry>  
         <oasis:entry colname="col2">Activate tidal potential forcing</oasis:entry>
       </oasis:row>
     </oasis:thead>
     <oasis:tbody>
       <oasis:row>  
         <oasis:entry colname="col1">key_dynspg_ts</oasis:entry>  
         <oasis:entry colname="col2">Free surface volume with time splitting</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">key_ldfslp</oasis:entry>  
         <oasis:entry colname="col2">Rotation of lateral mixing tensor</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">key_iomput</oasis:entry>  
         <oasis:entry colname="col2">Input output manager</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">key_vvl</oasis:entry>  
         <oasis:entry colname="col2">Variable volume layer</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">key_shelf</oasis:entry>  
         <oasis:entry colname="col2">Diagnostic switch for output</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">key_zdfgls</oasis:entry>  
         <oasis:entry colname="col2">Generic length-scale turbulence scheme</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">key_bdy</oasis:entry>  
         <oasis:entry colname="col2">Use open lateral boundaries</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">key_amm</oasis:entry>  
         <oasis:entry colname="col2">Dimensions for AMM domain</oasis:entry>
       </oasis:row>
       <oasis:row>  
         <oasis:entry colname="col1">key_levels=51</oasis:entry>  
         <oasis:entry colname="col2">Number of vertical levels</oasis:entry>
       </oasis:row>
     </oasis:tbody>
   </oasis:tgroup></oasis:table></table-wrap>

</app>

<app id="App1.Ch1.S2">
  <title>Adjusting the lateral open ocean boundary conditions</title>
      <p>The lateral open ocean boundary conditions are derived from three separate
<inline-formula><mml:math id="M112" display="inline"><mml:mrow><mml:mn mathvariant="normal">1</mml:mn><mml:mo>/</mml:mo><mml:msup><mml:mn mathvariant="normal">4</mml:mn><mml:mo>∘</mml:mo></mml:msup></mml:mrow></mml:math></inline-formula> ORCA025 experiments. The years 1981 to 1989 are also taken from
the GO5.0 <inline-formula><mml:math id="M113" display="inline"><mml:mrow><mml:mn mathvariant="normal">1</mml:mn><mml:mo>/</mml:mo><mml:msup><mml:mn mathvariant="normal">4</mml:mn><mml:mo>∘</mml:mo></mml:msup></mml:mrow></mml:math></inline-formula> ORCA025 hindcast <xref ref-type="bibr" rid="bib1.bibx24" id="paren.59"/>. The boundary
conditions from 1989 onwards are taken from the two separate Global Seasonal
Forecast system version 5 (GLOSEA5) <xref ref-type="bibr" rid="bib1.bibx22" id="paren.60"/> experiments spanning
1989–2003 and 2003–2012.</p>
      <p>Each of ORCA025 experiments had substantially different mean SSH. They needed
to be matched at the cross-over dates as closely as possible to prevent large
shocks. The free-running model GO5 experiment for the 1980s was shown to
have a long-term unrealistic drift in the mean SSH. This long-term trend is
removed from the data before deriving boundary conditions. Furthermore, the
first GLOSEA run does not have altimeter assimilation until 1992 and likewise
has an unrealistic drift removed from these initial years (1989–1992).</p>
      <p>Once the data are detrended, a mean SSH is calculated area wide at the
cross-over dates in 1989 and 2003. The second GLOSEA dataset is taken as the
reference. The difference in the mean SSH in the earlier detrended GO5.0
experiment at the 1989 crossover data is then subtracted from the entire
period (1981–1989). This, in effect, is a uniform shift in SSH so that at
the cross-over date the discrepancy is as reduced as possible. Similarly, the
difference in the mean between the first GLOSEA run and the second is used to
match the two in 2003. However, even after this prepossessing, there is still
some transient adjustment in SSH, particularly so at the 2003 cross-over.
<?xmltex \hack{\newpage}?></p>
</app>

<app id="App1.Ch1.S3">
  <title>Other inputs</title>
      <p>The bathymetry used in CO5 is made publicly available from
<ext-link xlink:href="https://doi.org/10.13140/RG.2.2.25799.50081" ext-link-type="DOI">10.13140/RG.2.2.25799.50081</ext-link> <xref ref-type="bibr" rid="bib1.bibx26" id="paren.61"/>.</p><?xmltex \hack{\clearpage}?>
</app>
  </app-group><notes notes-type="competinginterests">

      <p>The authors declare that they have no conflict of
interest.</p>
  </notes><ack><title>Acknowledgements</title><p>Funding support is gratefully acknowledged from the Ministry of Defence, the Public Weather Service,
the European Community's Seventh Framework Programme FP7/2007–2013 under grant agreement no. 283367
(MyOcean2) and from the Copernicus Marine Environment Monitoring Service.
We acknowledge use of the MONSooN system,
a collaborative facility supplied under the Joint Weather and Climate Research Programme,
a strategic partnership between the Met Office and the Natural Environment Research Council.
We also acknowledge the Centre for Environmental Data Analysis (CEDA) for the
use of JASMIN <xref ref-type="bibr" rid="bib1.bibx18" id="paren.62"/> for post-processing the model
data.<?xmltex \hack{\newline}?><?xmltex \hack{\newline}?>Edited by: Robert Marsh <?xmltex \hack{\newline}?>
Reviewed by: Bruce Hackett and Robinson Hordoir</p></ack><ref-list>
    <title>References</title>

      <ref id="bib1.bibx1"><label>Arakawa and Lamb(1981)</label><mixed-citation>
Arakawa, A. and Lamb, V. R.: A potential enstrophy and energy conserving
scheme for the shallow water equations, Mon. Weather Rev., 109, 18–36, 1981.</mixed-citation></ref>
      <ref id="bib1.bibx2"><label>Bersch et al.(2013)Bersch, Gouretski, Sadikni, and Hinrichs</label><mixed-citation>Bersch, M., Gouretski, V., Sadikni, R., and Hinrichs, I.: KLIWAS North Sea
Climatology of Hydrographic Data (Version 1.0), Tech. rep., Center for Earth
System Research and Sustainability (CEN), University of Hamburg,
<ext-link xlink:href="https://doi.org/10.1594/WDCC/KNSC_hyd_v1.0" ext-link-type="DOI">10.1594/WDCC/KNSC_hyd_v1.0</ext-link>,
2013.</mixed-citation></ref>
      <ref id="bib1.bibx3"><label>Canuto et al.(2001)Canuto, Howard, Cheng, and
Dubovikov</label><mixed-citation>
Canuto, V., Howard, A., Cheng, Y., and Dubovikov, M.: Ocean turbulence. Part
I:
One-point closure model-momentum and heat vertical diffusivities, J/
Phys/ Oceanogr., 31, 1413–1426, 2001.</mixed-citation></ref>
      <ref id="bib1.bibx4"><label>Casey et al.(2010)Casey, Brandon, Cornillon, and Evans</label><mixed-citation>Casey, K. S., Brandon, T. B., Cornillon, P., and Evans, R.: The Past,
Present,
and Future of the AVHRR Pathfinder SST Program,  Springer
Netherlands, Dordrecht, 273–287,  <ext-link xlink:href="https://doi.org/10.1007/978-90-481-8681-5_16" ext-link-type="DOI">10.1007/978-90-481-8681-5_16</ext-link>,
2010.</mixed-citation></ref>
      <ref id="bib1.bibx5"><label>Craig and Banner(1994)</label><mixed-citation>
Craig, P. D. and Banner, M. L.: Modeling wave-enhanced turbulence in the
ocean
surface layer, J. Phys. Oceanogr., 24, 2546–2559, 1994.</mixed-citation></ref>
      <ref id="bib1.bibx6"><label>Dee et al.(2011)Dee, Uppala, Simmons, Berrisford, Poli, Kobayashi,
Andrae, Balmaseda, Balsamo, Bauer et al.</label><mixed-citation>
Dee, D., Uppala, S., Simmons, A. et al.: The ERA-Interim
reanalysis: Configuration and performance of the data assimilation system,
Q. J. Roy. Meteorol. Soc., 137, 553–597, 2011.</mixed-citation></ref>
      <ref id="bib1.bibx7"><label>Donnelly et al.(2015)Donnelly, Andersson, and
Arheimer</label><mixed-citation>Donnelly, C., Andersson, J. C., and Arheimer, B.: Using flow signatures and
catchment similarities to evaluate the E-HYPE multi-basin model across
Europe, Hydrol. Sci. J., 61, 255–273, <ext-link xlink:href="https://doi.org/10.1080/02626667.2015.1027710" ext-link-type="DOI">10.1080/02626667.2015.1027710</ext-link>, 2015.</mixed-citation></ref>
      <ref id="bib1.bibx8"><label>Galperin et al.(1988)Galperin, Kantha, Hassid, and
Rosati</label><mixed-citation>
Galperin, B., Kantha, L., Hassid, S., and Rosati, A.: A quasi-equilibrium
turbulent energy model for geophysical flows, J. Atmos.
Sci., 45, 55–62, 1988.</mixed-citation></ref>
      <ref id="bib1.bibx9"><label>Good et al.(2013)Good, Martin, and Rayner</label><mixed-citation>Good, S. A., Martin, M. J., and Rayner, N. A.: EN4: Quality controlled ocean
temperature and salinity profiles and monthly objective analyses with
uncertainty estimates, J. Geophys. Res.-Oceans, 118,
6704–6716, <ext-link xlink:href="https://doi.org/10.1002/2013JC009067" ext-link-type="DOI">10.1002/2013JC009067</ext-link>,
2013.</mixed-citation></ref>
      <ref id="bib1.bibx10"><label>Gräwe et al.(2015)Gräwe, Holtermann, Klingbeil, and
Burchard</label><mixed-citation>Gräwe, U., Holtermann, P., Klingbeil, K., and Burchard, H.: Advantages of
vertically adaptive coordinates in numerical models of stratified shelf seas,
Ocean Model., 92, 56–68,
<ext-link xlink:href="https://doi.org/10.1016/j.ocemod.2015.05.008" ext-link-type="DOI">10.1016/j.ocemod.2015.05.008</ext-link>,
2015.</mixed-citation></ref>
      <ref id="bib1.bibx11"><label>Haney(1971)</label><mixed-citation>
Haney, R. L.: Surface thermal boundary condition for ocean circulation
models,
J. Phys. Oceanogr., 1, 241–248, 1971.</mixed-citation></ref>
      <ref id="bib1.bibx12"><label>Holt and Proctor(2008)</label><mixed-citation>Holt, J. and Proctor, R.: The seasonal circulation and volume transport on
the
northwest European continental shelf: A fine-resolution model study, J.
Geophys. Res.-Oceans, 113, <ext-link xlink:href="https://doi.org/10.1029/2006JC004034" ext-link-type="DOI">10.1029/2006JC004034</ext-link>, 2008.</mixed-citation></ref>
      <ref id="bib1.bibx13"><label>Holt et al.(2012)</label><mixed-citation>Holt, J., Hughes, S., Hopkins, J., Wakelin, S. L., Holliday, N. P., Dye, S.,
González-Pola, C., Hjøllo, S. S., Mork, K. A., Nolan, G., Proctor, R.,
Read, J., Shammon, T., Sherwin, T., Smyth, T., Tattersall, G., Ward, B., and
Wiltshire, K. H.: Multi-decadal variability and trends in the temperature of
the northwest European continental shelf: A model-data synthesis, Prog.
Oceanogr., 106, 96–117,
<ext-link xlink:href="https://doi.org/10.1016/j.pocean.2012.08.001" ext-link-type="DOI">10.1016/j.pocean.2012.08.001</ext-link>,
2012.</mixed-citation></ref>
      <ref id="bib1.bibx14"><label>Holt and James(2001)</label><mixed-citation>Holt, J. T. and James, I. D.: An s coordinate density evolving model of the
northwest European continental shelf: 1. Model description and density
structure, J. Geophys. Res.-Oceans, 106, 14015–14034,
<ext-link xlink:href="https://doi.org/10.1029/2000JC000304" ext-link-type="DOI">10.1029/2000JC000304</ext-link>,
2001.</mixed-citation></ref>
      <ref id="bib1.bibx15"><label>Howarth and Pugh(1983)</label><mixed-citation>Howarth, M. and Pugh, D.: Chapter 4 Observations of Tides Over the
Continental
Shelf of North-West Europe, Elsevier Oceanography Series, 35, 135–188,
<ext-link xlink:href="https://doi.org/10.1016/S0422-9894(08)70502-6" ext-link-type="DOI">10.1016/S0422-9894(08)70502-6</ext-link>,
1983.</mixed-citation></ref>
      <ref id="bib1.bibx16"><label>Ingleby and Huddleston(2007)</label><mixed-citation>Ingleby, B. and Huddleston, M.: Quality control of ocean temperature and
salinity profiles – Historical and real-time data, J. Marine Syst.,
65, 158–175, <ext-link xlink:href="https://doi.org/10.1016/j.jmarsys.2005.11.019" ext-link-type="DOI">10.1016/j.jmarsys.2005.11.019</ext-link>,
2007.</mixed-citation></ref>
      <ref id="bib1.bibx17"><label>Large and Yeager(2009)</label><mixed-citation>
Large, W. and Yeager, S.: The global climatology of an interannually varying
air–sea flux data set, Clim. Dynam., 33, 341–364, 2009.</mixed-citation></ref>
      <ref id="bib1.bibx18"><label>Lawrence et al.(2013)Lawrence, Bennett, Churchill, Juckes, Kershaw,
Pascoe, Pepler, Pritchard, and Stephens</label><mixed-citation>Lawrence, B. N., Bennett, V. L., Churchill, J., Juckes, M., Kershaw, P.,
Pascoe, S., Pepler, S., Pritchard, M., and Stephens, A.: Storing and
manipulating environmental big data with JASMIN, in: 2013 IEEE International
Conference on Big Data,   68–75, <ext-link xlink:href="https://doi.org/10.1109/BigData.2013.6691556" ext-link-type="DOI">10.1109/BigData.2013.6691556</ext-link>, 2013.</mixed-citation></ref>
      <ref id="bib1.bibx19"><label>Lengaigne et al.(2007)</label><mixed-citation>Lengaigne, M., Menkes, C., Aumont, O., Gorgues, T., Bopp, L., André, J.-M.,
and Madec, G.: Influence of the oceanic biology on the tropical Pacific
climate in a coupled general circulation model, Clim. Dynam., 28,
503–516, <ext-link xlink:href="https://doi.org/10.1007/s00382-006-0200-2" ext-link-type="DOI">10.1007/s00382-006-0200-2</ext-link>,
2007.</mixed-citation></ref>
      <ref id="bib1.bibx20"><label>Levier et al.(2007)Levier, Tréguier, Madec, and Garnier</label><mixed-citation>
Levier, B., Tréguier, A. M., Madec, G., and Garnier, V.: Free surface and
variable volume in the NEMO code, MESRSEA IP report WP09-CNRS-STR03-1A, 2007.</mixed-citation></ref>
      <ref id="bib1.bibx21"><label>Lindström et al.(2010)Lindström, Pers, Rosberg,
Strömqvist, and Arheimer</label><mixed-citation>Lindström, G., Pers, C., Rosberg, J., Strömqvist, J., and Arheimer,
B.:
Development and testing of the HYPE (Hydrological Predictions for the
Environment) water quality model for different spatial scales, Hydrol.
Res., 41, 295–319, <ext-link xlink:href="https://doi.org/10.2166/nh.2010.007" ext-link-type="DOI">10.2166/nh.2010.007</ext-link>,
2010.</mixed-citation></ref>
      <ref id="bib1.bibx22"><label>MacLachlan et al.(2015)MacLachlan, Arribas, Peterson, Maidens,
Fereday, Scaife, Gordon, Vellinga, Williams, Comer, Camp, Xavier, and
Madec</label><mixed-citation>MacLachlan, C., Arribas, A., Peterson, K. A., Maidens, A., Fereday, D.,
Scaife,
A. A., Gordon, M., Vellinga, M., Williams, A., Comer, R. E., Camp, J.,
Xavier, P., and Madec, G.: Global Seasonal forecast system version 5
(GloSea5): a high-resolution seasonal forecast system, Q. J. Roy. Meteor. Soc.,
141, 1072–1084, <ext-link xlink:href="https://doi.org/10.1002/qj.2396" ext-link-type="DOI">10.1002/qj.2396</ext-link>, 2015.</mixed-citation></ref>
      <ref id="bib1.bibx23"><label>Madec(2008)</label><mixed-citation>
Madec, G.: NEMO ocean engine: Note Du Pôle de Modél, Institut
Pierre-Simon Laplace (IPSL), France, No 27, 2008.</mixed-citation></ref>
      <ref id="bib1.bibx24"><label>Megann et al.(2014)Megann, Storkey, Aksenov, Alderson, Calvert,
Graham, Hyder, Siddorn, and Sinha</label><mixed-citation>Megann, A., Storkey, D., Aksenov, Y., Alderson, S., Calvert, D., Graham, T.,
Hyder, P., Siddorn, J., and Sinha, B.: GO5.0: the joint NERC–Met Office NEMO
global ocean model for use in coupled and forced applications, Geosci. Model
Dev., 7, 1069–1092, <ext-link xlink:href="https://doi.org/10.5194/gmd-7-1069-2014" ext-link-type="DOI">10.5194/gmd-7-1069-2014</ext-link>, 2014.</mixed-citation></ref>
      <ref id="bib1.bibx25"><label>Merchant et al.(2014)Merchant, Embury, Roberts-Jones, Fiedler,
Bulgin, Corlett, Good, McLaren, Rayner, Morak-Bozzo, and Donlon</label><mixed-citation>Merchant, C. J., Embury, O., Roberts-Jones, J., Fiedler, E., Bulgin, C. E.,
Corlett, G. K., Good, S., McLaren, A., Rayner, N., Morak-Bozzo, S., and
Donlon, C.: Sea surface temperature datasets for climate applications from
Phase 1 of the European Space Agency Climate Change Initiative (SST CCI),
Geoscience Data Journal, 1, 179–191, <ext-link xlink:href="https://doi.org/10.1002/gdj3.20" ext-link-type="DOI">10.1002/gdj3.20</ext-link>,
2014.</mixed-citation></ref>
      <ref id="bib1.bibx26"><label>O'Dea(2016a)</label><mixed-citation>O'Dea, E.: CO5 Bathymetry,<?xmltex \hack{\newline}?>
<ext-link xlink:href="https://doi.org/10.13140/RG.2.2.25799.50081" ext-link-type="DOI">10.13140/RG.2.2.25799.50081</ext-link>, 2016a.</mixed-citation></ref>
      <ref id="bib1.bibx27"><label>O'Dea(2016b)</label><mixed-citation>O'Dea, E.: CO5 AMM7 namelist,
<ext-link xlink:href="https://doi.org/10.13140/RG.2.2.17410.89286" ext-link-type="DOI">10.13140/RG.2.2.17410.89286</ext-link>, 2016b.</mixed-citation></ref>
      <ref id="bib1.bibx28"><label>O'Dea et al.(2012)O'Dea, Arnold, Edwards, Furner, Hyder, Martin,
Siddorn, Storkey, While, Holt, and Liu</label><mixed-citation>
O'Dea, E. J., Arnold, A. K., Edwards, K. P., Furner, R., Hyder, P., Martin,
M. J., Siddorn, J. R., Storkey, D., While, J., Holt, J. T., and Liu, H.: An
operational ocean forecast system incorporating NEMO and SST data
assimilation for the tidally driven European North-West shelf, Journal of
Operational Oceanography, 5, 3–17, 2012.</mixed-citation></ref>
      <ref id="bib1.bibx29"><label>Otto et al.(1990)Otto, Zimmerman, Furnes, Mork, Saetre, and
Becker</label><mixed-citation>Otto, L., Zimmerman, J., Furnes, G., Mork, M., Saetre, R., and Becker, G.:
Review of the physical oceanography of the North Sea, Neth. J.
Sea Res., 26, 161–238,
<ext-link xlink:href="https://doi.org/10.1016/0077-7579(90)90091-T" ext-link-type="DOI">10.1016/0077-7579(90)90091-T</ext-link>,
1990.</mixed-citation></ref>
      <ref id="bib1.bibx30"><label>Prandle et al.(1996)Prandle, Ballard, Flatt, Harrison, Jones, Knight,
Loch, McManus, Player, and Tappin</label><mixed-citation>Prandle, D., Ballard, G., Flatt, D., Harrison, A., Jones, S., Knight, P.,
Loch,
S., McManus, J., Player, R., and Tappin, A.: Combining modelling and
monitoring to determine fluxes of water, dissolved and particulate metals
through the Dover Strait, Cont. Shelf Res., 16, 237–257,
<ext-link xlink:href="https://doi.org/10.1016/0278-4343(95)00009-P" ext-link-type="DOI">10.1016/0278-4343(95)00009-P</ext-link>,
1996.</mixed-citation></ref>
      <ref id="bib1.bibx31"><label>Rodi(1987)</label><mixed-citation>
Rodi, W.: Examples of calculation methods for flow and mixing in stratified
fluids, J. Geophys. Res.-Oceans, 92, 5305–5328,
1987.</mixed-citation></ref>
      <ref id="bib1.bibx32"><label>Siddorn and Furner(2013)</label><mixed-citation>Siddorn, J. and Furner, R.: An analytical stretching function that combines
the
best attributes of geopotential and terrain-following vertical coordinates,
Ocean Model., 66, 1–13, 2013.
 </mixed-citation></ref><?xmltex \hack{\newpage}?>
      <ref id="bib1.bibx33"><label>Sikirić et al.(2013)Sikirić, Roland, Janeković,
Tomaz̆ić, and Kuzmić</label><mixed-citation>Sikirić, M. D., Roland, A., Janeković, I., Tomaz̆ić, I., and
Kuzmić, M.: Coupling of the Regional Ocean Modeling System (ROMS) and
Wind Wave Model, Ocean Model., 72, 59–73,
<ext-link xlink:href="https://doi.org/10.1016/j.ocemod.2013.08.002" ext-link-type="DOI">10.1016/j.ocemod.2013.08.002</ext-link>,
2013.</mixed-citation></ref>
      <ref id="bib1.bibx34"><label>Song and Haidvogel(1994)</label><mixed-citation>Song, Y. and Haidvogel, D.: A Semi-implicit Ocean Circulation Model Using a
Generalized Topography-following Coordinate System, J. Comput. Phys., 115,
228–244, <ext-link xlink:href="https://doi.org/10.1006/jcph.1994.1189" ext-link-type="DOI">10.1006/jcph.1994.1189</ext-link>, 1994.</mixed-citation></ref>
      <ref id="bib1.bibx35"><label>Tinker et al.(2015)Tinker, Lowe, Holt, Pardaens, and
Wiltshire</label><mixed-citation>Tinker, J., Lowe, J., Holt, J., Pardaens, A., and Wiltshire, A.: Validation
of
an ensemble modelling system for climate projections for the northwest
European shelf seas, Prog. Oceanogr., 138,   211–237,
<ext-link xlink:href="https://doi.org/10.1016/j.pocean.2015.07.002" ext-link-type="DOI">10.1016/j.pocean.2015.07.002</ext-link>,
2015.</mixed-citation></ref>
      <ref id="bib1.bibx36"><label>Umlauf and Burchard(2003)</label><mixed-citation>
Umlauf, L. and Burchard, H.: A generic length-scale equation for geophysical
turbulence models, J. Marine Res., 61, 235–265, 2003.</mixed-citation></ref>
      <ref id="bib1.bibx37"><label>Umlauf and Burchard(2005)</label><mixed-citation>
Umlauf, L. and Burchard, H.: Second-order turbulence closure models for
geophysical boundary layers. A review of recent work, Cont. Shelf
Res., 25, 795–827, 2005.</mixed-citation></ref>
      <ref id="bib1.bibx38"><label>Young and Holt(2007)</label><mixed-citation>Young, E. and Holt, J.: Prediction and analysis of long-term variability of
temperature and salinity in the Irish Sea, J. Geophys. Res.-Oceans, 112, <ext-link xlink:href="https://doi.org/10.1029/2005JC003386" ext-link-type="DOI">10.1029/2005JC003386</ext-link>,
2007.</mixed-citation></ref>
      <ref id="bib1.bibx39"><label>Zalesak(1979)</label><mixed-citation>
Zalesak, S. T.: Fully multidimensional flux-corrected transport algorithms
for
fluids, J. Comput. Phys., 31, 335–362, 1979.</mixed-citation></ref>
      <ref id="bib1.bibx40"><label>Zweng et al.(2013)Zweng, Reagan, Antonov, Locarnini, Mishonov, Boyer,
Garcia, Baranova, Johnson, Seidov, and Biddle</label><mixed-citation>Zweng, M., Reagan, J., Antonov, J., Locarnini, R., Mishonov, A., Boyer, T.,
Garcia, H., Baranova, O., Johnson, D., Seidov, D., and Biddle, M.: World
Ocean Atlas 2013, Volume 2: Salinity, Tech. Rep. NOAA Atlas NESDIS 74, NOAA,
Silver Springs, MD, available at:
<uri>http://http://data.nodc.noaa.gov/woa/WOA13/DOC/woa13_vol2.pdf</uri> (last access: 28 July 2017), 2013.</mixed-citation></ref>

  </ref-list><app-group content-type="float"><app><title/>

    </app></app-group></back>
    <!--<article-title-html>The CO5 configuration of the 7 km Atlantic Margin Model:  large-scale biases and sensitivity to forcing, physics options and vertical resolution</article-title-html>
<abstract-html><p class="p">We describe the physical model component of the standard Coastal
Ocean version 5 configuration (CO5) of the European north-west shelf (NWS).
CO5 was developed jointly between the Met Office and the National
Oceanography Centre. CO5 is designed with the seamless approach in mind,
which allows for modelling of multiple timescales for a variety of
applications from short-range ocean forecasting to climate
projections. The configuration constitutes the basis of the latest update to
the ocean and data assimilation components of the Met Office's operational
Forecast Ocean Assimilation Model (FOAM) for the NWS. A 30.5-year
non-assimilating control hindcast of CO5 was integrated from January 1981 to
June 2012. Sensitivity simulations were conducted with reference to the
control run. The control run is compared against a previous non-assimilating
Proudman Oceanographic Laboratory Coastal Ocean Modelling System (POLCOMS)
hindcast of the NWS. The CO5 control hindcast is shown to have much reduced
biases compared to POLCOMS. Emphasis in the system description is weighted to
updates in CO5 over previous versions. Updates include an increase in
vertical resolution, a new vertical coordinate stretching function, the
replacement of climatological riverine sources with the pan-European
hydrological model E-HYPE, a new Baltic boundary condition and switching from
directly imposed atmospheric model boundary fluxes to calculating the fluxes
within the model using a bulk formula. Sensitivity tests of the updates are
detailed with a view toward attributing observed changes in the new system from
the previous system and suggesting future directions of research to further
improve the system.</p></abstract-html>
<ref-html id="bib1.bib1"><label>Arakawa and Lamb(1981)</label><mixed-citation>
Arakawa, A. and Lamb, V. R.: A potential enstrophy and energy conserving
scheme for the shallow water equations, Mon. Weather Rev., 109, 18–36, 1981.
</mixed-citation></ref-html>
<ref-html id="bib1.bib2"><label>Bersch et al.(2013)Bersch, Gouretski, Sadikni, and Hinrichs</label><mixed-citation>
Bersch, M., Gouretski, V., Sadikni, R., and Hinrichs, I.: KLIWAS North Sea
Climatology of Hydrographic Data (Version 1.0), Tech. rep., Center for Earth
System Research and Sustainability (CEN), University of Hamburg,
<a href="https://doi.org/10.1594/WDCC/KNSC_hyd_v1.0" target="_blank">https://doi.org/10.1594/WDCC/KNSC_hyd_v1.0</a>,
2013.
</mixed-citation></ref-html>
<ref-html id="bib1.bib3"><label>Canuto et al.(2001)Canuto, Howard, Cheng, and
Dubovikov</label><mixed-citation>
Canuto, V., Howard, A., Cheng, Y., and Dubovikov, M.: Ocean turbulence. Part
I:
One-point closure model-momentum and heat vertical diffusivities, J/
Phys/ Oceanogr., 31, 1413–1426, 2001.
</mixed-citation></ref-html>
<ref-html id="bib1.bib4"><label>Casey et al.(2010)Casey, Brandon, Cornillon, and Evans</label><mixed-citation>
Casey, K. S., Brandon, T. B., Cornillon, P., and Evans, R.: The Past,
Present,
and Future of the AVHRR Pathfinder SST Program,  Springer
Netherlands, Dordrecht, 273–287,  <a href="https://doi.org/10.1007/978-90-481-8681-5_16" target="_blank">https://doi.org/10.1007/978-90-481-8681-5_16</a>,
2010.
</mixed-citation></ref-html>
<ref-html id="bib1.bib5"><label>Craig and Banner(1994)</label><mixed-citation>
Craig, P. D. and Banner, M. L.: Modeling wave-enhanced turbulence in the
ocean
surface layer, J. Phys. Oceanogr., 24, 2546–2559, 1994.
</mixed-citation></ref-html>
<ref-html id="bib1.bib6"><label>Dee et al.(2011)Dee, Uppala, Simmons, Berrisford, Poli, Kobayashi,
Andrae, Balmaseda, Balsamo, Bauer et al.</label><mixed-citation>
Dee, D., Uppala, S., Simmons, A. et al.: The ERA-Interim
reanalysis: Configuration and performance of the data assimilation system,
Q. J. Roy. Meteorol. Soc., 137, 553–597, 2011.
</mixed-citation></ref-html>
<ref-html id="bib1.bib7"><label>Donnelly et al.(2015)Donnelly, Andersson, and
Arheimer</label><mixed-citation>
Donnelly, C., Andersson, J. C., and Arheimer, B.: Using flow signatures and
catchment similarities to evaluate the E-HYPE multi-basin model across
Europe, Hydrol. Sci. J., 61, 255–273, <a href="https://doi.org/10.1080/02626667.2015.1027710" target="_blank">https://doi.org/10.1080/02626667.2015.1027710</a>, 2015.
</mixed-citation></ref-html>
<ref-html id="bib1.bib8"><label>Galperin et al.(1988)Galperin, Kantha, Hassid, and
Rosati</label><mixed-citation>
Galperin, B., Kantha, L., Hassid, S., and Rosati, A.: A quasi-equilibrium
turbulent energy model for geophysical flows, J. Atmos.
Sci., 45, 55–62, 1988.
</mixed-citation></ref-html>
<ref-html id="bib1.bib9"><label>Good et al.(2013)Good, Martin, and Rayner</label><mixed-citation>
Good, S. A., Martin, M. J., and Rayner, N. A.: EN4: Quality controlled ocean
temperature and salinity profiles and monthly objective analyses with
uncertainty estimates, J. Geophys. Res.-Oceans, 118,
6704–6716, <a href="https://doi.org/10.1002/2013JC009067" target="_blank">https://doi.org/10.1002/2013JC009067</a>,
2013.
</mixed-citation></ref-html>
<ref-html id="bib1.bib10"><label>Gräwe et al.(2015)Gräwe, Holtermann, Klingbeil, and
Burchard</label><mixed-citation>
Gräwe, U., Holtermann, P., Klingbeil, K., and Burchard, H.: Advantages of
vertically adaptive coordinates in numerical models of stratified shelf seas,
Ocean Model., 92, 56–68,
<a href="https://doi.org/10.1016/j.ocemod.2015.05.008" target="_blank">https://doi.org/10.1016/j.ocemod.2015.05.008</a>,
2015.
</mixed-citation></ref-html>
<ref-html id="bib1.bib11"><label>Haney(1971)</label><mixed-citation>
Haney, R. L.: Surface thermal boundary condition for ocean circulation
models,
J. Phys. Oceanogr., 1, 241–248, 1971.
</mixed-citation></ref-html>
<ref-html id="bib1.bib12"><label>Holt and Proctor(2008)</label><mixed-citation>
Holt, J. and Proctor, R.: The seasonal circulation and volume transport on
the
northwest European continental shelf: A fine-resolution model study, J.
Geophys. Res.-Oceans, 113, <a href="https://doi.org/10.1029/2006JC004034" target="_blank">https://doi.org/10.1029/2006JC004034</a>, 2008.
</mixed-citation></ref-html>
<ref-html id="bib1.bib13"><label>Holt et al.(2012)</label><mixed-citation>
Holt, J., Hughes, S., Hopkins, J., Wakelin, S. L., Holliday, N. P., Dye, S.,
González-Pola, C., Hjøllo, S. S., Mork, K. A., Nolan, G., Proctor, R.,
Read, J., Shammon, T., Sherwin, T., Smyth, T., Tattersall, G., Ward, B., and
Wiltshire, K. H.: Multi-decadal variability and trends in the temperature of
the northwest European continental shelf: A model-data synthesis, Prog.
Oceanogr., 106, 96–117,
<a href="https://doi.org/10.1016/j.pocean.2012.08.001" target="_blank">https://doi.org/10.1016/j.pocean.2012.08.001</a>,
2012.
</mixed-citation></ref-html>
<ref-html id="bib1.bib14"><label>Holt and James(2001)</label><mixed-citation>
Holt, J. T. and James, I. D.: An s coordinate density evolving model of the
northwest European continental shelf: 1. Model description and density
structure, J. Geophys. Res.-Oceans, 106, 14015–14034,
<a href="https://doi.org/10.1029/2000JC000304" target="_blank">https://doi.org/10.1029/2000JC000304</a>,
2001.
</mixed-citation></ref-html>
<ref-html id="bib1.bib15"><label>Howarth and Pugh(1983)</label><mixed-citation>
Howarth, M. and Pugh, D.: Chapter 4 Observations of Tides Over the
Continental
Shelf of North-West Europe, Elsevier Oceanography Series, 35, 135–188,
<a href="https://doi.org/10.1016/S0422-9894(08)70502-6" target="_blank">https://doi.org/10.1016/S0422-9894(08)70502-6</a>,
1983.
</mixed-citation></ref-html>
<ref-html id="bib1.bib16"><label>Ingleby and Huddleston(2007)</label><mixed-citation>
Ingleby, B. and Huddleston, M.: Quality control of ocean temperature and
salinity profiles – Historical and real-time data, J. Marine Syst.,
65, 158–175, <a href="https://doi.org/10.1016/j.jmarsys.2005.11.019" target="_blank">https://doi.org/10.1016/j.jmarsys.2005.11.019</a>,
2007.
</mixed-citation></ref-html>
<ref-html id="bib1.bib17"><label>Large and Yeager(2009)</label><mixed-citation>
Large, W. and Yeager, S.: The global climatology of an interannually varying
air–sea flux data set, Clim. Dynam., 33, 341–364, 2009.
</mixed-citation></ref-html>
<ref-html id="bib1.bib18"><label>Lawrence et al.(2013)Lawrence, Bennett, Churchill, Juckes, Kershaw,
Pascoe, Pepler, Pritchard, and Stephens</label><mixed-citation>
Lawrence, B. N., Bennett, V. L., Churchill, J., Juckes, M., Kershaw, P.,
Pascoe, S., Pepler, S., Pritchard, M., and Stephens, A.: Storing and
manipulating environmental big data with JASMIN, in: 2013 IEEE International
Conference on Big Data,   68–75, <a href="https://doi.org/10.1109/BigData.2013.6691556" target="_blank">https://doi.org/10.1109/BigData.2013.6691556</a>, 2013.
</mixed-citation></ref-html>
<ref-html id="bib1.bib19"><label>Lengaigne et al.(2007)</label><mixed-citation>
Lengaigne, M., Menkes, C., Aumont, O., Gorgues, T., Bopp, L., André, J.-M.,
and Madec, G.: Influence of the oceanic biology on the tropical Pacific
climate in a coupled general circulation model, Clim. Dynam., 28,
503–516, <a href="https://doi.org/10.1007/s00382-006-0200-2" target="_blank">https://doi.org/10.1007/s00382-006-0200-2</a>,
2007.
</mixed-citation></ref-html>
<ref-html id="bib1.bib20"><label>Levier et al.(2007)Levier, Tréguier, Madec, and Garnier</label><mixed-citation>
Levier, B., Tréguier, A. M., Madec, G., and Garnier, V.: Free surface and
variable volume in the NEMO code, MESRSEA IP report WP09-CNRS-STR03-1A, 2007.
</mixed-citation></ref-html>
<ref-html id="bib1.bib21"><label>Lindström et al.(2010)Lindström, Pers, Rosberg,
Strömqvist, and Arheimer</label><mixed-citation>
Lindström, G., Pers, C., Rosberg, J., Strömqvist, J., and Arheimer,
B.:
Development and testing of the HYPE (Hydrological Predictions for the
Environment) water quality model for different spatial scales, Hydrol.
Res., 41, 295–319, <a href="https://doi.org/10.2166/nh.2010.007" target="_blank">https://doi.org/10.2166/nh.2010.007</a>,
2010.
</mixed-citation></ref-html>
<ref-html id="bib1.bib22"><label>MacLachlan et al.(2015)MacLachlan, Arribas, Peterson, Maidens,
Fereday, Scaife, Gordon, Vellinga, Williams, Comer, Camp, Xavier, and
Madec</label><mixed-citation>
MacLachlan, C., Arribas, A., Peterson, K. A., Maidens, A., Fereday, D.,
Scaife,
A. A., Gordon, M., Vellinga, M., Williams, A., Comer, R. E., Camp, J.,
Xavier, P., and Madec, G.: Global Seasonal forecast system version 5
(GloSea5): a high-resolution seasonal forecast system, Q. J. Roy. Meteor. Soc.,
141, 1072–1084, <a href="https://doi.org/10.1002/qj.2396" target="_blank">https://doi.org/10.1002/qj.2396</a>, 2015.
</mixed-citation></ref-html>
<ref-html id="bib1.bib23"><label>Madec(2008)</label><mixed-citation>
Madec, G.: NEMO ocean engine: Note Du Pôle de Modél, Institut
Pierre-Simon Laplace (IPSL), France, No 27, 2008.
</mixed-citation></ref-html>
<ref-html id="bib1.bib24"><label>Megann et al.(2014)Megann, Storkey, Aksenov, Alderson, Calvert,
Graham, Hyder, Siddorn, and Sinha</label><mixed-citation>
Megann, A., Storkey, D., Aksenov, Y., Alderson, S., Calvert, D., Graham, T.,
Hyder, P., Siddorn, J., and Sinha, B.: GO5.0: the joint NERC–Met Office NEMO
global ocean model for use in coupled and forced applications, Geosci. Model
Dev., 7, 1069–1092, <a href="https://doi.org/10.5194/gmd-7-1069-2014" target="_blank">https://doi.org/10.5194/gmd-7-1069-2014</a>, 2014.
</mixed-citation></ref-html>
<ref-html id="bib1.bib25"><label>Merchant et al.(2014)Merchant, Embury, Roberts-Jones, Fiedler,
Bulgin, Corlett, Good, McLaren, Rayner, Morak-Bozzo, and Donlon</label><mixed-citation>
Merchant, C. J., Embury, O., Roberts-Jones, J., Fiedler, E., Bulgin, C. E.,
Corlett, G. K., Good, S., McLaren, A., Rayner, N., Morak-Bozzo, S., and
Donlon, C.: Sea surface temperature datasets for climate applications from
Phase 1 of the European Space Agency Climate Change Initiative (SST CCI),
Geoscience Data Journal, 1, 179–191, <a href="https://doi.org/10.1002/gdj3.20" target="_blank">https://doi.org/10.1002/gdj3.20</a>,
2014.
</mixed-citation></ref-html>
<ref-html id="bib1.bib26"><label>O'Dea(2016a)</label><mixed-citation>
O'Dea, E.: CO5 Bathymetry,
<a href="https://doi.org/10.13140/RG.2.2.25799.50081" target="_blank">https://doi.org/10.13140/RG.2.2.25799.50081</a>, 2016a.
</mixed-citation></ref-html>
<ref-html id="bib1.bib27"><label>O'Dea(2016b)</label><mixed-citation>
O'Dea, E.: CO5 AMM7 namelist,
<a href="https://doi.org/10.13140/RG.2.2.17410.89286" target="_blank">https://doi.org/10.13140/RG.2.2.17410.89286</a>, 2016b.
</mixed-citation></ref-html>
<ref-html id="bib1.bib28"><label>O'Dea et al.(2012)O'Dea, Arnold, Edwards, Furner, Hyder, Martin,
Siddorn, Storkey, While, Holt, and Liu</label><mixed-citation>
O'Dea, E. J., Arnold, A. K., Edwards, K. P., Furner, R., Hyder, P., Martin,
M. J., Siddorn, J. R., Storkey, D., While, J., Holt, J. T., and Liu, H.: An
operational ocean forecast system incorporating NEMO and SST data
assimilation for the tidally driven European North-West shelf, Journal of
Operational Oceanography, 5, 3–17, 2012.
</mixed-citation></ref-html>
<ref-html id="bib1.bib29"><label>Otto et al.(1990)Otto, Zimmerman, Furnes, Mork, Saetre, and
Becker</label><mixed-citation>
Otto, L., Zimmerman, J., Furnes, G., Mork, M., Saetre, R., and Becker, G.:
Review of the physical oceanography of the North Sea, Neth. J.
Sea Res., 26, 161–238,
<a href="https://doi.org/10.1016/0077-7579(90)90091-T" target="_blank">https://doi.org/10.1016/0077-7579(90)90091-T</a>,
1990.
</mixed-citation></ref-html>
<ref-html id="bib1.bib30"><label>Prandle et al.(1996)Prandle, Ballard, Flatt, Harrison, Jones, Knight,
Loch, McManus, Player, and Tappin</label><mixed-citation>
Prandle, D., Ballard, G., Flatt, D., Harrison, A., Jones, S., Knight, P.,
Loch,
S., McManus, J., Player, R., and Tappin, A.: Combining modelling and
monitoring to determine fluxes of water, dissolved and particulate metals
through the Dover Strait, Cont. Shelf Res., 16, 237–257,
<a href="https://doi.org/10.1016/0278-4343(95)00009-P" target="_blank">https://doi.org/10.1016/0278-4343(95)00009-P</a>,
1996.
</mixed-citation></ref-html>
<ref-html id="bib1.bib31"><label>Rodi(1987)</label><mixed-citation>
Rodi, W.: Examples of calculation methods for flow and mixing in stratified
fluids, J. Geophys. Res.-Oceans, 92, 5305–5328,
1987.
</mixed-citation></ref-html>
<ref-html id="bib1.bib32"><label>Siddorn and Furner(2013)</label><mixed-citation>
Siddorn, J. and Furner, R.: An analytical stretching function that combines
the
best attributes of geopotential and terrain-following vertical coordinates,
Ocean Model., 66, 1–13, 2013.

</mixed-citation></ref-html>
<ref-html id="bib1.bib33"><label>Sikirić et al.(2013)Sikirić, Roland, Janeković,
Tomaz̆ić, and Kuzmić</label><mixed-citation>
Sikirić, M. D., Roland, A., Janeković, I., Tomaz̆ić, I., and
Kuzmić, M.: Coupling of the Regional Ocean Modeling System (ROMS) and
Wind Wave Model, Ocean Model., 72, 59–73,
<a href="https://doi.org/10.1016/j.ocemod.2013.08.002" target="_blank">https://doi.org/10.1016/j.ocemod.2013.08.002</a>,
2013.
</mixed-citation></ref-html>
<ref-html id="bib1.bib34"><label>Song and Haidvogel(1994)</label><mixed-citation>
Song, Y. and Haidvogel, D.: A Semi-implicit Ocean Circulation Model Using a
Generalized Topography-following Coordinate System, J. Comput. Phys., 115,
228–244, <a href="https://doi.org/10.1006/jcph.1994.1189" target="_blank">https://doi.org/10.1006/jcph.1994.1189</a>, 1994.
</mixed-citation></ref-html>
<ref-html id="bib1.bib35"><label>Tinker et al.(2015)Tinker, Lowe, Holt, Pardaens, and
Wiltshire</label><mixed-citation>
Tinker, J., Lowe, J., Holt, J., Pardaens, A., and Wiltshire, A.: Validation
of
an ensemble modelling system for climate projections for the northwest
European shelf seas, Prog. Oceanogr., 138,   211–237,
<a href="https://doi.org/10.1016/j.pocean.2015.07.002" target="_blank">https://doi.org/10.1016/j.pocean.2015.07.002</a>,
2015.
</mixed-citation></ref-html>
<ref-html id="bib1.bib36"><label>Umlauf and Burchard(2003)</label><mixed-citation>
Umlauf, L. and Burchard, H.: A generic length-scale equation for geophysical
turbulence models, J. Marine Res., 61, 235–265, 2003.
</mixed-citation></ref-html>
<ref-html id="bib1.bib37"><label>Umlauf and Burchard(2005)</label><mixed-citation>
Umlauf, L. and Burchard, H.: Second-order turbulence closure models for
geophysical boundary layers. A review of recent work, Cont. Shelf
Res., 25, 795–827, 2005.
</mixed-citation></ref-html>
<ref-html id="bib1.bib38"><label>Young and Holt(2007)</label><mixed-citation>
Young, E. and Holt, J.: Prediction and analysis of long-term variability of
temperature and salinity in the Irish Sea, J. Geophys. Res.-Oceans, 112, <a href="https://doi.org/10.1029/2005JC003386" target="_blank">https://doi.org/10.1029/2005JC003386</a>,
2007.
</mixed-citation></ref-html>
<ref-html id="bib1.bib39"><label>Zalesak(1979)</label><mixed-citation>
Zalesak, S. T.: Fully multidimensional flux-corrected transport algorithms
for
fluids, J. Comput. Phys., 31, 335–362, 1979.
</mixed-citation></ref-html>
<ref-html id="bib1.bib40"><label>Zweng et al.(2013)Zweng, Reagan, Antonov, Locarnini, Mishonov, Boyer,
Garcia, Baranova, Johnson, Seidov, and Biddle</label><mixed-citation>
Zweng, M., Reagan, J., Antonov, J., Locarnini, R., Mishonov, A., Boyer, T.,
Garcia, H., Baranova, O., Johnson, D., Seidov, D., and Biddle, M.: World
Ocean Atlas 2013, Volume 2: Salinity, Tech. Rep. NOAA Atlas NESDIS 74, NOAA,
Silver Springs, MD, available at:
<a href="http://http://data.nodc.noaa.gov/woa/WOA13/DOC/woa13_vol2.pdf" target="_blank">http://http://data.nodc.noaa.gov/woa/WOA13/DOC/woa13_vol2.pdf</a> (last access: 28 July 2017), 2013.
</mixed-citation></ref-html>--></article>
