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Changeset 10465 – NEMO

Changeset 10465


Ignore:
Timestamp:
2019-01-08T11:00:28+01:00 (6 years ago)
Author:
deazer
Message:

Merge in latest trunk as verion we branched from fails some ORCA sette tests, latest version ok

Location:
NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX
Files:
3 deleted
12 edited
2 copied

Legend:

Unmodified
Added
Removed

  • NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/README.rst

    r10279 r10465  
    1 :Authors: NEMO System Team 
    21:Release: |release| 
    32:Date:    |today| 
    43 
    5 `NEMO`_ for *Nucleus for European Modelling of the Ocean* is a state-of-the-art modelling framework for 
    6 research activities and forecasting services in ocean and climate sciences. 
     4`NEMO`_ for *Nucleus for European Modelling of the Ocean* is a state-of-the-art modelling framework, 
     5for research activities and forecasting services in ocean and climate sciences, 
     6developed in a sustainable way by a European consortium since 2008. 
    77 
    88.. contents:: 
    … …  
    2121  (``./src/MBG``) :cite:`TOP_manual`. 
    2222 
    23 These physical core engines are described in their respective <reference publications> that must be cited for 
    24 any work related to their use. 
     23These physical core engines are described in their respective `reference publications`_, 
     24that must be cited for any work related to their use. 
    2525 
    26 Applications and capabilities 
    27 ============================= 
     26Assets and ready-to-use solutions 
     27================================= 
    2828 
    2929Not only does the NEMO framework model the ocean circulation, 
    3030it offers various features to enable 
    3131 
    32 - Create :doc:`embedded zooms <zooms>` seamlessly with 2-way nesting package `AGRIF`_. 
    33 - :doc:`Low cost biogeochemistry <coarsening>` and :doc:`alternative model opportunity <tracers>`. 
    34 - Versatile :doc:`assimilation <assimilation>`. 
    35 - :doc:`Output diagnostics <diagnostics>` with `XIOS`_ server. 
    36 - :doc:`Coupling <coupling>` via `OASIS`_ for Earth system modelling. 
     32- Create :doc:`embedded zooms <zooms>` seamlessly thanks to 2-way nesting package `AGRIF`_. 
     33- Opportunity to integrate an :doc:`alternative biogeochemistry model <tracers>` 
     34- Versatile :doc:`data_assimilation <data assimilation>`. 
     35- Generation of :doc:`diagnostics <diagnostics>` through effective `XIOS`_ server. 
     36- Roll-out Earth system modelling with :doc:`coupling interface <coupling>` to `OASIS`_. 
    3737 
    38 | Several :doc:`builtins configurations <configurations>` are provided to assess the skills and performances of 
     38| Several :doc:`built-in configurations <configurations>` are provided to evaluate the skills and performances of 
    3939   the model which can be used as templates for :doc:`setting up a new configuration <setup>` (``./cfgs``). 
    40 | The end user could also find some :doc:`idealised test cases <test_cases>` online to serve as templates and 
     40| The end user could also find online some :doc:`idealised test cases <test_cases>` to serve as templates and 
    4141   to study particular processes (``./tests``). 
    4242 
    4343A set of :doc:`utilities <tools>` is also provided to [pre|post]process your data (``./tools``). 
    4444 
    45 Literature 
    46 ========== 
     45Project literature 
     46================== 
    4747 
     48A tutorial  
    4849:doc:`install` 
    4950 
    … …  
    7677extensive :website:`bibliography <bibliography/publications>` published. 
    7778 
    78 Community development 
    79 ===================== 
     79Collaborative development 
     80========================= 
    8081 
    8182| The NEMO Consortium pulling together 5 European institutes (`CMCC`_, `CNRS`_, `MOI`_, `Met Office`_ and `NERC`_) 
    … …  
    8889When the need arises, :forge:`working groups <wiki/WorkingGroups>` are created or resumed to 
    8990gather the community expertise for advising on the development activities. 
     91 
     92:doc:`<contributing>` 

  • NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/cfgs/AGRIF_DEMO/README.rst

    r10279 r10465  
    1 ********************** 
    2 Embedded zooms (AGRIF) 
    3 ********************** 
     1************** 
     2Embedded zooms 
     3************** 
    44 
    55.. contents:: 

  • NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/cfgs/ORCA2_OFF_PISCES/EXPREF/file_def_nemo.xml

    r9909 r10465  
    130130          <field field_ref="LDlight"  /> 
    131131          <field field_ref="pdust"    /> 
    132           <field field_ref="Fe2"      /> 
    133132          <field field_ref="Fe3"      /> 
    134133          <field field_ref="FeL1"     /> 
    135           <field field_ref="FeL2"     /> 
    136           <field field_ref="FeP"      /> 
    137134          <field field_ref="TL1"      /> 
    138           <field field_ref="TL2"      /> 
    139135          <field field_ref="Sdenit"   /> 
    140136          <field field_ref="Totlig"   /> 

  • NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/cfgs/README.rst

    r10279 r10465  
    1 ***************************** 
    2 Run a reference configuration 
    3 ***************************** 
     1*************************** 
     2Run built-in configurations 
     3*************************** 
    44 
    55.. contents:: 
    … …  
    1414| :underline:`The NEMO System Team is in charge of these configurations`. 
    1515 
    16 +----------------------+-----+-----+-----+--------+-------+-------------------------------+ 
    17 |                      | OPA | SI3 | TOP | PISCES | AGRIF | Inputs                        | 
    18 +======================+=====+=====+=====+========+=======+===============================+ 
    19 | `AGRIF_DEMO`_        |  X  |  X  |     |        |   X   | - `AGRIF_DEMO_v4.0.tar`_      | 
    20 |                      |     |     |     |        |       | - `ORCA2_ICE_v4.0.tar`_       | 
    21 +----------------------+-----+-----+-----+--------+-------+-------------------------------+ 
    22 | `AMM12`_             |  X  |     |     |        |       | `AMM12_v4.0.tar`_             | 
    23 +----------------------+-----+-----+-----+--------+-------+-------------------------------+ 
    24 | `C1D_PAPA`_          |  X  |     |     |        |       | `INPUTS_C1D_PAPA_v4.0.tar`_  | 
    25 +----------------------+-----+-----+-----+--------+-------+-------------------------------+ 
    26 | `GYRE_BFM`_          |  X  |     |  X  |        |       | ``-``                         | 
    27 +----------------------+-----+-----+-----+--------+-------+-------------------------------+ 
    28 | `GYRE_PISCES`_       |  X  |     |  X  |   X    |       | ``-``                         | 
    29 +----------------------+-----+-----+-----+--------+-------+-------------------------------+ 
    30 | `ORCA2_ICE_PISCES`_  |  X  |  X  |  X  |   X    |       | - `ORCA2_ICE_v4.0.tar`_       | 
    31 |                      |     |     |     |        |       | - `INPUTS_PISCES_v4.0.tar`_  | 
    32 +----------------------+-----+-----+-----+--------+-------+-------------------------------+ 
    33 | `ORCA2_OFF_PISCES`_  |     |     |  X  |   X    |       | - `INPUTS_PISCES_v4.0.tar`_  | 
    34 |                      |     |     |     |        |       | - `ORCA2_OFF_v4.0.tar`_       | 
    35 +----------------------+-----+-----+-----+--------+-------+-------------------------------+ 
    36 | `ORCA2_OFF_TRC`_     |     |     |  X  |        |       | `ORCA2_OFF_v4.0.tar`_         | 
    37 +----------------------+-----+-----+-----+--------+-------+-------------------------------+ 
    38 | `ORCA2_SAS_ICE`_     |     |  X  |     |        |       | - `ORCA2_ICE_v4.0.tar`_       | 
    39 |                      |     |     |     |        |       | - `INPUTS_SAS_v4.0.tar`_      | 
    40 +----------------------+-----+-----+-----+--------+-------+-------------------------------+ 
    41 | `SPITZ12`_           |  X  |  X  |     |        |       | `SPITZ12_v4.0.tar`_           | 
    42 +----------------------+-----+-----+-----+--------+-------+-------------------------------+ 
     16+----------------------+-----+-----+-----+--------+-------+--------------------------+ 
     17|                      | OPA | SI3 | TOP | PISCES | AGRIF | Inputs                   | 
     18+======================+=====+=====+=====+========+=======+==========================+ 
     19| `AGRIF_DEMO`_        |  X  |  X  |     |        |   X   | - AGRIF_DEMO_v4.0.tar    | 
     20|                      |     |     |     |        |       | - ORCA2_ICE_v4.0.tar     | 
     21+----------------------+-----+-----+-----+--------+-------+--------------------------+ 
     22| `AMM12`_             |  X  |     |     |        |       | AMM12_v4.0.tar           | 
     23+----------------------+-----+-----+-----+--------+-------+--------------------------+ 
     24| `C1D_PAPA`_          |  X  |     |     |        |       | INPUTS_C1D_PAPA_v4.0.tar | 
     25+----------------------+-----+-----+-----+--------+-------+--------------------------+ 
     26| `GYRE_BFM`_          |  X  |     |  X  |        |       | ``-``                    | 
     27+----------------------+-----+-----+-----+--------+-------+--------------------------+ 
     28| `GYRE_PISCES`_       |  X  |     |  X  |   X    |       | ``-``                    | 
     29+----------------------+-----+-----+-----+--------+-------+--------------------------+ 
     30| `ORCA2_ICE_PISCES`_  |  X  |  X  |  X  |   X    |       | - ORCA2_ICE_v4.0.tar     | 
     31|                      |     |     |     |        |       | - INPUTS_PISCES_v4.0.tar | 
     32+----------------------+-----+-----+-----+--------+-------+--------------------------+ 
     33| `ORCA2_OFF_PISCES`_  |     |     |  X  |   X    |       | - INPUTS_PISCES_v4.0.tar | 
     34|                      |     |     |     |        |       | - ORCA2_OFF_v4.0.tar     | 
     35+----------------------+-----+-----+-----+--------+-------+--------------------------+ 
     36| `ORCA2_OFF_TRC`_     |     |     |  X  |        |       | ORCA2_OFF_v4.0.tar       | 
     37+----------------------+-----+-----+-----+--------+-------+--------------------------+ 
     38| `ORCA2_SAS_ICE`_     |     |  X  |     |        |       | - ORCA2_ICE_v4.0.tar     | 
     39|                      |     |     |     |        |       | - INPUTS_SAS_v4.0.tar    | 
     40+----------------------+-----+-----+-----+--------+-------+--------------------------+ 
     41| `SPITZ12`_           |  X  |  X  |     |        |       | SPITZ12_v4.0.tar         | 
     42+----------------------+-----+-----+-----+--------+-------+--------------------------+ 
    4343 
    4444AGRIF_DEMO 

  • NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/cfgs/SHARED/README.rst

    r10279 r10465  
    1 ****************** 
    2 Diagnostics (XIOS) 
    3 ****************** 
     1*********** 
     2Diagnostics 
     3*********** 
    44 
    55.. contents:: 

  • NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/latex/NEMO/subfiles/chap_misc.tex

    r10442 r10465  
    8181%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    8282 
     83%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
     84\begin{figure}[!tbp] 
     85  \begin{center} 
     86    \includegraphics[width=1.0\textwidth]{Fig_closea_mask_example} 
     87    \caption{ 
     88      \protect\label{fig:closea_mask_example} 
     89      Example of mask fields for the closea module. \textit{Left}: a 
     90      closea\_mask field; \textit{Right}: a closea\_mask\_rnf 
     91      field. In this example, if ln\_closea is set to .true., the mean 
     92      freshwater flux over each of the American Great Lakes will be 
     93      set to zero, and the total residual for all the lakes, if 
     94      negative, will be put into the St Laurence Seaway in the area 
     95      shown.  
     96    } 
     97  \end{center} 
     98\end{figure} 
     99%>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
    83100 
    84101% ================================================================ 
    … …  
    88105\label{sec:MISC_closea} 
    89106 
    90 \colorbox{yellow}{Add here a short description of the way closed seas are managed} 
    91  
     107Some configurations include inland seas and lakes as ocean 
     108points. This is particularly the case for configurations that are 
     109coupled to an atmosphere model where one might want to include inland 
     110seas and lakes as ocean model points in order to provide a better 
     111bottom boundary condition for the atmosphere. However there is no 
     112route for freshwater to run off from the lakes to the ocean and this 
     113can lead to large drifts in the sea surface height over the lakes. The 
     114closea module provides options to either fill in closed seas and lakes 
     115at run time, or to set the net surface freshwater flux for each lake 
     116to zero and put the residual flux into the ocean. 
     117 
     118Prior to NEMO 4 the locations of inland seas and lakes was set via 
     119hardcoded indices for various ORCA configurations. From NEMO 4 onwards 
     120the inland seas and lakes are defined using mask fields in the 
     121domain configuration file. The options are as follows. 
     122 
     123\begin{enumerate} 
     124\item{{\bf No ``closea\_mask'' field is included in domain configuration 
     125  file.} In this case the closea module does nothing.} 
     126 
     127\item{{\bf A field called closea\_mask is included in the domain 
     128configuration file and ln\_closea=.false. in namelist namcfg.} In this 
     129case the inland seas defined by the closea\_mask field are filled in 
     130(turned to land points) at run time. That is every point in 
     131closea\_mask that is nonzero is set to be a land point.} 
     132 
     133\item{{\bf A field called closea\_mask is included in the domain 
     134configuration file and ln\_closea=.true. in namelist namcfg.} Each 
     135inland sea or group of inland seas is set to a positive integer value 
     136in the closea\_mask field (see Figure \ref{fig:closea_mask_example} 
     137for an example). The net surface flux over each inland sea or group of 
     138inland seas is set to zero each timestep and the residual flux is 
     139distributed over the global ocean (ie. all ocean points where 
     140closea\_mask is zero).} 
     141 
     142\item{{\bf Fields called closea\_mask and closea\_mask\_rnf are 
     143included in the domain configuration file and ln\_closea=.true. in 
     144namelist namcfg.} This option works as for option 3, except that if 
     145the net surface flux over an inland sea is negative (net 
     146precipitation) it is put into the ocean at specified runoff points. A 
     147net positive surface flux (net evaporation) is still spread over the 
     148global ocean. The mapping from inland seas to runoff points is defined 
     149by the closea\_mask\_rnf field. Each mapping is defined by a positive 
     150integer value for the inland sea(s) and the corresponding runoff 
     151points. An example is given in Figure 
     152\ref{fig:closea_mask_example}. If no mapping is provided for a 
     153particular inland sea then the residual is spread over the global 
     154ocean.} 
     155 
     156\item{{\bf Fields called closea\_mask and closea\_mask\_emp are 
     157included in the domain configuration file and ln\_closea=.true. in 
     158namelist namcfg.} This option works the same as option 4 except that 
     159the nonzero net surface flux is sent to the ocean at the specified 
     160runoff points regardless of whether it is positive or negative. The 
     161mapping from inland seas to runoff points in this case is defined by 
     162the closea\_mask\_emp field.} 
     163\end{enumerate} 
     164 
     165There is a python routine to create the closea\_mask fields and append 
     166them to the domain configuration file in the utils/tools/DOMAINcfg directory.  
    92167 
    93168% ================================================================ 

  • NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/rst/source/NEMO_guide.rst

    r10279 r10465  
    4141 
    4242   zooms 
    43    coarsening 
    4443   coupling 
    4544   assimilation 
    … …  
    5655.. Next headings markup acording to readme.rst 
    5756 
    58 How to cite NEMO 
    59 ================ 
     57Reference publications 
     58====================== 
    6059 
    6160.. bibliography:: references.bib 

  • NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/rst/source/conf.py

    r10279 r10465  
    6363# directories to ignore when looking for source files. 
    6464# This pattern also affects html_static_path and html_extra_path . 
    65 exclude_patterns = ['global.rst'] 
     65exclude_patterns = ['global.rst', 'coarsening.rst'] 
    6666 
    6767# The name of the Pygments (syntax highlighting) style to use. 

  • NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/doc/rst/source/coupling.rst

    r10279 r10465  
    1 ********************** 
    2 Coupling (OASIS & SAS) 
    3 ********************** 
     1******** 
     2Coupling 
     3******** 
    44 
    55NEMO currently exploits OASIS-3-MCT to implement a generalised coupled interface 

  • NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/src/OFF/nemogcm.F90

    r10425 r10465  
    253253         ! 
    254254      ENDIF 
     255      ! open /dev/null file to be able to supress output write easily 
     256      CALL ctl_opn( numnul, '/dev/null', 'REPLACE', 'FORMATTED', 'SEQUENTIAL', -1, 6, .FALSE. ) 
     257      ! 
    255258      !                                      ! Domain decomposition 
    256259      CALL mpp_init                          ! MPP 

  • NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/src/SAS/nemogcm.F90

    r10425 r10465  
    302302         ! 
    303303      ENDIF 
     304      ! open /dev/null file to be able to supress output write easily 
     305      CALL ctl_opn( numnul, '/dev/null', 'REPLACE', 'FORMATTED', 'SEQUENTIAL', -1, 6, .FALSE. ) 
     306      ! 
    304307      !                                      ! Domain decomposition 
    305308      CALL mpp_init                          ! MPP 

  • NEMO/branches/UKMO/dev_10448_WAD_SBC_BUGFIX/src/TOP/README.rst

    r10279 r10465  
    1 ********************* 
    2 Oceanic tracers (TOP) 
    3 ********************* 
     1*************** 
     2Oceanic tracers 
     3*************** 
    44 
    55.. contents:: 
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