Changeset 11708


Ignore:
Timestamp:
2019-10-16T11:13:01+02:00 (11 months ago)
Author:
nicolasmartin
Message:

z

Location:
NEMO/trunk
Files:
5 edited

Legend:

Unmodified
Added
Removed
  • NEMO/trunk/INSTALL.rst

    r10991 r11708  
    2323- *Fortran* compiler (``ifort``, ``gfortran``, ``pgfortran``, ...), 
    2424- *Message Passing Interface (MPI)* implementation (e.g. |OpenMPI|_ or |MPICH|_). 
    25 - |NetCDF|_ library with its underlying |HDF|_  
     25- |NetCDF|_ library with its underlying |HDF|_ 
    2626 
    2727**NEMO, by default, takes advantage of some MPI features introduced into the MPI-3 standard.** 
     
    7474   | Combining older NetCDF-C versions with newer HDF5 1.10 versions will create superblock 3 files 
    7575     that are not readable by lots of older software. 
    76     
     76 
    7777Extract and install XIOS 
    7878======================== 
     
    9999   This version should be more stable (in terms of future code changes) than the XIOS trunk. 
    100100   It is also the version used by the NEMO system team when testing all developments and new releases. 
    101     
     101 
    102102   This particular version has its own branch and can be checked out and downloaded with: 
    103103 
     
    133133| ``src``   | Modelling routines                                         | 
    134134|           |                                                            | 
    135 |           | - ``ICE``: |SI3| for sea ice                               | 
     135|           | - ``ICE``: |NEMO-ICE| for sea ice                          | 
    136136|           | - ``NST``: AGRIF for embedded zooms                        | 
    137 |           | - ``OCE``: |OPA| for ocean dynamics                        | 
    138 |           | - ``TOP``: |TOP| for tracers                               | 
     137|           | - ``OCE``: |NEMO-OCE| for ocean dynamics                   | 
     138|           | - ``TOP``: |NEMO-MBG| for tracers                          | 
    139139+-----------+------------------------------------------------------------+ 
    140140| ``tests`` | :doc:`Test cases <test_cases>` (unsupported)               | 
     
    237237*   functions.sh : bash functions used by makenemo, for instance to create the WORK directory 
    238238*   cfg.txt : text list of configurations and source directories 
    239 *   bld.cfg : FCM rules to compile  
     239*   bld.cfg : FCM rules to compile 
    240240 
    241241Examples 
  • NEMO/trunk/README.rst

    r10991 r11708  
    33:SVN rev.: |revision| 
    44 
    5 NEMO_ for **Nucleus for European Modelling of the Ocean** is a state-of-the-art modelling framework for 
     5NEMO_ for *Nucleus for European Modelling of the Ocean* is a state-of-the-art modelling framework for 
    66research activities and forecasting services in ocean and climate sciences, 
    77developed in a sustainable way by a European consortium since 2008. 
     
    1515The NEMO ocean model has 3 major components: 
    1616 
    17 - |OPA| models the ocean {thermo}dynamics and solves the primitive equations 
    18   (``./src/OCE``) 
    19 - |SI3| simulates seaice {thermo}dynamics, brine inclusions and subgrid-scale thickness variations 
    20   (``./src/ICE``) 
    21 - |TOP| models the {on,off}line oceanic tracers transport and biogeochemical processes 
     17- |NEMO-OCE| models the ocean {thermo}dynamics and solves the primitive equations (``./src/OCE``) 
     18- |NEMO-ICE| simulates seaice {thermo}dynamics, brine inclusions and 
     19  subgrid-scale thickness variations (``./src/ICE``) 
     20- |NEMO-MBG| models the {on,off}line oceanic tracers transport and biogeochemical processes 
    2221  (``./src/TOP``) 
    2322 
    24 These physical core engines are described in their respective `references`_ that 
    25 must be cited for any work related to their use. 
     23These physical core engines are described in 
     24their respective `reference publications <#project-documentation>`_ that 
     25must be cited for any work related to their use (see :doc:`citations`). 
    2626 
    2727Assets and solutions 
     
    4242 
    4343The user can also checkout available :doc:`idealized test cases<test_cases>` that 
    44 address specific physical processes(``./tests``). 
     44address specific physical processes (``./tests``). 
    4545 
    4646A set of :doc:`utilities <tools>` is also provided to {pre,post}process your data (``./tools``). 
     
    5050 
    5151A walkthrough tutorial illustrates how to get code dependencies, compile and execute NEMO 
    52 (``./INSTALL.rst``) .  
     52(``./INSTALL.rst``). 
    5353 
    5454Reference manuals and quick start guide can be build from source and 
    5555exported to HTML or PDF formats (``./doc``) or 
    56 downloaded directly from the :website:`website<bibliography/documentation>`. 
     56downloaded directly from the :forge:`development platform<wiki/Documentations>`. 
    5757 
    58 =========== ===================== =============== 
    59  Component   Reference Manual      Quick start 
    60 =========== ===================== =============== 
    61  |OPA|       |NEMO manual|_        |NEMO guide| 
    62              :cite:`NEMO_manual` 
    63  |SI3|       |SI3 manual| 
    64              :cite:`SI3_manual` 
    65  |TOP|       |TOP manual| 
    66              :cite:`TOP_manual` 
    67 =========== ===================== =============== 
     58============ ================== ==================== 
     59 Component    Reference Manual   Quick start 
     60============ ================== ==================== 
     61 |NEMO-OCE|   |DOI man OCE|_     |DOI strt gui| 
     62 |NEMO-ICE|   |DOI man ICE| 
     63 |NEMO-MBG|   |DOI man MBG| 
     64============ ================== ==================== 
    6865 
    6966Since 2014 the project has a `Special Issue`_ in the open-access journal 
    70 Geoscientific Model Development (GMD) from the European Geosciences Union (EGU). 
     67Geoscientific Model Development (GMD) from the European Geosciences Union (EGU_). 
    7168The main scope is to collect relevant manuscripts covering various topics and 
    7269to provide a single portal to assess the model potential and evolution. 
     
    7976================= 
    8077 
    81 The NEMO Consortium pulling together 5 European institutes (CMCC_, CNRS_, MOI_, `Met Office`_ and NERC_) 
    82 plans the sustainable development in order to keep a reliable evolving framework since 2008. 
     78The NEMO Consortium pulling together 5 European institutes 
     79(CMCC_, CNRS_, MOI_, `Met Office`_ and NERC_) plans the sustainable development in order to 
     80keep a reliable evolving framework since 2008. 
    8381 
    84 It defines the |NEMO strategy|_ that is implemented by the System Team on a yearly basis in order to 
    85 release a new version almost every four years. 
     82It defines the |DOI dev stgy|_ that is implemented by the System Team on a yearly basis 
     83in order to release a new version almost every four years. 
    8684 
    8785When the need arises, :forge:`working groups<wiki/WorkingGroups>` are created or resumed to 
    8886gather the community expertise for advising on the development activities. 
    8987 
    90  
    91 .. Substitutions / Links 
    92  
    93 .. |NEMO manual| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1464816.svg 
    94 .. |NEMO guide|  image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1475325.svg 
    95 .. |SI3 manual|  image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1471689.svg 
    96 .. |TOP manual|  image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1471700.svg 
    97  
    98 .. |NEMO strategy| replace:: multi-year development strategy 
    99  
    100 .. _Special Issue: https://www.geosci-model-dev.net/special_issue40.html 
     88.. |DOI dev stgy| replace:: multi-year development strategy 
  • NEMO/trunk/cfgs/README.rst

    r10694 r11708  
    2525 
    2626.. code-block:: console 
    27                  
     27 
    2828   $ ./makenemo -r 'ORCA2_ICE_PISCES' -m 'my-fortran.fcm' -j '4' 
    2929 
     
    3434Then it will be possible to launch the execution of the model through a runscript 
    3535(opportunely adapted to the user system). 
    36     
     36 
    3737List of Configurations 
    3838====================== 
     
    4646 Configuration                     Component(s)                            Input & Forcing File(s) 
    4747---------------------- ---------------------------------- ------------------------------------------------ 
    48  Name                   OPA   SI3   TOP   PISCES   AGRIF 
     48 Name                   OCE   SI3   TOP   PISCES   AGRIF 
    4949====================== ===== ===== ===== ======== ======= ================================================ 
    5050 AGRIF_DEMO_             X     X                     X     AGRIF_DEMO_v4.0.tar, ORCA2_ICE_v4.0.tar 
     
    7373 
    7474The 1:1 grid can be used alone as a benchmark to check that 
    75 the model solution is not corrupted by grid exchanges.  
     75the model solution is not corrupted by grid exchanges. 
    7676Note that since grids interact only at the baroclinic time level, 
    7777numerically exact results can not be achieved in the 1:1 case. 
     
    8585a regular horizontal grid of ~12 km of resolution (see :cite:`ODEA2012`). 
    8686 
    87 This configuration allows to tests several features of NEMO specifically addressed to the shelf seas.  
     87This configuration allows to tests several features of NEMO specifically addressed to the shelf seas. 
    8888In particular, ``AMM12`` accounts for vertical s-coordinates system, GLS turbulence scheme, 
    8989tidal lateral boundary conditions using a flather scheme (see more in ``BDY``). 
     
    123123in the Beta-plane approximation with a regular 1° horizontal resolution and 31 vertical levels, 
    124124with PISCES BGC model :cite:`gmd-8-2465-2015`. 
    125 Analytical forcing for heat, freshwater and wind-stress fields are applied.   
     125Analytical forcing for heat, freshwater and wind-stress fields are applied. 
    126126 
    127127This configuration acts also as demonstrator of the **user defined setup** (``ln_read_cfg = .false.``) and 
     
    140140with the drawback of getting results that have a very limited physical meaning. 
    141141 
    142 GYRE grid resolution can be increased at runtime by setting a different value of ``nn_GYRE`` (integer multiplier scaling factor), as described in the following table:  
     142GYRE grid resolution can be increased at runtime by setting a different value of ``nn_GYRE`` (integer multiplier scaling factor), as described in the following table: 
    143143 
    144144=========== ========= ========== ============ =================== 
     
    154154Note that, it is necessary to set ``ln_bench = .true.`` in ``namusr_def`` to 
    155155avoid problems in the physics computation and that 
    156 the model timestep should be adequately rescaled.  
     156the model timestep should be adequately rescaled. 
    157157 
    158158For example if ``nn_GYRE = 150``, equivalent to an ORCA 1/12° grid, 
     
    161161Differently from previous versions of NEMO, 
    162162the code uses by default the time-splitting scheme and 
    163 internally computes the number of sub-steps.  
     163internally computes the number of sub-steps. 
    164164 
    165165ORCA2_ICE_PISCES 
     
    174174the ratio of anisotropy is nearly one everywhere 
    175175 
    176 this configuration uses the three components  
    177  
    178 - |OPA|, the ocean dynamical core  
    179 - |SI3|, the thermodynamic-dynamic sea ice model. 
    180 - |TOP|, passive tracer transport module and PISCES BGC model :cite:`gmd-8-2465-2015` 
     176this configuration uses the three components 
     177 
     178- |NEMO-OCE|, the ocean dynamical core 
     179- |NEMO-ICE|, the thermodynamic-dynamic sea ice model. 
     180- |NEMO-MBG|, passive tracer transport module and PISCES BGC model :cite:`gmd-8-2465-2015` 
    181181 
    182182All components share the same grid. 
     
    194194 
    195195.. code-block:: console 
    196                  
     196 
    197197        $ ./makenemo -r 'ORCA2_ICE_PISCES' -n 'AGRIF' add_key 'key_agrif' 
    198198 
     
    305305 
    306306.. Links and substitutions 
    307  
  • NEMO/trunk/doc/latex/NEMO/subfiles/chap_OBS.tex

    r11693 r11708  
    855855 
    856856%% ================================================================================================= 
    857 \section{Standalone observation operator} 
     857\section{Standalone observation operator (\texttt{SAO})} 
    858858\label{sec:OBS_sao} 
    859859 
  • NEMO/trunk/src/TOP/README.rst

    r10549 r11708  
    128128 
    129129.. literalinclude:: ../../namelists/namtrc_run 
     130   :language: fortran 
    130131 
    131132.. literalinclude:: ../../namelists/namtrc 
     133   :language: fortran 
    132134 
    133135.. literalinclude:: ../../namelists/namtrc_dta 
     136   :language: fortran 
    134137 
    135138.. literalinclude:: ../../namelists/namtrc_adv 
     139   :language: fortran 
    136140 
    137141.. literalinclude:: ../../namelists/namtrc_ldf 
     142   :language: fortran 
    138143 
    139144.. literalinclude:: ../../namelists/namtrc_rad 
     145   :language: fortran 
    140146 
    141147.. literalinclude:: ../../namelists/namtrc_snk 
     148   :language: fortran 
    142149 
    143150.. literalinclude:: ../../namelists/namtrc_dmp 
     151   :language: fortran 
    144152 
    145153.. literalinclude:: ../../namelists/namtrc_ice 
     154   :language: fortran 
    146155 
    147156.. literalinclude:: ../../namelists/namtrc_trd 
     157   :language: fortran 
    148158 
    149159.. literalinclude:: ../../namelists/namtrc_bc 
     160   :language: fortran 
    150161 
    151162.. literalinclude:: ../../namelists/namtrc_bdy 
     163   :language: fortran 
    152164 
    153165.. literalinclude:: ../../namelists/namage 
     166   :language: fortran 
    154167 
    155168Two main types of data structure are used within TOP interface to initialize tracer properties (1) and 
     
    321334 
    322335   bld::tool::fppkeys  key_iomput key_mpp_mpi key_top 
    323     
     336 
    324337   src::MYBGC::initialization         <MYBGCPATH>/initialization 
    325338   src::MYBGC::pelagic                <MYBGCPATH>/pelagic 
    326339   src::MYBGC::benthic                <MYBGCPATH>/benthic 
    327     
     340 
    328341   bld::pp::MYBGC      1 
    329342   bld::tool::fppflags::MYBGC   %FPPFLAGS 
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