- Timestamp:
- 2019-01-28T17:20:19+01:00 (5 years ago)
- Location:
- NEMO/trunk
- Files:
-
- 6 edited
Legend:
- Unmodified
- Added
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-
NEMO/trunk/INSTALL.rst
r10559 r10596 13 13 include: the AGRIF preprocessing program "conv"; the FCM build system and the 14 14 IOIPSL library for parts of the output. 15 |16 15 - Other requirements that your system needs to provide include: a Perl 5 interpreter; a modern 17 16 Fortran compiler (ifort, gfortran, pgfortran, ...) and (in most cases) a MPI library … … 24 23 features to those defined within the MPI-2 standard (but will lose some performance 25 24 benefits). 26 | 25 27 26 The following prerequisites may already be installed or be available from the 28 27 official repositories of your Linux distribution. However access to all the … … 40 39 netcdf-c-4.6.2 and netcdf-fortran-4.4.4, state the following requirements for netCDF-4 support: 41 40 42 * HDF5 1.8.9 or later. 43 * HDF5 1.10.1 or later. 44 * zlib 1.2.5 or later (for netCDF-4 compression) 45 * curl 7.18.0 or later (for DAP remote access client support) 46 47 | 41 - HDF5 1.8.9 or later. 42 - HDF5 1.10.1 or later. 43 - zlib 1.2.5 or later (for netCDF-4 compression) 44 - curl 7.18.0 or later (for DAP remote access client support) 45 48 46 `Important Note: When building netCDF-C library versions older than 4.4.1, 49 47 use only HDF5 1.8.x versions. Combining older netCDF-C versions with newer -
NEMO/trunk/README.rst
r10592 r10596 60 60 61 61 .. _external biogeochemistry model : http://forge.ipsl.jussieu.fr/nemo/wiki/WorkingGroups/TOP/TOP-UserQuickGuide 62 .. _NEMO : https://www.nemo-ocean.eu/63 .. _OASIS : https://portal.enes.org/oasis64 .. _XIOS : http://forge.ipsl.jussieu.fr/ioserver65 .. _AGRIF : https://www-ljk.imag.fr/MOISE/AGRIF/66 62 .. _working groups : https://forge.ipsl.jussieu.fr/nemo/wiki/WorkingGroups 67 63 .. _reference documentation : https://www.nemo-ocean.eu/bibliography/documentation/ … … 69 65 .. _associated projects : https://www.nemo-ocean.eu/projects/ 70 66 .. _bibliography : https://www.nemo-ocean.eu/wp-content/plugins/wp-bibtexbrowser/bibtexbrowser.php?bib=nemo.bib 71 .. _CMCC : https://www.cmcc.it/72 .. _CNRS : http://www.cnrs.fr/73 .. _MOI : https://www.mercator-ocean.fr74 .. _Met Office : https://www.metoffice.gov.uk/75 .. _NERC : https://nerc.ukri.org/76 .. _`NEMO manual` : http://zenodo.org/badge/DOI/10.5281/zenodo.1464816.svg77 .. _`NEMO guide` : http://zenodo.org/badge/DOI/10.5281/zenodo.1475325.svg78 .. _`SI3 manual` : http://zenodo.org/badge/DOI/10.5281/zenodo.1471689.svg79 .. _`TOP manual` : http://zenodo.org/badge/DOI/10.5281/zenodo.1471700.svg80 -
NEMO/trunk/RELEASE_NOTES.rst
r10595 r10596 12 12 - Lateral melting 13 13 - Melt ponds: constant or :doi:`10.1175/JCLI-D-11-00078.1 <Holland et al. 2012>` formulation (and soon topographic melt ponds) 14 - Ice-atm. drags from :doi:`10.1029/2012JD017630 <Lupkes et al. 2012>` (depending on ice concentration) or 15 :doi:`10.1002/2014JD022418 <Lupkes et al. 2015>` (depending on sea ice concentration and atm. stability) 14 - Ice-atm. drags from :doi:`10.1029/2012JD017630 <Lupkes et al. 2012>` (depending on ice concentration) or :doi:`10.1002/2014JD022418 <Lupkes et al. 2015>` (depending on sea ice concentration and atm. stability) 16 15 - Landfast ice (:doi:`10.1002/2016JC012006 <Lemieux et al. 2016>`) 17 16 … … 64 63 The first test cases available for now are: 65 64 - ``CANAL``: east-west periodic canal of variable size with several initial states and associated geostrophic currents (zonal jets or vortex) 66 - ``ICE_AGRIF``: east-west + north-south periodic channel. 67 The common configuration includes an AGRIF zoom (1:3) in the middle of the basin to test how an ice patch is advected through it but one can also test the advection schemes (Prather and Ultimate-Macho) by removing the key_agrif in the cpp keys. 68 - ``ISOMIP``: simple box configuration with an ice shelf with simple geometry on top. 69 The purpose of this test case is to evaluate the impact of various schemes and new development with iceshelf cavities. 70 The exact original setup is described here. 71 - ``LOCK-EXCHANGE``:classical fluid dynamics experiment that has been adapted by Haidvogel and Beckmann (1999) for testing advection schemes in ocean circulation models. 72 It has been used by several authors including Burchard and Bolding (2002) and Ilıcak et al. (2012). 73 The LOCK EXCHANGE experiment can in particular illustrate the impact of different choices of numerical schemes and/or subgrid closures on spurious interior mixing 74 - ``OVERFLOW``: illustrates the impact of different choices of numerical schemes and/or subgrid closures on spurious interior mixing close to bottom topography. 75 It is adapted from the non-rotating overflow configuration described in Haidvogel and Beckmann (1999) and further used by Ilıcak et al. (2012) 76 - ``VORTEX``: illustrates the propagation of an anticyclonic eddy over a Beta plan and flat bottom. 77 It is implemented here with an online refined subdomain (thanks to AGRIF library) out of which the vortex propagates. 78 It serves as a benchmark to diagnose nesting errors as in Debreu et al. (2012), Penven et al. (2006) and Spall and Holland (1991) 79 - ``WAD``: a set of simple closed basin geometries for testing the Wetting and drying capabilities. 80 Examples range from a closed channel with EW linear bottom slope to a parabolic EW channel with a Gaussian ridge. 65 - ``ICE_AGRIF``: east-west + north-south periodic channel. The common configuration includes an AGRIF zoom (1:3) in the middle of the basin to test how an ice patch is advected through it but one can also test the advection schemes (Prather and Ultimate-Macho) by removing the key_agrif in the cpp keys. 66 - ``ISOMIP``: simple box configuration with an ice shelf with simple geometry on top. The purpose of this test case is to evaluate the impact of various schemes and new development with iceshelf cavities. The exact original setup is described here. 67 - ``LOCK-EXCHANGE``:classical fluid dynamics experiment that has been adapted by Haidvogel and Beckmann (1999) for testing advection schemes in ocean circulation models. It has been used by several authors including Burchard and Bolding (2002) and Ilıcak et al. (2012). The LOCK EXCHANGE experiment can in particular illustrate the impact of different choices of numerical schemes and/or subgrid closures on spurious interior mixing 68 - ``OVERFLOW``: illustrates the impact of different choices of numerical schemes and/or subgrid closures on spurious interior mixing close to bottom topography. It is adapted from the non-rotating overflow configuration described in Haidvogel and Beckmann (1999) and further used by Ilıcak et al. (2012) 69 - ``VORTEX``: illustrates the propagation of an anticyclonic eddy over a Beta plan and flat bottom. It is implemented here with an online refined subdomain (thanks to AGRIF library) out of which the vortex propagates. It serves as a benchmark to diagnose nesting errors as in Debreu et al. (2012), Penven et al. (2006) and Spall and Holland (1991) 70 - ``WAD``: a set of simple closed basin geometries for testing the Wetting and drying capabilities. Examples range from a closed channel with EW linear bottom slope to a parabolic EW channel with a Gaussian ridge. 81 71 82 72 New Reference configurations … … 97 87 - The passive tracers transport component was redesigned toward a modular structure and users can enable each module directly through logical flags in namelist_top (no more fortran macros!). 98 88 - :doc:`tracers <TOP on-line user documentation>` 99 - TOPcurrently accounts for the following 5 modules:100 CFCcontains inorganic carbon tracers (CFC11/CFC12/SF6),101 MY_TRCis a template for new modules (or external couplings),102 AGEdeals with water age tracking,103 C14as a radiocarbon passive tracer, and104 the companion ecosystem model PISCES.89 - ``TOP`` currently accounts for the following 5 modules: 90 ``CFC`` contains inorganic carbon tracers (CFC11/CFC12/SF6), 91 ``MY_TRC`` is a template for new modules (or external couplings), 92 ``AGE`` deals with water age tracking, 93 ``C14`` as a radiocarbon passive tracer, and 94 the companion ecosystem model ``PISCES``. 105 95 - A generalized infrastructure was developed to handle the prescription of either surface, coastal, or open boundaries conditions for each passive tracer. 106 96 - A new configuration, named ORCA2_OFF_TRC, was created to provide a benchmark simulation environment to deal with inert carbon tracers dynamics by exploiting the offline coupling with NEMO. -
NEMO/trunk/cfgs/README.rst
r10541 r10596 80 80 -------- 81 81 82 GYRE_BFM shares the same physical setup of GYRE_PISCES_, but NEMO is coupled with the `BFM <http://www.bfm-community.eu/>`_ biogeochemical model as described in : trac:`source:/NEMO/trunk/cfgs/GYRE_BFM/README`.82 GYRE_BFM shares the same physical setup of GYRE_PISCES_, but NEMO is coupled with the `BFM <http://www.bfm-community.eu/>`_ biogeochemical model as described in :forge:`browser/NEMO/trunk/cfgs/GYRE_BFM/README`. 83 83 84 84 … … 100 100 / 101 101 102 Note that, the default grid size is 30x20 grid points (with ``nn_GYRE = 1``) and vertical levels are set by ``jpkglo``. The specific code changes can be inspected at : trac:`source:/NEMO/trunk/src/OCE/USR`102 Note that, the default grid size is 30x20 grid points (with ``nn_GYRE = 1``) and vertical levels are set by ``jpkglo``. The specific code changes can be inspected at :forge:`browser/NEMO/trunk/src/OCE/USR` 103 103 104 104 **Running GYRE as a benchmark** : this simple configuration can be used as a benchmark since it is easy to increase resolution, with the drawback of getting results that have a very limited physical meaning. … … 217 217 Note that, this configuration default uses linear free surface (``ln_linssh = .true.``) assuming that model mesh is not varying in time and it includes the bottom boundary layer parameterization (``ln_trabbl = .true.``) that requires the provision of bbl coefficients through ``sn_ubl`` and ``sn_vbl`` fields. 218 218 219 It is also possible to activate PISCES model (see ORCA2_OFF_PISCES_) or a user defined set of tracers and source-sink terms with ``ln_my_trc = .true.`` (and adaptation of : trac:`source:/NEMO/trunk/src/TOP/MY_TRC` routines).219 It is also possible to activate PISCES model (see ORCA2_OFF_PISCES_) or a user defined set of tracers and source-sink terms with ``ln_my_trc = .true.`` (and adaptation of :forge:`browser/NEMO/trunk/src/TOP/MY_TRC` routines). 220 220 221 221 In addition, the offline module (OFF) allows for the provision of further fields: … … 235 235 236 236 237 More details can be found by inspecting the offline data manager at : trac:`source:/NEMO/trunk/src/OFF/dtadyn.F90`237 More details can be found by inspecting the offline data manager at :forge:`browser/NEMO/trunk/src/OFF/dtadyn.F90` 238 238 239 239 -
NEMO/trunk/doc/rst/source/NEMO_guide.rst
r10593 r10596 43 43 zooms 44 44 coupling 45 assimilation45 data_assimilation 46 46 tracers 47 47 -
NEMO/trunk/doc/rst/source/global.rst
r10557 r10596 16 16 .. Institutes 17 17 18 .. _CMCC: http ://www.cmcc.it19 .. _CNRS: http ://www.cnrs.fr20 .. _Mercator Ocean: http ://www.mercator-ocean.fr21 .. _Met Office: http ://www.metoffice.gov.uk22 .. _MOI: http ://www.mercator-ocean.fr23 .. _NERC: http ://nerc.ukri.org18 .. _CMCC: https://www.cmcc.it 19 .. _CNRS: https://www.cnrs.fr 20 .. _Mercator Ocean: https://www.mercator-ocean.fr 21 .. _Met Office: https://www.metoffice.gov.uk 22 .. _MOI: https://www.mercator-ocean.fr 23 .. _NERC: https://nerc.ukri.org 24 24 25 25 .. Models / Softwares 26 26 27 .. _AGRIF: http ://agrif.imag.fr28 .. _OASIS: http ://verc.enes.org/oasis29 .. _XIOS: http ://forge.ipsl.jussieu.fr/ioserver27 .. _AGRIF: https://agrif.imag.fr 28 .. _OASIS: https://portal.enes.org/oasis 29 .. _XIOS: https://forge.ipsl.jussieu.fr/ioserver 30 30 31 31 .. NEMO 32 32 33 .. _NEMO: http ://www.nemo-ocean.eu34 .. _NEMO strategy: http ://doi.org/10.5281/zenodo.147166335 .. _NEMO guide: http ://doi.org/10.5281/zenodo.147532536 .. _NEMO manual: http ://doi.org/10.5281/zenodo.146481637 .. _SI3 manual: http ://doi.org/10.5281/zenodo.147168938 .. _TOP manual: http ://doi.org/10.5281/zenodo.147170033 .. _NEMO: https://www.nemo-ocean.eu 34 .. _NEMO strategy: https://doi.org/10.5281/zenodo.1471663 35 .. _NEMO guide: https://doi.org/10.5281/zenodo.1475325 36 .. _NEMO manual: https://doi.org/10.5281/zenodo.1464816 37 .. _SI3 manual: https://doi.org/10.5281/zenodo.1471689 38 .. _TOP manual: https://doi.org/10.5281/zenodo.1471700
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