ROMS_AGRIF is based on the Regional Ocean Modeling System (ROMS) and has benefited from developments made by the ROMS community. If not done yet, we encourage you to also register at the  official ROMS website. ROMSTOOLS is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. ROMSTOOLS is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ROMSTOOLS uses several Matlab Utilities, and Datasets available for download.

See Change Log section for Known problems and Fixes.


ROMS_AGRIF and ROMS_TOOLS VERSIONS ARE NOT EVOLVING ANYMORE

 

Roms_Agrif v3.1.1 : Latest stable version, 07 July 2014

./Roms_tools/Roms_Agrif/
Date: 07/07/2014
Compatible with Romstools.

DOWNLOAD ROMS_AGRIF V3.1.1 SOURCE FILES

See the changelog section


Roms_Agrif v3.1 : 03 February 2014

./Roms_tools/Roms_Agrif/
Date: 03/02/2014
Compatible with Romstools.

DOWNLOAD ROMS_AGRIF V3.1 SOURCE FILES

See the changelog section


Roms_Agrif v3.0  :

./Roms_tools/Roms_Agrif/

Date: 21/12/2012
Compatible with Romstools.

DOWNLOAD ROMS_AGRIF V3.0 SOURCE FILES

See the changelog section

Known problems and Fixes

  • 27 Aug. 2013: Error in wrt_avg for ubar, vbar and zeta. It writes the instantaneous value instead of the averaged value in the averaged output files. Thanks to S. Pous. Here is the fixed routine wrt_avg.F.fix_27Aug2013 (to be renamed wrt_avg.F)
  • 22 Mar. 2013: In set_global_definitions.h, change the default diffusion tensor rotation for the TS_HADV_RSUP3 and TS_HADV_RSUP5 tracer advection/diffusion scheme. The default rotation is now a geopotential rotation =>  # define TS_MIX_GEO. Please download the fix set_global_definition.h.fix ( to replace the original set_global_definitions.h)
  • 07 Mar. 2013Bug in OBC with NChlPZD and N2ChPZD2 model.  The anaytical value for the BGC variable not found in the netCDF lateral boundary files were not read in case of “BRY”-type netcdf files as they are supposed to do.  Please download the get_bry_bio.F.fix and analytical.F.fix . In Roms_tools/Roms_Agrif, replace the original get_bry_bio.F and analytical.F .
  • 04 Feb. 2013: Bug in def_his.F routines, for the writing of the fields Aks in the average netCDF files. The patch is here  (patch_def_his_Aks_04022013.diff). Download it, then go in Roms_tools/Roms_Agrif directory and type the command  patch -p0 < patch_def_his_aks_04022013.diff  to apply it.
  • 21 Jan. 2013: Bug in bulk_flux.F routines in case of non-fairall parametrization. The patch to apply (by doing patch < the_patch_file) in Roms_tools/Roms_Agrif is here  (patch_bulk_flux_21012013.diff)

Roms_Agrif v2.2  :

./Roms_tools/Roms_Agrif/
Date: 16/03/2012
Compatible with Romstools.

DOWNLOAD ROMS_AGRIF V2.2 SOURCE FILES | 16 March 2012


Roms_Agrif v2.1 :

./Roms_tools/Roms_Agrif/
./Roms_tools/Run_v.2.1/
Date: 20/07/2010
Compatible with Romstools.  

DOWNLOAD ROMS_AGRIF V2.1 SOURCE FILES | 20 July 2010

Known Problems and Fixes for V2.1

Bug fixes (12 April 2011)

  • Possibility to use the BRY files AND the biology modules (NPZD type model and PISCES). Better biogeochemical tracer management : some recoding did using a loop on the bgc tracers.
  • Unconsistency in Run_v2.1/roms_inter.in on the VSPONGE coefficient.  
  • Status : Fixed 
  • Solution: download this patch, untar it in ../Roms_tools. See the README_patch_romsagrif_12_04_2011.txt for more details and modified routines

Bug fixes (10 March 2011)

  • Avoid OpenMP false sharing. It was leading to non-reproductability of the model solution in case of OpenMP parallelization.
  • PSOURCE and ANA_PSOURCE in case of MPI
  • BULK and TIDES management
  • Unconsistency in roms_inter.in
  • Wrong declaration of flags wrtdia and wrtdia_avg in case of DIAGNOSTICS_BIO
  • Status : Fixed
  • Solution: download this patch, untar it in ../Roms_tools. See the README_patch_romsagrif_10_03_2011.txt for more details and modified routines

Unconsistency in the roms_inter.in, roms_forecasts.in and roms_hindcast.in file concerning the tracer equation and momentum equation diagnostics terms flags. (08 Oct 2010)

  • Status : Fixed
  • Solution: download this patch, untar it and place its content in the Roms_tools/RunV2.1 directory.

Problems of array dimensions for bry forcing in parallel mode. (27 Sept 2010)

  • Description : Serial/OpenMP vs MPI because of the extended bounds needed by MPI to do the message passing.
  • Status : Fixed
  • Solution: download this patch, untar it and place its content in the Roms_tools/Roms_Agrif sources directory

 


Roms_agrif users mailing list : mailing list used to exchange informations between the roms_agrif users.

2014

Date: 07 July 2014

Category : Release v3.1.1

Description: This is the latest official ROMS_AGRIF release.

ROMS_AGRIF v3.1.1 includes mainly many bug fixes for the previous release v3.1 and a few developments. We thank the developers who helped build this new version and users who helped testing previous one and beta versions.

The main bug fixes of ROMS_AGRIF v3.1.1 are:

  • KPP numerical closure new implementation (2005) : fix to limit extrapolation of Akv at level N and avoid negative values
  • Fixes to enable options of nudging SST or/and SSS towards prescribed ones when using BULK_FLUX
  • GLS_MIXING : bug fixes in MPI parallelization
  • Various bug corrections, mainly concerning parallelization

The main updates ROMS_AGRIF v3.1.1 are:

  • Updated PISCES biogeochemical model.
  • Improved WENO5 : from Borges et al. (2008) providing smoothness indicators of higher order, i.e., a scheme with less dissipation and better monotonicity preservation than the classical WENO5

Known problems, fixes and patches:

  • 18 July 2014: Typo bug fix in get_bry.F and get_bry_bio.F in Roms_Agrif/ directory . You only need these patches if you download ROMS_AGRIF v3.1.1 before the 18 July 2014.

Date: 03 February 2014

Category : Release v3.1

The main new features of the v3.1 release are:

  • New online ocean-atmosphere coupling between ROMS_AGRIF and the Weather Research and Forecasting Model (WRF) through the generic coupler OASIS3-MCT.
  • A new biogeochemical model BioEBUS: It is a 12 component nitrogen-based model including Nitrate, Nitrite, Ammonium, Dissolved Organic Nitrogen, Oxygen, Nitrous oxide, 2 Phytoplankton (Small and Large), 2 Zooplankton and 2 Detritus components. It is an advanced code of moderate complexity (compared with PISCES for example) particularly suited to upwelling regions and minimum oxygen zones.
  • New fifth-order Weighted Essentially Non-Oscillatory (WENO5) advection scheme. Advantages: high accuracy, positive definiteness, monotonicity, stability; it is well suited for simulation of frontal dynamics, especially with biogeochemical tracers. The advection scheme can be activated for biogeochemical tracers only if desired to avoid negative values caused by numerical overshoot.
  • Wave-Current interaction (MRL_WCI): The UCLA scheme presented in Uchiyama et al. (2010) was implemented in ROMS_AGRIF with addition of wetting/drying and nesting facilities. It includes a ray-theory spectrum-peak propagation and refraction model (WKB_WWAVE) for coupled studies or can use a forcing data set from stand alone wave models. This is still a work in progress but two new test cases can be used for testing: SHOREFACE and RIP.
  • GLS_MIXING: the Generalized Length Scale turbulent closure scheme was implemented (adapted from Warner et al., 2005)
  • WETTING_DRYING schemes: The John Warner scheme available in Rutgers ROMS was implemented in ROMS_AGRIF. It only works with the new coordinate system: NEW_S_COORD.
  • Various bug corrections, mainly concerning parallelization

Known problems, fixes and patches:

2012

Date: 21 December 2012

Author : P. Marchesiello, G. Cambon, L. Debreu, P. Penven
Category : Release v3.0
Description: Official ROMS_AGRIF release.

ROMS_AGRIF V3.0 includes many improvements, especially on the stability of lateral advection/diffusion. We thank the developers who helped build this release and users who helped testing previous releases and beta versions.

  • New NetCDF I/O file format for CF Convention compliance
    • New metric variables (horizontal and vertical) in grid file
    • New attributes (standard name, axis, etc …)
    • Possibility of defining a fillvalue in the land mask area
  • New advection schemes for tracers:
    • New RSUP3 (Upstream 3rd order advection with split and rotated diffusion) following Lemarié et al. (2012): there is now an implicit correction that removes all former stability constraints due to the rotation of bilaplacian diffusion. Bilaplacian diffusion can now be rotated along iso-neutral surfaces thanks to the stability treatment.
    • New 5th order advection scheme (UP5): this scheme required the addition of 1 layer of extra ghost cells (passing from 2 to 3) in MPI parallelization. That will be useful for future high-order scheme implementation. UP5 is cheaper than RSUP3 and requires fewer vertical levels but still shows significant diapycnal mixing above steep slopes (much less than UP3 though).
  • New vertical coordinate transformation (Vtransform =2) from UCLA code. This vertical sigma coordinate allows more geopotential orientation in the thermocline (less errors in pressure gradient and lateral mixing).
  • New KPP scheme from UCLA code. Built with fewer logical (IF) statements to reduce threshold effects.
  • Realistic river flow data can now be read from a NetCDF file (with CPP key PSOURCE_NCFILES)
  • Online-bulk forcing: allows reading atmospheric data files on their native grids. In this case, spatial interpolation on ROMS grid is done online and the usual bulk formulation is used with these data.
  • SST skin: a new routine computes a sea surface skin temperature using the prognostic scheme of Zeng and Beljaars (2005). The skin temperature replaces (with CPP key defined) the model top temperature in the bulk formulation.
  • Bug corrections: there were a few. An important one concerned using explicit viscosity with AGRIF. Most other bugs were in the parallelization.
  • Cleaning in NPZD type BGC model
    • N2P2Z2D2 model removed
    • Bug fixes in diagnostics bio
  • New jobcomp script, more robust

Known problems and Fixes:

  • 27 Aug. 2013: Error in wrt_avg for ubar, vbar and zeta. It writes the instantaneous value instead of the averaged value in the averaged output files. Thanks to S. Pous. Here is the fixed routine wrt_avg.F.fix_27Aug2013 (to be renamed wrt_avg.F)
  • 22 Mar. 2013: In set_global_definitions.h, change the default diffusion tensor rotation for the TS_HADV_RSUP3 and TS_HADV_RSUP5 tracer advection/diffusion scheme. The default rotation is now a geopotential rotation => # define TS_MIX_GEO. Please download the fix set_global_definition.h.fix ( to replace the original set_global_definitions.h)
  • 07 Mar. 2013: Bug in OBC with NChlPZD and N2ChPZD2 model. The anaytical value for the BGC variable not found in the netCDF lateral boundary files were not read in case of “BRY”-type netcdf files as they are supposed to do. Please download the get_bry_bio.F.fix and analytical.F.fix . In Roms_tools/Roms_Agrif, replace the original get_bry_bio.F and analytical.F .
  • 04 Feb. 2013: Bug in def_his.F routines, for the writing of the fields Aks in the average netCDF files. The patch is here (patch_def_his_Aks_04022013.diff). Download it, then go in Roms_tools/Roms_Agrif directory and type the command patch -p0 < patch_def_his_aks_04022013.diff to apply it.
  • 21 Jan. 2013: Bug in bulk_flux.F routines in case of non-fairall parametrization. The patch to apply (by doing patch < the_patch_file) in Roms_tools/Roms_Agrif is here (patch_bulk_flux_21012013.diff)

Date: 16 March 2012

Author : P. Marchesiello, G. Cambon, L. Debreu, P. Penven
Category : Release v2.2
Description: Official ROMS_AGRIF release v2.2

Known problems:

  • with AGRIF nesting, keep TNU2 and VISC2 values to zero. This problem is corrected in the next release.

2010

Date: 20 July 2010

Author : L. Debreu, P. Marchesiello, G. Cambon, P. Penven
Category : Release v2.1, for more informations, see documentation

  • AGRIF 2 way nesting with a full barotropic-baroclinic 2-way nesting.
  • AGRIF allows MPI parallelization of nesting, in addition to added flexibility and portability. In particular AGRIF executable conv (for generation of nested code) is auto-configured and amr.in is now transparent to ROMS developments (AGRIF manages the include files and variables to be interpolated).
  • New RSUP3 advection/diffusion schemes for tracers to reduce diapycnal diffusion along slopes.
  • Online diagnostics are added for tracers and momentum equations
  • New fields in outputs files: zonal and meridional wind stresses, wind speed, heat fluxes.
  • New bulk formulae for heat fluxes and wind stresses calculation (Fairall, 1996)
  • New biology models : NchlPZD, N2ChlPZD2, N2P2Z2D2
  • New biogeochemical models : PISCES
  • New parallelization optimization procesure : autotiling

Known problems:

  • with AGRIF nesting, keep TNU2 and VISC2 values to zero. This problem is corrected in the next release.

ROMSTOOLS V3.1.1 : Latest stable version, 07 July 2014.

  • ./Roms_tools/Aforc_NCEP/
  • ./Roms_tools/Aforc_QuikSCAT/
  • ./Roms_tools/Diagnostic_tools/
  • ./Roms_tools/Forecast_tools/
  • ./Roms_tools/Nesting_tools/
  • ./Roms_tools/Oforc_OGCM/
  • ./Roms_tools/Opendap_tools/
  • ./Roms_tools/Preprocessing_tools/
  • ./Roms_tools/Tides/
  • ./Roms_tools/Rivers/
  • ./Roms_tools/RUNOFF_DAI/
  • ./Roms_tools/Visualization_tools/
  • ./Roms_tools/

IMPORTANT : CHECK THE changelog section for eventual bug fixes

DOWNLOAD Matlab TOOLBOX ROMSTOOLS V3.1.1


ROMSTOOLS V3.1 : 03 February 2014.

See the changelog section 

DOWNLOAD Matlab TOOLBOX ROMSTOOLS V3.1

 Download the last complete patch here  (to be untar in Roms_tools/ directory) | 14 Feb. 2014

ROMSTOOLS V3.0 : 21 December 2012.

See the changelog section 

DOWNLOAD Matlab TOOLBOX ROMSTOOLS V3.0


ROMSTOOLS V2.2 : 16 March 2012.

DOWNLOAD Matlab TOOLBOX ROMSTOOLS V2.2


ROMSTOOLS V2.1 : 20 July 2010.

DOWNLOAD Matlab TOOLBOX ROMSTOOLS V2.1

Known Problems and Fixes for V2.1

UPDATES of Nesting_tools, Diagnostics_tools, Oforc_OGCM, Preprocessing_tools and Forecast_tools (15 April 2011)

  • Diagnostics_tools
    • copycsf.csh : a little problem with ncgen and the date attribute !! Correction of wrong interp_OGCM.m routine in the 12 April 2011 patch!!
  • Oforc_OGCM :
    • copycsf.csh : a little problem with ncgen and the date attribute !! Correction of wrong interp_OGCM.m routine in the 12 April 2011 patch!!
    • Url update
    • Speedup of interanual bry files processing
    • Some bug fixes in the local data processing of OBC file from local data (No OpenDAP)
  • Nesting_tools :
    • Better management of NPZD and/or PISCES initial files processing in nestgui.
  • Preprocessing_tools :
    • Possibility to create bry files for the NPZD biology module => make_bry_bgc.m
  • Forecast_tools :
    • Bug correction on GFS time ( ==> shift of 3 hours in atm; foring fields) : get_GFS.m and get_GDAS.m
    • Add some atm fields to be fully compatible with Roms_Agrif_v2.1
    • Add some missing scripts
  • Solution : download this patch and place it above Roms_tools directory to untar it (../Roms_tools)

Bug in make_NCEP.m : make_NCEP.m, get_NCEP_grid.m (16 February 2011)

  • Description
    •  make_NCEP.m : Bug fix in sms_time and bulk_time in case of overlap at the end using the next month
    • get_NCEP_grid.m : Bug in extraction of the NCEP data on the roms domain in case of Get_My_Data=1
  • Status : Fixed
  • Solution : download this patch and place it above Roms_tools directory to untar it (../Roms_tools)

Unconsistency in the roms_inter.in, roms_forecast.in and roms_hindcast.in file concerning the tracer equation and momentum equation diagnostics terms flags. (08 Oct 2010)

  • Status : Fixed
  • Solution: download this patch here, untar it and place its content in the Roms_tools/Run directory.

Bug in tides processing : make_tides.m script (27 Sept 2010)

  • Description : Error between tidal wave rank in the TPXO global tides and the tidal rank in ROMS forcing file containing the barotropic forcings imposed at the open boundary of the domain.
  • Status : Fixed
  • Solution : download this patch here, and place its contents in the Roms_tools/Tides directory

2016

4 Feb. 2016 : In Aforc_NCEP/, if you were using the ROMSTOOLS v3.1.1, there was a bug in the download_CFSR.m routines.

  • We were downloading heat fluxes variable for Upward Long wave, Downward and Upward Short wave. We were using the variables AT THE TOP OF THE ATMOSPHERE that was inducing large biais in SST in all the CFSR simulation. To use the right fluxes at THE SURFACE OF THE OCEAN, the vname values in download_CFSR.m
    -Upward_Long-Wave_Rad_Flux_surface
    -Downward_Short-Wave_Rad_Flux_surface
    -Upward_Short-Wave_Rad_Flux_surface
  • Here are the fixes:

2014

Date : 07 July 2014 Object : ROMSTOOLS release v3.1.1 Category : Release v3.1.1 Description : Compatible with ROMS_AGRIF v3.1.1 The main changes and updates are:

  • ECCO2 (mitgcm) oceanic reanalysis processing (0.5°x 0.5° resolution, every 3-days)
  • New procedure to compute daily averaged solar short wave radiation for PISCES biogeochemical model
  • Various cleaning (biogeochemical model pre-processing, etc …)

Known problems, fixes and patches:

  • 15 July 2014: In Aforc_NCEP/, additional routine add_radswbio_CFSR.m . It is useful to compute radswbio interannual atmopheric forcing, without diurnal cycle, needed by the biogeochemical model PISCES. You only need to download it if you download the ROMSTOOLS v3.1.1 release before the 16 July 2014.

Date : 03 February 2014 Object : ROMSTOOLS release v3.1 Author : G. Cambon, P. Penven, P. Marchesiello and R. Benshila Category : Release v3.1 Description : Compatible with ROMS_AGRIF v3.1 The major developments are:

  • New river runoff pre-processing tools:
    • New runoff global monthly climatology (Dai and Trenberth, 2002) including river position (the 925 main ones) and their runoff cycle.
    • Variable river flow and tracer concentrations are available
    • Automatic positioning of runoffs
  • Nesting_tools: update to manage the new biogeochemical model BioEBUS
  • Various cleaning (romstools_param.m, biogeochemical model pre-processing, etc …)

Known problems, fixes and patches: Download the last complete patch here (to be untar in Roms_tools/ directory) | 14 Feb. 2014

  • 14 Fev 2014: In Oforc_OGCM/, repair the oceanic boundary confition pre-processing coming from ECCO2 (MIT-GCM) global oceanic reanalysis update it to ECC2 version (higher resolution in space : 0.5° and time: every 3-days)
  • 12 Feb 2014: In Preprocessing_tools/, bug in make_n2o_biobus.m
  • 04 Feb. 2014: In Preprocessing_tools/, bugs in function names for add_bry_npzd.m and add_bry_bioebus.m.

2012

Date : 21 December 2012 Object : ROMSTOOLS release v3.0 Author : G. Cambon Category : Release v3.0 Description : Compatible with ROMS_AGRIF v3.0.

  • Various cleaning (romstools_param.m, overlapping period, etc ..)
  • New vertical sigma coordinate transformation
  • Nesting_tools: update to avoid masking problems with 2-way nesting
  • Interannual forcing: NCEP, CFSR, SODA (with the new SODA 2 reanalysis)
  • New WOAPICES datasets with Iron dust monthly climatology needed by PISCES (available in the DATASETS subsection of the “Download section”)

Known problems:

  • 10 Jan. 2014: In Run, update romstools_param.m to take into account the corrected/updated QSCAT/SCOW wind stress climatology file.
  • 04 Feb. 2013 : In Nesting_tools, backward compatibility problems with old matlab versions
    • Get the file nestgui.fig compatible : nestgui.fig
    • Get the patch for specific routines here : patch_nesting_tools_04022013.diff. Then, go in Roms_tools directory and type this command : patch -p1 -d ./Nesting_tools/ < patch_nesting_tools_04022013.diff

Source code

Documentation 

  • V3.0  (HTML, still under construction…)
  • V1.0  (PDF, P. Penven, 2000)

Old svn access, not maintained anymore:

Available on ROMS_AGRIF project on Inria Gforge

Register on Gforge Inria

First register on Gforge INRIA: https://gforge.inria.fr/projects/romsagrif/. Go to section New account, provide requested information, and use AIRSEA (Laurent Debreu’s research Team in LJK, Grenoble) as identification for Inria Team.

ROMS_AGRIF updates are listed here : http://lists.gforge.inria.fr/cgi-bin/mailman/private/romsagrif-commits/

Join the project ROMSAGRIF

The second step is to join the romsagrif project team. On your personal page, search for the project romsagrif, and ask to join it. An email will be sent to the project administrators.

How to download the code

You can download the trunk directory on our SVN server located at:

https://scm.gforge.inria.fr/svn/romsagrif/Roms_tools

You will download the source code of the ROMS AGRIF project (ROMS_AGRIF source code and Roms_tools matlab files). For that you have must use the version control system  Subversion (after installing it on your computer if needed), also called svn. More details can be found on the Inria Gforge help pages, online tutorial and FAQ:

  •  The “standard” users (it is the default status, only downloads allowed) will get the source code via the https procedure: 
    •  svn checkout –username your_login https://scm.gforge.inria.fr/authscm/your_login/svn/romsagrif/Roms_tools
  • The “developer” users (downloads and developments uploads allowed) will get the source code via the svn+ssh procedure:
    •  svn checkout svn+ssh://your_login@scm.gforge.inria.fr/svnroot/romsagrif/Roms_tools
  • Take care of the subversion configuration file : ~/.subversion/servers, in the section concerning the http-proxy :http-proxy-host and http-proxy-port
  • Changes related to Inriagforge SCM urls update after the June 2, 2015 migration:  here

How to update the code

  • Simply go to your romsagrif download directory and execute svn update romsagrif

NOTES: On Linux, you can use a graphical client to SVN such as  kdesvn that can help manage updates; other tools exist like TortoiseSVN, RapidSVN, … For more information:  http://siteadmin.gforge.inria.fr/FAQ.html.