CHANGE LOG FOR ROMS_AGRIF
Date: 20 July 2010
Author : L. Debreu, P. Marchesiello, G. Cambon, P. Penven
Category : Release v2.1, for more informations, see
documentation
Description: This is the latest official ROMS_AGRIF release.
- 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
CHANGE LOG FOR ROMSTOOLS
2010
Date : 20 July 2010
Object : ROMSTOOLS release v2.1
Author : G. Cambon
Category : Release
Description : Compatible with ROMS_AGRIF v2.1
Some small bugs fixed and cleaning.
Date : 12 Mar. 2010
Object : ROMSTOOLS release 2.0-r588
Author : G. Cambon
Category : Release
Description : Updated version of ROMSTOOLS release V2.0 : Some cleaning and small bugs fixed
Date : 9 Mar. 2010
Author : G. Cambon and B. Le Vu
Category : Bug fix
Description : Update WOA2005 (not WOA2001): Bad fields for the NO3 seasonal fields, it was not the seasonnal means but the four first monthly means.
Date : 15 Feb. 2010
Object : ROMSTOOLS release V2.0
Author : G. Cambon, P. Penven, P. Marchesiello
Category: Release
Description: Updated version of ROMSTOOLS.
- Interannual preprocessing tools: Aforc_NCEP, Aforc_QuikSCAT and Oforc_OGCM
- Capabilities to use either OpenDap procedure or direct FTP procedure.
- Capabilities to set the overlapping parameters between monthly forcing files (atmopsheric surface forcing or oceanic boundary forcing).
- Capabilities to use QuikSCAT windspeed in the NCEP bulk files generation.
- Nesting_tools : take in account biogeochemical and biological model in nested forcing files generation creation.
- Forecast tools : add forecast capabilities using Mercator french operational system.
2008
Date : 29 September 2008 ! Change in the romstools associated to roms 2.0 !
Author : G. Cambon
Category: Cleaning
Description: Synchronisation of jobcomp between Roms_Agrif and Run. Add warning on/off in make_grid.m. Add drawnow command in test_clim and test_forcing.m
Date : 15 July 2008 ! Change in the romstools associated to roms2.0 !
Author : L. Renault & G. Cambon
Category : Update real time for NCEP bulk forcing file to compute the outgoing long wave online(roms_WW_alpha). Preprocessing_tools/create_bulk.f Aforc_NCEP_Update/interp_NCEP.m Description
Date : 9 July 2008 ! Change in the romstools associated to roms2.0 !
Author : G. Cambon
Category : Cleaning
Description : Modification and cleaning of PISCES preprocessing matlab routines. Preprocessing_tools/make_clim_pisces.m, make_bry_pisces.., add WOAPISCES data file.
Date: 30 April 2008
Author : S. Illig & G. Cambon
Category : Update and bug corrections
Description : Modify the NCEP bulk/frc file using the QuikSCAT daily data. Possibility to add the u-wind, v-wind, and wind speed fields in the QuikSCAT daily forcing files. Bugs corrections in make_NCEP.m
Modified files : make_QSCAT_daily.m, download_QSCAT.m, create_forcing_QSCAT.m, romstools_param.m, make_NCEP.m, make_NCEP_withQSCAT_daily.m.
Date: 28 April 2008
Author : N. Grima & G. Cambon
Category : bug fix
Description : Remove the NaN value in the QuikSCAT climatology.
Modified files : QSCAT_global_clim_jul99_aug06.nc changed in QSCAT_global_clim_2000_2007.nc
Date: 18 March 2008
Author : P. Penven & G. Cambon
Category : update
Description : Update Oforc_OGCM to use new SODA data v2p0p2-3.
Modified files : create_SODA.m, make_OGCM.m, extract_SODA.m
Date: 18 March 2008
Author : G. Cambon
Category : update
Description : Update Aforc_QuikSCAT : bug in download_QuikSCAT.m
Modified files : download_QuikSCAT.m
Date: 17 March 2008
Author : J. Lefèvre & G. Cambon
Category : update
Description : Update Aforc_NCEP scripts (Aforc_NCEP_Update.tar.gz file) to use nomads3 server.
Modified files : download_NCEP.m, extract_NCEP.m, get_NCEP_grid.m, interp_NCEP.m, make_NCEP.m, write_NCEP.m
2007
Date: 17 January 2007
Author : P. Penven
Category : update
Description : change run_roms_inter.csh to be able to use QuikSCAT wind stress with a bulk file from NCEP.
Modified files : run_roms_inter.csh
Date: 17 January 2007
Author : P. Penven
Category : bug fix
Description : keep OGCM=ECCO in make_OGCM_frcst.
Modified files : make_OGCM_frcst.m.
Date: 16 January 2007
Author : P. Penven
Category : update
Description : Use of OpenDAP for daily MWF QuikSCAT winds. New QuikSCAT climatology.
Modified files : romstools_param.m, start.m, Aforc_QSCAT directory, Preprocessing tools directory, QuikSCAT_clim directory.
Date: 15 January 2007
Author : T. Tan and P. Penven
Category : update
Description : Update of the documentation.
Modified files : Documentation_tools.
2006
Date: 15 November 2006
Author : P. Penven
Category : bug fix and update
Description : Correction in the mixed layer computation scripts + Lorbacher & Dommenget MLD routine added.
Modified files : Visualization_tools.
Date: 10 November 2006
Author : P. Penven
Category : update
Description : Test and update of the different test cases. Put a TEST_CASES directory into the run directory.
Modified files : Run and Testcases directories.
Date: 02 November 2006
Author : P. Penven
Category : update
Description : use of "Yorig" time in roms_gui and roms_anim.
Modified files : Visualization_tools & Diagnostic_tools directories.
Date: 31 October 2006
Author : P. Penven and M. Messier
Category : update
Description : several updates in ROMS_GUI: plot button, time_series, vertical profiles, several derived variables...
Modified files : Visualization_tools directory.
Date: 26 October 2006
Author : P. Penven
Category : update
Description : change add_ini_no3 and add_ini_chla so we can start a biological simulation after a spinup of the physics alone. + correction in NO3: below a certain value(1) NO3 is set to zero to prevent blooms at initialisation.
Modified files : add_ini_no3.m, add_ini_chla.m, make_biol.m .
Date: 25 October 2006
Author : P. Penven
Category : bug fix
Description : corrections in get_Meddy and get_Seddy
Modified files : Diagnostic_tools.
Date: 25 October 2006
Author : P. Penven
Category : bug fix
Description : wrong file names for SeaWifs
Modified files : SeaWifs dir.
Date: 25 October 2006
Author : P. Penven
Category : bug fix and update
Description : uwnd and vwnd reintroduced in the bulk file. uwnd and vwnd are added in the COADS05 dir and in the NCEP opendap tools
Modified files : COADS05, Aforc_NCEP, Preprocessing tools.
Date: 24 October 2006
Author : P. Penven
Category : update
Description : generalisation of the diagnostic tools to all roms variables (biology, etc..)
Modified files : Diagnostic_tools, Run
Date: 24 October 2006
Author : P. Penven
Category : update
Description : added editmask in make_grid
Modified files : make_grid.m
Date: 24 October 2006
Author : P. Penven
Category : update
Description : seawifs colormap changed, works now with vertical sections.
Modified files : Preprocessing_tools, Visualization_tools
Date: 24 October 2006
Author : J. Hermes
Category : bug fix
Description : change dl to allow zonal and meridian vertical sections.
Modified files : Visualization_tools
Date: 20 October 2006
Author : P. Penven and O. Aumont
Category : implementation
Description : Added 2 more datasets: WOA2005 and a SeaWifs global climatology (since chlorophylle is not included in WOA2005 yet).
Modified files : WOA2005 dir, SeaWifs dir
Date: 5 October 2006
Author : P. Penven
Category : bug fix and update
Description : cleaning of the forecast system and the scripts for climatology and inter_annual experiements.
Modified files : Forecast dir, Run dir
Date: 5 October 2006
Author : P. Penven
Category : bug fix and update
Description : problem for m_contour.m and m_contourf.m with matlab release 2006. add m_ellipse.m to make nice ellipses with m_map.
Modified files : m_map: m_contour.m m_contourf.m m_ellipse.m
Date: 5 October 2006
Author : P. Penven
Category : bug fix and update
Description : add a salinity test in the interpolation procedures to prevent the generation negative salinities close to rivers. correction of problem with add_topo at low resolution.
Modified files : Preprocessing tools (add_topo.m, ext_tracers.m,...)
Date: 5 October 2006
Author : P. Penven
Category : update
Description : Update of make_tides. Cleaning. Put the time in "Yorig" time (i.e. in days since 1 Jan Yorig). Use of TPXO6 and TPXO7.
Modified files : Tides directory + 2 new directories TPXO6 and TPXO7.
Date: 2 October 2006
Author : P. Penven
Category : update
Description : adapted x. capet storage of distance matrices for the objective analysis of pathfinder data. cleaning of pathfinder_sst.m
Modified files : pathfinder_sst.m, get_missing_val.m, oainterp.m, ext_data.m
Date: 2 October 2006
Author : P. Penven
Category : update and bug fix
Description : change 'title' variable name in romstools_param.m to avoid conflicts. This forced to change several files.
Modified files : Run/romstools_param.m + all make_XXX.m files.
Date: 2 October 2006
Author : P. Penven
Category : update
Description : Added a loaddap mex file for fedora in 32 bits, start.m is updated accordingly. loaddap needs a libdap library to be installed on the system
Modified files : Opendap_tools/FEDORA/* Run/start.m
Date: 29 September 2006
Author : P. Penven
Category : implementation
Description : add 3 buttons in nestgui: for the bulk files, to create a roms.in.# file and to creat an AGRIF_FixedGrids.in file
Modified files : Nesting_tools
Date: 29 September 2006
Author : P. Penven
Category : bug fix
Description : correction of the cpp keys for use with AGRIF + update start.m
Modified files : Run/cppdefs.h
Date: 29 September 2006
Author : P. Penven
Category : update
Description : put make_bulk.m and create_bulk.m in the Preprocessing tools directory. Add a test for the plots in make_bulk.m. remove Aforc_bulk.
Modified files : Aforc_bulk/ Preprocessing_tools/
Date: 28 September 2006
Author : P. Penven
Category : implementation
Description : interpolations for bulk files
Modified files : Nesting_tools
Date: 27 September 2006
Author : P. Penven
Category : bug fix and update
Description : use of the new grid filtering with nestgui + update system to prevent errors + cosmetics
Modified files : Nesting_tools
Date: 26 September 2006
Author : P. Penven
Category : bug fix
Description : ... missing at disp(['GET_MISSING_VAL: only ',num2str(sum(sum(isdata))),
Modified files : get_missing_val.m
Date: 26 September 2006
Author : Hector Hito Andres Sepulveda Allende and P. Penven
Category : bug fix
Description : correction for a non-integer day index
Modified files : Forecast_tools/extract_ECCO_frcst.m
Date: 26 September 2006
Author : P. Penven
Category : bug fix
Description : replace make_clim=1 make_bry=1, make_ini=1, make_frc=1, make_blk=1 and make_plot=1 by makeclim=1 makebry=1, makeini=1, makefrc=1, makeblk=1 and makeplot=1 to avoid conflicts between variable names and m-files names.
Modified files : romstools_param.m, make_OGCM_frcst.m, make_OGCM.m, make_NCEP.m, make_GFS.m, make_clim.m, make_forcing.m, make_grid.m
Date: 22 September 2006
Author : P. Penven
Category : update
Description : start.m check if the system is 64 bits or 32 bits and the matlab version for the use of mexnc or mexcdf and for the opendap library (for the moment, only the version for a readhat 64 bits is availlable).
Modified files : start.m
Date: 10 September 2006
Author : P. Penven, X Capet
Category : update
Description : Improved topography filtering in deep-sea areas in make_grid.m
Date: 10 September 2006
Author : P. Penven
Category : implementation
Description : Use of OpenDAP to get ECCO and GFS data for forecasts.
New files : Forecast_tools: download_ECCO_frcst.m get_GFS_fname.m interp_OGCM_frcst.m write_GFS.m download_GFS.m get_GFS.m make_GFS.m extract_ECCO_frcst.m get_GFS_subgrid.m make_OGCM_frcst.m
Date: 10 September 2006
Author : P. Penven
Category : implementation
Description : Generalisation of the use of romstools_param.h for the input parameters of ROMSTOOLS
Modified files : romstools_param.m, make_grid.m, make_forcing.m, make_clim.m, make_bry.m, make_tides.m, make_bulk.m, make_NCEP.m, make_OGCM.m
Date: 10 September 2006
Author : P. Penven
Category : implementation
Description : Matlab/Opendap routines for interannual simulations. Update of of make_ECCO: replacement by a more general make_OGCM which works for the moment with ECCO and SODA. Update of make_NCEP.
New files : Aforc_NCEP, Oforc_OGCM, Opendap_tools
Date: 10 September 2006
Author : P. Penven
Category : update
Description : GPL license added to ROMSTOOLS
Modified files : almost all files
2005
Date: 22 September 2005
Author : P. Marchesiello
Category : implementation
Description : implementation of routines to interpolate ECCO data on 2d boundary arrays (roms_ecco_bry.nc); There is now make_ecco_ini.m to create initial file without the whole make_ecco_clim process.
New files : ECCO: get_missing_val_ecco_bry.m hinterp_ecco_bry.m make_ecco_bry.m vinterp_ecco_bry.m; Preprocessing_tools: test_bry.m
Date: 15 September 2005
Author : P. Penven and P. Marchesiello
Category : implementation
Description : implementation of routines to interpolate clim data on 2d boundary arrays (roms_bry.nc); There is now make_ini.m to create initial file without the whole make_clim process.
New files : Preprocessing_tools: bry_interp.m create_bryfile.m create_bry_Z.m geost_currents_bry.m getpot_bry.m make_bry.m vinterp_bry.m
Date: 13 September 2005
Author : P. Penven and P. Marchesiello
Category : update
Description : update Roms_tools for matlab7.
New files : Preprocessing_tools: geost_currents.m make_clim.m make_coast.m make_grid.m smoothgrid.m; Netcdf_matlab/ncutility: mexcdf.m ncmex.m; Nesting_tools: vert_correct.m nested_clim.m nested_grid.m; ECCO: make_ecco_clim.m ext_data_ecco.m
Date: 15 June 2005
Author : P. Marchesiello
Category : cleaning
Description : replace lines mask=mask./mask for portability.
New files : make_grid.m, ... in Preprocessing_tools
Date: 15 April 2005
Author : L. Debreu
Category : cleaning
Description : Clean initialisation in case tini is different from clim times
New files : vinterp_clm.m make_clim.m in Preprocessing_tools
Date: 26 January 2005
Author : P. Marchesiello
Category : update
Description : add zooplankton pre-processing for BIOLOGY
initialization and boundary conditions
New files : Preprocessing_tools/add_zoo.m add_ini_zoo.m
2004
Date: 25 November 2004
Author : L. Debreu
Category : cleaning
Description : jobcomp in Run directory
New files : Run/jobcomp
Date: 24 November 2004
Author : P. Marchesiello
Category : cleaning
Description : jobcomp in Run directory was not updated
New files : Run/jobcomp
Date: 9 November 2004
Author : P. Marchesiello
Category : upgrade
Description : added the Bulk_forcing package to prepare COADS05 atmospheric fields
for heat flux bulk formulation in Roms_Agrif
New files : Bulk_forcing/create_bulk.m Bulk_forcing/make_bulk.m test_bulk.m as_consts.m
Date: 9 November 2004
Author : P. Marchesiello
Category : cleaning
Description : the (cheap) PERU regional case is default in both Run and
Preprocessing_tools
Modified files : Preprocessing_tools/make_grid.m Preprocessing_tools/make_clim.m
Run/param.h Run/cppdefs.h Run/roms.in Run/roms.in.1
Date: 13 September 2004
Author : P. Marchesiello
Category : Bug fixed in Nesting_tools and update in Run
Description : coma was missing in interp_restart; Roms_Agrif files were not up to date in Run
Modified files : Nesting_tools/interp_restart.m Run/jobcomp Run/param.h Run/cppdefs.h
Date: 10 September 2004
Author : P. Marchesiello
Category : upgrade Preprocessing_tools
Description : Replacement/Interpolation of Equatorial velocity values as an approximation to using the meridional differentiated form of the geostrophic equation.
Modified files : Preprocessing_tools/geost_currents.m
Date: 26 July 2004
Author : Pierrick Penven
Category : upgrade Nesting_tools
Description : Add a few capabilities to nestgui: display imin,imax,jmin,jmax values, possibility of a different hmin for the child, a button for the topogaphy, a button for volume corrections, a button for vertical corrections, a button for extrapolations of values under the mask, a button for biology, a button to get Isrc and Jsrc values for the rivers for the parent and the child.
modified files : Nesting_tools/*
Date: 26 July 2004
Author : Laurent Debreu, Pierrick Penven
Category : upgrade Nesting_tools
Description : Add a correction to the topography in order to get the same volume and the same section at the parent-child boundaries. Make sure that the mask is identical at the 2 first points close to parent-child boundaries
modified files : Nesting_tools/connect_volume.m, Nesting_tools/nested_grid.m, Nesting_tools/get_alpha.m, Nesting_tools/connect_topo.m
Date: 29 June 2004
Author : Patrick Marchesiello
Category : upgrade
Description : define biological variables and attributes in initial netcdf file
modified files : create_nestedinitial.m
Date: 21 June 2004
Author : Patrick Marchesiello
Category : upgrade
Description : replace scrum_mask with roms_mask developped by A. Shcherbina from UCSD
modified files : make_coast.m now produces coastfile_i_2.mat to be used by roms_mask; roms_mask makes a call to make_coast; make_grid is changed accordingly
Date: 26 May 2004
Author : Pierrick Penven
Category : upgrade
Description : add potential density (Rpot) and Brunt Vaissala Frequency (Bvf) in roms_gui
modified files : roms_gui.fig vertslice.m get_bvf.m bvf_eos.m get_pot.m rho_pot.m
Date: 26 May 2004
Author : Pierrick Penven
Category : bug fix
Description : correct get_psi in case of masking in the south-west corner (psi(1,1); case unconsidered previously)
modified files : get_psi.m
Date: 26 May 2004
Author : Pierrick Penven
Category : upgrade
Description : add quickscat wind climatology
modified files : Quickscat_wind/ directory added, start.m
Date: 26 May 2004
Author : Patrick Marchesiello, Pierrick Penven
Category : upgrade
Description : generate mpeg animations also
modified files : animation.m
Date: 26 May 2004
Author : Pierrick Penven
Category : upgrade
Description : make_forcing now handle rotated grids (use angle)
modified files : make_forcing.m
Date: 26 May 2004
Author : Pierrick Penven, Vincent Echevin
Category : upgrade
Description : Add a directory for the interpolation of Mercator Global Operational Model (POG) data at model boundaries
modified files : Mercator_interp/ directory added, start.m
Date: 26 May 2004
Author : Patrick Marchesiello, Xavier Capet, Pierrick Penven
Category : upgrade
Description : PATHFINDER SST data added for heat flux computation
modified files : SST_pathfinder/ directory added, start.m
Date: 26 May 2004
Author : Patrick Marchesiello, Hernan Arango
Category : upgrade
Description : scrum_mask added to the directory tree
modified files : mask/ directory added, start.m
Date: 26 May 2004
Author : Pierrick Penven
Category : upgrade
Description : Problem for the grids that cross the greenwich meridian or the 180 meridian solved.
modified files : ext_tracers.m, ext_data.m, add_topo.m
Date: 26 May 2004
Author : Patrick Marchesiello
Category : upgrade
Description : new netcdf library for IFC, compatible with fedora.
modified files : netcdf_ifc/libnetcdf.a
Date: 1 April 2004
Author : Laurent Debreu, Pierrick Penven
Category : upgrade
Description : roms_gui resizable
modified files : roms_gui.fig
Date: 1 April 2004
Author : Pierrick Penven
Category : upgrade
Description : add computation of potential temperature from in-situ
data (WOA2001)
modified files : theta.m getpot.m make_clim.m
Date: March 31 2004
Author : Pierrick Penven
Category : upgrade
Description : use of WOA2001 ocean atlas
modified files : WOA2001 directory
Date: March 31 2004
Author : Patrick Marchesiello
Category : bug fix
Description : use of 'nearest' Matlab data extrapolation instead
of oainterp. This is less costly for large domains.
modified files : get_missing_val.m
Date: March 31 2004
Author : Pierrick Penven
Category : upgrade
Description : add nesting graphic user interface
modified files : Nesting_tools directory
Date: March 31 2004
Author : Pierrick Penven, Patrick Marchesiello
Category : upgrade
Description : add tidal data
modified files : Tides directory
Date: March 31 2004
Author : Pierrick Penven
Category : upgrade
Description : add biological data capabilities
modified files : make_biol.m add_no3.m add_chla.m add_phyto.m
add_ini_no3.m add_ini_chla.m add_ini_phyto.m
Date: March 31 2004
Author : Pierrick Penven
Category : bug fix
Description : Possibility of crossing greenwitch meridian.
replacement of lognitude arrays from [0 360] to [-180 180].
modified files : all data netcdf files
CHANGE LOG FOR ROMSTOOLS UTILITIES
Date: 13 July 2010
Author : G. Cambon
Category : Release v2.1
Description :
- Update m_map version
- Update netcdf librairy for Matlab : change mexnc/ and netcdf_toolbox by mexcdf/netcdf_toolbox and mexcdf/mexnc, works on Matlab 7 and Matlab 8 (tested on R2008a), on both 32 and 64 bits plateforms.
- Add (but not used yet) mexcdf/snc_tools
- Replace mex60 by netcdf_matlab_60 , for Matlab 6 : work on both 32 and 64 bits plateforms.
