------------------------------------------------------------------------ r1153 | vgarnier | 2011-01-28 19:44:31 +0100 (ven. 28 janv. 2011) | 1 ligne V8.18 highly recommended Version, stable for more than 1 year ! Final V8. At last cd ..cd ..! ------------------------------------------------------------------------ r1155 | vgarnier | 2011-01-29 14:05:24 +0100 (sam. 29 janv. 2011) | 1 ligne Bug on zize of obc_tide_sshw ------------------------------------------------------------------------ r1156 | vgarnier | 2011-01-30 11:21:47 +0100 (dim. 30 janv. 2011) | 1 ligne evolution of MARS environment to link toolcpp.h routine ------------------------------------------------------------------------ r1161 | vgarnier | 2011-03-03 11:29:31 +0100 (jeu. 03 mars 2011) | 1 ligne R. Ramel (Alyotech) : tools in python to check the variables of the code and detail the useful indexes ------------------------------------------------------------------------ r1162 | vgarnier | 2011-03-03 16:45:55 +0100 (jeu. 03 mars 2011) | 4 lignes Introduction of libraries netcdf4 (sequential, mpiifort and ifort+mpt Introduction l_parnc4 : to save in netcdf4 format l_iopack : to compact the variables in output files ------------------------------------------------------------------------ r1166 | vgarnier | 2011-03-03 23:32:19 +0100 (jeu. 03 mars 2011) | 1 ligne R. Ramel (Alyotech) : evolution of connect. Much much faster cd TOOLS/CONNECT/! ------------------------------------------------------------------------ r1167 | vgarnier | 2011-03-03 23:47:21 +0100 (jeu. 03 mars 2011) | 29 lignes R. Ramel (Alyotech) Creation of ionc4 librairie --------------------------- - update of ionetcdf in fortran 90 - the library is a module of MARS - A library can be linked. See directory LIB/libionc4 Compilation (Makefile.XX) ------------------------- - According to the type parallel I/O with intel compilor select: DIRNC = /home1/caparmor/rramel/netcdf4.1.2 ---> sequential I/O with intel compiler DIRNC = /home1/caparmor/rramel/netcdf4.1.2_par ---> parallel I/O with intel compiler DIRNC = /home1/caparmor/rramel/netcdf4.1.2_mpt ---> parallel I/O with intel compiler and MPT This third solution is much faster if you write your output files onto caparmor - For Agrif, remove the compilation of comionc4 and ionc4 routine, and define the variables DIRIONC and IONETCDF in the Makefile DIRIONC = $(HOMEMARS)/../LIB/libionc4/intel-seq ---> sequential I/O with intel compiler DIRIONC = $(HOMEMARS)/../LIB/libionc4/intel-mpi ---> parallel I/O with intel compiler DIRIONC = $(HOMEMARS)/../LIB/libionc4/intel-mpt ---> parallel I/O with intel compiler and MPT Parametrization for the output files ------------------------------------ Select l_out_nc4 to save the data in netcdf4 format Select l_out_pack to compress the value in netcdf output files (offset and scale are automatically computed from valid_min, valid_max and fill_value) ------------------------------------------------------------------------ r1168 | vgarnier | 2011-03-04 15:51:19 +0100 (ven. 04 mars 2011) | 1 ligne compilation avec -large des librairies ionc4 intel-mpi et intel ------------------------------------------------------------------------ r1169 | vgarnier | 2011-03-04 15:53:04 +0100 (ven. 04 mars 2011) | 3 lignes l_parnc4 becomes l_out_nc4par l_iopack becomes l_out_pack ------------------------------------------------------------------------ r1170 | vgarnier | 2011-03-04 15:59:40 +0100 (ven. 04 mars 2011) | 1 ligne V9.01 ! R. Ramel (Alyotech) Librairie ionc4 - ecriture/lecture parallele ------------------------------------------------------------------------ r1171 | vgarnier | 2011-03-04 16:48:07 +0100 (ven. 04 mars 2011) | 7 lignes svn merge -r1157:1165 /home/flamingo/vgarnier/MARS/CODE/branches/V8 changes into the trunk Modifications relative to the ecosystem: - advection scheme for the settling velocity (the cpp key named key_subs_part_eqsubdt is recommanded and works) - separation of the trajectory and Individual Based Model (M. Huret) - important modifications - traject2d is not maintained anymore ------------------------------------------------------------------------ r1173 | vg056b7 | 2011-03-19 14:58:15 +0100 (sam. 19 mars 2011) | 1 ligne R. Ramel (Alyotech) - ionc4 - complement for trajectory and stationnary point ------------------------------------------------------------------------ r1174 | vg056b7 | 2011-03-19 14:59:37 +0100 (sam. 19 mars 2011) | 1 ligne R. Ramel (Alyotech) - ionc4 - compilation of the ionc4 library with compilation option of the user ------------------------------------------------------------------------ r1175 | vg056b7 | 2011-03-20 11:01:38 +0100 (dim. 20 mars 2011) | 6 lignes F. Dumas - Continuum of the bottom stress between 2D and 3D dynamics (removing of strkler variable) - removing of igdu=2,3 (wet cell on the right(left) and dry cell on the left(right) WARNING : modification of the results ------------------------------------------------------------------------ r1177 | vg056b7 | 2011-03-21 12:47:19 +0100 (lun. 21 mars 2011) | 13 lignes Evolution of update functionality = merging changes of the reference MARS code into the user s routines In the .cshrc define : setenv HTTPSVNROOT https://forge.ifremer.fr/svn/mars3d (the path has chnged) setenv extranet_login yours To update the user routine, type the unique command gmake update "OLDREV=XXX" "NEWREV=XXX" (instead of gmake install "OLDREV=XXX" "NEWREV=XXX" ; update -s) ------------------------------------------------------------------------ r1178 | vg056b7 | 2011-03-21 12:48:03 +0100 (lun. 21 mars 2011) | 1 ligne removing of dh43 ------------------------------------------------------------------------ r1179 | vg056b7 | 2011-03-22 15:58:40 +0100 (mar. 22 mars 2011) | 1 ligne removing of libionetcdf because replaced by libionc4 ------------------------------------------------------------------------ r1180 | vg056b7 | 2011-03-22 16:16:17 +0100 (mar. 22 mars 2011) | 13 lignes Choose the number of cpu (total number MPI+OMP) echo usage : runmpi_connect name_run name_file number_cpu number_omp "1(one file)/2(several files)" concatdir echo at the end of each job, you will get name_run0.oJOB_NUMBER and name_run1.oJOB_NUMBER echo name_file is name_suffix, with name defined in output.dat and suffix defined in paracom.txt echo echo number_omp is the number of cpus used for OMP - must be lower than 8 - echo echo To gather files faster, it is better to write CPU parts into a global file created under echo a /home directory. You can specify the directory of concatenation through a 5th argument. exit 1 endif ------------------------------------------------------------------------ r1181 | vg056b7 | 2011-03-22 16:32:52 +0100 (mar. 22 mars 2011) | 13 lignes runmpiomp_connect : the evolution concerns the choice of the number of cpu of the same node using the OMP parallelisation usage : runmpi_connect name_run name_file number_cpu number_omp "1(one file)/2(several files)" concatdir (1) at the end of each job, you will get name_run0.oJOB_NUMBER and name_run1.oJOB_NUMBER (2) name_file is name_suffix, with name defined in output.dat and suffix defined in paracom.txt (3) number_cpu is the totale number of cpu (number of nodes * number of OMP cpus) (4) number_omp is the number of cpus used for OMP - must be lower than 8 - (5) To gather files faster, it is better to write CPU parts into a global file created under a /home directory. You can specify the directory of concatenation through a 5th argument. ------------------------------------------------------------------------ r1182 | vg056b7 | 2011-03-22 16:50:59 +0100 (mar. 22 mars 2011) | 3 lignes Correct fill_value for hx qnd hy in bathy_verif.nc file ------------------------------------------------------------------------ r1185 | vg056b7 | 2011-03-29 11:56:10 +0200 (mar. 29 mars 2011) | 8 lignes Initialisation of the arrays of surface drag and thermal exchange coefficients to take into account the dependence on air-sea temperature difference for the surface if imeteo_exchtype=1 only Such initialization allows future bilinear interpolation for Luyten & De Mulder (1992) (-Dkey_sflx_turb_luyten) and default (-Dkey_sflx_turb_default) formulations of latent and sensible heat fluxes estimate ------------------------------------------------------------------------ r1191 | vg056b7 | 2011-03-29 16:24:01 +0200 (mar. 29 mars 2011) | 6 lignes merge -r1186:1190 /home/flamingo/vgarnier/MARS/CODE/branches/V8/ changes into the trunk - Introduction of a new test case : castidalflat2dv - bug sedim.F90 - evolution contareaddat.F90 ------------------------------------------------------------------------ r1193 | vg056b7 | 2011-03-30 10:40:41 +0200 (mer. 30 mars 2011) | 1 ligne Introduction of a new test case : castidalflat2dv END ------------------------------------------------------------------------ r1195 | vg056b7 | 2011-03-30 16:16:14 +0200 (mer. 30 mars 2011) | 4 lignes merge -r1192:1194 /home/flamingo/vgarnier/MARS/CODE/branches/V8/ changes into the trunk - trajectories : modification (M. Huret) ------------------------------------------------------------------------ r1198 | vg056b7 | 2011-04-02 16:47:32 +0200 (sam. 02 avril 2011) | 9 lignes merge -r1194:1197 /home/flamingo/vgarnier/MARS/CODE/branches/V8/ changes into the trunk P. Le Hir, F. Dumas : Estimate and use of the percent of a cell that is wet. pwetmin must be as small as possible (0.01) to use this functionality. pwetmin=1.0_rsh means this functionality is off WARNING : this introduction might change the results even with aacmin=1, but it has not been observed. ------------------------------------------------------------------------ r1200 | vg056b7 | 2011-04-03 11:44:19 +0200 (dim. 03 avril 2011) | 1 ligne correction of r1198 : Estimate and use of the percent of wetting ------------------------------------------------------------------------ r1208 | vg056b7 | 2011-04-07 12:43:20 +0200 (jeu. 07 avril 2011) | 1 ligne elimination argument of test case subroutines ------------------------------------------------------------------------ r1209 | vg056b7 | 2011-04-07 13:28:28 +0200 (jeu. 07 avril 2011) | 13 lignes merge -r1201:1207 /home/flamingo/vgarnier/MARS/CODE/branches/V8/ changes into the trunk * correction initialisation latmax,latmin,lonmin,lonmax (bathy.F90) * complement for the introduction of the real wet surface (contasinksource.F90, submassbalance.F90) * correction bug on the vertical integration of concentations over small depths < hm (parsubeqhm.F90,tssubeqhm.F90) * (most of the routines) pwetmin becomes fwetmin ! fraction of minimum wetting pwetp becomes fwetp ! fraction of wet surface at previous time set pwet becomes fwet ! fraction of wet surface ------------------------------------------------------------------------ r1210 | vg056b7 | 2011-04-08 10:53:05 +0200 (ven. 08 avril 2011) | 1 ligne Important bug corrected on tosx and tosx in case l_meteo_stat=.true. or l_meteo_hom=.true. and l_sflx_solarcst=.true.i (was multiplied by cd and rhoair twice). WARNING : Change results for sure ! ------------------------------------------------------------------------ r1212 | vg056b7 | 2011-04-08 16:41:00 +0200 (ven. 08 avril 2011) | 1 ligne initialisation of latmin,latmax,lonmin,lonmax from locale variable lon2d et lat2d even for key_grid_rotated ------------------------------------------------------------------------ r1213 | vg056b7 | 2011-04-08 16:45:14 +0200 (ven. 08 avril 2011) | 8 lignes Precise ,l_out_nc4par=.true. as argument of ionc4_openr for all the files for which each cpu reads a small part of the global field WARNING, pay attention to choose DIRNC according to the FC - ifort with sequential netcdf library, - mpiifort with parallel netcdf library ------------------------------------------------------------------------ r1214 | vg056b7 | 2011-04-08 16:54:19 +0200 (ven. 08 avril 2011) | 1 ligne precise useful modules for the compilation with mpt ------------------------------------------------------------------------ r1215 | vg056b7 | 2011-04-11 08:25:59 +0200 (lun. 11 avril 2011) | 1 ligne sedim : introduction of ionc4_read_subzxyt and ionc4_read_subzzxyt ------------------------------------------------------------------------ r1219 | vg056b7 | 2011-04-17 22:04:51 +0200 (dim. 17 avril 2011) | 1 ligne upgrade of Makefile.linux to be used on flamingo ------------------------------------------------------------------------ r1220 | vg056b7 | 2011-04-17 22:31:51 +0200 (dim. 17 avril 2011) | 3 lignes merge -r1211:1218 /home/flamingo/vgarnier/MARS/CODE/branches/V8/ changes into the trunk (=V8.19 without ionc4 and arguments on test case routines (cas*.F90) ------------------------------------------------------------------------ r1223 | vg056b7 | 2011-04-19 17:14:21 +0200 (mar. 19 avril 2011) | 3 lignes merge -r1218:1222 /home/flamingo/vgarnier/MARS/CODE/branches/V8/ changes into the trunk (=V8.19 without ionc4 and arguments on test case routines (cas*.F90) ------------------------------------------------------------------------ r1224 | vg056b7 | 2011-04-20 16:02:53 +0200 (mer. 20 avril 2011) | 7 lignes V9.02 with corection sedim.F90 =V8.19 without ionc4 and arguments on test case routines (cas*.F90) ------------------------------------------------------------------------ r1225 | vg056b7 | 2011-04-22 10:46:42 +0200 (ven. 22 avril 2011) | 11 lignes Modifications relative to compilations in gfortran (gcc version 4.4.1 20090725 (Red Hat 4.4.1-2) sur flamingo) : - truncation of long lines - ionc4 introduced in ibm - small corrections linked to ionc4 - Errors in submassbalance.F90 (part of the subroutine is removed when using gfortran), sedim.F90 (-Dkey_sedim_mixsed), with -Dkey_agrif - Warning with -Dkey_dyn_pg_djcs, -Dkey_substance and ibm.F90 Add the key_gfortran cpp key to compile in gfortran ------------------------------------------------------------------------ r1227 | vg056b7 | 2011-04-22 16:31:56 +0200 (ven. 22 avril 2011) | 1 ligne bug on the time interpolation of substances at the open boundaries ------------------------------------------------------------------------ r1228 | vg056b7 | 2011-04-26 20:59:57 +0200 (mar. 26 avril 2011) | 5 lignes Bug in sflxsurf (phicon_atm). Concern people using substance and flux of substance through the air-sea interface outputsave.F90 : Removing of useless declaration paraspec.txt : Removing of useless description ------------------------------------------------------------------------ r1232 | vg056b7 | 2011-04-29 18:04:09 +0200 (ven. 29 avril 2011) | 2 lignes P. Lazure : Estimation and saving of all the terms of the dynamics (3D) equations ------------------------------------------------------------------------ r1234 | vg056b7 | 2011-05-03 22:22:31 +0200 (mar. 03 mai 2011) | 1 ligne correction relative the fraction of wet cell (fwetp) and the flux sflx_s2w from the sediment module : removing of fwetp in tssub* parsub* ------------------------------------------------------------------------ r1236 | vg056b7 | 2011-05-03 23:07:01 +0200 (mar. 03 mai 2011) | 1 ligne correction bug -Dkey_sedim_mixsed ------------------------------------------------------------------------ r1237 | vg056b7 | 2011-05-09 17:08:08 +0200 (lun. 09 mai 2011) | 6 lignes End of P. Lazure modification : Estimation and saving of all the terms of the dynamics (3D) equations : Correct creation of the output file with the new ionc4 + Removing of saving of Hà;hx,hx in case of agrif use, due to spurious effect. To see with L. Debreu. ------------------------------------------------------------------------ r1239 | vg056b7 | 2011-05-18 19:03:18 +0200 (mer. 18 mai 2011) | 1 ligne BUG in turbulence k- epsilon equation (turb_nbeq=2, turb_2eq_option=2) ------------------------------------------------------------------------ r1240 | vg056b7 | 2011-05-19 18:12:11 +0200 (jeu. 19 mai 2011) | 1 ligne backup before r1239 : no bug in turbulence k- epsilon equation (turb_nbeq=2, turb_2eq_option=2) actually ------------------------------------------------------------------------ r1241 | vg056b7 | 2011-05-19 18:13:27 +0200 (jeu. 19 mai 2011) | 1 ligne type correction on number. WARNING, May modify the results if use of turbulence k- epsilon equation (turb_nbeq=2, turb_2eq_option=2) ------------------------------------------------------------------------ r1243 | vg056b7 | 2011-06-06 14:58:40 +0200 (lun. 06 juin 2011) | 1 ligne BUG with the use of key_siggen (river discharge multiplied by 2). MODIFY the results ! ------------------------------------------------------------------------ r1244 | vg056b7 | 2011-06-06 15:04:56 +0200 (lun. 06 juin 2011) | 1 ligne Reading of the real date for the departure of the run from init_fromfile file, in order to allocate and initialize the tchrono variable correctly. May MODIFY and AVOID array exceeding during the time interpolation of data read from a *.dat file (i.e. river discharges, outflow...) ------------------------------------------------------------------------ r1245 | vg056b7 | 2011-06-06 15:05:49 +0200 (lun. 06 juin 2011) | 1 ligne test if value of the outflow remain positive. Stop the run if not ------------------------------------------------------------------------ r1250 | vg056b7 | 2011-06-07 15:59:30 +0200 (mar. 07 juin 2011) | 1 ligne correct initialisation of phimax and save time (add j index) ------------------------------------------------------------------------ r1251 | vg056b7 | 2011-06-07 16:00:14 +0200 (mar. 07 juin 2011) | 1 ligne removing of useless variables ------------------------------------------------------------------------ r1252 | vg056b7 | 2011-06-14 10:56:12 +0200 (mar. 14 juin 2011) | 4 lignes V9.02 init.F90 : postponing of checking on the compatibility between dates EXAMPLES/MENOR/paraspec.txt : modication of date_start3d (= date in file_init) ------------------------------------------------------------------------ r1253 | vg056b7 | 2011-06-14 10:57:20 +0200 (mar. 14 juin 2011) | 7 lignes V9.03 init.F90 : postponing of the checking on the compatibility between dates EXAMPLES/MENOR/paraspec.txt : modication of date_start3d (= date in file_init) obc2drankdefault.F90 : modification of the error message outflow.F90 : CALL_MPI ------------------------------------------------------------------------ r1255 | vg056b7 | 2011-06-23 15:29:45 +0200 (jeu. 23 juin 2011) | 1 ligne remove public declaration of internal variables ------------------------------------------------------------------------ r1256 | vg056b7 | 2011-06-24 11:04:47 +0200 (ven. 24 juin 2011) | 2 lignes Add intent everywhere but in PHYS/TIDE PHYS/AGRIF ------------------------------------------------------------------------ r1258 | vg056b7 | 2011-08-08 18:00:50 +0200 (lun. 08 août 2011) | 13 lignes NetCDF : introduction of the norme COMODO based on NetCDF Climate and Forecast (CF) Metadata Convention (1.4) MyOcean Information System and Service Desk specifications : Gridded Data Formats. MYO-MIS-TN-INT-GRIDS, 19/03/2010, v1.0/r0.3 CD-OCO Csv & Netcdf OCO user's manuel. COR-DO/DTI-MUT/07.159, 27/01/2011, Version 1.3 The modifications concern : - Dimensions are ni,nj - longitude and latitude are 2D variables and saved at location t,u,v,f - dx,dy are saved at location t,u,v,f - atributes content and coordinates ------------------------------------------------------------------------ r1259 | vg056b7 | 2011-08-09 12:54:15 +0200 (mar. 09 août 2011) | 17 lignes Update of mars_envir_manual.ppt manual (netcdf4 installation and mpi use on caparmor) Correction of the previous log (r1258) NetCDF : introduction of the COMODO-0.1 norm based on *CR des réunions et ateliers du projet MARMO. v1.1, 02/09/2010 *NetCDF Climate and Forecast (CF) Metadata Convention (1.4) *MyOcean Information System and Service Desk specifications : Gridded Data Formats. MYO-MIS-TN-INT-GRIDS, 19/03/2010, v1.0/r0.3 *CD-OCO Csv & Netcdf OCO user's manuel. COR-DO/DTI-MUT/07.159, 27/01/2011, Version 1.3 The modifications concern : - Dimensions are ni,nj - longitude and latitude are 2D variables and saved at location t,u,v,f - dx,dy are saved at location t,u,v,f - atributes content and coordinates ------------------------------------------------------------------------ r1260 | vg056b7 | 2011-08-10 09:32:09 +0200 (mer. 10 août 2011) | 1 ligne stop run if pb with mpi.txt file ------------------------------------------------------------------------ r1261 | vg056b7 | 2011-08-12 12:30:53 +0200 (ven. 12 août 2011) | 1 ligne back to r1259 because any MPI job is stopped with the previous addingsvn status! ------------------------------------------------------------------------ r1263 | vg056b7 | 2011-08-15 00:29:17 +0200 (lun. 15 août 2011) | 12 lignes Generalization of the initialization of the grid to irregular or rotated grids. - Readding of the longitude and latitude at locations t,u,v,f (bathy.F90) - Calculations of dx,dy,dx_u,dy_u,dx_v,dy_v,dx_p,dy_p in gridmetrics.F90 fron the latitude and longitude values IMPORTANT WARNING : the bathymetric files must be upgraded from MARS code if not issued from BMGTool (see notice_V9.03_V9.04) IMPORTANT : * tool_latlon2ij must be modified to find correct i,j in generic grids. DO NOT specify river or outflow locations by the geographical positions ! * tool_ind2lat, tool_ind2lon usefull for trajectory or ibm only (to find the precise location inside a cell). Not ready yet ! * In the future (after the evolution of the above tools), the head.CONF file will be dedicated to the specification of the locations of the 2d obc (rank purpose) ------------------------------------------------------------------------ r1264 | vg056b7 | 2011-08-16 20:59:14 +0200 (mar. 16 août 2011) | 8 lignes To manage with sleeping cpus, the initialization of arrays, for which the spatial extension is larger than the cpu domain, must be direct and can not results from an MPI exchange. In gridmetric.F90, all the dx,dy,dx_u... arrays must be assigned over their global domain. (All exchanges have been removed) In different routines of allocation, the following variables are set to 0 : zr,pr,buoy2d,htx,hty,u,v,whx,why ------------------------------------------------------------------------ r1265 | vg056b7 | 2011-08-18 23:57:21 +0200 (jeu. 18 août 2011) | 1 ligne minor correction for toolind2lon/lat (in case of rotated grid) ------------------------------------------------------------------------ r1268 | vg056b7 | 2011-08-21 18:28:26 +0200 (dim. 21 août 2011) | 6 lignes The spatial extension if ssh (xe,xeu,xev,xec...) becomes liminm1:limaxp1,ljminm1:ljmaxp1 because the non orthogonal curvilinear calculations use i-1 and j-1 indexes as weel as the BRGM module. ps AGRIF : exchanges of ssh have been added in agrifobcssh.F90 routine but results in MPI still differ from the sequential ones. ------------------------------------------------------------------------ r1269 | vg056b7 | 2011-08-21 18:29:37 +0200 (dim. 21 août 2011) | 1 ligne BRES config : reading of HX,HY ------------------------------------------------------------------------ r1270 | vg056b7 | 2011-08-23 08:52:59 +0200 (mar. 23 août 2011) | 1 ligne initxe.F90 : global first initialization to valmanq of ssh ------------------------------------------------------------------------ r1273 | vg056b7 | 2011-08-25 15:50:43 +0200 (jeu. 25 août 2011) | 1 ligne complement of revision 575 : introduction of the surge functionality in 3d ------------------------------------------------------------------------ r1274 | vg056b7 | 2011-08-25 15:51:36 +0200 (jeu. 25 août 2011) | 1 ligne Initialisation to 0 of diagnostic variables ------------------------------------------------------------------------ r1275 | vg056b7 | 2011-08-25 15:52:43 +0200 (jeu. 25 août 2011) | 1 ligne Introduction of the earth radius as a parameter (rt becomes radearth) ------------------------------------------------------------------------ r1276 | vg056b7 | 2011-09-04 19:16:56 +0200 (dim. 04 sept. 2011) | 1 ligne Correction OMP for P. Lazure modification : Estimation and saving of all the terms of the dynamics (3D) equations ------------------------------------------------------------------------ r1277 | vg056b7 | 2011-10-11 12:24:22 +0200 (mar. 11 oct. 2011) | 1 ligne Complement r1275 : Introduction of the earth radius as a parameter (rt becomes radearth) ------------------------------------------------------------------------ r1278 | vg056b7 | 2011-10-11 12:26:41 +0200 (mar. 11 oct. 2011) | 1 ligne Complement r1268 : The spatial extension of ssh (xe,xeu,xev,xec...) becomes liminm1:limaxp1,ljminm1:ljmaxp1 ------------------------------------------------------------------------ r1279 | vg056b7 | 2011-10-12 15:50:42 +0200 (mer. 12 oct. 2011) | 1 ligne Important correction for surges. WARNING : modify the results ! ------------------------------------------------------------------------ r1280 | vg056b7 | 2011-10-12 15:50:55 +0200 (mer. 12 oct. 2011) | 1 ligne Introduction of OMP into turbkl_gasp.F90 ------------------------------------------------------------------------ r1281 | vg056b7 | 2011-10-12 15:51:27 +0200 (mer. 12 oct. 2011) | 1 ligne Modification of the turbulent flux formulation Fairall about the unit of the rain ------------------------------------------------------------------------ r1282 | vg056b7 | 2011-10-12 17:05:48 +0200 (mer. 12 oct. 2011) | 1 ligne addition of ionc4_sync to avoid the loose of data in case of run crash ------------------------------------------------------------------------ r1283 | vg056b7 | 2011-10-12 17:07:11 +0200 (mer. 12 oct. 2011) | 1 ligne Complete line for the parametrization of ionc_conv_distribution_statement ------------------------------------------------------------------------ r1284 | vg056b7 | 2011-10-12 18:03:18 +0200 (mer. 12 oct. 2011) | 1 ligne output of the real concentrations and not the max of the concentration and 1.0e-30 ------------------------------------------------------------------------ r1285 | vg056b7 | 2011-10-13 14:32:28 +0200 (jeu. 13 oct. 2011) | 9 lignes Modifications of the test on icon to come back to the original meaning of icon : icon defines whether buoyancy effects are taken into account - 0 : no salinity, temperature and buoyancy computation - 1 : salinity, temperature and buoyancy are computed but the internal pressure gradient is not accounted for. - 2 : salinity, temperature and buoyancy are computed and the internal pressure gradient is accounted for. WARNING This modification may change the results of your simulation if icon==1 ------------------------------------------------------------------------ r1286 | vg056b7 | 2011-10-14 11:05:27 +0200 (ven. 14 oct. 2011) | 1 ligne MPI : amelioration with the initialization of fxeau ------------------------------------------------------------------------ r1287 | vg056b7 | 2011-10-14 14:24:26 +0200 (ven. 14 oct. 2011) | 1 ligne adding of MPI_FINALIZE before the exit of the main program at the end of the run ------------------------------------------------------------------------ r1288 | vg056b7 | 2011-10-14 14:25:28 +0200 (ven. 14 oct. 2011) | 1 ligne Complement r1268 and r1278 : The spatial extension of ssh (xe,xeu,xev,xec...) becomes liminm1:limaxp1,ljminm1:ljmaxp1 ------------------------------------------------------------------------ r1289 | vg056b7 | 2011-10-17 12:19:49 +0200 (lun. 17 oct. 2011) | 1 ligne FINAL complement r1268, r1278 and r1288 (correction bug on the spatial initialization of obc_tide_u*) : The spatial extension of ssh (xe,xeu,xev,xec...) becomes liminm1:limaxp1,ljminm1:ljmaxp1 ------------------------------------------------------------------------ r1290 | vg056b7 | 2011-10-17 12:29:46 +0200 (lun. 17 oct. 2011) | 5 lignes Correction incoherence of test on the location on the boundary child/mother In case of exact locations between the mother and child, this inconsistency induces disparities between jobs in seq and MPI. WARNING : may modify the results ------------------------------------------------------------------------ r1291 | vg056b7 | 2011-10-17 12:38:37 +0200 (lun. 17 oct. 2011) | 1 ligne correction of the bottom stress parametrisation : removing of the gravity (the bottom stress was 10 times too large !) - WARNING modify the results in 2D and over small depths in 3D ------------------------------------------------------------------------ r1292 | vg056b7 | 2011-10-17 12:39:17 +0200 (lun. 17 oct. 2011) | 1 ligne correction of the bottom stress parametrisation : removing of the gravity (the bottom stress was 10 times too large !) - WARNING modify the results in 2D and over small depths in 3D ------------------------------------------------------------------------ r1293 | vg056b7 | 2011-10-17 12:40:36 +0200 (lun. 17 oct. 2011) | 3 lignes correction declaration of ionc4_close (outputdiag.F90) correction mkconfdir to get the same output files in the chain of validation ------------------------------------------------------------------------ r1294 | vg056b7 | 2011-10-18 22:47:36 +0200 (mar. 18 oct. 2011) | 1 ligne turbulence 2 equations : introduction of OMP ------------------------------------------------------------------------ r1295 | vg056b7 | 2011-10-19 15:18:09 +0200 (mer. 19 oct. 2011) | 1 ligne Correction bug 6 : Initialization phieau and phicon. No pb for phisal and phieau ------------------------------------------------------------------------ r1296 | vg056b7 | 2011-10-20 09:55:41 +0200 (jeu. 20 oct. 2011) | 1 ligne Adaptation due to r1295 : initialization of phieau in initflux for test cases 5 and 6 (casevap, caschannel) ------------------------------------------------------------------------ r1297 | vg056b7 | 2011-10-20 10:05:58 +0200 (jeu. 20 oct. 2011) | 6 lignes FINAL complement r1268, r1278, r1288 and r1289 (correction for AGRIF) : The spatial extension of ssh (xe,xeu,xev,xec...) becomes liminm1:limaxp1,ljminm1:ljmaxp1 -Correction of the spatial extension of some variables (ssh,h0,hx,hy) to achiieve coherence within the code. -Declaration of the ID for hx,hy,h0 before the call of agrif_update_variable. -Exchanges of ssh added in r1268 have been removed. ------------------------------------------------------------------------ r1298 | vg056b7 | 2011-10-21 14:57:13 +0200 (ven. 21 oct. 2011) | 1 ligne tool to create a file of bathymetry compatible with the V9.04 (we need to estimate and save the longitude and latitude variables at locations t,u,v,f) ------------------------------------------------------------------------ r1299 | vg056b7 | 2011-10-21 15:00:09 +0200 (ven. 21 oct. 2011) | 1 ligne ionc4 : Introduction of ionc4_var_exists routine to check the existence of a variable in a netcdf file ------------------------------------------------------------------------ r1300 | vg056b7 | 2011-10-21 15:01:47 +0200 (ven. 21 oct. 2011) | 1 ligne key_tide_shom : introduction of a bilinear interpolation for high resolution grids (key_tide_shom_bilinear ------------------------------------------------------------------------ r1301 | vg056b7 | 2011-10-21 19:44:18 +0200 (ven. 21 oct. 2011) | 3 lignes - format COMODO0.1 for file bathy_verif.nc - shorten long lines of obcogcm.F90 in order to compile with gfortran ------------------------------------------------------------------------ r1302 | vg056b7 | 2011-10-21 19:45:42 +0200 (ven. 21 oct. 2011) | 1 ligne Evolution bathy_V8_to_V9.04.f90 : test on the existence of h0 ------------------------------------------------------------------------ r1303 | vg056b7 | 2011-10-21 19:57:02 +0200 (ven. 21 oct. 2011) | 1 ligne add batches to run with MPT ------------------------------------------------------------------------ r1307 | vg056b7 | 2011-10-27 12:50:46 +0200 (jeu. 27 oct. 2011) | 1 ligne introduction of OMP directives in parsub_budget_flxcum routine ------------------------------------------------------------------------ r1308 | vg056b7 | 2011-10-27 17:28:55 +0200 (jeu. 27 oct. 2011) | 1 ligne correction bug if river mouth on tidal flat. WARNING may modify the results ! ------------------------------------------------------------------------ r1311 | vg056b7 | 2011-10-27 18:33:58 +0200 (jeu. 27 oct. 2011) | 1 ligne Velocities set to valmanq in the output files. WARNING : Post-processing may require an adaptation ------------------------------------------------------------------------ r1312 | vg056b7 | 2011-10-28 07:47:19 +0200 (ven. 28 oct. 2011) | 1 ligne Decoupe tool : evolution to make sure ig,id,jb,jh are in active cpus ------------------------------------------------------------------------ r1313 | vg056b7 | 2011-10-28 07:58:19 +0200 (ven. 28 oct. 2011) | 1 ligne V9.04 (V8.19 without bugs 1-9 + ionc4 + COMODO0.1 norm + generic readding of grids (regular, rotated, curvilinear) + monitoring of terms in momentum equation + velocities set to valmanq over land in output file (Be careful in post-processing) ------------------------------------------------------------------------ r1314 | vg056b7 | 2011-10-28 14:24:05 +0200 (ven. 28 oct. 2011) | 16 lignes Trajectories and IBM modules : parallelisation MPI for simple sigma (not ready for generalized sigma yet) Has required the broadening of the spatial extension of the following variables : htx(liminm2:limaxp2,ljminm2:ljmaxp2) | liminm1:limax ,ljminm1:ljmaxp1 before hty(liminm2:limaxp2,ljminm2:ljmaxp2) | liminm1:limaxp1,ljminm1:ljmax before wz(0:kmax,liminm1:limaxp1,ljminm1:ljmaxp1) | limin:limaxp1,ljmin:ljmaxp1 before dx(liminm1:limaxp1,ljminm1:ljmaxp1) | liminm1:limaxp1,ljmin:ljmax before dy(liminm1:limaxp1,ljminm1:ljmaxp1) | liminm1:limaxp1,ljmin:ljmax before hc_sig(liminm2:limaxp2,ljminm2:ljmaxp2) | liminm1:limaxp1,ljminm1:ljmaxp1 before kz(kmax,liminm1:limaxp1,ljminm1:ljmaxp1) | limin:limax ,ljmin:ljmax before casbcvortex.F90 : Initialistion of correct longitudes and latitudes, different initialisation for rsh=8 (modification of limit) traject2d is not parallelized and is not upholded anymore. ------------------------------------------------------------------------ r1315 | vg056b7 | 2011-11-02 13:51:45 +0100 (mer. 02 nov. 2011) | 8 lignes Spatial extension de ssh to manage with trajectories and generalized sigma : ssh(liminm1:limaxp1,ljminm1:ljmaxp1) becomes ssh(liminm2:limaxp2,ljminm2:ljmaxp2) WARNINGS : - the case of cyclic conditions has not evolved. It seems it works but... - the Schwiderski model of tide has not been upgraded to this configuration - this modification implies a larged extension of h0, pa... next commit ------------------------------------------------------------------------ r1316 | vg056b7 | 2011-11-02 16:12:16 +0100 (mer. 02 nov. 2011) | 5 lignes Due to the new spatial extension of ssh (and obc_tide_ssh*), the variables h0 and pa must be extented to (liminm2:limaxp2,ljminm2:ljmaxp2) h0(liminm1:limaxp2,ljminm1:ljmaxp2) becomes h0(liminm2:limaxp2,ljminm2:ljmaxp2) pa(limin:limaxp1,ljmin:ljmaxp1) pa(liminm2:limaxp2,ljminm2:ljmaxp2) ------------------------------------------------------------------------ r1319 | vg056b7 | 2011-11-02 18:25:42 +0100 (mer. 02 nov. 2011) | 1 ligne correction Spatial extension of ssh for MPI ------------------------------------------------------------------------ r1320 | vg056b7 | 2011-11-03 10:05:08 +0100 (jeu. 03 nov. 2011) | 1 ligne correction declaration due to the Spatial extension of ssh for MPI ------------------------------------------------------------------------ r1321 | vg056b7 | 2011-11-03 10:05:41 +0100 (jeu. 03 nov. 2011) | 1 ligne Evolutions for gfortran ------------------------------------------------------------------------ r1324 | vg056b7 | 2011-11-04 12:11:45 +0100 (ven. 04 nov. 2011) | 1 ligne Evolution Makefile for eco3m on Caparmor ------------------------------------------------------------------------ r1325 | vg056b7 | 2011-11-04 12:15:23 +0100 (ven. 04 nov. 2011) | 1 ligne Evolution sedimentology : introduction of flx_w2s_sum ------------------------------------------------------------------------ r1326 | vg056b7 | 2011-11-04 16:07:41 +0100 (ven. 04 nov. 2011) | 5 lignes ~Generic~ search of the name of the dimensions in netcdf file in order to get the dimensions along X and Y of a file (JF Le Roux) The tested names are lon,longitude,LON,LONGITUDE and lat,latitude,LAT,LATITUDE ------------------------------------------------------------------------ r1327 | vg056b7 | 2011-11-04 18:06:36 +0100 (ven. 04 nov. 2011) | 1 ligne Evolution of submassbalance to save results in separate files (if to many variables) and to estimate the surface and volume of each area (B. Thouvenin) ------------------------------------------------------------------------ r1328 | vg056b7 | 2011-11-04 18:51:59 +0100 (ven. 04 nov. 2011) | 1 ligne New solution for tides : the OSU TOPEX/Poseidon Global Inverse Solution TPX0 (P. Douillet) ------------------------------------------------------------------------ r1329 | vg056b7 | 2011-11-04 19:00:05 +0100 (ven. 04 nov. 2011) | 1 ligne Correction r1328 : problem of compilation ------------------------------------------------------------------------ r1330 | vg056b7 | 2011-11-04 19:05:49 +0100 (ven. 04 nov. 2011) | 1 ligne removing of the obligation to use upwind scheme for the sandy variables ------------------------------------------------------------------------ r1331 | vg056b7 | 2011-11-10 11:22:48 +0100 (jeu. 10 nov. 2011) | 1 ligne Complement r1325 - Evolution sedimentology : introduction of flx_w2s_sum ------------------------------------------------------------------------ r1332 | vg056b7 | 2011-11-10 11:25:15 +0100 (jeu. 10 nov. 2011) | 1 ligne V9.05m + light modification of runmpiomp_connect and batch_mpiomp (idem for mpt) to correct the chain of validation of MARS ------------------------------------------------------------------------ r1333 | vg056b7 | 2011-11-16 18:47:06 +0100 (mer. 16 nov. 2011) | 1 ligne compilation of the ionc4 library with the options of compilation used for the MARS code ------------------------------------------------------------------------ r1334 | vg056b7 | 2011-11-18 16:03:54 +0100 (ven. 18 nov. 2011) | 1 ligne information to compile and run with the -mcmodel=large -shared-intel compilation options ------------------------------------------------------------------------ r1335 | vg056b7 | 2011-11-18 16:05:43 +0100 (ven. 18 nov. 2011) | 1 ligne minor corrections : unit of the salinity, PRINT_DBG ------------------------------------------------------------------------ r1336 | vg056b7 | 2011-11-18 17:09:02 +0100 (ven. 18 nov. 2011) | 1 ligne correction bug on the vertical integration of phicon over small depths < hm ------------------------------------------------------------------------ r1337 | vg056b7 | 2011-11-21 09:58:14 +0100 (lun. 21 nov. 2011) | 1 ligne Vertical repartition of phicon_atm for small depths (B. Thouvenin) ------------------------------------------------------------------------ r1338 | vg056b7 | 2011-11-21 15:15:06 +0100 (lun. 21 nov. 2011) | 1 ligne review of the attributes of the variables according to COMODO-0.1, CF-1.5 and CD-OCO-V1.3 ------------------------------------------------------------------------ r1339 | vg056b7 | 2011-11-21 17:25:44 +0100 (lun. 21 nov. 2011) | 1 ligne generic names name_in_longitude,name_in_longitude_u,... to read any bathymetric file ------------------------------------------------------------------------ r1340 | vg056b7 | 2011-11-21 18:27:55 +0100 (lun. 21 nov. 2011) | 1 ligne evolution packing : review of such valid_max/min and adding of valid_min/max_dx/dy ------------------------------------------------------------------------ r1341 | vg056b7 | 2011-11-22 10:10:17 +0100 (mar. 22 nov. 2011) | 1 ligne review of the value of valid_min_sal ------------------------------------------------------------------------ r1342 | vg056b7 | 2011-11-22 10:14:15 +0100 (mar. 22 nov. 2011) | 1 ligne evolution sedimentology and caschan* et castidalflat (F. Cayocca, B. Thouve) ------------------------------------------------------------------------ r1343 | vg056b7 | 2011-11-23 19:10:40 +0100 (mer. 23 nov. 2011) | 1 ligne evolution of the initialisation in output.F90 to run with l_out_precdate (precise date for output) or l_out_demer (demerliac filter) even though the choice of the firt date of the output is not correct (before or equal to the begining of the run) ------------------------------------------------------------------------ r1344 | vg056b7 | 2011-11-25 10:27:22 +0100 (ven. 25 nov. 2011) | 1 ligne correction OBC : characteristics method - WARNING : modify the results for l_obc_char ------------------------------------------------------------------------ r1345 | vg056b7 | 2011-11-25 10:34:09 +0100 (ven. 25 nov. 2011) | 1 ligne correction OBC : characteristics method - WARNING : modify the results for l_obc_char ------------------------------------------------------------------------ r1346 | vg056b7 | 2011-11-25 11:28:31 +0100 (ven. 25 nov. 2011) | 1 ligne l_obc_cycl : correction of a bug. Maybe not important because the cyclic obc is also applied just after this correction ------------------------------------------------------------------------ r1347 | vg056b7 | 2011-11-25 21:18:32 +0100 (ven. 25 nov. 2011) | 1 ligne correct the spatial extension on which the QUICK and QUICKEST schemes (momentum equation) can be estimated : a line or column less at the Southern and Western open boundary (F. Vandermeirsch) ------------------------------------------------------------------------ r1348 | vg056b7 | 2011-12-10 14:14:38 +0100 (sam. 10 déc. 2011) | 1 ligne evolution sedim ------------------------------------------------------------------------ r1349 | vg056b7 | 2011-12-10 14:17:52 +0100 (sam. 10 déc. 2011) | 1 ligne correction of mass balance ------------------------------------------------------------------------ r1350 | vg056b7 | 2011-12-10 14:21:40 +0100 (sam. 10 déc. 2011) | 5 lignes Management of outflows (atmospheric and oceanic) over wet-drying cells. - no atmospheric outflow over a dry cell - oceanic outflow is saved during the wetting and rejected when the cell becomes wet (introduction of phicon_drycell). This functionality is only available with the key_dyn_wetdry_fct cpp key. ------------------------------------------------------------------------ r1351 | vg056b7 | 2011-12-17 15:16:08 +0100 (sam. 17 déc. 2011) | 1 ligne complement OMP for revision r1350 (not sufficient nevertheless...) ------------------------------------------------------------------------ r1352 | vg056b7 | 2011-12-17 15:34:17 +0100 (sam. 17 déc. 2011) | 1 ligne Introduction of key_out_grid_smallsize cpp key in order to not save longitude_f, latitude_f and dx* grid variables ------------------------------------------------------------------------ r1353 | vg056b7 | 2011-12-17 16:05:23 +0100 (sam. 17 déc. 2011) | 1 ligne introduction of relaxation of tracer along open boundaries (commented) ------------------------------------------------------------------------ r1354 | vg056b7 | 2011-12-18 23:38:36 +0100 (dim. 18 déc. 2011) | 1 ligne Vertical repartition of the river ------------------------------------------------------------------------ r1355 | vg056b7 | 2011-12-18 23:55:35 +0100 (dim. 18 déc. 2011) | 1 ligne coorection erosion (from F. Dufois) ------------------------------------------------------------------------ r1356 | vg056b7 | 2011-12-19 00:07:47 +0100 (lun. 19 déc. 2011) | 1 ligne suite r1355 : correction of erosion for mudsand ------------------------------------------------------------------------ r1357 | vg056b7 | 2011-12-19 00:56:41 +0100 (lun. 19 déc. 2011) | 1 ligne complement initialisation for revision r1350 (not sufficient nevertheless for OMP...) ------------------------------------------------------------------------ r1358 | vg056b7 | 2011-12-23 23:16:37 +0100 (ven. 23 déc. 2011) | 1 ligne modif to remvoe a fort.XX file in MPI run ------------------------------------------------------------------------ r1359 | vg056b7 | 2011-12-23 23:19:41 +0100 (ven. 23 déc. 2011) | 3 lignes To have a correct name of the ouput file if a file by date and at a precise date Removing of isor : to be finished in castest*.F90 ------------------------------------------------------------------------ r1360 | vg056b7 | 2011-12-28 22:10:45 +0100 (mer. 28 déc. 2011) | 1 ligne complete modif r1358 to remove a fort.XX file for MPI run ------------------------------------------------------------------------ r1361 | vg056b7 | 2011-12-30 11:04:53 +0100 (ven. 30 déc. 2011) | 1 ligne complement r1355 for the chain of validation : correction of erosion for mudsand ------------------------------------------------------------------------ r1362 | vg056b7 | 2011-12-30 11:27:50 +0100 (ven. 30 déc. 2011) | 7 lignes Evoution of the test cases relative to the sedimentology : compilation of caschansed, caschansub and caschanconta in a unique test case : caschansed - to use additional substances (old caschansub) add the cpp key -Dkey_castestsub - to use the contaminant module (old caschanconta), add the cpp keys -Dkey_castestsub -Dkey_contaminant -Dkey_castestconta The parametrisation of caschansed and castidalflat2dv has been improved (WARNING : the results are changed for these test cases !) ------------------------------------------------------------------------ r1363 | vg056b7 | 2011-12-30 13:19:45 +0100 (ven. 30 déc. 2011) | 9 lignes A/ Review of the bottom stress in the 3d equations of the dynamics (S. Petton, F. Dumas, P. Lazure, V. Garnier) - Implicitation of the bottom stress (consistence between 2d and 3d) - removing of min , max in the formulation of the bottom stress, but adding of a safety catch : the bottom stress is estimated at a distance from the bottom further than z0 - the degree of implicitation is tuned by the coefficients cfroe and cfroi in parameters.F90 B/ Over small depths (igd=5), the 3d velocity profile is distributed according to a log profile WARNING : modify all the results in 3d ! ------------------------------------------------------------------------ r1364 | vg056b7 | 2011-12-31 16:53:54 +0100 (sam. 31 déc. 2011) | 1 ligne correction r1363 : bottom stress for small depth : log profile ------------------------------------------------------------------------ r1365 | vg056b7 | 2012-01-02 14:01:04 +0100 (lun. 02 janv. 2012) | 3 lignes IBM : evolutions MPI : management of buoy washed up ------------------------------------------------------------------------ r1366 | vg056b7 | 2012-01-02 18:19:45 +0100 (lun. 02 janv. 2012) | 1 ligne Removing of isor ------------------------------------------------------------------------ r1367 | vg056b7 | 2012-01-03 14:49:03 +0100 (mar. 03 janv. 2012) | 5 lignes OBC of tracers (T, S, substances) : introduction of the coefficient obc_coefrel to allow a pure prescription of OGCM values or a relaxation with a time scale of 1/obc_coefrel - obc_coefrel=0, pure prescription of T,S,substances (obc_sw...) - obc_coefrel/=0, relaxation towards OGCM values according to the coef dt*obc_coefrel (sal(k,i,j)*(1.0_rsh-dtrelax)+obc_sw(k,1,j)*dtrelax) ------------------------------------------------------------------------ r1368 | vg056b7 | 2012-01-04 07:50:20 +0100 (mer. 04 janv. 2012) | 3 lignes Introduction of 4 variables (nbvartraj_int,log,rsh,rlg) to specify the number of variables describing a particule according to their type (MPI purpose) ------------------------------------------------------------------------ r1369 | vg056b7 | 2012-01-04 08:04:39 +0100 (mer. 04 janv. 2012) | 4 lignes Introduction of the cpp key key_phicondrycell to save outflow amount during the drying and keep the balance Caschansed.F90 : hm=1 (WARNING : modify the result of this test case) ------------------------------------------------------------------------ r1370 | vg056b7 | 2012-01-04 08:07:35 +0100 (mer. 04 janv. 2012) | 1 ligne complement r1369 : management of the outflow (phicon) over tidal flat has been moved into outflow.F90 ------------------------------------------------------------------------ r1371 | vg056b7 | 2012-01-05 20:15:49 +0100 (jeu. 05 janv. 2012) | 1 ligne cpp program obsolete ans useless ------------------------------------------------------------------------ r1372 | vg056b7 | 2012-01-05 20:23:52 +0100 (jeu. 05 janv. 2012) | 1 ligne correction of the estimate of hz over small depth. WARNING : may modify the results for key_siggen and wet-drying ------------------------------------------------------------------------ r1373 | vg056b7 | 2012-01-05 21:02:01 +0100 (jeu. 05 janv. 2012) | 1 ligne evolution for gfortran ------------------------------------------------------------------------ r1374 | vg056b7 | 2012-01-05 21:15:28 +0100 (jeu. 05 janv. 2012) | 1 ligne initialisation of the time variable (t) if l_initfromfile=.true. but l_init_rtime=.false. ------------------------------------------------------------------------ r1375 | vg056b7 | 2012-01-06 09:18:29 +0100 (ven. 06 janv. 2012) | 1 ligne evolution of Malefile.linux for gfortran ------------------------------------------------------------------------ r1376 | vg056b7 | 2012-01-06 09:20:00 +0100 (ven. 06 janv. 2012) | 1 ligne evolution of the tidalflat test case ------------------------------------------------------------------------ r1377 | vg056b7 | 2012-01-06 09:20:56 +0100 (ven. 06 janv. 2012) | 1 ligne sedim : management of the erosion ------------------------------------------------------------------------ r1378 | vg056b7 | 2012-01-06 09:25:26 +0100 (ven. 06 janv. 2012) | 5 lignes Fluxes and MPI - test to make sure that an area of 2*2 from the meteorological file is read in parallel - initialisation of the wint, sat... variables to zero (before the reading) - evolution of estimate of the drag coefficient (charnock formulation) to avoid nul coefficient ------------------------------------------------------------------------ r1379 | vg056b7 | 2012-01-13 14:40:14 +0100 (ven. 13 janv. 2012) | 1 ligne wall at the eastern boundary for rank 0 is removed since the bathymetry of the rank 0 over the North East Atlantic is correct in V9.04 (/export/home11/mars/CONFIG/TOBY/DATA/hxhy_rang0_oco1.4.nc) ------------------------------------------------------------------------ r1380 | vg056b7 | 2012-01-16 10:35:30 +0100 (lun. 16 janv. 2012) | 4 lignes zoom and MPI : - if l_out_nc4par=.true. (writing in parallel by all the cpus at the same time), a new communicator must be defined and used : it includes only the cpus active over the area of the zoom. - to specify the attributes min/max of the bathymetry, a reduction is called. It uses all the cpus (MPI_COMM_WORLD) by default. The new communicator (of active cpus over the zoom) must be specified and is given through an optional argument. ------------------------------------------------------------------------ r1381 | vg056b7 | 2012-01-16 10:48:05 +0100 (lun. 16 janv. 2012) | 3 lignes IMPORTANT CORRECTION to allow a wind forcing cst in space and time throughout the simulation. WARNING, modify the results for l_meteo_stat=.true. and wind_veloc/=0 ------------------------------------------------------------------------ r1382 | vg056b7 | 2012-01-16 10:49:53 +0100 (lun. 16 janv. 2012) | 2 lignes Tests on the parametrization of the wind forcing to force the user to parametrize properly and to decide by himself about the atmosphrical forcing. ------------------------------------------------------------------------ r1383 | vg056b7 | 2012-01-17 21:34:44 +0100 (mar. 17 janv. 2012) | 1 ligne correction r1380 (zoom) for sedimoutput.F90 ------------------------------------------------------------------------ r1384 | vg056b7 | 2012-01-17 21:36:38 +0100 (mar. 17 janv. 2012) | 1 ligne test on departure time : adding of 1 seconde to manage with decimal times ------------------------------------------------------------------------ r1385 | vg056b7 | 2012-01-18 08:58:23 +0100 (mer. 18 janv. 2012) | 1 ligne config TOBY : wind forcing constant in space and time and equal to 5 m/s ------------------------------------------------------------------------ r1386 | vg056b7 | 2012-01-25 13:07:39 +0100 (mer. 25 janv. 2012) | 1 ligne TRAJ : correction ------------------------------------------------------------------------ r1387 | vg056b7 | 2012-01-25 13:08:52 +0100 (mer. 25 janv. 2012) | 1 ligne OUTPUT : correction of bugs for diagnostics and demerliac functinality ------------------------------------------------------------------------ r1388 | vg056b7 | 2012-01-25 13:09:41 +0100 (mer. 25 janv. 2012) | 1 ligne SFLX Large and Yeager formula : correction bug (minor) ------------------------------------------------------------------------ r1389 | vg056b7 | 2012-01-25 13:10:44 +0100 (mer. 25 janv. 2012) | 1 ligne Chain of valaidation : evolution of output.dat files to test the restart, demerliac and zoom functionalities ------------------------------------------------------------------------ r1390 | vg056b7 | 2012-01-25 19:31:44 +0100 (mer. 25 janv. 2012) | 1 ligne Improvement of the copyconfig command (S. Theetten) ------------------------------------------------------------------------ r1391 | vg056b7 | 2012-01-26 16:52:29 +0100 (jeu. 26 janv. 2012) | 1 ligne complement of r1390 : Improvement of the copyconfig command (S. Theetten) ------------------------------------------------------------------------ r1392 | vg056b7 | 2012-01-26 19:30:07 +0100 (jeu. 26 janv. 2012) | 1 ligne Evolution of the test case btcurrent : the current is oblique ------------------------------------------------------------------------ r1393 | vg056b7 | 2012-01-30 10:48:37 +0100 (lun. 30 janv. 2012) | 1 ligne Evolution of the test case btcurrent : the initial condition is perturbated to see if it converges or not ------------------------------------------------------------------------ r1394 | vg056b7 | 2012-01-31 15:22:08 +0100 (mar. 31 janv. 2012) | 1 ligne evolution of the chain of validation for MENOR ------------------------------------------------------------------------ r1395 | vg056b7 | 2012-02-02 19:01:17 +0100 (jeu. 02 févr. 2012) | 1 ligne Initialization of dx and dy at the corners (limaxp1:ljmaxp1...) for trajectory needs ------------------------------------------------------------------------ r1396 | vg056b7 | 2012-02-03 10:28:57 +0100 (ven. 03 févr. 2012) | 16 lignes Important modification of the estimation of the viscosity and diffusivity coefficients (A.C Bennis, F. Dumas) resolution with 2 equations of turbulence : ------------------------------------------- - Introduction of the mixing length due to surface waves - corrections - duplication of nz and kz at kmax (= nz/kz(kmax-1)). We increase the mixing at the surface. equation of Gaspard (1 equation of turbulence solved) : ------------------------------------------------------- - Introduction of the mixing length due to surface waves and bottom rugosity - duplication of nz and kz at kmax (= nz/kz(kmax-1)). We increase the mixing at the surface. WARNING : Results are modified for turb_nbeq = 1 or 2 ------------------------------------------------------------------------ r1397 | vg056b7 | 2012-02-06 14:02:59 +0100 (lun. 06 févr. 2012) | 4 lignes Complement of the implicitation of the bottom stress (consistence between 2D en 3D) to assure no bottom stress (key_no_bottom_stress) (F. Vandermeirsch) ------------------------------------------------------------------------ r1398 | vg056b7 | 2012-02-07 08:18:07 +0100 (mar. 07 févr. 2012) | 3 lignes lchain=200 warning (only and no stop) if l_meteo_stat=l_meteo_hom=l_sflx_rwind=.false. ------------------------------------------------------------------------ r1399 | vg056b7 | 2012-02-07 16:21:06 +0100 (mar. 07 févr. 2012) | 1 ligne Test on other names of dimensions : nav_lon, nav_lat ------------------------------------------------------------------------ r1400 | vg056b7 | 2012-02-07 16:22:31 +0100 (mar. 07 févr. 2012) | 1 ligne Only the MASTER writes warnings ------------------------------------------------------------------------ r1401 | vg056b7 | 2012-02-07 16:33:30 +0100 (mar. 07 févr. 2012) | 1 ligne modification of the Makefile to allow the MASTER to write the warnings only ------------------------------------------------------------------------ r1402 | vg056b7 | 2012-02-07 16:41:29 +0100 (mar. 07 févr. 2012) | 5 lignes Check if values read from a netcdf file of initial conditions are correct, i.e. bounded by maximum and minimum values (prescribed by the modellers in paramain.txt) Allow to verify the Initial Condition issued from extract (or from a restart file) is not filled by abnormal values in the wetting domain. ------------------------------------------------------------------------ r1403 | vg056b7 | 2012-02-07 16:52:01 +0100 (mar. 07 févr. 2012) | 7 lignes Verifications and reading of the correct record done by the MASTER only - sflxread.F90 - obcogcm.F90 Not sure it speed the starting of the MPI jobs toolmpi.F90 : adding of BCAST_MPI procedures (for rsh,rlg,int,char) to diffuse the information (real,integer or chain of character) to all the cpus ------------------------------------------------------------------------ r1404 | vg056b7 | 2012-02-07 17:19:02 +0100 (mar. 07 févr. 2012) | 1 ligne complement r1400 (warning writted by MASTER) for OMP ------------------------------------------------------------------------ r1405 | vg056b7 | 2012-02-14 10:31:38 +0100 (mar. 14 févr. 2012) | 1 ligne complement to r1403 (BCAST_MPI procedures) to manage with rsh=rlg=8 ------------------------------------------------------------------------ r1406 | vg056b7 | 2012-02-14 10:32:45 +0100 (mar. 14 févr. 2012) | 1 ligne Modification of the chain of validation : MENOR uses MED12 as initial and open boundary conditions and valmanq=999. ------------------------------------------------------------------------ r1407 | vg056b7 | 2012-02-14 16:52:33 +0100 (mar. 14 févr. 2012) | 1 ligne complement r1406 and checking on valmanq and rg_valmanq_io : they must be equal ! ------------------------------------------------------------------------ r1408 | vg056b7 | 2012-02-14 17:00:18 +0100 (mar. 14 févr. 2012) | 1 ligne set velocities to 0 over land ------------------------------------------------------------------------ r1409 | vg056b7 | 2012-02-14 17:02:07 +0100 (mar. 14 févr. 2012) | 1 ligne outsaverestart.F90 : to allow parallel writing l_out_nc4par=.true. ------------------------------------------------------------------------ r1410 | vg056b7 | 2012-02-14 17:03:53 +0100 (mar. 14 févr. 2012) | 1 ligne outputsave.F90 : to allow writing of small output files (l_out_nc4par=.false.) over smaller area (zoom or points) ------------------------------------------------------------------------ r1411 | vg056b7 | 2012-02-14 17:04:46 +0100 (mar. 14 févr. 2012) | 1 ligne evolution of PRINT_DBG ------------------------------------------------------------------------ r1412 | vg056b7 | 2012-02-14 17:25:13 +0100 (mar. 14 févr. 2012) | 1 ligne sedimoutput.F90,outputdiag.F90 : to allow writing of small output files over smaller area (zoom or points), complement r1410 ------------------------------------------------------------------------ r1413 | vg056b7 | 2012-02-15 08:57:23 +0100 (mer. 15 févr. 2012) | 1 ligne connect : correction to gather ni and nj values properly ------------------------------------------------------------------------ r1414 | vg056b7 | 2012-02-15 11:26:33 +0100 (mer. 15 févr. 2012) | 4 lignes sflxread.F90 : OMPMPI evolution to diffuse the information (real,integer or chain of character) to all the cpus (CALL BCAST) other routines : review of the messages with key_printdbg ------------------------------------------------------------------------ r1415 | vg056b7 | 2012-02-15 21:19:52 +0100 (mer. 15 févr. 2012) | 4 lignes Evolution for trajectories and ibm modules (M. Huret) + Reading of a netCDF file as an initial condition ------------------------------------------------------------------------ r1416 | vg056b7 | 2012-02-15 21:52:14 +0100 (mer. 15 févr. 2012) | 2 lignes compilation gfortran ------------------------------------------------------------------------ r1417 | vg056b7 | 2012-02-16 22:29:34 +0100 (jeu. 16 févr. 2012) | 1 ligne Evolution sedimento : outputs and corrections in the module ------------------------------------------------------------------------ r1418 | vg056b7 | 2012-02-18 12:06:13 +0100 (sam. 18 févr. 2012) | 1 ligne Evolution sedimento : outputs, correction type ------------------------------------------------------------------------ r1419 | vg056b7 | 2012-02-18 13:53:53 +0100 (sam. 18 févr. 2012) | 1 ligne the record to be read is assigned by irec ------------------------------------------------------------------------ r1420 | vg056b7 | 2012-02-18 14:04:43 +0100 (sam. 18 févr. 2012) | 1 ligne Diagnostic of the physical vertical velocity (P. Garreau) ------------------------------------------------------------------------ r1421 | vg056b7 | 2012-02-18 16:26:01 +0100 (sam. 18 févr. 2012) | 1 ligne Test for very very small depths : igd set to 4 (land no calculation) ------------------------------------------------------------------------ r1422 | vg056b7 | 2012-02-21 19:35:41 +0100 (mar. 21 févr. 2012) | 1 ligne Formulation Fairall 03 and Large et Yeager 04 : rubber to avoid divisions by zeros that occur very rarely ------------------------------------------------------------------------ r1423 | vg056b7 | 2012-02-25 14:51:06 +0100 (sam. 25 févr. 2012) | 1 ligne Evolution sedimento : outputs and tflat test case ------------------------------------------------------------------------ r1424 | vg056b7 | 2012-03-02 12:01:10 +0100 (ven. 02 mars 2012) | 1 ligne Add content attribute to each variable ------------------------------------------------------------------------ r1425 | vg056b7 | 2012-03-02 19:28:21 +0100 (ven. 02 mars 2012) | 1 ligne complement environment for the IBM module ------------------------------------------------------------------------ r1426 | vg056b7 | 2012-03-06 14:23:51 +0100 (mar. 06 mars 2012) | 1 ligne complement r1409 outsaverestart.F90 : to allow parallel writing l_out_nc4par=.true. ------------------------------------------------------------------------ r1427 | vg056b7 | 2012-03-06 21:36:14 +0100 (mar. 06 mars 2012) | 1 ligne Decoupe MPI domains : evolutions and introduction of ionc4. To be used with a bathymetry in the V9 format ------------------------------------------------------------------------ r1428 | vg056b7 | 2012-03-07 13:17:59 +0100 (mer. 07 mars 2012) | 1 ligne correction of the outputs for offline functionality ------------------------------------------------------------------------ r1429 | vg056b7 | 2012-03-19 13:30:59 +0100 (lun. 19 mars 2012) | 1 ligne dx_p dy_p become dx_f dy_f ------------------------------------------------------------------------ r1430 | vg056b7 | 2012-03-20 12:29:01 +0100 (mar. 20 mars 2012) | 1 ligne Reading of wave fields (R. Verney) ------------------------------------------------------------------------ r1431 | vg056b7 | 2012-03-20 12:31:20 +0100 (mar. 20 mars 2012) | 1 ligne NetCDF files : introduction of ni_u,nj_u,ni_v,nj_v,ni_f,nj_f dimensions to comply with the COMODO norme for the variables-dimensions ------------------------------------------------------------------------ r1432 | vg056b7 | 2012-03-22 15:47:53 +0100 (jeu. 22 mars 2012) | 1 ligne Correction of NetCDF files : introduction of ni_u,nj_u,ni_v,nj_v,ni_f,nj_f dimensions to comply with the COMODO norme for the variables-dimensions ------------------------------------------------------------------------ r1433 | vg056b7 | 2012-03-23 16:24:46 +0100 (ven. 23 mars 2012) | 1 ligne Correction of NetCDF files : valid_min, valid_max ------------------------------------------------------------------------ r1434 | vg056b7 | 2012-03-23 16:28:31 +0100 (ven. 23 mars 2012) | 1 ligne Vertical repartition of the 3D velocity over very small depths : uz=u if Hz(1)