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Read and write the whole pctsrf array in (re)startphy.nc, instead of splitting it into FTER, FLIC, FOCE, FSIC.
In procedure calcul_fluxs, rename coef1lay to cdragh (following LMDZ). Use named constant min_wind_speed (following LMDZ). Change name of NetCDF variable soll to CF standard rls.
Variable fevap of physiq is not used. Remove it from physiq and from the restart file. Remove the corresponding argument evap of pbl_surface. Use directly yqsurf instead of qairsol in pbl_surface.
Move Sources/* to root directory.
Promoted lmt_pas from local variable of physiq to variable of module conf_gcm_m. Removed variable run_off of module interface_surf. Was not used. Called run_off_ter in LMDZ, but not used nor printed there either. Simplified logic in interfoce_lim. The way it was convoluted with interfsurf_hq and clmain was quite a mess. Extracted reading of SST into a separate procedure: read_sst. We do not need SST and pctsrf_new at the same time: SST is not needed for sea-ice surface. I did not like this programming: going through the procedure repeatedly for different purposes and testing inside whether there was something to do or it was already done. Reading is now only controlled by itap and lmt_pas, instead of debut, jour, jour_lu and deja_lu. Now we do not copy from pct_tmp to pctsrf_new every time step. Simplified processing of pctsrf in clmain and below. It was quite troubling: pctsrf_new was intent out in interfoce_lim but only defined for ocean and sea-ice. Also the idea of having arrays for all surfaces, pcsrf and pctsrf_new, in interfsurf_hq, which is called for a particular surface, was troubling. pctsrf_new for all surfaces was intent out in intefsurf_hq, but not defined for all surfaces at each call. Removed argument pctsrf_new of clmain: was a duplicate of pctsrf on output, and not used in physiq. Replaced pctsrf_new in clmain by pctsrf_new_oce and pctsrf_new_sic, which were the only ones modified.
Extracted the call to read_comdissnew out of conf_gcm. Made ok_instan a variable of module clesphys, itau_phy a variable of module phyetat0_m, nid_ins a variable of module ini_histins_m, itap a variable of new module time_phylmdz, so that histwrite_phy can be called from any procedure without the need to cascade those variables into that procedure. Made itau_w a variable of module time_phylmdz so that it is computed only once per time step of physics. Extracted variables of module clesphys which were in namelist conf_phys_nml into their own namelist, clesphys_nml, and created procedure read_clesphys reading clesphys_nml, to avoid side effect. No need for double precision in procedure getso4fromfile. Assume there is a single variable for the whole year in the NetCDF file instead of one variable per month. Created generic procedure histwrite_phy and removed procedure write_histins, following LMDZ. histwrite_phy has only two arguments, can be called from anywhere, and should manage the logic of writing or not writing into various history files with various operations. So the test on ok_instan goes inside histwrite_phy. Test for raz_date in phyetat0 instead of physiq to avoid side effect. Created procedure increment_itap to avoid side effect. Removed unnecessary differences between procedures readsulfate and readsulfate_pi.
Added argument itau_phy to ini_histins, phyetat0, phytrac and phyredem0. Removed variable itau_phy of module temps. Avoiding side effect in etat0 and phyetat0. The procedures ini_histins, phyetat0, phytrac and phyredem0 are all called by physiq so there is no cascading variable penalty. In procedure inifilr, made the condition on colat0 weaker to allow for rounding error. Removed arguments flux_o, flux_g and t_slab of clmain, flux_o and flux_g of clqh and interfsurf_hq, tslab and seaice of phyetat0 and phyredem. NetCDF variables TSLAB and SEAICE no longer in restartphy.nc. All these variables were related to the not-implemented slab ocean. seaice and tslab were just set to 0 in phyetat0 and never used nor changed. flux_o and flux_g were computed in clmain but never used in physiq. Removed argument swnet of clqh. Was used only to compute a local variable, swdown, which was not used.
Just encapsulated SUBROUTINE vlsplt in a module and cleaned it. In procedure vlx, local variables dxqu and adxqu only need indices iip2:ip1jm. Otherwise, just cleaned vlx. Procedures dynredem0 and dynredem1 no longer have argument fichnom, they just operate on a file named "restart.nc". The programming guideline here is that gcm should not be more complex than it needs by itself, other programs (ce0l etc.) just have to adapt to gcm. So ce0l now creates files "restart.nc" and "restartphy.nc". In order to facilitate decentralizing the writing of "restartphy.nc", created a procedure phyredem0 out of phyredem. phyredem0 creates the NetCDF header of "restartphy.nc" while phyredem writes the NetCDF variables. As the global attribute itau_phy needs to be filled in phyredem0, at the beginnig of the run, we must compute its value instead of just using itap. So we have a dummy argument lmt_pas of phyredem0. Also, the ncid of "startphy.nc" is upgraded from local variable of phyetat0 to dummy argument. phyetat0 no longer closes "startphy.nc". Following the same decentralizing objective, the ncid of "restart.nc" is upgraded from local variable of dynredem0 to module variable of dynredem0_m. "restart.nc" is not closed at the end of dynredem0 nor opened at the beginning of dynredem1. In procedure etat0, instead of creating many vectors of size klon which will be filled with zeroes, just create one array null_array. In procedure phytrac, instead of writing trs(: 1) to a text file, write it to "restartphy.nc" (following LMDZ). This is better because now trs(: 1) is next to its coordinates. We can write to "restartphy.nc" from phytrac directly, and not add trs(: 1) to the long list of variables in physiq, thanks to the decentralizing of "restartphy.nc". In procedure phyetat0, we no longer write to standard output the minimum and maximum values of read arrays. It is ok to check input and abort on invalid values but just printing statistics on input seems too much useless computation and out of place clutter.
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