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Changed all ".f90" suffixes to ".f".
Moved procedure inigeom into module comgeom. In disvert, renamed s_sampling to vert_sampling, following LMDZ. Removed choice strato1. In case read, read ap and bp instead of s (following LMDZ). Added argument phis to start_init_orog and start_init_dyn, and removed variable phis of module start_init_orog_m. In etat0 and start_init_orog, renamed relief to zmea_2d. In start_init_dyn, renamed psol to ps. In start_init_orog, renamed relief_hi to relief. No need to set phis(iim + 1, :) = phis(1, :), already done in grid_noro. Documentation for massbar out of SVN, in massbar.txt. Documentation was duplicated in massdair, but not relevant in massdair. In conflx, no need to initialize pen_[ud] and pde_[ud]. In flxasc, used intermediary variable fact (following LMDZ). In grid_noro, added local variable zmea0 for zmea not smoothed and computed zphi from zmea instead of zmea0 (following LMDZ). This changes the results of ce0l. Removed arguments pen_u and pde_d of phytrac and nflxtr, which were not used.
Moved everything out of libf.
Renamed tpot to teta and psol to ps in etat0. Replaced calls to flincom by calls to NetCDF95 in startdyn. lon_ini, lat_ini and levdyn_ini are now pointers.
NaN to signalling NaN in gfortran_debug.mk. Removed unused procedures in getincom and getincom2. In procedure conf_interface, replaced call to getincom by new namelist. Moved procedure conf_interface into module interface_surf. Added variables sig1 and w01 to startphy.nc and restartphy.nc, for procedure cv_driver. Renamed (ema_)?work1 and (ema_)?work2 to sig1 and w01 in concvl and physiq. Deleted unused arguments of clmain, clqh and intersurf_hq, among which (y)?sollwdown. Following LMDZ, in physiq, read sollw instead of sollwdown from startphy.nc, write sollw instead of sollwdown to restartphy.nc. In procedure sw, initialized zfs[ud][pn]a[di], for runs where ok_ade and ok_aie are false. (Following LMDZ.) Added dimension klev to startphy.nc and restartphy.nc, and deleted dimension horizon_vertical. Made t_ancien and q_ancien two-dimensional NetCDF variables. Bug fix: in phyetat0, define ratqs, clwcon and rnebcon for vertical levels >=2. Bug fix: set mfg, p[de]n_[ud] to 0. when iflag_con >= 3. (Following LMDZ.)
Changed handling of compiler in compilation system. Removed the prefix letters "y", "p", "t" or "z" in some names of variables. Replaced calls to NetCDF by calls to NetCDF95. Extracted "ioget_calendar" procedures from "calendar.f90" into a separate file. Extracted to a separate file, "mathop2.f90", procedures that were not part of the generic interface "mathop" in "mathop.f90". Removed computation of "dq" in "bilan_dyn", which was not used. In "iniadvtrac", removed schemes 20 Slopes and 30 Prather. Was not compatible with declarations of array sizes. In "clcdrag", "ustarhb", "vdif_kcay", "yamada4" and "coefkz", changed the size of some arrays from "klon" to "knon". Removed possible call to "conema3" in "physiq". Removed unused argument "cd" in "yamada".
Removed Numerical Recipes procedure "ran1". Replaced calls to "ran1" in "inidissip" by calls to intrinsic procedures. Split file "interface_surf.f90" into a file with a module containing only variables, "interface_surf", and single-procedure files. Gathered files into directory "Interface_surf". Added argument "cdivu" to "gradiv" and "gradiv2", "cdivh" to "divgrad2" and "divgrad", and "crot" to "nxgraro2" and "nxgrarot". "dissip" now uses variables "cdivu", "cdivh" and "crot" from module "inidissip_m", so it can pass them to "gradiv2", etc. Thanks to this modification, we avoid a circular dependency betwwen "inidissip.f90" and "gradiv2.f90", etc. The value -1. used by "gradiv2", for instance, during computation of eigenvalues is not the value "cdivu" computed by "inidissip". Extracted procedure "start_inter_3d" from module "startdyn", to its own module. In "inidissip", unrolled loop on "ii". I find it clearer now. Moved variables "matriceun", "matriceus", "matricevn", "matricevs", "matrinvn" and "matrinvs" from module "parafilt" to module "inifilr_m". Moved variables "jfiltnu", "jfiltnv", "jfiltsu", "jfiltsv" from module "coefils" to module "inifilr_m".
"start_init_phys" is now called directly by "etat0" instead of through "start_init_dyn". "qsol_2d" is no longer a variable of module "start_init_phys_m", it is an argument of "start_init_phys". "start_init_dyn" now receives "tsol_2d" from "etat0". Split file "vlspltqs.f" into "vlspltqs.f90", "vlxqs.f90" and ""vlyqs.f90". In "start_init_orog", replaced calls to "flin*" by calls to NetCDF95.
Corrected bug in "phyredem.f90" that was introduced in revision 20.
Deleted argument "presnivs" of "physiq", "ini_histhf", "ini_histhf3d", "ini_histday", "ini_histins", "ini_histrac", "phytrac". Access it from "comvert" instead. Replaced calls to NetCDF Fortran 77 interface by calls to Fortran 90 interface or to NetCDF95. Procedure "gr_phy_write_3d" now works with a variable of arbitrary size in the second dimension. Annotated use statements with "only" clause. Replaced calls to NetCDF interface version 2 by calls to Fortran 90 interface in "guide.f90" and "read_reanalyse.f". In "write_histrac", replaced calls to "gr_fi_ecrit" by calls to "gr_phy_write_2d" and "gr_phy_write_3d".
Inlined procedures "regr_pr_av" and "regr_pr_int" in "regr_pr_o3", "regr_pr_av_coefoz" and "regr_pr_int_coefoz".
-- Minor modification of input/output: Added variable "Sigma_O3_Royer" to "histday.nc". "ecrit_day" is not modified in "physiq". Removed variables "pyu1", "pyv1", "ftsol1", "ftsol2", "ftsol3", "ftsol4", "psrf1", "psrf2", "psrf3", "psrf4" "mfu", "mfd", "en_u", "en_d", "de_d", "de_u", "coefh" from "histrac.nc". Variable "raz_date" of module "conf_gcm_m" has logical type instead of integer type. -- Should not change any result at run time: Modified calls to "IOIPSL_Lionel" procedures because the interfaces of these procedures have been simplified. Changed name of variable in module "start_init_orog_m": "masque" to "mask". Created a module containing procedure "phyredem". Removed arguments "punjours", "pdayref" and "ptimestep" of procedure "iniphysiq". Renamed procedure "gr_phy_write" to "gr_phy_write_2d". Created procedure "gr_phy_write_3d". Removed procedures "ini_undefstd", "moy_undefSTD", "calcul_STDlev", "calcul_divers".
-- Minor change of behaviour: "etat0" does not compute "rugsrel" nor "radpas". Deleted arguments "radpas" and "rugsrel" of "phyredem". Deleted argument "rugsrel" of "phyetat0". "startphy.nc" does not contain the variable "RUGSREL". In "physiq", "rugoro" is set to 0 if not "ok_orodr". The whole program "etat0_lim" does not use "clesphys2". -- Minor modification of input/output: Created subroutine "read_clesphys2". Variables of "clesphys2" are read in "read_clesphys2" instead of "conf_gcm". "printflag" does not print variables of "clesphys2". -- Should not change any result at run time: References to module "numer_rec" instead of individual modules of "Numer_rec_Lionel". Deleted argument "clesphy0" of "calfis", "physiq", "conf_gcm", "leapfrog", "phyetat0". Deleted variable "clesphy0" in "gcm". "phyetat0" does not modify variables of "clesphys2". The program unit "gcm" does not modify "itau_phy". Added some "intent" attributes. "regr11_lint" does not call "polint".
-- Minor modification of input/output: Created procedure "read_logic". Variables of module "logic" are read by "read_logic" instead of "conf_gcm". Variable "offline" of module "conf_gcm" is read from namelist instead of "*.def". Deleted arguments "dtime", "co2_ppm_etat0", "solaire_etat0", "tabcntr0" and local variables "radpas", "tab_cntrl" of "phyetat0". "phyetat0" does not read "controle" in "startphy.nc" any longer. "phyetat0" now reads global attribute "itau_phy" from "startphy.nc". "phyredem" does not create variable "controle" in "startphy.nc" any longer. "phyredem" now writes global attribute "itau_phy" of "startphy.nc". Deleted argument "tabcntr0" of "printflag". Removed diagnostic messages written by "printflag" for comparison of the variable "controle" of "startphy.nc" and the variables read from "*.def" or namelist input. -- Removing unwanted functionality: Removed variable "lunout" from module "iniprint", replaced everywhere by standard output. Removed case "ocean == 'couple'" in "clmain", "interfsurf_hq" and "physiq". Removed procedure "interfoce_cpl". -- Should not change anything at run time: Automated creation of graphs in documentation. More documentation on input files. Converted Fortran files to free format: "phyredem.f90", "printflag.f90". Split module "clesphy" into "clesphys" and "clesphys2". Removed variables "conser", "leapf", "forward", "apphys", "apdiss" and "statcl" from module "logic". Added arguments "conser" to "advect", "leapf" to "integrd". Added local variables "forward", "leapf", "apphys", "conser", "apdiss" in "leapfrog". Added intent attributes. Deleted arguments "dtime" of "phyredem", "pdtime" of "flxdtdq", "sh" of "phytrac", "dt" of "yamada". Deleted local variables "dtime", "co2_ppm_etat0", "solaire_etat0", "length", "tabcntr0" in "physiq". Replaced all references to "dtime" by references to "pdtphys".
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