Index: trunk/LMDZ.COMMON/libf/evolution/changelog.txt =================================================================== --- trunk/LMDZ.COMMON/libf/evolution/changelog.txt (revision 4089) +++ trunk/LMDZ.COMMON/libf/evolution/changelog.txt (revision 4090) @@ -886,2 +886,5 @@ == 18/02/2026 == JBC Fallback for 128-bit integers since this type is not supported by Intel Fortran. + +== 27/02/2026 == JBC +Update README and change "startpem.nc" into "startevol.nc". Index: trunk/LMDZ.COMMON/libf/evolution/clim_state_init.F90 =================================================================== --- trunk/LMDZ.COMMON/libf/evolution/clim_state_init.F90 (revision 4089) +++ trunk/LMDZ.COMMON/libf/evolution/clim_state_init.F90 (revision 4090) @@ -308,5 +308,5 @@ ! ! DESCRIPTION -! Read the file "startpem.nc" which stores the PEM state. +! Read the file "startevol.nc" which stores the PEM state. ! ! AUTHORS & DATE @@ -367,6 +367,6 @@ integer(di) :: i, islope, k, nb_str_max, nsoil_startpem real(dp) :: delta ! Depth of the interface regolith/breccia, breccia/bedrock [m] -real(dp), dimension(ngrid,nsoil,nslope) :: TI_startpem ! Soil thermal inertia saved in the startpem [SI] -real(dp), dimension(ngrid,nsoil,nslope) :: tsoil_startpem ! Soil temperature saved in the startpem [K] +real(dp), dimension(ngrid,nsoil,nslope) :: TI_startpem ! Soil thermal inertia saved in the startevol [SI] +real(dp), dimension(ngrid,nsoil,nslope) :: tsoil_startpem ! Soil temperature saved in the startevol [K] real(dp), dimension(:,:,:,:), allocatable :: layerings_array ! Array for layerings Index: trunk/LMDZ.COMMON/libf/evolution/clim_state_rec.F90 =================================================================== --- trunk/LMDZ.COMMON/libf/evolution/clim_state_rec.F90 (revision 4089) +++ trunk/LMDZ.COMMON/libf/evolution/clim_state_rec.F90 (revision 4090) @@ -25,5 +25,5 @@ ! VARIABLES ! --------- -logical(k4), private :: is_restartpem = .false. ! Flag to know if "restartpem.nc" exists +logical(k4), private :: is_restartpem = .false. ! Flag to know if "restartevol.nc" exists contains @@ -397,4 +397,5 @@ call check_nc(nf90_put_att(ncid,varid,'title','Layering ice pore volume fraction'),'putting title attribute for stratif_poreice_volfrac') end if + ! Global attributes call check_nc(nf90_put_att(ncid,nf90_global,'title','PEM start file'),'putting global attribute') @@ -421,5 +422,5 @@ ! ! DESCRIPTION -! Write the file "restartpem.nc". +! Write the file "restartevol.nc". ! ! AUTHORS & DATE Index: trunk/LMDZ.COMMON/libf/evolution/deftank/README =================================================================== --- trunk/LMDZ.COMMON/libf/evolution/deftank/README (revision 4089) +++ trunk/LMDZ.COMMON/libf/evolution/deftank/README (revision 4090) @@ -24,5 +24,5 @@ Options with example: 1) [local] : root name of arch files, assuming that they have been set up for your configuration; - 2) [planet] : mars to use the Mars planet physics package; + 2) [planet] : mars to use the PEM dedicated to the Mars planet; 3) [dimensions]: 64x48x54 to define the grid you want to use (longitude x latitude x atmospheric layers). To run the PEM, you need a PCM working with XIOS and consistent options. To compile it, in "LMDZ.COMMON", do: ./makelmdz_fcm -arch [local] -p [planet] -parallel mpi_omp -io xios -d [dimensions] -j 8 gcm @@ -45,24 +45,24 @@ > the def files you want to run the PCM: "run.def", "callphys.def", "traceur.def", etc. /!\ Do not forget to rename the PCM "run.def" into "run_pcm.def"; - > the starting files you want to run the PCM: "startfi.nc", "start.nc"/"start1D.txt"/profiles; + > the starting files you want to run the PCM: "startfi.nc" and "start.nc"/"start1D.txt"; > the necessary PEM files: "pem_workflow.sh", "pem_workflow_lib.sh", "pcm_run.job", "pem_run.job", "run_pem.def" and "obl_ecc_lsp.asc"; - > the optional PEM files: "diagevol.def" to define the PEM variables to be ouputted and "startpem.nc" to set the initial state of the PEM. + > the optional PEM files: "diagevol.def" to define the PEM variables to be ouputted and "startevol.nc" to set the initial state of the PEM. The PEM files can be found in the deftank folder. Before a simulation, you have to set up some parameters/options in: - > "pem_workflow.sh"; - > "pcm_run.job"; - > "pem_run.job"; - > def files, especially for "run_pem.def", "run_pcm.def", "callphys.def". -In addition, the user has to provide a "startfi.nc" whose orbital parameters are consistent with the initial date set in "run_pem.def". The script "ini_pem_orbit.sh" can do it automatically with "obl_ecc_lsp.asc". + > "pem_workflow.sh" (see below for details); + > "pcm_run.job" (see below for details); + > "pem_run.job" (see below for details); + > def files, especially for "run_pem.def", "run_pcm.def" and "callphys.def" which must be consistent. In particular, "run_pem.def" needs to include some definitions for the physics in file "run_pcm.def" with "INCLUDEDEF=run_pcm.def". +In addition, the user has to provide a "startfi.nc" whose orbital parameters are consistent with the initial date set in "run_pem.def". The script "ini_pem_orbit.sh" can do it automatically reading "obl_ecc_lsp.asc". Outputs: -------- The PEM simulation generates the following files: - > the usual outputs of the PCM: "restartfi.nc", "restart.nc", "diagfi.nc", etc; + > the usual outputs of the PCM: "restartfi.nc", "restart.nc"/"restart1D.txt", "diagfi.nc", etc; > the XIOS outputs of the PCM: "Xoutdaily4pem*.nc"/"Xoutyearly4pem*.nc"; > the outputs of the chained simulation: "pem_workflow.log", "pem_workflow.sts" and possibly "kill_pem_workflow.sh"; - > the usual outputs of the PEM: "restartfi.nc", "restart.nc"/"restart1D.txt" and "diagevol.nc". + > the usual outputs of the PEM: "restartevol.nc", "restartfi.nc", "restart.nc"/"restart1D.txt" and "diagevol.nc". During the simulation, the PCM/PEM run files are renamed conveniently and stored in the sub-directories "logs" (log files), "starts" (starting files) and "diags" (diagnostic files). If you run a simulation by submitting jobs, the script "kill_pem_workflow.sh" is automatically generated. It can be used to kill the jobs related to your chained simulation in the queue of the job scheduler. @@ -73,8 +73,8 @@ Bash script file to launch the chained simulation of PEM and PCM runs. The user has to specify: - > n_mars_years, n_earth_years -> the number of Mars/Earth years to be simulated in total (> 0); - > n_pcm_runs_ini -> the number of initial PCM years (>= 2); - > n_pcm_runs -> the number of PCM years between each PEM run (>= 2, usually 2); - > exec_mode -> the execution mode (0 = "processing scripts"; any other values = "submitting jobs"). The former option is usually used to process the script on a local machine while the latter is used to submit jobs on a supercomputer with SLURM or PBS/TORQUE. + > 'n_planetary_years' or 'n_earth_years' -> the number of Planetary/Earth years to be simulated in total (> 0); + > 'n_pcm_runs_ini' -> the number of initial PCM years (>= 2); + > 'n_pcm_runs' -> the number of PCM years between each PEM run (>= 2, usually 2); + > 'exec_mode' -> the execution mode (0 = "processing scripts"; any other values = "submitting jobs"). The former option is usually used to process the script on a local machine while the latter is used to submit jobs on a supercomputer with SLURM or PBS/TORQUE. The script can take an argument: 1) None: to start a simulation from scratch; @@ -89,6 +89,6 @@ > The headers correspond to the ADASTRA supercomputer and should be changed for other machines and job schedulers. In case of "processing scripts" execution mode, the headers are naturally omitted. > The path to source the arch file should be adapted to the machine. - > The name of the PCM executable file should be adapted. - > The execution command should also be adapted according to the set-up. + > 'pcm_exe', the name of the PCM executable file should be adapted. + > 'exec_cmd', the execution command should also be adapted according to the set-up. # pem_run.job: @@ -97,10 +97,10 @@ > The headers correspond to the ADASTRA supercomputer and should be changed for other machines and job schedulers. In case of "processing scripts" execution mode, the headers are naturally omitted. > The path to source the arch file should be adapted to the machine. - > The name of the PEM executable file should be adapted. - > The PEM executable can have an optional argument which should be specified according to the set-up ("--auto-exit" for SLURM and PBS/TORQUE | "" when the script is not run as a job). + > 'pem_exe', the name of the PEM executable file should be adapted. + > 'pem_arg', the PEM executable can have an optional argument which should be specified according to the set-up ("--auto-exit" for SLURM and PBS/TORQUE | "" when the script is not run as a job). # run_pem.def All the possible parameters to define a PEM run (read in "config.F90"). - It needs to include in "run_pcm.def" with "INCLUDEDEF=run_pem.def". + It needs to include some definitions for the physics in file "run_pcm.def" with "INCLUDEDEF=run_pcm.def". # obl_ecc_lsp.asc [default], obl_ecc_lsp_pos.asc [future years] @@ -126,6 +126,6 @@ # visu_layering.py: - Python script file to output the stratification data from the "startpem.nc" files. + Python script file to output the stratification data from the "startevol.nc" files. # visu_layering_evol.py: - Python script file to output the stratification data over time from the "startpem.nc" files. + Python script file to output the stratification data over time from the "startevol.nc" files. Index: trunk/LMDZ.COMMON/libf/evolution/deftank/clean.sh =================================================================== --- trunk/LMDZ.COMMON/libf/evolution/deftank/clean.sh (revision 4089) +++ trunk/LMDZ.COMMON/libf/evolution/deftank/clean.sh (revision 4090) @@ -35,6 +35,6 @@ cp starts/start1D.txt . fi -if [ -f "starts/startpem.nc" ]; then - cp starts/startpem.nc . +if [ -f "starts/startevol.nc" ]; then + cp starts/startevol.nc . fi # Cleaning of files in the sub-folders Index: trunk/LMDZ.COMMON/libf/evolution/deftank/pem_run.job =================================================================== --- trunk/LMDZ.COMMON/libf/evolution/deftank/pem_run.job (revision 4089) +++ trunk/LMDZ.COMMON/libf/evolution/deftank/pem_run.job (revision 4090) @@ -48,6 +48,6 @@ mv diagevol_soil.nc diags/diagevol_soil${i_pem_run}.nc fi -cp restartpem.nc starts/restartpem${i_pem_run}.nc -mv restartpem.nc startpem.nc +cp restartevol.nc starts/restartevol${i_pem_run}.nc +mv restartevol.nc startevol.nc cp restartfi.nc starts/restartfi_postPEM${i_pem_run}.nc mv restartfi.nc startfi.nc Index: trunk/LMDZ.COMMON/libf/evolution/deftank/pem_workflow_lib.sh =================================================================== --- trunk/LMDZ.COMMON/libf/evolution/deftank/pem_workflow_lib.sh (revision 4089) +++ trunk/LMDZ.COMMON/libf/evolution/deftank/pem_workflow_lib.sh (revision 4090) @@ -285,6 +285,6 @@ cp start1D.txt starts/ fi - if [ -f "startpem.nc" ]; then - cp startpem.nc starts/ + if [ -f "startevol.nc" ]; then + cp startevol.nc starts/ fi @@ -468,8 +468,8 @@ cleanup starts/restart_postPEM .nc $(($i_pem_run - 1)) cleanup starts/restartfi_postPEM .nc $(($i_pem_run - 1)) - cleanup starts/restartpem .nc $(($i_pem_run - 1)) - rm -f startpem.nc - if [ -f "starts/startpem.nc" ]; then - cp starts/startpem.nc . + cleanup starts/restartevol .nc $(($i_pem_run - 1)) + rm -f startevol.nc + if [ -f "starts/startevol.nc" ]; then + cp starts/startevol.nc . fi if [ $i_resume -eq $(($n_pcm_runs_ini - 1)) ]; then @@ -498,6 +498,6 @@ cleanup starts/restart_postPEM .nc $(($i_pem_run - 1)) cleanup starts/restartfi_postPEM .nc $(($i_pem_run - 1)) - cleanup starts/restartpem .nc $(($i_pem_run - 1)) - cp starts/restartpem$(($i_pem_run - 1)).nc startpem.nc + cleanup starts/restartevol .nc $(($i_pem_run - 1)) + cp starts/restartevol$(($i_pem_run - 1)).nc startevol.nc if [ $il -eq $(($n_pcm_runs - 1)) ]; then # Second to last PCM run cp diags/Xoutdaily4pem${i_resume}.nc Xoutdaily4pem_Y1.nc @@ -537,6 +537,6 @@ cleanup starts/restart_postPEM .nc $i_resume cleanup starts/restartfi_postPEM .nc $i_resume - cleanup starts/restartpem .nc $i_resume - cp starts/restartpem${i_resume}.nc startpem.nc + cleanup starts/restartevol .nc $i_resume + cp starts/restartevol${i_resume}.nc startevol.nc cp starts/restartfi_postPEM${i_resume}.nc startfi.nc if [ -f "starts/restart_postPEM${i_resume}.nc" ]; then Index: trunk/LMDZ.COMMON/libf/evolution/deftank/run_pem.def =================================================================== --- trunk/LMDZ.COMMON/libf/evolution/deftank/run_pem.def (revision 4089) +++ trunk/LMDZ.COMMON/libf/evolution/deftank/run_pem.def (revision 4090) @@ -2,7 +2,4 @@ # Run control parameters for the PEM # #------------------------------------# - -#---------- Planet type ----------# -planet_type=mars #---------- Output parameters ----------# @@ -77,5 +74,5 @@ #---------- Ice management parameters ----------# -# Amount of H2O ice to initialize the huge reservoir if the variable is not present in "startpem.nc". Default = 9200. kg.m-2 (= 10 m) +# Amount of H2O ice to initialize the huge reservoir if the variable is not present in "startevol.nc". Default = 9200. kg.m-2 (= 10 m) # h2oice_huge_ini=9200. Index: trunk/LMDZ.COMMON/libf/evolution/deftank/visu_layering.py =================================================================== --- trunk/LMDZ.COMMON/libf/evolution/deftank/visu_layering.py (revision 4089) +++ trunk/LMDZ.COMMON/libf/evolution/deftank/visu_layering.py (revision 4090) @@ -1,5 +1,5 @@ #!/usr/bin/env python3 ####################################################################################### -### Python script to output the stratification data from the "restartpem#.nc" files ### +### Python script to output the stratification data from the "restartevol#.nc" files ### ####################################################################################### Index: trunk/LMDZ.COMMON/libf/evolution/deftank/visu_layering_evol.py =================================================================== --- trunk/LMDZ.COMMON/libf/evolution/deftank/visu_layering_evol.py (revision 4089) +++ trunk/LMDZ.COMMON/libf/evolution/deftank/visu_layering_evol.py (revision 4090) @@ -1,5 +1,5 @@ #!/usr/bin/env python3 ####################################################################################################### -### Python script to output stratification data over time from "restartpem#.nc" files ### +### Python script to output stratification data over time from "restartevol#.nc" files ### ### and to plot orbital parameters from "obl_ecc_lsp.asc" ### ####################################################################################################### @@ -21,5 +21,5 @@ Prompt the user for: - folder_path: directory containing NetCDF files (default: "starts") - - base_name: base filename (default: "restartpem") + - base_name: base filename (default: "restartevol") - infofile: name of the PEM info file (default: "pem_workflow.sts") Validates existence of folder and infofile before returning. @@ -37,6 +37,6 @@ base_name = input( "Enter the base name of the NetCDF files " - "(press Enter for default [restartpem]): " - ).strip() or "restartpem" + "(press Enter for default [restartevol]): " + ).strip() or "restartevol" infofile = input( Index: trunk/LMDZ.COMMON/libf/evolution/io_netcdf.F90 =================================================================== --- trunk/LMDZ.COMMON/libf/evolution/io_netcdf.F90 (revision 4089) +++ trunk/LMDZ.COMMON/libf/evolution/io_netcdf.F90 (revision 4090) @@ -32,5 +32,5 @@ character(11), parameter :: start1D_name = 'start1D.txt' character(10), parameter :: startfi_name = 'startfi.nc' -character(11), parameter :: startpem_name = 'startpem.nc' +character(12), parameter :: startpem_name = 'startevol.nc' character(19), parameter :: xios_day_name1 = 'Xoutdaily4pem_Y1.nc' ! XIOS daily output file, second to last PCM year character(19), parameter :: xios_day_name2 = 'Xoutdaily4pem_Y2.nc' ! XIOS daily output file, last PCM year Index: trunk/LMDZ.COMMON/libf/evolution/pem.F90 =================================================================== --- trunk/LMDZ.COMMON/libf/evolution/pem.F90 (revision 4089) +++ trunk/LMDZ.COMMON/libf/evolution/pem.F90 (revision 4090) @@ -203,5 +203,5 @@ call compute_maxyr_orbit(n_yr_sim,nmax_yr_runorb) -! Read the "startpem.nc" +! Read the "startevol.nc" allocate(h2o_ice(ngrid,nslope),co2_ice(ngrid,nslope)) allocate(h2o_ads_reg(ngrid,nsoil,nslope),co2_ads_reg(ngrid,nsoil,nslope),delta_h2o_ads(ngrid),delta_co2_ads(ngrid)) @@ -492,5 +492,5 @@ call build4PCM_surf_rad_prop(h2o_ice,co2_ice,albedo4PCM,emissivity4PCM) -! Write the "startpem.nc" +! Write the "startevol.nc" call write_restartpem(h2o_ice,co2_ice,tsoil_avg,TI,icetable_depth,icetable_thickness,ice_porefilling,h2o_ads_reg,co2_ads_reg,layerings_map) Index: trunk/LMDZ.COMMON/libf/evolution/soil_temp.F90 =================================================================== --- trunk/LMDZ.COMMON/libf/evolution/soil_temp.F90 (revision 4089) +++ trunk/LMDZ.COMMON/libf/evolution/soil_temp.F90 (revision 4090) @@ -551,5 +551,5 @@ !======================================================================= -SUBROUTINE evolve_soil_temp(tsoil_avg, tsurf_avg, tsoil_ts, tsoil_ts_old, h2o_soildensity_avg) +SUBROUTINE evolve_soil_temp(tsoil_avg,tsurf_avg,tsoil_ts,tsoil_ts_old,h2o_soildensity_avg) !----------------------------------------------------------------------- ! NAME Index: trunk/LMDZ.COMMON/libf/evolution/xios_data.F90 =================================================================== --- trunk/LMDZ.COMMON/libf/evolution/xios_data.F90 (revision 4089) +++ trunk/LMDZ.COMMON/libf/evolution/xios_data.F90 (revision 4090) @@ -73,4 +73,5 @@ character(:), allocatable :: num ! To read slope variables real(dp), dimension(ngrid,nsoil,nslope,nday) :: h2o_soildensity_ts + ! CODE ! ---- @@ -143,4 +144,5 @@ end if end do + ! Close the NetCDF file of XIOS outputs call close_nc(xios_yr_name2)