Index: /trunk/LMDZ.MARS/README =================================================================== --- /trunk/LMDZ.MARS/README (revision 2812) +++ /trunk/LMDZ.MARS/README (revision 2813) @@ -3757,2 +3757,5 @@ Bug fix in jthermcalc_e107 (wrong indexes used in some computations involving NO2 and H2). + +== 08/11/2022 == RV +Update startarchive2icosa repertory for new version of Dynamico Index: /trunk/LMDZ.MARS/util/startarchive2icosa/README =================================================================== --- /trunk/LMDZ.MARS/util/startarchive2icosa/README (revision 2812) +++ /trunk/LMDZ.MARS/util/startarchive2icosa/README (revision 2813) @@ -6,4 +6,5 @@ Run a dynamico simulation (with startphy_file=false for example) with the desired resolution to get start.nc and startfi.nc. These files will be used as reference (rename as *_ref.nc) in the script. +You can use the files named *_no_start to have an example of callphys etc to run without startfiles Job_mpi is the file you need to run start_archive2icosa on Occigen @@ -18,8 +19,8 @@ -------------- 1) input file start_archive.nc needs some minor adaptations: -- variable "nivsigs" needs be renamed "sigs" (XIOS requires CF-compliant files) +- variable "nivsigs" needs be renamed "sigs" (XIOS requires CF-compliant files) (RV: No neeeded anymore) ncrename -vnivsigs,sigs start_archive.nc - input file start_archive.nc need be converted to NetCDF4 format -nccopy -k 'netCDF-4' start_archive.nc start_archive_nc4.nc +nccopy -k 4 start_archive.nc start_archive_nc4.nc 2) script "compile" can be used to compile main tool start_archive2icosa.f90 as well as rearrange_startphy.f90 Index: /trunk/LMDZ.MARS/util/startarchive2icosa/callphys.def_no_start =================================================================== --- /trunk/LMDZ.MARS/util/startarchive2icosa/callphys.def_no_start (revision 2813) +++ /trunk/LMDZ.MARS/util/startarchive2icosa/callphys.def_no_start (revision 2813) @@ -0,0 +1,175 @@ +##General options +##~~~~~~~~~~~~~~~ +#Run with or without tracer transport ? +tracer=.true. + +#Diurnal cycle ? if diurnal=False, diurnal averaged solar heating +diurnal=.true. + +#Seasonal cycle ? if season=False, Ls stays constant, to value set in "start" +season = .true. + +#write some more output on the screen ? +lwrite = .false. + +#Save statistics in file "stats.nc" ? +callstats =.false. + +#Save EOF profiles in file "profiles" for Climate Database? +calleofdump = .false. + +#Directory where external input files are: +datadir=datadir + +## use (read/write) a startfi.nc file? (default=.true.) +startphy_file = .false. +surfemis =0.5 +surfalbedo =0.5 + +## Dust scenario. Used if the dust is prescribed (i.e. if tracer=F or active=F) +## ~~~~~~~~~~~~~ +# =1 Dust opt.deph read in startfi; =2 Viking scenario; =3 MGS scenario, +# =4 Mars Year 24 from TES assimilation (old version of MY24; dust_tes.nc file) +# =6 "cold" (low dust) scenario ; =7 "warm" (high dust) scenario +# =8 "clim" scenario +# =24 Mars Year 24 from TES assimilation (ie: MCD reference case) +# =25 Mars Year 25 from TES assimilation (ie: a year with a global dust storm) +# =26 Mars Year 26 from TES assimilation +iaervar = 8 +# Dust opacity at 700 Pa (when constant, i.e. for the iaervar=1 case) +tauvis=0.5 +# Dust vertical distribution: +# (=0: old distrib. (Pollack90), =1: top set by "topdustref", +# =2: Viking scenario; =3 MGS scenario) +iddist = 3 +# Dust top altitude (km). (Matters only if iddist=1) +topdustref = 55. + +## Physical Parameterizations : +## ~~~~~~~~~~~~~~~~~~~~~~~~~~ +# call radiative transfer ? +callrad = .false. +# call NLTE radiative schemes ? matters only if callrad=T +callnlte = .false. +# NLTE 15um scheme to use. +# 0-> Old scheme, static oxygen +# 1-> Old scheme, dynamic oxygen +# 2-> New scheme +nltemodel = 0 +# call CO2 NIR absorption ? matters only if callrad=T +callnirco2 = .false. +# NIR NLTE correction ? matters only if callnirco2=T +nircorr=0 +# call turbulent vertical diffusion ? +calldifv = .false. +# call convective adjustment ? +calladj = .false. +# Thermals +calltherm = .false. +callrichsl = .false. +# call CO2 condensation ? +callcond =.false. +# call thermal conduction in the soil ? +callsoil = .false. +# call Lott's gravity wave/subgrid topography scheme ? +calllott = .false. +calllott_nonoro = .false. +# Impose polar cap surface albedos as observed by TES? +TESicealbedo = .true. +## Coefficient for Northern cap albedoes +TESice_Ncoef=1.6 +## Coefficient for Southern cap albedoes +TESice_Scoef=1.6 + + +## Radiative transfer options : +## ~~~~~~~~~~~~~~~~~~~~~~~~~~ +# the rad.transfer is computed every "iradia" physical timestep +iradia = 1 +# Output of the exchange coefficient mattrix ? for diagnostic only +callg2d = .false. +# Rayleigh scattering : (should be .false. for now) +rayleigh = .false. + +## Tracer (dust water, ice and/or chemical species) options (used if tracer=T): +## ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +# DUST: Transported dust ? (if >0, use 'dustbin' dust bins) +dustbin = 0 +# DUST: Radiatively active dust ? (matters if dustbin>0) +active = .false. +# DUST: use mass and number mixing ratios to predict dust size ? +doubleq = .false. +# DUST: lifted by GCM surface winds ? +lifting = .false. +# DUST: lifted by dust devils ? +callddevil = .false. +# DUST: Scavenging by H2O snowfall ? +scavenging = .false. +# DUST: Scavenging by instantaneous CO2 snowfall ? +scavco2cond = .false. + +# DUST: freedust ? +freedust=.false. +# DUST: dust injection scheme (if >0, use 'dustinjection') +dustinjection=0 +# DUST: dust injection scheme coefficient +coeff_injection=0.25 +# DUST: Rocket Dust Storm scheme +rdstorm=.false. +# DUST: slpwind scheme +slpwind = .false. + +# DUST/WATERICE: Gravitationnal sedimentation ? +sedimentation = .false. + + +# WATERICE: Radiatively active transported atmospheric water ice ? +activice = .false. +# WATER: Compute water cycle +water = .false. +# WATER: Microphysical scheme for water-ice clouds? +microphys = .false. +# WATER: Microphysical time step for water-ice clouds? (30 by default) +#imicro = 100 +# WATER: parameter contact +mteta = 0.95 +# WATER: current permanent caps at both poles. True IS RECOMMENDED +# (with .true., North cap is a source of water and South pole +# is a cold trap) +caps = .true. +# WATER: Water ice albedo ? +albedo_h2o_ice = 0.35 +# WATER: Water ice thermal inertia +inert_h2o_ice = 800 +# WATER: Frost thickness threshold for albedo +frost_albedo_threshold = 0.005 +nuice_sed=0.1 +# PHOTOCHEMISTRY: include chemical species +photochem = .false. +#WATER: subgrid clouds +CLFvarying=.false. +#WATER: subgrid clouds +CLFfixval=1 +#WATER: naerkind +naerkind=0 + +## Thermospheric options (relevant if tracer=T) : +##~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +# call thermosphere ? +callthermos = .false. +# WATER: included without cycle (only if water=.false.) +thermoswater = .false. +# call thermal conduction ? (only if callthermos=.true.) +callconduct = .false. +# call EUV heating ? (only if callthermos=.true.) +calleuv=.false. +# call molecular viscosity ? (only if callthermos=.true.) +callmolvis = .false. +# call molecular diffusion ? (only if callthermos=.true.) +callmoldiff = .false. +# call thermospheric photochemistry ? (only if callthermos=.true.) +thermochem = .false. +# date for solar flux calculation: (1985 < date < 2002) +## (Solar min=1996.4 ave=1993.4 max=1990.6) +solarcondate = 1993.4 + Index: /trunk/LMDZ.MARS/util/startarchive2icosa/compile =================================================================== --- /trunk/LMDZ.MARS/util/startarchive2icosa/compile (revision 2812) +++ /trunk/LMDZ.MARS/util/startarchive2icosa/compile (revision 2813) @@ -1,12 +1,12 @@ #!/usr/bin/bash -source /scratch/cnt0027/lmd1167/adelavois/models/code/XIOS/arch.env -source /scratch/cnt0027/lmd1167/adelavois/models/code/XIOS/arch.path +source ../../../../../trunk_Dynamico/trunk/XIOS/arch.env +source ../../../../../trunk_Dynamico/trunk/XIOS/arch.path mpif90 -g -traceback start_archive2icosa.f90 \ $NETCDF_INCDIR $NETCDF_LIBDIR $NETCDF_LIB \ $HDF5_INCDIR $HDF5_LIBDIR $HDF5_LIB \ --I /scratch/cnt0027/lmd1167/adelavois/models/code/XIOS/inc \ --L /scratch/cnt0027/lmd1167/adelavois/models/code/XIOS/lib -lxios -lstdc++ \ +-I ../../../../../trunk_Dynamico/trunk/XIOS/inc \ +-L ../../../../../trunk_Dynamico/trunk/XIOS/lib -lxios -lstdc++ \ -o start_archive2icosa @@ -14,6 +14,6 @@ $NETCDF_INCDIR $NETCDF_LIBDIR $NETCDF_LIB \ $HDF5_INCDIR $HDF5_LIBDIR $HDF5_LIB \ --I /scratch/cnt0027/lmd1167/adelavois/models/code/XIOS/inc \ --L /scratch/cnt0027/lmd1167/adelavois/models/code/XIOS/lib -lxios -lstdc++ \ +-I ../../../../../trunk_Dynamico/trunk/XIOS/inc \ +-L ../../../../../trunk_Dynamico/trunk/XIOS/lib -lxios -lstdc++ \ -o rearrange_startphy Index: /trunk/LMDZ.MARS/util/startarchive2icosa/icosa_finalize.bash =================================================================== --- /trunk/LMDZ.MARS/util/startarchive2icosa/icosa_finalize.bash (revision 2812) +++ /trunk/LMDZ.MARS/util/startarchive2icosa/icosa_finalize.bash (revision 2813) @@ -7,6 +7,7 @@ # load nco module module purge -source /scratch/cnt0027/lmd1167/adelavois/models/code/XIOS/arch.env -module load nco/4.7.9-gcc-4.8.5-hdf5-1.8.18-openmpi-2.0.4 +source /scratch/cnt0027/lmd1167/adelavois/models/code/XIOS/arch.env #You have to adapt to your own path +#module load nco/4.7.9-gcc-4.8.5-hdf5-1.8.18-openmpi-2.0.4 #Example of version of the module needed +module load nco #conversion to netcdf 3 in order to rename and add variables, not properly done with netcdf4 files @@ -24,11 +25,14 @@ #Temporay soildepth array from Dynamico restartfi ncks -A -v soildepth \ - ../../mars_dynamico_update_basic/startfi_0.nc startphy_nc3.nc + ../../mars_dynamico_update_basic/startfi_0.nc startphy_nc3.nc #You have to adapt to your own path -nccopy -k 'netCDF-4' startphy_nc3.nc startfi.nc +nccopy -k 4 startphy_nc3.nc startfi.nc #Temporary Time variable from start2archive; should be added with xios -ncks -A -v Time \ - start_archive_nc4.nc startfi.nc +#ncks -A -v Time \ +# start_archive_nc4.nc startfi.nc +ncks -O -x -v time_counter startfi.nc startfi.nc_tmp +ncks -A -v Time start.nc startfi.nc_tmp +cp startfi.nc_tmp startfi.nc rearrange_startphy > rearrange_startphy.out 2>&1 @@ -47,4 +51,21 @@ start_icosa_ref.nc start_icosa.nc +# In the current version of Dynamico, the variable q for tracer is needed but unused. +# To create this unused variable simply run this short python code + +#import numpy as np +#import netCDF4 as nc + +#fn = 'start_icosa.nc' +#ds = nc.Dataset(fn, 'a', format='NETCDF4') +#nq = ds.createDimension('nq', 7) + +#q = ds.createVariable('q', 'f8', ('nq','lev', 'cell_mesh',)) +#nqq = ds.createVariable('nq', 'f8', ('nq',)) +#q[:,:,:]=0. +#q.online_operation = "once" +#q.coordinates = "lat lon" +#ds.close() + # cleanup rm -rf startphy_icosa_nc3.nc startphy_nc3.nc Index: /trunk/LMDZ.MARS/util/startarchive2icosa/run_icosa.def_no_start =================================================================== --- /trunk/LMDZ.MARS/util/startarchive2icosa/run_icosa.def_no_start (revision 2813) +++ /trunk/LMDZ.MARS/util/startarchive2icosa/run_icosa.def_no_start (revision 2813) @@ -0,0 +1,249 @@ +#INCLUDEDEF=saturn_const.def + +##mpi_threading_mode=serialized +#mpi_threading_mode=funneled + +#halo_i=0 +#halo_j=1 +# ------------------------------- Mesh --------------------------------- + +# Number of subdivision on a main triangle (nbp) : integer (default=40) +#nbp=160 +nbp=20 + +# Earth as reference ? +# nbp 20 40 80 160 +# T-edge length (km) 500 250 120 60 + +## sub splitting of main rhombus : integer (default=1) +#nsplit_i=1 +#nsplit_j=1 +#omp_level_size=1 +########################################### +## There must be less MPIxOpenMP processes than the 10 x nsplit_i x nsplit_j tiles +## typically for pure MPI runs, let nproc = 10 x nsplit_i x nsplit_j +## it is better to have nbp/split >~ 10 +########################################### +## 10 procs +nsplit_i=1 +nsplit_j=2 +#### 50 noeuds de 24 processeurs = 1200 procs +#nsplit_i=10 +#nsplit_j=12 + +# Number of vertical layer (llm) : integer (default=19) +#llm=64 +llm=73 + +# disvert : vertical discretisation : string (default='std') : std, ncar, ncar30l +#disvert=read_apbp +disvert=plugin + +# optim_it : mesh optimisation : number of iteration : integer (default=0) +#optim_it=1000 +optim_it=100 + +# ---------------------------------- Time--------------------------------- + +## scheme type : string : euler, leapfrog_matsuno, runge_kutta ) +# time_scheme = ARK2.3 (RK 2nd order at 3 levels) | leapfrog_matsuno | ... +time_scheme = ARK2.3 + +## matsuno period : integer ( default=5) Only used for leapfrog_matsuno scheme +matsuno_period = 10 + +# timestep : real (default=480s) +# dt = 92.473958333334 +### attention 3 chiffres significatifs dans XIOS +# number of dynamical steps per day (instead of dt) +day_step=960 + +# advection called every itau_adv time steps : integer (default 2) +# standard : umax=100m/s vs c=340m/s (ratio 1:3) +# in JW06 umax=35m/s vs c=340m/s (ratio 1:10) +itau_adv=3 + +# number of timestep (default 100) (ignored if run_length is set) +#itaumax = 10 + +# run length : real (default=dt*itaumax) + +#################################### + +## 1 martian day +#run_length = 88775 +#run_length = 887750 + +## 1 martian year : 59212925s +## first martian month (61sols):5415275s + +# number of days to run +ndays=1 + +#################################### + +##activate IO (default = true) +#enable_io = false + +## output with XIOS (only if compiled with XIOS): true/false (default true) +#xios_output=false + +# output field period (valid XIOS or not) : integer (default none) +# [should be equal to dt if XIOS dynamical outputs are wanted] +# [because write_period sets synchronization frequency with XIOS] +write_period = 92.473958333 + + +#itau_write_etat0=380520 + +# ---------------------------------- Misc -------------------------------- + +# number of tracer (nqtot) : integer (default 1) +nqtot=1 + +# pression value where output is interpolated : real (default=0, no output) +###out_pression_level=85000 + +# etat0 : initial state : string (default=jablonowsky06) : +# jablonowsky06, academic, ncar + +#etat0=start_file +#etat0_start_file_colocated=true + +## -- to cross the 2y limit +#etat0_start_iteration=0 +#run_length=38052 + +etat0=isothermal +etat0_isothermal_temp=200 + +# start file name (default is start.nc) +# restart file name (default is restart.nc) +#start_file_name=start_icosa +restart_file_name=restart_icosa + +#etat0_start_iteration_reset=true +#etat0_start_iteration=0 + +##### for one-day run from a profile to create a start +#etat0=temperature_profile +#temperature_profile_file=temp_profile.txt +#run_length=38052 + +# ------------------------------ Dynamics -------------------------------- + +# caldyn : computation type for gcm equation : string (default=gcm) : gcm, adv +caldyn=gcm + +# caldyn_conserv : string (default=energy) : energy,enstrophy +caldyn_conserv=energy + +# caldyn_exner : scheme for computing Exner function : string (default=direct) : direct,lmdz +caldyn_exner=direct + +# caldyn_hydrostat : scheme for computing geopotential : string (default=direct) : direct,lmdz +caldyn_hydrostat=direct + +# guided_type : string (default=none) : none, ncar +guided_type=none + +#Sponge layer +### iflag_sponge=0 for no sponge +### iflag_sponge=1 for sponge over 4 topmost layers +### iflag_sponge=2 for sponge from top to ~1% of top layer pressure +### tau_sponge --> damping frequency at last layer +### e-5 medium / e-4 strong yet reasonable / e-3 very strong +### mode_sponge=1 for u,v --> 0 +### mode_sponge=2 for u,v --> zonal mean (NOT IMPLEMENTED) +### mode_sponge=3 for u,v,h --> zonal mean (NOT IMPLEMENTED) +#iflag_sponge = 1 +iflag_sponge = 1 +tau_sponge = 1.e-4 +#mode_sponge = 1 + + +# ---------------------------------- Dissipation --------------------------------- + +# dissipation time graddiv : real (default=5000) +tau_graddiv = 2000 + +# number of iteration for graddiv : integer (default=1) +nitergdiv = 2 + +# dissipation time nxgradrot (default=5000) +tau_gradrot = 4000 + +# number of iteration for nxgradrot : integer (default=1) +nitergrot=2 + +# dissipation time divgrad (theta) (default=5000) +tau_divgrad= 4000 +# number of iteration for divgrad : integer (default=1) +niterdivgrad=2 + +# Vertical evolution of the dissipation coefficient +# vert_prof_dissip_type=legacy +vert_prof_dissip_type=plugin + +# vertical dissipation setup (none|altitude|pressure) +vert_prof_dissip_setup=altitude +dissip_fac_mid=3. +dissip_fac_up=30. +dissip_startalt=70. +dissip_deltaz=30. + +#Vertical coefficient for dissipation: 1 is for Earth, 2 Mars, 3 Venus, default is basic scheme +#vert_prof_dissip=2 +#fac_mid=3. +#fac_up=30. +#dissip_deltaz=30. +#startalt=70. + +# Rayleigh friction : string (default=none) : none, dcmip2_schaer_noshear, dcmip2_schaer_shear +rayleigh_friction_type=none +#rayleigh_friction_type=giant_liu_schneider +#rayleigh_limlat = 33. +#rayleigh_friction_tau = 8640000. + +# -------------------------------- Physics ------------------------------------- + +# (itau_physics=160)*(dt=118.9125) --> half a saturn day as physical timestep +# ---- for some reason (day consistency, physical timestep must be less a day) +# ---- change also in run.def +itau_physics=5 + +# kind of physics : string : none, dcmip (default=none) +physics=phys_external + +## testcase physics for dcmip : INTEGER : 1, 2 (default=1) +#dcmip_physics=1 + +# -------------------- parameters for NCAR test cases ------------------------ + +# NCAR advection test, initial tracer : string ( default='cos_bell') +# const, slotted_cyl, cos_bell, dbl_cos_bell_q1, dbl_cos_bell_q2, complement, hadley +ncar_adv_shape=cos_bell + +# NCAR advection test, wind field : string (default='deform') : solid, deform, hadley +ncar_adv_wind=solid + +# ncar_T0 : reference temperature for NCAR test cases : real (default=300) +# also used by disvert if disvert=ncar +ncar_T0=300 + +# ncar_p0 : reference pressure for NCAR test cases : real (default=1e5) +# also used by disvert if disvert=ncar +ncar_p0=1e5 + +# ncar_disvert_c : exponent for B(eta) : integer (default=1) +# used by disvert if disvert=ncar + +ncar_disvert_c=1 + +# dcmip 4 testcase : integer (default=1) : 1, 2 +dcmip4_testcase=1 +#----------------------------------------------------------------------- + + +check_conservation = detailed +itau_check_conserv = 320 Index: /trunk/LMDZ.MARS/util/startarchive2icosa/traceur.def_no_start =================================================================== --- /trunk/LMDZ.MARS/util/startarchive2icosa/traceur.def_no_start (revision 2813) +++ /trunk/LMDZ.MARS/util/startarchive2icosa/traceur.def_no_start (revision 2813) @@ -0,0 +1,2 @@ +1 +co2