Index: /trunk/LMDZ.MARS/libf/phymars/xios_output_mod.F90 =================================================================== --- /trunk/LMDZ.MARS/libf/phymars/xios_output_mod.F90 (revision 2940) +++ /trunk/LMDZ.MARS/libf/phymars/xios_output_mod.F90 (revision 2941) @@ -27,4 +27,5 @@ USE regular_lonlat_mod, ONLY: lon_reg, lat_reg USE nrtype, ONLY: pi + use comslope_mod, ONLY: nslope,def_slope_mean #ifdef CPP_XIOS USE xios @@ -62,4 +63,7 @@ CALL xios_set_axis_attr("soil_layers", n_glo=size(mlayer), value=mlayer,& unit="m",positive="down") + IF (prt_level>=10) WRITE(lunout,*) "initialize_xios_output: call xios_set_axis_attr for subslope" + CALL xios_set_axis_attr("subslope", n_glo=nslope, value=def_slope_mean,& + unit="degree",positive="up") ! 2. Declare horizontal domain Index: /trunk/LMDZ.MARS/util/startarchive2icosa/README =================================================================== --- /trunk/LMDZ.MARS/util/startarchive2icosa/README (revision 2940) +++ /trunk/LMDZ.MARS/util/startarchive2icosa/README (revision 2941) @@ -6,5 +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 +You can use the files named *_no_start to have an example of files to run without startfiles Job_mpi is the file you need to run start_archive2icosa on Occigen Index: unk/LMDZ.MARS/util/startarchive2icosa/callphys.def_no_start =================================================================== --- /trunk/LMDZ.MARS/util/startarchive2icosa/callphys.def_no_start (revision 2940) +++ (revision ) @@ -1,175 +1,0 @@ -##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 2940) +++ /trunk/LMDZ.MARS/util/startarchive2icosa/compile (revision 2941) @@ -1,12 +1,12 @@ #!/usr/bin/bash -source ../../../../../trunk_Dynamico/trunk/XIOS/arch.env -source ../../../../../trunk_Dynamico/trunk/XIOS/arch.path +source ../../../XIOS/arch.env +source ../../../XIOS/arch.path mpif90 -g -traceback start_archive2icosa.f90 \ $NETCDF_INCDIR $NETCDF_LIBDIR $NETCDF_LIB \ $HDF5_INCDIR $HDF5_LIBDIR $HDF5_LIB \ --I ../../../../../trunk_Dynamico/trunk/XIOS/inc \ --L ../../../../../trunk_Dynamico/trunk/XIOS/lib -lxios -lstdc++ \ +-I ../../../XIOS/inc \ +-L ../../../XIOS/lib -lxios -lstdc++ \ -o start_archive2icosa @@ -14,6 +14,6 @@ $NETCDF_INCDIR $NETCDF_LIBDIR $NETCDF_LIB \ $HDF5_INCDIR $HDF5_LIBDIR $HDF5_LIB \ --I ../../../../../trunk_Dynamico/trunk/XIOS/inc \ --L ../../../../../trunk_Dynamico/trunk/XIOS/lib -lxios -lstdc++ \ +-I ../../../XIOS/inc \ +-L ../../../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 2940) +++ /trunk/LMDZ.MARS/util/startarchive2icosa/icosa_finalize.bash (revision 2941) @@ -7,5 +7,5 @@ # load nco module module purge -source /scratch/cnt0027/lmd1167/adelavois/models/code/XIOS/arch.env #You have to adapt to your own path +source ../trunk/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 @@ -18,23 +18,22 @@ ncrename -v lon,longitude -v lat,latitude -d cell,physical_points\ startphy_icosa_nc3.nc startphy_nc3.nc -# Temporarily added because program is not yet able to read topography -# SSO parameters are now taken from a dedicated startarchive.nc -# see start2archive_SSO.f90 -#ncks -A -v albedodat,ZMEA,ZSTD,ZSIG,ZGAM,ZTHE \ -# startphy_icosa_ref.nc startphy_nc3.nc #Temporay soildepth array from Dynamico restartfi -ncks -A -v soildepth \ - ../../mars_dynamico_update_basic/startfi_0.nc startphy_nc3.nc #You have to adapt to your own path +ncks -A -v soildepth restartfi.nc startphy_nc3.nc #You have to adapt to your own path +ncks -A -v subslope_dist restartfi.nc startphy_nc3.nc +ncks -A -v def_slope restartfi.nc startphy_nc3.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 -O -x -v time_counter startfi.nc startfi.nc_tmp ncks -A -v Time start.nc startfi.nc_tmp +ncks -A -v flux_geo restartfi.nc startfi.nc_tmp +ncks -A -v wstar restartfi.nc startfi.nc_tmp +ncks -A -v hmons restartfi.nc startfi.nc_tmp +ncks -A -v summit restartfi.nc startfi.nc_tmp +ncks -A -v base restartfi.nc startfi.nc_tmp cp startfi.nc_tmp startfi.nc -rearrange_startphy > rearrange_startphy.out 2>&1 +./rearrange_startphy > rearrange_startphy.out 2>&1 # make a proper start.nc file based on start_icosa.nc @@ -51,21 +50,9 @@ start_icosa_ref.nc start_icosa.nc +ncks -A -v W,geopot,q,nq 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/iodef.xml =================================================================== --- /trunk/LMDZ.MARS/util/startarchive2icosa/iodef.xml (revision 2940) +++ /trunk/LMDZ.MARS/util/startarchive2icosa/iodef.xml (revision 2941) @@ -11,6 +11,17 @@ + + + + + + + + + + + + - @@ -22,12 +33,8 @@ - - - - - - - - + + + + @@ -50,9 +57,17 @@ + + + + - + + + + + @@ -69,17 +84,5 @@ operation="instant" > - - - - - - - - - - - - @@ -91,4 +94,23 @@ + + + + + + + + + + + + + + + + + + + + + + + + + - - @@ -200,5 +245,12 @@ + + + + + + @@ -212,5 +264,5 @@ + @@ -261,4 +314,12 @@ + + + + + + + + @@ -277,4 +338,14 @@ + + + + + + + + + + @@ -289,4 +360,8 @@ + + + + @@ -301,4 +376,9 @@ + + + + + Index: /trunk/LMDZ.MARS/util/startarchive2icosa/rearrange_startphy.f90 =================================================================== --- /trunk/LMDZ.MARS/util/startarchive2icosa/rearrange_startphy.f90 (revision 2940) +++ /trunk/LMDZ.MARS/util/startarchive2icosa/rearrange_startphy.f90 (revision 2941) @@ -6,5 +6,5 @@ INTEGER :: ncid -INTEGER :: dimids(4) +INTEGER :: dimids(9) INTEGER :: varid INTEGER :: ierr @@ -12,7 +12,10 @@ INTEGER :: ndim CHARACTER(LEN=100) :: varname -INTEGER :: varname_dimids(5) +INTEGER :: varname_dimids(9) INTEGER :: i,j,k,nb_cells,nlev,nsoil,nvertex,nlev_p1 + +INTEGER :: physical_points, subslope, index_, inter_slope, subsurface_layer, lev_p1, Time, nslope + INTEGER,ALLOCATABLE :: cell_index(:) REAL,ALLOCATABLE :: ref_lon(:) @@ -25,4 +28,6 @@ REAL,ALLOCATABLE :: ref_field_soil(:,:),field_soil(:,:) REAL,ALLOCATABLE :: ref_field_vertex(:,:),field_vertex(:,:) +REAL,ALLOCATABLE :: ref_field_subslope(:,:),field_subslope(:,:) +REAL,ALLOCATABLE :: ref_field_soil_subslope(:,:,:),field_soil_subslope(:,:,:) REAL :: lati,loni REAL :: diff_lat,diff_lon @@ -121,25 +126,47 @@ ! load, rearrange and write variables ierr=NF90_INQ_DIMID(ncid,"physical_points",dimids(1)) - ierr=NF90_INQ_DIMID(ncid,"lev",dimids(2)) - ierr=NF90_INQUIRE_DIMENSION(ncid, dimids(2), len=nlev) - ierr=NF90_INQ_DIMID(ncid,"subsurface_layers",dimids(3)) - ierr=NF90_INQUIRE_DIMENSION(ncid, dimids(3), len=nsoil) - ierr=NF90_INQ_DIMID(ncid,"nvertex",dimids(4)) - ierr=NF90_INQUIRE_DIMENSION(ncid, dimids(4), len=nvertex) - ierr=NF90_INQ_DIMID(ncid,"lev_p1",dimids(5)) - ierr=NF90_INQUIRE_DIMENSION(ncid, dimids(2), len=nlev_p1) + ierr=NF90_INQUIRE_DIMENSION(ncid, dimids(1), len=physical_points) + ierr=NF90_INQ_DIMID(ncid,"nvertex",dimids(2)) + ierr=NF90_INQUIRE_DIMENSION(ncid, dimids(2), len=nvertex) + ierr=NF90_INQ_DIMID(ncid,"subslope",dimids(3)) + ierr=NF90_INQUIRE_DIMENSION(ncid, dimids(3), len=subslope) + ierr=NF90_INQ_DIMID(ncid,"index",dimids(4)) + ierr=NF90_INQUIRE_DIMENSION(ncid, dimids(4), len=index_) + ierr=NF90_INQ_DIMID(ncid,"inter_slope",dimids(5)) + ierr=NF90_INQUIRE_DIMENSION(ncid, dimids(5), len=inter_slope) + ierr=NF90_INQ_DIMID(ncid,"subsurface_layers",dimids(6)) + ierr=NF90_INQUIRE_DIMENSION(ncid, dimids(6), len=subsurface_layer) + ierr=NF90_INQ_DIMID(ncid,"lev_p1",dimids(7)) + ierr=NF90_INQUIRE_DIMENSION(ncid, dimids(7), len=lev_p1) + ierr=NF90_INQ_DIMID(ncid,"Time",dimids(8)) + ierr=NF90_INQUIRE_DIMENSION(ncid, dimids(8), len=Time) + ierr=NF90_INQ_DIMID(ncid,"nslope",dimids(9)) + ierr=NF90_INQUIRE_DIMENSION(ncid, dimids(9), len=nslope) ierr=NF90_INQUIRE(ncid,nVariables=nvar) + + +! ierr=NF90_INQ_DIMID(ncid,"lev",dimids(2)) +! ierr=NF90_INQUIRE_DIMENSION(ncid, dimids(2), len=nlev) +! ierr=NF90_INQ_DIMID(ncid,"subsurface_layers",dimids(3)) +! ierr=NF90_INQUIRE_DIMENSION(ncid, dimids(3), len=nsoil) +! ierr=NF90_INQ_DIMID(ncid,"nvertex",dimids(4)) +! ierr=NF90_INQUIRE_DIMENSION(ncid, dimids(4), len=nvertex) +! ierr=NF90_INQ_DIMID(ncid,"lev_p1",dimids(5)) +! ierr=NF90_INQUIRE_DIMENSION(ncid, dimids(2), len=nlev_p1) + write(*,*) "nvar=",nvar - allocate(ref_field(nb_cells),field(nb_cells)) - allocate(ref_field_3D(nb_cells,nlev),field_3D(nb_cells,nlev)) - allocate(ref_field_3D_p1(nb_cells,nlev_p1),field_3D_p1(nb_cells,nlev_p1)) - allocate(ref_field_soil(nb_cells,nsoil),field_soil(nb_cells,nsoil)) - allocate(ref_field_vertex(nvertex,nb_cells),field_vertex(nvertex,nb_cells)) + allocate(ref_field(physical_points),field(physical_points)) + allocate(ref_field_3D_p1(physical_points,lev_p1),field_3D_p1(physical_points,lev_p1)) + allocate(ref_field_subslope(physical_points,subslope),field_subslope(physical_points,subslope)) + allocate(ref_field_soil(physical_points,subsurface_layer),field_soil(physical_points,subsurface_layer)) + allocate(ref_field_vertex(nvertex,physical_points),field_vertex(nvertex,physical_points)) + allocate(ref_field_soil_subslope(physical_points,subsurface_layer,subslope),field_soil_subslope(physical_points,subsurface_layer,subslope)) write(*,*) "dimids :", dimids + ! loop over variables: do k=1,nvar varname_dimids(:)=0 ierr=NF90_INQUIRE_VARIABLE(ncid,k,name=varname,ndims=ndim,dimids=varname_dimids) - write(*,*) "name: ",trim(varname),"; dimensions:",varname_dimids + write(*,*) "name: ",trim(varname),";ndim=",ndim,"; dimensions:",varname_dimids if (ierr /= nf90_noerr) then write(*,*) "error for variable k=",k @@ -159,6 +186,6 @@ ierr=NF90_PUT_VAR(ncid,varid,field) - ! Processing 3D variables : bounds_lon and bounds_lat - else if ((ndim==2).and.(varname_dimids(1)==dimids(4))) then + ! Processing vertex variables : bounds_lon and bounds_lat + else if ((ndim==2).and.(varname_dimids(1)==dimids(2))) then write(*,*) "processing ",trim(varname) ! load field_3D @@ -174,23 +201,39 @@ ierr=NF90_PUT_VAR(ncid,varid,field_vertex) if (ierr /= nf90_noerr) print*,"error putvar ",trim(varname) - + + ! Processing 3D variables : subslope + else if ((ndim==2).and.(varname_dimids(2)==dimids(3))) then + write(*,*) "processing ",trim(varname) + ! load field_3D + ierr=NF90_INQ_VARID(ncid,varname,varid) + if (ierr /= nf90_noerr) print*,"error inqvarid ",trim(varname) + ierr=NF90_GET_VAR(ncid,varid,ref_field_subslope) + if (ierr /= nf90_noerr) print*,"error get_var ",trim(varname) + ! rearrange field_3D + do i=1,nb_cells + field_subslope(cell_index(i),:)=ref_field_subslope(i,:) + enddo + ! write field_3D + ierr=NF90_PUT_VAR(ncid,varid,field_subslope) + if (ierr /= nf90_noerr) print*,"error putvar ",trim(varname) + ! Processing 3D variables : altitude - else if ((ndim==2).and.(varname_dimids(2)==dimids(2))) then - write(*,*) "processing ",trim(varname) - ! load field_3D - ierr=NF90_INQ_VARID(ncid,varname,varid) - if (ierr /= nf90_noerr) print*,"error inqvarid ",trim(varname) - ierr=NF90_GET_VAR(ncid,varid,ref_field_3D) - if (ierr /= nf90_noerr) print*,"error get_var ",trim(varname) - ! rearrange field_3D - do i=1,nb_cells - field_3D(cell_index(i),:)=ref_field_3D(i,:) - enddo - ! write field_3D - ierr=NF90_PUT_VAR(ncid,varid,field_3D) + else if ((ndim==2).and.(varname_dimids(2)==dimids(7))) then + write(*,*) "processing ",trim(varname) + ! load field_3D + ierr=NF90_INQ_VARID(ncid,varname,varid) + if (ierr /= nf90_noerr) print*,"error inqvarid ",trim(varname) + ierr=NF90_GET_VAR(ncid,varid,ref_field_3D_p1) + if (ierr /= nf90_noerr) print*,"error get_var ",trim(varname) + ! rearrange field_3D + do i=1,nb_cells + field_3D_p1(cell_index(i),:)=ref_field_3D_p1(i,:) + enddo + ! write field_3D + ierr=NF90_PUT_VAR(ncid,varid,field_3D_p1) if (ierr /= nf90_noerr) print*,"error putvar ",trim(varname) ! Processing 3D variables : soil - else if ((ndim==2).and.(varname_dimids(2)==dimids(3))) then + else if ((ndim==2).and.(varname_dimids(2)==dimids(6))) then write(*,*) "processing ",trim(varname) ! load field_soil @@ -207,19 +250,22 @@ if (ierr /= nf90_noerr) print*,"error putvar ",trim(varname) - ! Processing 3D variables : q2 with lev_p1 as vertical axis - else if ((ndim==2).and.(varname_dimids(2)==dimids(5))) then - write(*,*) "processing ",trim(varname) - ! load field_3D - ierr=NF90_INQ_VARID(ncid,varname,varid) - if (ierr /= nf90_noerr) print*,"error inqvarid ",trim(varname) - ierr=NF90_GET_VAR(ncid,varid,ref_field_3D_p1) - if (ierr /= nf90_noerr) print*,"error get_var ",trim(varname) - ! rearrange field_3D - do i=1,nb_cells - field_3D_p1(cell_index(i),:)=ref_field_3D_p1(i,:) - enddo - ! write field_3D - ierr=NF90_PUT_VAR(ncid,varid,field_3D_p1) - if (ierr /= nf90_noerr) print*,"error putvar ",trim(varname) + ! Processing 3D variables : tsoil + else if ((ndim==3).and.(varname_dimids(3)==dimids(3))) then + write(*,*) "processing ",trim(varname) + ! load field_3D + ierr=NF90_INQ_VARID(ncid,varname,varid) + if (ierr /= nf90_noerr) print*,"error inqvarid ",trim(varname) + ierr=NF90_GET_VAR(ncid,varid,ref_field_soil_subslope) + if (ierr /= nf90_noerr) print*,"error get_var ",trim(varname) + ! rearrange field_3D + do i=1,nb_cells + field_soil_subslope(cell_index(i),:,:)=ref_field_soil_subslope(i,:,:) + enddo + ! write field_3D + ierr=NF90_PUT_VAR(ncid,varid,field_soil_subslope) + if (ierr /= nf90_noerr) print*,"error putvar ",trim(varname) + else + print *, "Nothing to do with ", trim(varname), " ndim=", ndim, " varname_dimids(:)=", varname_dimids(:) + endif enddo Index: /trunk/LMDZ.MARS/util/startarchive2icosa/run_icosa.def_no_start =================================================================== --- /trunk/LMDZ.MARS/util/startarchive2icosa/run_icosa.def_no_start (revision 2940) +++ /trunk/LMDZ.MARS/util/startarchive2icosa/run_icosa.def_no_start (revision 2941) @@ -1,249 +1,106 @@ -#INCLUDEDEF=saturn_const.def -##mpi_threading_mode=serialized -#mpi_threading_mode=funneled +#---------------- Mesh ---------------- -#halo_i=0 -#halo_j=1 -# ------------------------------- Mesh --------------------------------- +# Number of subdivisions on a main triangle : integer (default=40) +nbp = 60 -# Number of subdivision on a main triangle (nbp) : integer (default=40) -#nbp=160 -nbp=20 +# Number of vertical layers : integer (default=19) +llm = 54 -# 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 +# Vertical grid : [std|ncar|ncarl30] (default=std) #disvert=read_apbp disvert=plugin -# optim_it : mesh optimisation : number of iteration : integer (default=0) -#optim_it=1000 -optim_it=100 +# Mesh optimisation : number of iterations : integer (default=0) +optim_it = 1000 -# ---------------------------------- Time--------------------------------- +# Sub splitting of main rhombus : integer (default=1) +nsplit_i = 1 +nsplit_j = 1 -## scheme type : string : euler, leapfrog_matsuno, runge_kutta ) -# time_scheme = ARK2.3 (RK 2nd order at 3 levels) | leapfrog_matsuno | ... -time_scheme = ARK2.3 +#number of openmp task on vertical level +omp_level_size=1 -## matsuno period : integer ( default=5) Only used for leapfrog_matsuno scheme -matsuno_period = 10 +#---------------- Numerics ---------------- -# 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) +itau_adv = 1 -# 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 +# Time step in s : real (default=480) +# dt = 720 +# Alternative to specifying "dt", specify number of steps per day : day_step +day_step = 960 -# 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 +# Number of tracers : integer (default=1) +nqtot = 11 -#itau_write_etat0=380520 +#---------------- Time and output ---------------- -# ---------------------------------- Misc -------------------------------- +# Time style : [none|dcmip] (default=dcmip) +time_style = none -# number of tracer (nqtot) : integer (default 1) -nqtot=1 +# Run length in s : real (default=??) +# run_length = 103680000 +run_length = 462.369791666 +# Alternative to specifying "run_length", specify number of days to run : ndays +# ndays=1 -# pression value where output is interpolated : real (default=0, no output) -###out_pression_level=85000 +# Interval in s between two outputs : integer (default=0) +#write_period = 10800 +# output every dyn time step => dt = day_length/day_step ; 88775/960=92.4739583333 +write_period= 92.4739583333333 -# etat0 : initial state : string (default=jablonowsky06) : -# jablonowsky06, academic, ncar + +# Initial state : +# [jablonowsky06|academic|dcmip[1-4]|heldsz|dcmip2_schaer_noshear] (default=jablonowsky06) +etat0=isothermal +etat0_isothermal_temp=200 +# pertub initial state by a factor of ... +etat0_ps_white_noise=0.01 +etat0_theta_rhodz_white_noise=0.01 #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 +start_file_name=start_icosa restart_file_name=restart_icosa -#etat0_start_iteration_reset=true -#etat0_start_iteration=0 +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 +# Dissipation time for grad(div) : real (default=5000) +tau_graddiv = 18000 -# ------------------------------ 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) +# Exponent of grad(div) disspation : integer (default=1) nitergdiv = 2 -# dissipation time nxgradrot (default=5000) -tau_gradrot = 4000 +# Dissipation time for curl(curl) : real (default=5000) +tau_gradrot = 18000 -# number of iteration for nxgradrot : integer (default=1) -nitergrot=2 +# Exponent of curl(curl) disspation : integer (default=1) +nitergrot = 2 -# dissipation time divgrad (theta) (default=5000) -tau_divgrad= 4000 -# number of iteration for divgrad : integer (default=1) -niterdivgrad=2 +# Dissipation time for div(grad) : real (default=5000) +tau_divgrad = 18000 -# Vertical evolution of the dissipation coefficient -# vert_prof_dissip_type=legacy -vert_prof_dissip_type=plugin +# Exponent of div(grad) disspation : integer (default=1) +niterdivgrad = 2 -# 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. +#---------------- Planet ---------------- -#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. +INCLUDEDEF=mars_const.def # -------------------------------- 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 +# Physics package : [none|held_suarez|dcmip] (default=none) +physics = phys_external + +# call physics every itau_physics (dynamical) time step itau_physics=5 +#itau_physics=10 -# 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 +# physics initial state (startfi.nc) if startphy_file=.true. +startphy_file=.false. Index: /trunk/LMDZ.MARS/util/startarchive2icosa/start_archive2icosa.f90 =================================================================== --- /trunk/LMDZ.MARS/util/startarchive2icosa/start_archive2icosa.f90 (revision 2940) +++ /trunk/LMDZ.MARS/util/startarchive2icosa/start_archive2icosa.f90 (revision 2941) @@ -23,11 +23,13 @@ INTEGER :: src_nj, src_nj_glo, src_topo_nj, src_topo_nj_glo INTEGER :: src_nlev ! number of vertical layers - INTEGER :: src_nq=7 ! number of tracers + INTEGER :: src_nq=11 ! number of tracers INTEGER :: src_nt=1 ! number of time steps INTEGER :: src_nsoil=18 ! number of soil layers + INTEGER :: src_nslope=1 ! number of subslope DOUBLE PRECISION,ALLOCATABLE :: lev_values(:) ! vertical axis DOUBLE PRECISION,ALLOCATABLE :: lev_p1_values(:) ! vertical axis DOUBLE PRECISION,ALLOCATABLE :: nq_values(:) ! tracer # axis DOUBLE PRECISION,ALLOCATABLE :: soil_layers_values(:) ! soil axis + DOUBLE PRECISION,ALLOCATABLE :: subslope_values(:) ! subslope axis DOUBLE PRECISION,ALLOCATABLE :: src_lon(:) ! mesh center coordinate DOUBLE PRECISION,ALLOCATABLE :: src_lat(:) @@ -36,4 +38,5 @@ DOUBLE PRECISION,ALLOCATABLE :: src_controle(:) DOUBLE PRECISION,ALLOCATABLE :: src_field_2D(:,:) + DOUBLE PRECISION,ALLOCATABLE :: src_field_2D_subslope(:,:,:) DOUBLE PRECISION,ALLOCATABLE :: src_pk(:,:) DOUBLE PRECISION,ALLOCATABLE :: src_field_3D(:,:,:) @@ -44,4 +47,5 @@ DOUBLE PRECISION,ALLOCATABLE :: src_topo(:,:) DOUBLE PRECISION,ALLOCATABLE :: src_field_3D_soil(:,:,:) ! 3D grid in soil, for tsoil et inertia + DOUBLE PRECISION,ALLOCATABLE :: src_field_3D_soil_subslope(:,:,:,:) ! 3D grid in soil, for tsoil et inertia DOUBLE PRECISION,ALLOCATABLE :: src_soil_layers(:) ! soil_depth DOUBLE PRECISION,ALLOCATABLE :: src_field_3D_p1(:,:,:) !q2 field @@ -60,5 +64,5 @@ INTEGER :: dst_nvertex INTEGER :: ncid - INTEGER :: dimids(4) + INTEGER :: dimids(5) INTEGER :: varid @@ -140,5 +144,7 @@ write(*,*) "rank=",rank,"dimids tsoil =",dimids ierr=NF90_INQUIRE_DIMENSION(ncid, dimids(3), len=src_nsoil) + ierr=NF90_INQUIRE_DIMENSION(ncid, dimids(4), len=src_nslope) write(*,*) "rank=",rank," src_nsoil=",src_nsoil ! number of vertical layers + write(*,*) "rank=",rank," src_nslope=",src_nslope ! number of subslope ! assume domain splitup with MPI only along latitudes @@ -161,8 +167,10 @@ ALLOCATE(src_lat(src_nj)) ALLOCATE(src_field_2D(src_ni,src_nj)) + ALLOCATE(src_field_2D_subslope(src_ni,src_nj,src_nslope)) ALLOCATE(src_pk(src_ni,src_nj)) ALLOCATE(src_field_3D(src_ni,src_nj,src_nlev)) ALLOCATE(src_field_3D_p1(src_ni,src_nj,src_nlev+1)) ALLOCATE(src_field_3D_soil(src_ni,src_nj,src_nsoil)) + ALLOCATE(src_field_3D_soil_subslope(src_ni,src_nj,src_nsoil,src_nslope)) ! ALLOCATE(src_field_soil_layers(src_nsoil)) ALLOCATE(src_pressure(src_ni,src_nj,src_nlev+1)) @@ -283,4 +291,7 @@ soil_layers_values=(/ (l,l=1,src_nsoil) /) CALL xios_set_axis_attr("soil_layers",n_glo=src_nsoil,value=soil_layers_values) + ALLOCATE(subslope_values(src_nslope)) + subslope_values=(/ (l,l=1,src_nslope) /) + CALL xios_set_axis_attr("subslope",n_glo=src_nslope,value=subslope_values) ! Set domains @@ -367,7 +378,7 @@ ! surface temperature: - CALL xios_recv_field("src_tsurf",src_field_2D) - WRITE(*,*) rank,":src_tsurf(1:2,1:3)=",src_field_2D(1:2,1:3) - CALL xios_send_field("tsurf_clean",src_field_2D(1:src_ni-1,1:src_nj)) + CALL xios_recv_field("src_tsurf",src_field_2D_subslope) + WRITE(*,*) rank,":src_tsurf(1:2,1:3,1)=",src_field_2D_subslope(1:2,1:3,1) + CALL xios_send_field("tsurf_clean",src_field_2D_subslope(1:src_ni-1,1:src_nj,:)) ! co2 ice coverage: @@ -377,7 +388,7 @@ ! emissivity: - CALL xios_recv_field("src_emis",src_field_2D) - WRITE(*,*) rank,":src_emis(1:2,1:3)=",src_field_2D(1:2,1:3) - CALL xios_send_field("emis_clean",src_field_2D(1:src_ni-1,1:src_nj)) + CALL xios_recv_field("src_emis",src_field_2D_subslope) + WRITE(*,*) rank,":src_emis(1:2,1:3,1)=",src_field_2D_subslope(1:2,1:3,1) + CALL xios_send_field("emis_clean",src_field_2D_subslope(1:src_ni-1,1:src_nj,:)) ! q2 : q2surf for first layer of q2, the rest is q2atm @@ -422,50 +433,74 @@ CALL xios_send_field("co2_clean", & src_field_3D(1:src_ni-1,1:src_nj,1:src_nlev)) - CALL xios_recv_field("src_co2_surf",src_field_2D) + CALL xios_recv_field("src_co2_surf",src_field_2D_subslope) CALL xios_send_field("co2_surf_clean", & - src_field_2D(1:src_ni-1,1:src_nj)) + src_field_2D_subslope(1:src_ni-1,1:src_nj,:)) elseif (i==2) THEN CALL xios_send_field("dust_number_clean", & src_field_3D(1:src_ni-1,1:src_nj,1:src_nlev)) - CALL xios_recv_field("src_dust_number_surf",src_field_2D) + CALL xios_recv_field("src_dust_number_surf",src_field_2D_subslope) CALL xios_send_field("dust_number_surf_clean", & - src_field_2D(1:src_ni-1,1:src_nj)) + src_field_2D_subslope(1:src_ni-1,1:src_nj,:)) elseif (i==3) THEN CALL xios_send_field("dust_mass_clean", & src_field_3D(1:src_ni-1,1:src_nj,1:src_nlev)) - CALL xios_recv_field("src_dust_mass_surf",src_field_2D) + CALL xios_recv_field("src_dust_mass_surf",src_field_2D_subslope) CALL xios_send_field("dust_mass_surf_clean", & - src_field_2D(1:src_ni-1,1:src_nj)) + src_field_2D_subslope(1:src_ni-1,1:src_nj,:)) elseif (i==4) THEN CALL xios_send_field("ccn_number_clean", & src_field_3D(1:src_ni-1,1:src_nj,1:src_nlev)) - CALL xios_recv_field("src_ccn_number_surf",src_field_2D) + CALL xios_recv_field("src_ccn_number_surf",src_field_2D_subslope) CALL xios_send_field("ccn_number_surf_clean", & - src_field_2D(1:src_ni-1,1:src_nj)) + src_field_2D_subslope(1:src_ni-1,1:src_nj,:)) elseif (i==5) THEN CALL xios_send_field("ccn_mass_clean", & src_field_3D(1:src_ni-1,1:src_nj,1:src_nlev)) - CALL xios_recv_field("src_ccn_mass_surf",src_field_2D) + CALL xios_recv_field("src_ccn_mass_surf",src_field_2D_subslope) CALL xios_send_field("ccn_mass_surf_clean", & - src_field_2D(1:src_ni-1,1:src_nj)) + src_field_2D_subslope(1:src_ni-1,1:src_nj,:)) elseif (i==6) THEN CALL xios_send_field("h2o_ice_clean", & src_field_3D(1:src_ni-1,1:src_nj,1:src_nlev)) - CALL xios_recv_field("src_h2o_ice_surf",src_field_2D) + CALL xios_recv_field("src_h2o_ice_surf",src_field_2D_subslope) CALL xios_send_field("h2o_ice_surf_clean", & - src_field_2D(1:src_ni-1,1:src_nj)) + src_field_2D_subslope(1:src_ni-1,1:src_nj,:)) elseif (i==7) THEN CALL xios_send_field("h2o_vap_clean", & src_field_3D(1:src_ni-1,1:src_nj,1:src_nlev)) - CALL xios_recv_field("src_h2o_vap_surf",src_field_2D) + CALL xios_recv_field("src_h2o_vap_surf",src_field_2D_subslope) CALL xios_send_field("h2o_vap_surf_clean", & - src_field_2D(1:src_ni-1,1:src_nj)) + src_field_2D_subslope(1:src_ni-1,1:src_nj,:)) + elseif (i==8) THEN + CALL xios_send_field("stormdust_number_clean", & + src_field_3D(1:src_ni-1,1:src_nj,1:src_nlev)) + CALL xios_recv_field("src_stormdust_number_surf",src_field_2D_subslope) + CALL xios_send_field("stormdust_number_surf_clean", & + src_field_2D_subslope(1:src_ni-1,1:src_nj,:)) + elseif (i==9) THEN + CALL xios_send_field("stormdust_mass_clean", & + src_field_3D(1:src_ni-1,1:src_nj,1:src_nlev)) + CALL xios_recv_field("src_stormdust_mass_surf",src_field_2D_subslope) + CALL xios_send_field("stormdust_mass_surf_clean", & + src_field_2D_subslope(1:src_ni-1,1:src_nj,:)) + elseif (i==10) THEN + CALL xios_send_field("topdust_number_clean", & + src_field_3D(1:src_ni-1,1:src_nj,1:src_nlev)) + CALL xios_recv_field("src_topdust_number_surf",src_field_2D_subslope) + CALL xios_send_field("topdust_number_surf_clean", & + src_field_2D_subslope(1:src_ni-1,1:src_nj,:)) + elseif (i==11) THEN + CALL xios_send_field("topdust_mass_clean", & + src_field_3D(1:src_ni-1,1:src_nj,1:src_nlev)) + CALL xios_recv_field("src_topdust_mass_surf",src_field_2D_subslope) + CALL xios_send_field("topdust_mass_surf_clean", & + src_field_2D_subslope(1:src_ni-1,1:src_nj,:)) ENDIF ENDDO ! soil temperature - CALL xios_recv_field("src_tsoil",src_field_3D_soil) + CALL xios_recv_field("src_tsoil",src_field_3D_soil_subslope) CALL xios_send_field("tsoil_clean", & - src_field_3D_soil(1:src_ni-1,1:src_nj,1:src_nsoil)) + src_field_3D_soil_subslope(1:src_ni-1,1:src_nj,1:src_nsoil,:)) ! soil thermal intertia CALL xios_recv_field("src_inertiedat",src_field_3D_soil) Index: /trunk/LMDZ.MARS/util/startarchive2icosa/tracer.def_no_start =================================================================== --- /trunk/LMDZ.MARS/util/startarchive2icosa/tracer.def_no_start (revision 2941) +++ /trunk/LMDZ.MARS/util/startarchive2icosa/tracer.def_no_start (revision 2941) @@ -0,0 +1,14 @@ +&version=1.0 +&dynamico +default parent=air phases=g scheme=vanleer default_init_value=0.00 +co2 default_init_value=0.95 +dust_number default_init_value=1.e7 +dust_mass default_init_value=1.e-6 +stormdust_number default_init_value=1.e4 +stormdust_mass default_init_value=1.e-9 +topdust_number default_init_value=1.e4 +topdust_mass default_init_value=1.e-9 +h2o_vap default_init_value=1.e-5 +h2o_ice default_init_value=1.e-6 +ccn_number default_init_value=1.e6 +ccn_mass default_init_value=1.e-6 Index: unk/LMDZ.MARS/util/startarchive2icosa/traceur.def_no_start =================================================================== --- /trunk/LMDZ.MARS/util/startarchive2icosa/traceur.def_no_start (revision 2940) +++ (revision ) @@ -1,2 +1,0 @@ -1 -co2