Merge pull request #15 from fetch4/add-rundecks

Add `GISS_GC_14.R` rundeck to repo

.github/rundecks/GISS_GC_14.R

@@ -0,0 +1,266 @@
+GISS_GC_14.R GISS ModelE Lat-Lon Atmosphere Model, 1850 atm./ocean
+
+! GISS_GC_14 is based on E6F40 with updated aerosol/ozone input files for CMIP6
+! simulations
+!
+! It uses GEOS-Chem at version 14.3.1
+!
+! Lat-lon: 2x2.5 degree horizontal resolution
+! F40: 40 vertical layers with standard hybrid coordinate, top at .1 mb
+! Atmospheric composition for year 1850
+! Ocean climatology prescribed from years 1876-1885, CMIP6
+! Uses turbulence scheme (no dry conv), grav.wave drag
+! timesteps: dynamics 3.75 min leap frog; physics 30 min.; radiation 2.5 hrs
+! Filters: U,V in E-W and N-S direction (after every physics timestep)
+!          U,V in E-W direction near poles (after every dynamics timestep)
+!          sea level pressure (after every physics timestep)
+
+Preprocessor Options
+#define STDHYB                   ! standard hybrid vertical coordinate
+#define ATM_LAYERING L40         ! 40 layers, top at .1 mb
+#define NEW_IO                   ! new I/O (netcdf) on
+#define IRRIGATION_ON
+#define MODIS_LAI
+#define NEW_BCdalbsn
+#define NEW_IO_SUBDD
+#define CACHED_SUBDD
+#define GCAP
+#define CALCULATE_LIGHTNING
+#define TRACERS_GC               ! tracers using GISS-GC coupling
+#define MERRA_NUDGING
+#define NUDGE_ON
+End Preprocessor Options
+
+Object modules:
+
+! resolution-specific source codes
+Atm144x90                           ! horizontal resolution 144x90 -> 2x2.5deg
+AtmLayering                         ! vertical resolution
+DIAG_RES_F                          ! diagnostics
+FFT144                              ! Fast Fourier Transform
+
+IO_DRV                              ! new i/o
+
+! GISS dynamics with gravity wave drag
+ATMDYN MOMEN2ND                     ! atmospheric dynamics
+QUS_DRV QUS3D                       ! advection of Q/tracers
+STRATDYN STRAT_DIAG                 ! stratospheric dynamics (incl. gw drag)
+NUDGE
+
+! latitude-longitude grid specific source codes
+AtmRes
+GEOM_B                              ! model geometry
+DIAG_ZONAL GCDIAGb                  ! grid-dependent code for lat-circle diags
+DIAG_PRT POUT                       ! diagn/post-processing output
+MODEL_COM                           ! calendar, timing variables
+MODELE_DRV                          ! ModelE cap
+MODELE                              ! initialization and main loop
+ATM_COM                             ! main atmospheric variables
+ATM_DRV                             ! driver for atmosphere-grid components
+ATMDYN_COM                          ! atmospheric dynamics
+ATM_UTILS                           ! utilities for some atmospheric quantities
+CHEM_DRV CHEM_COM                   ! GEOS-Chem
+QUS_COM QUSDEF                      ! T/Q moments, 1D QUS
+CLOUDS2 CLOUDS2_DRV CLOUDS_COM      ! clouds modules
+SURFACE SURFACE_LANDICE FLUXES      ! surface calculation and fluxes
+GHY_COM GHY_DRV                     ! land surface and soils + snow model
+VEG_DRV                             ! vegetation
+ENT_DRV ENT_COM                     ! new vegetation
+PBL_COM PBL_DRV PBL                 ! atmospheric pbl
+IRRIGMOD                            ! irrigation module
+ATURB                               ! turbulence in whole atmosphere
+LAKES_COM LAKES                     ! lake modules
+SEAICE SEAICE_DRV                   ! seaice modules
+LANDICE LANDICE_COM LANDICE_DRV     ! land ice modules
+ICEDYN_DRV ICEDYN                   ! ice dynamics modules
+RAD_COM RAD_DRV RADIATION           ! radiation modules
+RAD_UTILS ALBEDO READ_AERO ocalbedo ! radiation and albedo
+DIAG_COM DIAG DEFACC                ! diagnostics
+OCN_DRV                             ! driver for ocean-grid components
+OCEAN OCNML                         ! ocean modules
+
+lightning
+SUBDD
+
+Components:
+shared MPI_Support solvers giss_LSM
+dd2d
+Ent
+
+Component Options:
+OPTS_Ent = ONLINE=YES PS_MODEL=FBB PFT_MODEL=ENT
+
+Data input files:
+! Atmospheric initial conditions for automatic relayering to model vertical grid
+AIC=NCARIC.144x90.D7712010_ext.nc
+! Ground initial condition
+GIC=GIC.144X90.DEC01.1.ext_1.nc
+
+OSST=OST_144x90.1876-1885avg.CMIP6.nc       ! climatological ocean temperature
+SICE=SICE_144x90.1876-1885avg.CMIP6.nc      ! climatological sea ice cover
+ZSIFAC=ZSIfac_144x90.1876-1885avg.CMIP6.nc  ! climatological sea ice thickness
+TOPO=Z2HX2fromZ1QX1N.BS1.nc                 ! ocean frac. and surface topography
+RVR=RD_Fd.nc                                ! river direction file
+NAMERVR=RD_Fd.names.txt                     ! named river outlets
+
+CDN=CD144X90.ext.nc
+VEG=V144x90_EntMM16_lc_max_trimmed_scaled_nocrops.ext.nc
+LAIMAX=V144x90_EntMM16_lai_max_trimmed_scaled_ext.nc
+HITEent=V144x90_EntMM16_height_trimmed_scaled_ext.nc
+LAI=V144x90_EntMM16_lai_trimmed_scaled_ext.nc
+CROPS=CROPS_and_pastures_Pongratz_to_Hurtt_144X90N_nocasp.nc
+IRRIG=Irrig144x90_1848to2100_FixedFuture_v3.nc
+SOIL=S144X900098M.ext.nc
+TOP_INDEX=top_index_144x90_a.ij.ext.nc
+ZVAR=ZVAR2X25A.nc ! topographic variation for gravity wave drag
+
+! probably need these (should convert to 144x90)
+soil_textures=soil_textures_top30cm_2x2.5
+SOILCARB_global=soilcarb_top30cm_2x2.5.nc
+GLMELT=GLMELT_144X90_gas.OCN.nc
+RADN1=sgpgxg.table8                           ! rad.tables and history files
+RADN2=LWTables33k_lowH2O_CO2_O3_planck_1-800  ! rad.tables and history files
+RADN4=LWCorrTables33k                         ! rad.tables and history files
+RADN5=H2Ocont_MT_CKD  ! Mlawer/Tobin_Clough/Kneizys/Davies H2O continuum table
+RADN3=miescatpar.abcdv2
+
+RH_QG_Mie=oct2003.relhum.nr.Q633G633.table
+RADN7=STRATAER.VOL.1850-2014_CMIP6_hdr                  ! needs MADVOL=2
+RADN8=cloud.epsilon4.72x46
+RADN9=solar.CMIP6official.ann1850-2299_with_E3_fastJ.nc ! needs KSOLAR=2
+RADNE=topcld.trscat8
+
+ISCCP=ISCCP.tautables
+GHG=GHG.CMIP6.1-2014.txt  !  GreenHouse Gases for CMIP6 runs up to 2014
+CO2profile=CO2profile.Jul16-2017.txt ! scaling of CO2 in stratosphere
+dH2O=dH2O_by_CH4_monthly
+
+! NINT E2.1 input files
+BCdalbsn=cmip6_nint_inputs_E14TomaOCNf10_4av_decadal/BCdalbsn
+DUSTaer=cmip6_nint_inputs_E14TomaOCNf10_4av_decadal/DUST
+TAero_SUL=cmip6_nint_inputs_E14TomaOCNf10_4av_decadal/SUL
+TAero_SSA=cmip6_nint_inputs_E14TomaOCNf10_4av_decadal/SSA
+TAero_NIT=cmip6_nint_inputs_E14TomaOCNf10_4av_decadal/NIT
+TAero_OCA=cmip6_nint_inputs_E14TomaOCNf10_4av_decadal/OCA
+TAero_BCA=cmip6_nint_inputs_E14TomaOCNf10_4av_decadal/BCA
+TAero_BCB=cmip6_nint_inputs_E14TomaOCNf10_4av_decadal/BCB
+u2014.nc=nudging/merra2/uwnd.2014.MERRA2onGISSE2.nc4
+v2014.nc=nudging/merra2/vwnd.2014.MERRA2onGISSE2.nc4
+u2015.nc=nudging/merra2/uwnd.2015.MERRA2onGISSE2.nc4
+v2015.nc=nudging/merra2/vwnd.2015.MERRA2onGISSE2.nc4
+u2016.nc=nudging/merra2/uwnd.2016.MERRA2onGISSE2.nc4
+v2016.nc=nudging/merra2/vwnd.2016.MERRA2onGISSE2.nc4
+O3file=cmip6_nint_inputs_E14TomaOCNf10_4av_decadal/O3
+Ox_ref=o3_2010_shindell_144x90x49_April1850.nc
+
+MSU_wts=MSU_SSU_RSS_weights.txt   ! MSU-diag
+REG=REG2X2.5                      ! special regions-diag
+
+Label and Namelist:  (next 2 lines)
+GISS_GC_14 (LLF40 + updated aerosol/ozone input files for CMIP6 simulations, 1850 atm/ocean)
+
+&&PARAMETERS
+! parameters set for choice of ocean model:
+KOCEAN=0        ! ocean is prescribed
+Kvflxo=0        ! usually set to 1 only during a prescr.ocn run by editing "I"
+variable_lk=1   ! variable lakes
+
+! drag params if gravity wave drag is not used and top is at .01mb
+X_SDRAG=.002,.0002  ! used above P(P)_sdrag mb (and in top layer)
+C_SDRAG=.0002       ! constant SDRAG above PTOP=150mb
+P_sdrag=1.          ! linear SDRAG only above 1mb (except near poles)
+PP_sdrag=1.         ! linear SDRAG above PP_sdrag mb near poles
+P_CSDRAG=1.         ! increase CSDRAG above P_CSDRAG to approach lin. drag
+Wc_JDRAG=30.        ! crit.wind speed for J-drag (Judith/Jim)
+ANG_sdrag=1     ! if 1: SDRAG conserves ang.momentum by adding loss below PTOP
+! vsdragl is a tuning coefficient for SDRAG starting at LS1
+! layer:   24    25    26    27   28    29    30    31   32   33   34   35   36  37  38   39 40
+vsdragl=0.000,0.000,0.000,0.000,0.00,0.000,0.000,0.000,0.00,0.00,0.00,0.00,0.00,0.3,0.6,0.83,1.
+
+! Gravity wave parameters
+PBREAK = 200.       ! the level for GW breaking above.
+DEFTHRESH=0.000055  ! threshold (1/s) for triggering deformation waves
+PCONPEN=400.        ! penetrating convection defn for GWDRAG
+CMC = 0.0000002     ! parameter for GW Moist Convective drag
+CSHEAR=10.          ! shear drag coefficient
+CMTN=0.1            ! default is 0.5
+CDEF=1.6            ! tuning factor for deformation -> momentum flux
+XCDNST=400.,10000.  ! strat. gw drag parameters
+QGWMTN=1            ! mountain waves ON
+QGWDEF=1            ! deformation waves ON
+QGWSHR=0            ! shear drag OFF
+QGWCNV=0            ! convective drag OFF
+
+! following two lines are only used when aerosol/radiation interactions are off
+FS8OPX=1.,1.,1.,1.,1.5,1.5,1.,1.
+FT8OPX=1.,1.,1.,1.,1.,1.,1.3,1.
+
+! increasing U00a decreases the high cloud cover (tune first)
+U00a=0.655 ! above 850mb w/o MC region; tune to get 30-35% high clouds
+! increasing U00b decreases net rad at TOA (tune last)
+U00b=1.00  ! below 850mb and MC regions; tune this to get radiative balance
+WMUI_multiplier=2.
+use_vmp=1
+radius_multiplier=1.1
+
+PTLISO=0.   ! pressure(mb) above which radiation assumes isothermal layers
+H2ObyCH4=1. ! activates stratospheric H2O generated by CH4 without interactive chemistry
+KSOLAR=2    ! use long annual mean file
+
+! parameters that control the atmospheric/boundary conditions
+! if set to 0, the current (day/) year is used: transient run
+master_yr=0        ! transient run
+volc_yr=-1
+od_cdncx=0.        ! do not include 1st indirect effect
+cc_cdncx=0.        ! do not include 2nd indirect effect (used 0.0036)
+dalbsnX=1.
+
+MADVOL=2
+
+! GEOS-Chem Operators (1=true, 0=false) ! TODO: Turn these on
+! DoGCConv=1
+! DoGCEmis=1
+! DoGCTend=0
+! DoGCTurb=1
+! DoGCChem=1
+! DoGCDryDep=1
+! DoGCWetDep=1
+
+DTsrc=1800.      ! physics timestep (cannot be changed after a run starts)
+DT=225.          ! advection timestep
+
+! parameters that control the Shapiro filter
+DT_XUfilter=225. ! Shapiro filter on U in E-W direction; usually same as DT
+DT_XVfilter=225. ! Shapiro filter on V in E-W direction; usually same as DT
+DT_YVfilter=0.   ! Shapiro filter on V in N-S direction
+DT_YUfilter=0.   ! Shapiro filter on U in N-S direction
+
+NIsurf=2         ! surface interaction computed NIsurf times per source timestep
+NRAD=1           ! radiation computed NRAD times per source timestep
+! parameters that affect at most diagn. output:  standard if DTsrc=1800. (sec)
+TAero_aod_diag=2 ! save band6 only
+aer_rad_forc=0   ! turn off aerosol radiative forcing diagnostics
+cloud_rad_forc=1 ! turn on cloud radiative forcing diagnostics
+
+! diagnostics
+! SUBDD='OH:4 NO:4 O3:4 NO2:4 CO:4 CH4:4 PS:4' ! TODO: Turn these on
+SUBDD='SAT:6i'
+NSUBDD=1         ! saving sub-daily diags every NSUBDD-th physics timestep
+DAYS_PER_FILE=1
+KCOPY=1          ! save accumulated diagnostics files
+KRSF=12          ! save restart file at the beginning of every 12 months
+isccp_diags=1    ! include all key diagnostics
+nda5d=13
+nda5s=13
+ndaa=13
+nda5k=13
+nda4=48
+Nssw=2
+Ndisk=960        ! write fort.1.nc or fort.2.nc every NDISK source timestep
+&&END_PARAMETERS
+
+&INPUTZ
+ YEARI=2016,MONTHI=7,DATEI=1,HOURI=0,
+ YEARE=2016,MONTHE=8,DATEE=1,HOURE=0,     KDIAG=13*0,
+ ISTART=2,IRANDI=0, YEARE=2016,MONTHE=7,DATEE=2,HOURE=0,
+/